From 45100528adbaa9dcfd1dee3db13d837982dd8ae0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 08:54:53 -0400 Subject: [PATCH 01/72] Update pair_coul.rst --- doc/src/pair_coul.rst | 79 +++++++++++++++++++------------------------ 1 file changed, 35 insertions(+), 44 deletions(-) diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4874bf044e..37193d752c 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -1,58 +1,55 @@ .. index:: pair_style coul/cut +.. index:: pair_style coul/cut/gpu +.. index:: pair_style coul/cut/kk +.. index:: pair_style coul/cut/omp +.. index:: pair_style coul/debye +.. index:: pair_style coul/debye/gpu +.. index:: pair_style coul/debye/kk +.. index:: pair_style coul/debye/omp +.. index:: pair_style coul/dsf +.. index:: pair_style coul/dsf/gpu +.. index:: pair_style coul/dsf/kk +.. index:: pair_style coul/dsf/omp +.. index:: pair_style coul/long +.. index:: pair_style coul/long/omp +.. index:: pair_style coul/long/kk +.. index:: pair_style coul/long/gpu +.. index:: pair_style coul/msm +.. index:: pair_style coul/msm/omp +.. index:: pair_style coul/streitz +.. index:: pair_style coul/wolf +.. index:: pair_style coul/wolf/kk +.. index:: pair_style coul/wolf/omp +.. index:: pair_style tip4p/cut +.. index:: pair_style tip4p/cut/omp +.. index:: pair_style tip4p/long +.. index:: pair_style tip4p/long/omp + pair_style coul/cut command =========================== -pair_style coul/cut/gpu command -=============================== - -pair_style coul/cut/kk command -============================== - -pair_style coul/cut/omp command -=============================== +Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp* pair_style coul/debye command ============================= -pair_style coul/debye/gpu command -================================= - -pair_style coul/debye/kk command -================================ - -pair_style coul/debye/omp command -================================= +Accelerator Variants: *coul/debye/gpu*, *coul/debye/kk*, *coul/debye/omp* pair_style coul/dsf command =========================== -pair_style coul/dsf/gpu command -=============================== - -pair_style coul/dsf/kk command -============================== - -pair_style coul/dsf/omp command -=============================== +Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp* pair_style coul/long command ============================ -pair_style coul/long/omp command -================================ - -pair_style coul/long/gpu command -================================ - -pair_style coul/long/kk command -=============================== +Accelerator Variants: *coul/long/omp*, *coul/long/kk*, *coul/long/gpu* pair_style coul/msm command =========================== -pair_style coul/msm/omp command -=============================== +Accelerator Variants: *coul/msm/omp* pair_style coul/streitz command =============================== @@ -60,23 +57,17 @@ pair_style coul/streitz command pair_style coul/wolf command ============================ -pair_style coul/wolf/kk command -=============================== - -pair_style coul/wolf/omp command -================================ +Accelerator Variants: *coul/wolf/kk*, *coul/wolf/omp* pair_style tip4p/cut command ============================ +Accelerator Variants: *tip4p/cut/omp* + pair_style tip4p/long command ============================= -pair_style tip4p/cut/omp command -================================ - -pair_style tip4p/long/omp command -================================= +Accelerator Variants: *tip4p/long/omp* Syntax """""" From 7e733913d798f7b8b0b2fe37db284619ed74f67a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:03:00 -0400 Subject: [PATCH 02/72] Update pair_fep_soft.rst --- doc/src/pair_fep_soft.rst | 71 ++++++++++++++++++++++----------------- 1 file changed, 41 insertions(+), 30 deletions(-) diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index bd38fe1ec9..be35f84508 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -1,64 +1,75 @@ .. index:: pair_style lj/cut/soft +.. index:: pair_style lj/cut/soft/omp +.. index:: pair_style lj/cut/coul/cut/soft +.. index:: pair_style lj/cut/coul/cut/soft/omp +.. index:: pair_style lj/cut/coul/long/soft +.. index:: pair_style lj/cut/coul/long/soft/omp +.. index:: pair_style lj/cut/tip4p/long/soft +.. index:: pair_style lj/cut/tip4p/long/soft/omp +.. index:: pair_style lj/charmm/coul/long/soft +.. index:: pair_style lj/charmm/coul/long/soft/omp +.. index:: pair_style lj/class2/soft +.. index:: pair_style lj/class2/coul/cut/soft +.. index:: pair_style lj/class2/coul/long/soft +.. index:: pair_style coul/cut/soft +.. index:: pair_style coul/cut/soft/omp +.. index:: pair_style coul/long/soft +.. index:: pair_style coul/long/soft/omp +.. index:: pair_style tip4p/long/soft +.. index:: pair_style tip4p/long/soft/omp +.. index:: pair_style morse/soft pair_style lj/cut/soft command ============================== -pair_style lj/cut/soft/omp command -================================== +Accelerator Styles: *lj/cut/soft/omp* pair_style lj/cut/coul/cut/soft command ======================================= -pair_style lj/cut/coul/cut/soft/omp command -=========================================== +Accelerator Styles: *lj/cut/coul/cut/soft/omp* pair_style lj/cut/coul/long/soft command ======================================== -pair_style lj/cut/coul/long/soft/omp command -============================================ +Accelerator Styles: *lj/cut/coul/long/soft/omp* pair_style lj/cut/tip4p/long/soft command -========================================== +========================================= -pair_style lj/cut/tip4p/long/soft/omp command -============================================== +Accelerator Styles: *lj/cut/tip4p/long/soft/omp* pair_style lj/charmm/coul/long/soft command -============================================ - -pair_style lj/charmm/coul/long/soft/omp command -================================================ - -pair_style lj/class2/soft command -================================== - -pair_style lj/class2/coul/cut/soft command =========================================== -pair_style lj/class2/coul/long/soft command -============================================ +Accelerator Styles: *lj/charmm/coul/long/soft/omp* -pair_style coul/cut/soft command +pair_style lj/class2/soft command ================================= -pair_style coul/cut/soft/omp command -===================================== +pair_style lj/class2/coul/cut/soft command +========================================== + +pair_style lj/class2/coul/long/soft command +=========================================== + +pair_style coul/cut/soft command +================================ + +Accelerator Styles: *coul/cut/soft/omp* pair_style coul/long/soft command -================================== +================================= -pair_style coul/long/soft/omp command -====================================== +Accelerator Styles: *coul/long/soft/omp* pair_style tip4p/long/soft command -=================================== +================================== -pair_style tip4p/long/soft/omp command -======================================= +Accelerator Styles: *tip4p/long/soft/omp* pair_style morse/soft command -============================== +============================= Syntax """""" From a9cf25db4cdff396b0ad5515da63fa4aa9314153 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:13:59 -0400 Subject: [PATCH 03/72] Update pair_eam.rst --- doc/src/pair_eam.rst | 64 +++++++++++++++----------------------------- 1 file changed, 22 insertions(+), 42 deletions(-) diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index c5f9b26435..56eed64d01 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -1,40 +1,33 @@ .. index:: pair_style eam +.. index:: pair_style eam/gpu +.. index:: pair_style eam/intel +.. index:: pair_style eam/kk +.. index:: pair_style eam/omp +.. index:: pair_style eam/opt +.. index:: pair_style eam/alloy +.. index:: pair_style eam/alloy/gpu +.. index:: pair_style eam/alloy/intel +.. index:: pair_style eam/alloy/kk +.. index:: pair_style eam/alloy/omp +.. index:: pair_style eam/alloy/opt +.. index:: pair_style eam/cd +.. index:: pair_style eam/cd/old +.. index:: pair_style eam/fs +.. index:: pair_style eam/fs/gpu +.. index:: pair_style eam/fs/intel +.. index:: pair_style eam/fs/kk +.. index:: pair_style eam/fs/omp +.. index:: pair_style eam/fs/opt pair_style eam command ====================== -pair_style eam/gpu command -========================== - -pair_style eam/intel command -============================ - -pair_style eam/kk command -========================= - -pair_style eam/omp command -========================== - -pair_style eam/opt command -========================== +Accelerator Styles: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* pair_style eam/alloy command ============================ -pair_style eam/alloy/gpu command -================================ - -pair_style eam/alloy/intel command -================================== - -pair_style eam/alloy/kk command -=============================== - -pair_style eam/alloy/omp command -================================ - -pair_style eam/alloy/opt command -================================ +Accelerator Styles: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* pair_style eam/cd command ========================= @@ -45,20 +38,7 @@ pair_style eam/cd/old command pair_style eam/fs command ========================= -pair_style eam/fs/gpu command -============================= - -pair_style eam/fs/intel command -=============================== - -pair_style eam/fs/kk command -============================ - -pair_style eam/fs/omp command -============================= - -pair_style eam/fs/opt command -============================= +Accelerator Styles: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* Syntax """""" From 77f803b366f7ca60fcb73d6a30e945d9bfda4b50 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:14:20 -0400 Subject: [PATCH 04/72] Update pair_charmm.rst --- doc/src/pair_charmm.rst | 49 +++++++++++++++++------------------------ 1 file changed, 20 insertions(+), 29 deletions(-) diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index 183311e34d..cef1b333fb 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -1,49 +1,40 @@ .. index:: pair_style lj/charmm/coul/charmm +.. index:: pair_style lj/charmm/coul/charmm/intel +.. index:: pair_style lj/charmm/coul/charmm/kk +.. index:: pair_style lj/charmm/coul/charmm/omp +.. index:: pair_style lj/charmm/coul/charmm/implicit +.. index:: pair_style lj/charmm/coul/charmm/implicit/kk +.. index:: pair_style lj/charmm/coul/charmm/implicit/omp +.. index:: pair_style lj/charmm/coul/long +.. index:: pair_style lj/charmm/coul/long/gpu +.. index:: pair_style lj/charmm/coul/long/intel +.. index:: pair_style lj/charmm/coul/long/kk +.. index:: pair_style lj/charmm/coul/long/opt +.. index:: pair_style lj/charmm/coul/long/omp +.. index:: pair_style lj/charmm/coul/msm +.. index:: pair_style lj/charmm/coul/msm/omp +.. index:: pair_style lj/charmmfsw/coul/charmmfsh +.. index:: pair_style lj/charmmfsw/coul/long pair_style lj/charmm/coul/charmm command ========================================= -pair_style lj/charmm/coul/charmm/intel command -=============================================== - -pair_style lj/charmm/coul/charmm/kk command -============================================ - -pair_style lj/charmm/coul/charmm/omp command -============================================= +Accelerator Styles: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* pair_style lj/charmm/coul/charmm/implicit command ================================================== -pair_style lj/charmm/coul/charmm/implicit/kk command -===================================================== - -pair_style lj/charmm/coul/charmm/implicit/omp command -====================================================== +Accelerator Styles: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* pair_style lj/charmm/coul/long command ======================================= -pair_style lj/charmm/coul/long/gpu command -=========================================== - -pair_style lj/charmm/coul/long/intel command -============================================= - -pair_style lj/charmm/coul/long/kk command -========================================== - -pair_style lj/charmm/coul/long/opt command -=========================================== - -pair_style lj/charmm/coul/long/omp command -=========================================== +Accelerator Styles: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* pair_style lj/charmm/coul/msm command ====================================== -pair_style lj/charmm/coul/msm/omp command -========================================== +Accelerator Styles: *lj/charmm/coul/msm/omp* pair_style lj/charmmfsw/coul/charmmfsh command =============================================== From dce7a39021ac99ddb6e4a85891417af9d8540fb7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:47:32 -0400 Subject: [PATCH 05/72] Update pair_buck.rst --- doc/src/pair_buck.rst | 56 ++++++++++++++++--------------------------- 1 file changed, 21 insertions(+), 35 deletions(-) diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index e8a1475ccb..6ff5f84fe2 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,55 +1,41 @@ .. index:: pair_style buck +.. index:: pair_style buck +.. index:: pair_style buck/gpu +.. index:: pair_style buck/intel +.. index:: pair_style buck/kk +.. index:: pair_style buck/omp +.. index:: pair_style buck/coul/cut +.. index:: pair_style buck/coul/cut/gpu +.. index:: pair_style buck/coul/cut/intel +.. index:: pair_style buck/coul/cut/kk +.. index:: pair_style buck/coul/cut/omp +.. index:: pair_style buck/coul/long +.. index:: pair_style buck/coul/long/gpu +.. index:: pair_style buck/coul/long/intel +.. index:: pair_style buck/coul/long/kk +.. index:: pair_style buck/coul/long/omp +.. index:: pair_style buck/coul/msm +.. index:: pair_style buck/coul/msm/omp pair_style buck command ======================== -pair_style buck/gpu command -============================ - -pair_style buck/intel command -============================== - -pair_style buck/kk command -=========================== - -pair_style buck/omp command -============================ +Accelerator Styles: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* pair_style buck/coul/cut command ================================= -pair_style buck/coul/cut/gpu command -===================================== - -pair_style buck/coul/cut/intel command -======================================= - -pair_style buck/coul/cut/kk command -==================================== - -pair_style buck/coul/cut/omp command -===================================== +Accelerator Styles: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* pair_style buck/coul/long command ================================== -pair_style buck/coul/long/gpu command -====================================== - -pair_style buck/coul/long/intel command -======================================== - -pair_style buck/coul/long/kk command -===================================== - -pair_style buck/coul/long/omp command -====================================== +Accelerator Styles: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* pair_style buck/coul/msm command ================================= -pair_style buck/coul/msm/omp command -===================================== +Accelerator Styles: *buck/coul/msm/omp* Syntax """""" From 7ae98ffae11ee3b75ea2bba13e89db49444f5d02 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 09:50:16 -0400 Subject: [PATCH 06/72] Update fix_rigid.rst --- doc/src/fix_rigid.rst | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index a143817303..8756e72db1 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -1,40 +1,49 @@ .. index:: fix rigid +.. index:: fix rigid/omp +.. index:: fix rigid/nve +.. index:: fix rigid/nve/omp +.. index:: fix rigid/nvt +.. index:: fix rigid/nvt/omp +.. index:: fix rigid/npt +.. index:: fix rigid/npt/omp +.. index:: fix rigid/nph +.. index:: fix rigid/nph/omp +.. index:: fix rigid/small +.. index:: fix rigid/small/omp +.. index:: fix rigid/nve/small +.. index:: fix rigid/nvt/small +.. index:: fix rigid/npt/small +.. index:: fix rigid/nph/small fix rigid command ================= -fix rigid/omp command -===================== +Accelerator Styles: *rigid/omp* fix rigid/nve command ===================== -fix rigid/nve/omp command -========================= +Accelerator Styles: *rigid/nve/omp* fix rigid/nvt command ===================== -fix rigid/nvt/omp command -========================= +Accelerator Styles: *rigid/nvt/omp* fix rigid/npt command ===================== -fix rigid/npt/omp command -========================= +Accelerator Styles: *rigid/npt/omp* fix rigid/nph command ===================== -fix rigid/nph/omp command -========================= +Accelerator Styles: *rigid/nph/omp* fix rigid/small command ======================= -fix rigid/small/omp command -=========================== +Accelerator Styles: *rigid/small/omp* fix rigid/nve/small command =========================== From a6a49d80b27a5b0f3c2acc1ef899e700a1b37adb Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:19:20 -0400 Subject: [PATCH 07/72] Update pair_sdk.rst --- doc/src/pair_sdk.rst | 26 +++++++++++--------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 501ce6cd85..02fed36130 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -1,31 +1,27 @@ .. index:: pair_style lj/sdk +.. index:: pair_style lj/sdk/gpu +.. index:: pair_style lj/sdk/kk +.. index:: pair_style lj/sdk/omp +.. index:: pair_style lj/sdk/coul/long +.. index:: pair_style lj/sdk/coul/long/gpu +.. index:: pair_style lj/sdk/coul/long/omp +.. index:: pair_style lj/sdk/coul/msm +.. index:: pair_style lj/sdk/coul/msm/omp pair_style lj/sdk command ========================= -pair_style lj/sdk/gpu command -============================= - -pair_style lj/sdk/kk command -============================ - -pair_style lj/sdk/omp command -============================= +Accelerator Styles: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* pair_style lj/sdk/coul/long command =================================== -pair_style lj/sdk/coul/long/gpu command -======================================= - -pair_style lj/sdk/coul/long/omp command -======================================= +Accelerator Styles: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* pair_style lj/sdk/coul/msm command ================================== -pair_style lj/sdk/coul/msm/omp command -====================================== +Accelerator Styles: *lj/sdk/coul/msm/omp* Syntax """""" From e5f1f58aab04cf013f277760981ae82e1a72d8f8 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:26:37 -0400 Subject: [PATCH 08/72] Update pair_born.rst --- doc/src/pair_born.rst | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 761b40b812..15ce4ac560 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -1,41 +1,40 @@ .. index:: pair_style born +.. index:: pair_style born/omp +.. index:: pair_style born/gpu +.. index:: pair_style born/coul/long +.. index:: pair_style born/coul/long/gpu +.. index:: pair_style born/coul/long/omp +.. index:: pair_style born/coul/msm +.. index:: pair_style born/coul/msm/omp +.. index:: pair_style born/coul/wolf +.. index:: pair_style born/coul/wolf/gpu +.. index:: pair_style born/coul/wolf/omp +.. index:: pair_style born/coul/dsf pair_style born command ======================= -pair_style born/omp command -=========================== - -pair_style born/gpu command -=========================== +Accelerator Styles: *born/omp*, *born/gpu* pair_style born/coul/long command ================================= -pair_style born/coul/long/gpu command -===================================== - -pair_style born/coul/long/omp command -===================================== +Accelerator Styles: *born/coul/long/gpu*, *born/coul/long/omp* pair_style born/coul/msm command ================================ -pair_style born/coul/msm/omp command -==================================== +Accelerator Styles: *born/coul/msm/omp* pair_style born/coul/wolf command ================================= -pair_style born/coul/wolf/gpu command -===================================== - -pair_style born/coul/wolf/omp command -===================================== +Accelerator Styles: *born/coul/wolf/gpu*, *born/coul/wolf/omp* pair_style born/coul/dsf command ================================ + Syntax """""" From 4d6be195eca30d8e3979059687e3cbf5dfa1942d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:29:29 -0400 Subject: [PATCH 09/72] Add utility to fixup doc headers --- doc/utils/fixup_headers.py | 63 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100755 doc/utils/fixup_headers.py diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py new file mode 100755 index 0000000000..9cb11e9cb5 --- /dev/null +++ b/doc/utils/fixup_headers.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python3 +# Utility script to fix headers in doc pages and generate "Accelerator Styles" portion +import shutil +import re +import argparse + +pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") + +parser = argparse.ArgumentParser(description='Fixup headers in docs') +parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') +args = parser.parse_args() + +for orig_file in args.files: + command_type = "unknown" + styles = [] + headings = {} + new_file = f"{orig_file}.tmp" + + with open(orig_file, 'r') as reader, open(new_file, 'w') as writer: + for line in reader: + if line.startswith("Syntax"): + break + + m = pattern.match(line) + if m: + command_type = m.group(1) + style = m.group(2) + + styles.append(style) + + base_name = '/'.join(style.split('/')[0:-1]) + ext = style.split('/')[-1] + + if ext not in ('omp', 'intel', 'kk', 'gpu', 'opt'): + headings[style] = [] + else: + headings[base_name].append(style) + + # write new header + for s in styles: + print(f".. index:: {command_type} {s}", file=writer) + + print(file=writer) + + for s, variants in headings.items(): + header = f"{command_type} {s} command" + print(header, file=writer) + print("="*len(header), file=writer) + print(file=writer) + + if len(variants) > 0: + print("Accelerator Styles: ", end="", file=writer) + print(", ".join([f"*{v}*" for v in variants]), file=writer) + + print(file=writer) + + # write rest of reader + print(line, end="", file=writer) + for line in reader: + print(line, end="", file=writer) + + # override original file + shutil.move(new_file, orig_file) From 3a22f26e87b39a35dd2a1626b191fd80a7ccf027 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:29:46 -0400 Subject: [PATCH 10/72] Update pair_cs.rst --- doc/src/pair_cs.rst | 56 +++++++++++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 22 deletions(-) diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 8efd49197d..ae5c29aa32 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -1,37 +1,49 @@ .. index:: pair_style born/coul/dsf/cs +.. index:: pair_style born/coul/long/cs +.. index:: pair_style born/coul/long/cs/gpu +.. index:: pair_style born/coul/wolf/cs +.. index:: pair_style born/coul/wolf/cs/gpu +.. index:: pair_style buck/coul/long/cs +.. index:: pair_style coul/long/cs +.. index:: pair_style coul/long/cs/gpu +.. index:: pair_style coul/wolf/cs +.. index:: pair_style lj/cut/coul/long/cs +.. index:: pair_style lj/class2/coul/long/cs pair_style born/coul/dsf/cs command -==================================== +=================================== + pair_style born/coul/long/cs command -===================================== - -pair_style born/coul/long/cs/gpu command -========================================= - -pair_style born/coul/wolf/cs command -===================================== - -pair_style born/coul/wolf/cs/gpu command -========================================= - -pair_style buck/coul/long/cs command -===================================== - -pair_style coul/long/cs command -================================ - -pair_style coul/long/cs/gpu command ==================================== +Accelerator Styles: *born/coul/long/cs/gpu* + +pair_style born/coul/wolf/cs command +==================================== + +Accelerator Styles: *born/coul/wolf/cs/gpu* + +pair_style buck/coul/long/cs command +==================================== + + +pair_style coul/long/cs command +=============================== + +Accelerator Styles: *coul/long/cs/gpu* + pair_style coul/wolf/cs command -================================ +=============================== + pair_style lj/cut/coul/long/cs command -======================================= +====================================== + pair_style lj/class2/coul/long/cs command -========================================== +========================================= + Syntax """""" From 49a6bf5e30b45b7c27228c2502d8e0174e990858 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:30:31 -0400 Subject: [PATCH 11/72] Update pair_class2.rst --- doc/src/pair_class2.rst | 34 +++++++++++++--------------------- 1 file changed, 13 insertions(+), 21 deletions(-) diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 66a696938f..6fcdd4f533 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -1,37 +1,29 @@ .. index:: pair_style lj/class2 +.. index:: pair_style lj/class2/gpu +.. index:: pair_style lj/class2/kk +.. index:: pair_style lj/class2/omp +.. index:: pair_style lj/class2/coul/cut +.. index:: pair_style lj/class2/coul/cut/kk +.. index:: pair_style lj/class2/coul/cut/omp +.. index:: pair_style lj/class2/coul/long +.. index:: pair_style lj/class2/coul/long/gpu +.. index:: pair_style lj/class2/coul/long/kk +.. index:: pair_style lj/class2/coul/long/omp pair_style lj/class2 command ============================ -pair_style lj/class2/gpu command -================================ - -pair_style lj/class2/kk command -=============================== - -pair_style lj/class2/omp command -================================ +Accelerator Styles: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* pair_style lj/class2/coul/cut command ===================================== -pair_style lj/class2/coul/cut/kk command -======================================== - -pair_style lj/class2/coul/cut/omp command -========================================= +Accelerator Styles: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* pair_style lj/class2/coul/long command ====================================== -pair_style lj/class2/coul/long/gpu command -========================================== - -pair_style lj/class2/coul/long/kk command -========================================= - -pair_style lj/class2/coul/long/omp command -========================================== +Accelerator Styles: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* Syntax """""" From 3c60a9e08e7d5b9e5abc82e15c8acf44e5bcecba Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:31:21 -0400 Subject: [PATCH 12/72] Update fix_nh.rst --- doc/src/fix_nh.rst | 34 +++++++++++++--------------------- 1 file changed, 13 insertions(+), 21 deletions(-) diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 64a3c3b061..3e23c46e61 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -1,37 +1,29 @@ .. index:: fix nvt +.. index:: fix nvt/intel +.. index:: fix nvt/kk +.. index:: fix nvt/omp +.. index:: fix npt +.. index:: fix npt/intel +.. index:: fix npt/kk +.. index:: fix npt/omp +.. index:: fix nph +.. index:: fix nph/kk +.. index:: fix nph/omp fix nvt command =============== -fix nvt/intel command -===================== - -fix nvt/kk command -================== - -fix nvt/omp command -=================== +Accelerator Styles: *nvt/intel*, *nvt/kk*, *nvt/omp* fix npt command =============== -fix npt/intel command -===================== - -fix npt/kk command -================== - -fix npt/omp command -=================== +Accelerator Styles: *npt/intel*, *npt/kk*, *npt/omp* fix nph command =============== -fix nph/kk command -================== - -fix nph/omp command -=================== +Accelerator Styles: *nph/kk*, *nph/omp* Syntax """""" From e4790331098575c57efccf5a17a19e7e4e027a51 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:51:47 -0400 Subject: [PATCH 13/72] Avoid breaking already fixed headers --- doc/utils/fixup_headers.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 9cb11e9cb5..7bdd11a607 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -4,6 +4,7 @@ import shutil import re import argparse +index_pattern = re.compile(r"^.. index:: (fix|pair_style)\s+([a-zA-Z0-9/_]+)$") pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') @@ -21,19 +22,25 @@ for orig_file in args.files: if line.startswith("Syntax"): break - m = pattern.match(line) + m = index_pattern.match(line) + + if not m: + m = pattern.match(line) + if m: command_type = m.group(1) style = m.group(2) - styles.append(style) + if style not in styles: + styles.append(style) base_name = '/'.join(style.split('/')[0:-1]) ext = style.split('/')[-1] if ext not in ('omp', 'intel', 'kk', 'gpu', 'opt'): - headings[style] = [] - else: + if style not in headings: + headings[style] = [] + elif style not in headings[base_name]: headings[base_name].append(style) # write new header @@ -49,7 +56,7 @@ for orig_file in args.files: print(file=writer) if len(variants) > 0: - print("Accelerator Styles: ", end="", file=writer) + print("Accelerator Variants: ", end="", file=writer) print(", ".join([f"*{v}*" for v in variants]), file=writer) print(file=writer) From e5e2abe44628ac8a5e0493bd5c0ff92057f801cb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 10:51:55 -0400 Subject: [PATCH 14/72] update include file policy file and policy for pointers.h special case --- doc/include-file-conventions.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index e3448cb8ce..ea4e07eb59 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -91,21 +91,21 @@ statements should follow the "include what you use" principle. Include files should be included in this order: * the header matching the implementation (`some_class.h` for file `some_class.cpp`) -* mpi.h -* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* mpi.h (only if needed) * LAMMPS local headers (preferably in alphabetical order) +* system and library headers (anything that is using angular brackets; C-library headers first, then C++) ### Special Cases and Exceptions #### pointers.h -The `pointer.h` header file also includes `cstdio`, `cstddef`, -`string`, `lmptype.h`, and `utils.h` (and through those indirectly - `stdint.h`, `intttypes.h`, cstdlib, and `climits`). +The `pointer.h` header file also includes (in this order) `lmptype.h`, +`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h` +and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`. This means any header including `pointers.h` can assume that `FILE`, -`NULL`, `INT_MAX` are defined, they may freely use std::string -and functions from the utils namespace without including the -corresponding header files. +`NULL`, `INT_MAX` are defined, and the may freely use the std::string +for arguments. Corresponding implementation files do not need to include +those headers. ## Tools From cc594c0613b263caf0d4549ee4cb6c7a3134774e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 10:52:10 -0400 Subject: [PATCH 15/72] include fmt/format.h into pointers.h --- src/pointers.h | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/pointers.h b/src/pointers.h index 4b91e009ac..04f682f045 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,13 +21,14 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" // IWYU pragma: export -#include // IWYU pragma: export -#include // IWYU pragme: export -#include // IWYU pragma: export -#include // IWYU pragma: export -#include "lammps.h" // IWYU pragma: export -#include "utils.h" // IWYU pragma: export +#include "lmptype.h" // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragme: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include "lammps.h" // IWYU pragma: export +#include "utils.h" // IWYU pragma: export +#include "fmt/format.h" // IWYU pragma: export namespace LAMMPS_NS { From 09bc686f714ceaa3e3c372afcd9e71acf88b0330 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:55:04 -0400 Subject: [PATCH 16/72] Avoid extra newline --- doc/utils/fixup_headers.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 7bdd11a607..884511bd32 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -58,8 +58,7 @@ for orig_file in args.files: if len(variants) > 0: print("Accelerator Variants: ", end="", file=writer) print(", ".join([f"*{v}*" for v in variants]), file=writer) - - print(file=writer) + print(file=writer) # write rest of reader print(line, end="", file=writer) From 8d1a117b75482c8ea8358e3946dbe1dab6e0c8d2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 10:59:01 -0400 Subject: [PATCH 17/72] Apply header fix to all remaining pair styles docs --- doc/src/pair_adp.rst | 4 ++-- doc/src/pair_agni.rst | 6 ++--- doc/src/pair_airebo.rst | 26 +++++++++------------ doc/src/pair_beck.rst | 8 +++---- doc/src/pair_born.rst | 9 ++++--- doc/src/pair_brownian.rst | 9 +++---- doc/src/pair_buck.rst | 21 ++++++++--------- doc/src/pair_buck6d_coul_gauss.rst | 1 + doc/src/pair_buck_long.rst | 6 ++--- doc/src/pair_charmm.rst | 24 +++++++++---------- doc/src/pair_class2.rst | 6 ++--- doc/src/pair_coeff.rst | 4 ---- doc/src/pair_colloid.rst | 8 +++---- doc/src/pair_comb.rst | 5 ++-- doc/src/pair_coul.rst | 1 - doc/src/pair_coul_diel.rst | 4 ++-- doc/src/pair_coul_slater.rst | 5 ++++ doc/src/pair_cs.rst | 11 +++------ doc/src/pair_dipole.rst | 23 +++++++++--------- doc/src/pair_dpd.rst | 21 +++++++---------- doc/src/pair_dpd_fdt.rst | 5 ++-- doc/src/pair_eam.rst | 6 ++--- doc/src/pair_edip.rst | 5 ++-- doc/src/pair_eim.rst | 4 ++-- doc/src/pair_exp6_rx.rst | 4 ++-- doc/src/pair_fep_soft.rst | 16 ++++++------- doc/src/pair_gauss.rst | 13 +++++------ doc/src/pair_gayberne.rst | 12 ++++------ doc/src/pair_gran.rst | 18 +++++++------- doc/src/pair_gromacs.rst | 21 +++++++---------- doc/src/pair_gw.rst | 1 + doc/src/pair_hbond_dreiding.rst | 9 +++---- doc/src/pair_hybrid.rst | 9 +++---- doc/src/pair_lj.rst | 1 - doc/src/pair_lj96.rst | 8 +++---- doc/src/pair_lj_cubic.rst | 8 +++---- doc/src/pair_lj_cut_coul.rst | 2 +- doc/src/pair_lj_cut_tip4p.rst | 1 - doc/src/pair_lj_expand.rst | 17 ++++++-------- doc/src/pair_lj_long.rst | 17 ++++++-------- doc/src/pair_lj_smooth.rst | 4 ++-- doc/src/pair_lj_smooth_linear.rst | 4 ++-- doc/src/pair_lubricate.rst | 9 +++---- doc/src/pair_lubricateU.rst | 1 + doc/src/pair_mdf.rst | 2 ++ doc/src/pair_meam_spline.rst | 4 ++-- doc/src/pair_mesodpd.rst | 3 +++ doc/src/pair_mesont_tpm.rst | 2 +- doc/src/pair_mie.rst | 4 ++-- doc/src/pair_mm3_switch3_coulgauss_long.rst | 2 +- doc/src/pair_modify.rst | 4 ---- doc/src/pair_morse.rst | 21 +++++++---------- doc/src/pair_multi_lucy_rx.rst | 4 ++-- doc/src/pair_nm.rst | 18 +++++++------- doc/src/pair_oxdna.rst | 4 ++++ doc/src/pair_oxdna2.rst | 5 ++++ doc/src/pair_oxrna2.rst | 5 ++++ doc/src/pair_peri.rst | 11 +++++---- doc/src/pair_reaxc.rst | 8 +++---- doc/src/pair_resquared.rst | 8 +++---- doc/src/pair_sdk.rst | 6 ++--- doc/src/pair_smd_triangulated_surface.rst | 2 +- doc/src/pair_smd_ulsph.rst | 2 +- doc/src/pair_snap.rst | 4 ++-- doc/src/pair_soft.rst | 8 +++---- doc/src/pair_spin_dipole.rst | 1 + doc/src/pair_spin_magelec.rst | 2 +- doc/src/pair_style.rst | 4 ---- doc/src/pair_sw.rst | 16 ++++--------- doc/src/pair_table.rst | 12 ++++------ doc/src/pair_table_rx.rst | 4 ++-- doc/src/pair_tersoff.rst | 23 +++++++----------- doc/src/pair_tersoff_mod.rst | 19 +++++++-------- doc/src/pair_tersoff_zbl.rst | 12 ++++------ doc/src/pair_thole.rst | 5 ++-- doc/src/pair_ufm.rst | 12 ++++------ doc/src/pair_vashishta.rst | 17 ++++++-------- doc/src/pair_write.rst | 4 ---- doc/src/pair_yukawa.rst | 12 ++++------ doc/src/pair_yukawa_colloid.rst | 8 +++---- doc/src/pair_zbl.rst | 12 ++++------ 81 files changed, 309 insertions(+), 378 deletions(-) diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 7017549925..5eec0004bf 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -1,10 +1,10 @@ .. index:: pair_style adp +.. index:: pair_style adp/omp pair_style adp command ====================== -pair_style adp/omp command -========================== +Accelerator Variants: *adp/omp* Syntax """""" diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index ee69f40d80..087c39e8f9 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -1,10 +1,10 @@ .. index:: pair_style agni +.. index:: pair_style agni/omp pair_style agni command -======================== +======================= -pair_style agni/omp command -============================ +Accelerator Variants: *agni/omp* Syntax """""" diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index f3be0e85de..d631d0a3d0 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -1,31 +1,27 @@ .. index:: pair_style airebo +.. index:: pair_style airebo/intel +.. index:: pair_style airebo/omp +.. index:: pair_style airebo/morse +.. index:: pair_style airebo/morse/intel +.. index:: pair_style airebo/morse/omp +.. index:: pair_style rebo +.. index:: pair_style rebo/intel +.. index:: pair_style rebo/omp pair_style airebo command ========================= -pair_style airebo/intel command -=============================== - -pair_style airebo/omp command -============================= +Accelerator Variants: *airebo/intel*, *airebo/omp* pair_style airebo/morse command =============================== -pair_style airebo/morse/intel command -===================================== - -pair_style airebo/morse/omp command -=================================== +Accelerator Variants: *airebo/morse/intel*, *airebo/morse/omp* pair_style rebo command ======================= -pair_style rebo/intel command -============================= - -pair_style rebo/omp command -=========================== +Accelerator Variants: *rebo/intel*, *rebo/omp* Syntax """""" diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 0e63fe77ba..44bc317138 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -1,13 +1,11 @@ .. index:: pair_style beck +.. index:: pair_style beck/gpu +.. index:: pair_style beck/omp pair_style beck command ======================= -pair_style beck/gpu command -=========================== - -pair_style beck/omp command -=========================== +Accelerator Variants: *beck/gpu*, *beck/omp* Syntax """""" diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 15ce4ac560..65be948f82 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -14,27 +14,26 @@ pair_style born command ======================= -Accelerator Styles: *born/omp*, *born/gpu* +Accelerator Variants: *born/omp*, *born/gpu* pair_style born/coul/long command ================================= -Accelerator Styles: *born/coul/long/gpu*, *born/coul/long/omp* +Accelerator Variants: *born/coul/long/gpu*, *born/coul/long/omp* pair_style born/coul/msm command ================================ -Accelerator Styles: *born/coul/msm/omp* +Accelerator Variants: *born/coul/msm/omp* pair_style born/coul/wolf command ================================= -Accelerator Styles: *born/coul/wolf/gpu*, *born/coul/wolf/omp* +Accelerator Variants: *born/coul/wolf/gpu*, *born/coul/wolf/omp* pair_style born/coul/dsf command ================================ - Syntax """""" diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index ea311d603e..43c17c9087 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -1,16 +1,17 @@ .. index:: pair_style brownian +.. index:: pair_style brownian/omp +.. index:: pair_style brownian/poly +.. index:: pair_style brownian/poly/omp pair_style brownian command =========================== -pair_style brownian/omp command -================================ +Accelerator Variants: *brownian/omp* pair_style brownian/poly command ================================ -pair_style brownian/poly/omp command -==================================== +Accelerator Variants: *brownian/poly/omp* Syntax """""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 6ff5f84fe2..5f255ece39 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,5 +1,4 @@ .. index:: pair_style buck -.. index:: pair_style buck .. index:: pair_style buck/gpu .. index:: pair_style buck/intel .. index:: pair_style buck/kk @@ -18,24 +17,24 @@ .. index:: pair_style buck/coul/msm/omp pair_style buck command -======================== +======================= -Accelerator Styles: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* +Accelerator Variants: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* pair_style buck/coul/cut command -================================= +================================ -Accelerator Styles: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* +Accelerator Variants: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* pair_style buck/coul/long command -================================== - -Accelerator Styles: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* - -pair_style buck/coul/msm command ================================= -Accelerator Styles: *buck/coul/msm/omp* +Accelerator Variants: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* + +pair_style buck/coul/msm command +================================ + +Accelerator Variants: *buck/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 7d3e5b9a22..5f96a93fee 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -1,4 +1,5 @@ .. index:: pair_style buck6d/coul/gauss/dsf +.. index:: pair_style buck6d/coul/gauss/long pair_style buck6d/coul/gauss/dsf command ======================================== diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index c0dd81d78f..1883cee637 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -1,10 +1,10 @@ .. index:: pair_style buck/long/coul/long +.. index:: pair_style buck/long/coul/long/omp pair_style buck/long/coul/long command -======================================= +====================================== -pair_style buck/long/coul/long/omp command -=========================================== +Accelerator Variants: *buck/long/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index cef1b333fb..6d81266a35 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -17,30 +17,30 @@ .. index:: pair_style lj/charmmfsw/coul/long pair_style lj/charmm/coul/charmm command -========================================= +======================================== -Accelerator Styles: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* +Accelerator Variants: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* pair_style lj/charmm/coul/charmm/implicit command -================================================== +================================================= -Accelerator Styles: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* +Accelerator Variants: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* pair_style lj/charmm/coul/long command -======================================= - -Accelerator Styles: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* - -pair_style lj/charmm/coul/msm command ====================================== -Accelerator Styles: *lj/charmm/coul/msm/omp* +Accelerator Variants: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* + +pair_style lj/charmm/coul/msm command +===================================== + +Accelerator Variants: *lj/charmm/coul/msm/omp* pair_style lj/charmmfsw/coul/charmmfsh command -=============================================== +============================================== pair_style lj/charmmfsw/coul/long command -========================================== +========================================= Syntax """""" diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 6fcdd4f533..cfa085cc28 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -13,17 +13,17 @@ pair_style lj/class2 command ============================ -Accelerator Styles: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* +Accelerator Variants: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* pair_style lj/class2/coul/cut command ===================================== -Accelerator Styles: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* +Accelerator Variants: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* pair_style lj/class2/coul/long command ====================================== -Accelerator Styles: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* +Accelerator Variants: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index ea62d839ab..7c72bb5843 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -1,7 +1,3 @@ -.. index:: pair_coeff - -pair_coeff command -================== Syntax """""" diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 4bb82e9615..040bea2487 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style colloid +.. index:: pair_style colloid/gpu +.. index:: pair_style colloid/omp pair_style colloid command ========================== -pair_style colloid/gpu command -============================== - -pair_style colloid/omp command -============================== +Accelerator Variants: *colloid/gpu*, *colloid/omp* Syntax """""" diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 441f982996..2e164d46fc 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -1,10 +1,11 @@ .. index:: pair_style comb +.. index:: pair_style comb/omp +.. index:: pair_style comb3 pair_style comb command ======================= -pair_style comb/omp command -=========================== +Accelerator Variants: *comb/omp* pair_style comb3 command ======================== diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 37193d752c..4def43647f 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -25,7 +25,6 @@ .. index:: pair_style tip4p/long .. index:: pair_style tip4p/long/omp - pair_style coul/cut command =========================== diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index e979ceef31..bcf0c48e4d 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -1,10 +1,10 @@ .. index:: pair_style coul/diel +.. index:: pair_style coul/diel/omp pair_style coul/diel command ============================ -pair_style coul/diel/omp command -================================ +Accelerator Variants: *coul/diel/omp* Syntax """""" diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index cc8e6f243c..a4d8b253b1 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -1,4 +1,9 @@ .. index:: pair_style coul/slater +.. index:: pair_style coul/slater/cut +.. index:: pair_style coul/slater/long + +pair_style coul/slater command +============================== pair_style coul/slater/cut command ================================== diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index ae5c29aa32..f41d840216 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -13,38 +13,33 @@ pair_style born/coul/dsf/cs command =================================== - pair_style born/coul/long/cs command ==================================== -Accelerator Styles: *born/coul/long/cs/gpu* +Accelerator Variants: *born/coul/long/cs/gpu* pair_style born/coul/wolf/cs command ==================================== -Accelerator Styles: *born/coul/wolf/cs/gpu* +Accelerator Variants: *born/coul/wolf/cs/gpu* pair_style buck/coul/long/cs command ==================================== - pair_style coul/long/cs command =============================== -Accelerator Styles: *coul/long/cs/gpu* +Accelerator Variants: *coul/long/cs/gpu* pair_style coul/wolf/cs command =============================== - pair_style lj/cut/coul/long/cs command ====================================== - pair_style lj/class2/coul/long/cs command ========================================= - Syntax """""" diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 21548be4f0..602c374d9f 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -1,28 +1,27 @@ .. index:: pair_style lj/cut/dipole/cut +.. index:: pair_style lj/cut/dipole/cut/gpu +.. index:: pair_style lj/cut/dipole/cut/omp +.. index:: pair_style lj/sf/dipole/sf +.. index:: pair_style lj/sf/dipole/sf/gpu +.. index:: pair_style lj/sf/dipole/sf/omp +.. index:: pair_style lj/cut/dipole/long +.. index:: pair_style lj/cut/dipole/long/gpu +.. index:: pair_style lj/long/dipole/long pair_style lj/cut/dipole/cut command ==================================== -pair_style lj/cut/dipole/cut/gpu command -======================================== - -pair_style lj/cut/dipole/cut/omp command -======================================== +Accelerator Variants: *lj/cut/dipole/cut/gpu*, *lj/cut/dipole/cut/omp* pair_style lj/sf/dipole/sf command ================================== -pair_style lj/sf/dipole/sf/gpu command -====================================== - -pair_style lj/sf/dipole/sf/omp command -====================================== +Accelerator Variants: *lj/sf/dipole/sf/gpu*, *lj/sf/dipole/sf/omp* pair_style lj/cut/dipole/long command ===================================== -pair_style lj/cut/dipole/long/gpu command -========================================= +Accelerator Variants: *lj/cut/dipole/long/gpu* pair_style lj/long/dipole/long command ====================================== diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 94c9fa9bea..d1d84407c4 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -1,25 +1,20 @@ .. index:: pair_style dpd +.. index:: pair_style dpd/gpu +.. index:: pair_style dpd/intel +.. index:: pair_style dpd/omp +.. index:: pair_style dpd/tstat +.. index:: pair_style dpd/tstat/gpu +.. index:: pair_style dpd/tstat/omp pair_style dpd command ====================== -pair_style dpd/gpu command -========================== - -pair_style dpd/intel command -============================ - -pair_style dpd/omp command -========================== +Accelerator Variants: *dpd/gpu*, *dpd/intel*, *dpd/omp* pair_style dpd/tstat command ============================ -pair_style dpd/tstat/gpu command -================================ - -pair_style dpd/tstat/omp command -================================ +Accelerator Variants: *dpd/tstat/gpu*, *dpd/tstat/omp* Syntax """""" diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index e0659a7b78..bb810b0fe6 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -1,4 +1,6 @@ .. index:: pair_style dpd/fdt +.. index:: pair_style dpd/fdt/energy +.. index:: pair_style dpd/fdt/energy/kk pair_style dpd/fdt command ========================== @@ -6,8 +8,7 @@ pair_style dpd/fdt command pair_style dpd/fdt/energy command ================================= -pair_style dpd/fdt/energy/kk command -==================================== +Accelerator Variants: *dpd/fdt/energy/kk* Syntax """""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 56eed64d01..690b387bad 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -22,12 +22,12 @@ pair_style eam command ====================== -Accelerator Styles: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* +Accelerator Variants: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* pair_style eam/alloy command ============================ -Accelerator Styles: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* +Accelerator Variants: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* pair_style eam/cd command ========================= @@ -38,7 +38,7 @@ pair_style eam/cd/old command pair_style eam/fs command ========================= -Accelerator Styles: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* +Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* Syntax """""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index d8e747ddf4..8f8d70f2f6 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -1,10 +1,11 @@ .. index:: pair_style edip +.. index:: pair_style edip/omp +.. index:: pair_style edip/multi pair_style edip command ======================= -pair_style edip/omp command -=========================== +Accelerator Variants: *edip/omp* pair_style edip/multi command ============================= diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index aef7dba3a4..8360dbab64 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -1,10 +1,10 @@ .. index:: pair_style eim +.. index:: pair_style eim/omp pair_style eim command ====================== -pair_style eim/omp command -========================== +Accelerator Variants: *eim/omp* Syntax """""" diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d6fe4850ce..49a4c5436f 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style exp6/rx +.. index:: pair_style exp6/rx/kk pair_style exp6/rx command ========================== -pair_style exp6/rx/kk command -============================= +Accelerator Variants: *exp6/rx/kk* Syntax """""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index be35f84508..109ddfdf21 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -22,27 +22,27 @@ pair_style lj/cut/soft command ============================== -Accelerator Styles: *lj/cut/soft/omp* +Accelerator Variants: *lj/cut/soft/omp* pair_style lj/cut/coul/cut/soft command ======================================= -Accelerator Styles: *lj/cut/coul/cut/soft/omp* +Accelerator Variants: *lj/cut/coul/cut/soft/omp* pair_style lj/cut/coul/long/soft command ======================================== -Accelerator Styles: *lj/cut/coul/long/soft/omp* +Accelerator Variants: *lj/cut/coul/long/soft/omp* pair_style lj/cut/tip4p/long/soft command ========================================= -Accelerator Styles: *lj/cut/tip4p/long/soft/omp* +Accelerator Variants: *lj/cut/tip4p/long/soft/omp* pair_style lj/charmm/coul/long/soft command =========================================== -Accelerator Styles: *lj/charmm/coul/long/soft/omp* +Accelerator Variants: *lj/charmm/coul/long/soft/omp* pair_style lj/class2/soft command ================================= @@ -56,17 +56,17 @@ pair_style lj/class2/coul/long/soft command pair_style coul/cut/soft command ================================ -Accelerator Styles: *coul/cut/soft/omp* +Accelerator Variants: *coul/cut/soft/omp* pair_style coul/long/soft command ================================= -Accelerator Styles: *coul/long/soft/omp* +Accelerator Variants: *coul/long/soft/omp* pair_style tip4p/long/soft command ================================== -Accelerator Styles: *tip4p/long/soft/omp* +Accelerator Variants: *tip4p/long/soft/omp* pair_style morse/soft command ============================= diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 8c7ce74174..9b516cce7b 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -1,19 +1,18 @@ .. index:: pair_style gauss +.. index:: pair_style gauss/gpu +.. index:: pair_style gauss/omp +.. index:: pair_style gauss/cut +.. index:: pair_style gauss/cut/omp pair_style gauss command ======================== -pair_style gauss/gpu command -============================ - -pair_style gauss/omp command -============================ +Accelerator Variants: *gauss/gpu*, *gauss/omp* pair_style gauss/cut command ============================ -pair_style gauss/cut/omp command -================================ +Accelerator Variants: *gauss/cut/omp* Syntax """""" diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 1e8094feef..309e949f97 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -1,16 +1,12 @@ .. index:: pair_style gayberne +.. index:: pair_style gayberne/gpu +.. index:: pair_style gayberne/intel +.. index:: pair_style gayberne/omp pair_style gayberne command =========================== -pair_style gayberne/gpu command -=============================== - -pair_style gayberne/intel command -================================= - -pair_style gayberne/omp command -=============================== +Accelerator Variants: *gayberne/gpu*, *gayberne/intel*, *gayberne/omp* Syntax """""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 9aacfdfa31..d3f87839e8 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -1,25 +1,25 @@ .. index:: pair_style gran/hooke +.. index:: pair_style gran/hooke/omp +.. index:: pair_style gran/hooke/history +.. index:: pair_style gran/hooke/history/omp +.. index:: pair_style gran/hooke/history/kk +.. index:: pair_style gran/hertz/history +.. index:: pair_style gran/hertz/history/omp pair_style gran/hooke command ============================= -pair_style gran/hooke/omp command -================================= +Accelerator Variants: *gran/hooke/omp* pair_style gran/hooke/history command ===================================== -pair_style gran/hooke/history/omp command -========================================= - -pair_style gran/hooke/history/kk command -======================================== +Accelerator Variants: *gran/hooke/history/omp*, *gran/hooke/history/kk* pair_style gran/hertz/history command ===================================== -pair_style gran/hertz/history/omp command -========================================= +Accelerator Variants: *gran/hertz/history/omp* Syntax """""" diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index a4c065e24d..88cb4ce880 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -1,25 +1,20 @@ .. index:: pair_style lj/gromacs +.. index:: pair_style lj/gromacs/gpu +.. index:: pair_style lj/gromacs/kk +.. index:: pair_style lj/gromacs/omp +.. index:: pair_style lj/gromacs/coul/gromacs +.. index:: pair_style lj/gromacs/coul/gromacs/kk +.. index:: pair_style lj/gromacs/coul/gromacs/omp pair_style lj/gromacs command ============================= -pair_style lj/gromacs/gpu command -================================= - -pair_style lj/gromacs/kk command -================================ - -pair_style lj/gromacs/omp command -================================= +Accelerator Variants: *lj/gromacs/gpu*, *lj/gromacs/kk*, *lj/gromacs/omp* pair_style lj/gromacs/coul/gromacs command ========================================== -pair_style lj/gromacs/coul/gromacs/kk command -============================================= - -pair_style lj/gromacs/coul/gromacs/omp command -============================================== +Accelerator Variants: *lj/gromacs/coul/gromacs/kk*, *lj/gromacs/coul/gromacs/omp* Syntax """""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 544d13df9b..d0a7e69b00 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -1,4 +1,5 @@ .. index:: pair_style gw +.. index:: pair_style gw/zbl pair_style gw command ===================== diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 0d821fa946..5e7183a348 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -1,16 +1,17 @@ .. index:: pair_style hbond/dreiding/lj +.. index:: pair_style hbond/dreiding/lj/omp +.. index:: pair_style hbond/dreiding/morse +.. index:: pair_style hbond/dreiding/morse/omp pair_style hbond/dreiding/lj command ==================================== -pair_style hbond/dreiding/lj/omp command -======================================== +Accelerator Variants: *hbond/dreiding/lj/omp* pair_style hbond/dreiding/morse command ======================================= -pair_style hbond/dreiding/morse/omp command -=========================================== +Accelerator Variants: *hbond/dreiding/morse/omp* Syntax """""" diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 924e19a8b3..558c326175 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -1,16 +1,17 @@ .. index:: pair_style hybrid +.. index:: pair_style hybrid/kk +.. index:: pair_style hybrid/overlay +.. index:: pair_style hybrid/overlay/kk pair_style hybrid command ========================= -pair_style hybrid/kk command -============================ +Accelerator Variants: *hybrid/kk* pair_style hybrid/overlay command ================================= -pair_style hybrid/overlay/kk command -==================================== +Accelerator Variants: *hybrid/overlay/kk* Syntax """""" diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index b8c5be3940..22f0d0dd37 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/opt .. index:: pair_style lj/cut/omp - pair_style lj/cut command ========================= diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 7ea3c2c9c1..3f1172618b 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj96/cut +.. index:: pair_style lj96/cut/gpu +.. index:: pair_style lj96/cut/omp pair_style lj96/cut command =========================== -pair_style lj96/cut/gpu command -=============================== - -pair_style lj96/cut/omp command -=============================== +Accelerator Variants: *lj96/cut/gpu*, *lj96/cut/omp* Syntax """""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 800de20e6f..e220e6e67c 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj/cubic +.. index:: pair_style lj/cubic/gpu +.. index:: pair_style lj/cubic/omp pair_style lj/cubic command =========================== -pair_style lj/cubic/gpu command -=============================== - -pair_style lj/cubic/omp command -=============================== +Accelerator Variants: *lj/cubic/gpu*, *lj/cubic/omp* Syntax """""" diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index ec34777d8d..f729c2016e 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -30,7 +30,7 @@ Accelerator Variants: *lj/cut/coul/cut/gpu*, *lj/cut/coul/cut/kk*, *lj/cut/coul/ pair_style lj/cut/coul/debye command ==================================== -Accelerator Variants: *lj/cut/coul/debye/gpu*, lj/cut/coul/debye/kk, *lj/cut/coul/debye/omp* +Accelerator Variants: *lj/cut/coul/debye/gpu*, *lj/cut/coul/debye/kk*, *lj/cut/coul/debye/omp* pair_style lj/cut/coul/dsf command ================================== diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 14e970a59e..4f55f3b14e 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/tip4p/long/omp .. index:: pair_style lj/cut/tip4p/long/opt - pair_style lj/cut/tip4p/cut command =================================== diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 8defbc3635..4d619a67e2 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/expand +.. index:: pair_style lj/expand/gpu +.. index:: pair_style lj/expand/kk +.. index:: pair_style lj/expand/omp +.. index:: pair_style lj/expand/coul/long +.. index:: pair_style lj/expand/coul/long/gpu pair_style lj/expand command ============================ -pair_style lj/expand/gpu command -================================ - -pair_style lj/expand/kk command -=============================== - -pair_style lj/expand/omp command -================================ +Accelerator Variants: *lj/expand/gpu*, *lj/expand/kk*, *lj/expand/omp* pair_style lj/expand/coul/long command ====================================== -pair_style lj/expand/coul/long/gpu command -========================================== +Accelerator Variants: *lj/expand/coul/long/gpu* Syntax """""" diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index ff6d834ad6..3609d093d9 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/long/coul/long +.. index:: pair_style lj/long/coul/long/intel +.. index:: pair_style lj/long/coul/long/omp +.. index:: pair_style lj/long/coul/long/opt +.. index:: pair_style lj/long/tip4p/long +.. index:: pair_style lj/long/tip4p/long/omp pair_style lj/long/coul/long command ==================================== -pair_style lj/long/coul/long/intel command -========================================== - -pair_style lj/long/coul/long/omp command -======================================== - -pair_style lj/long/coul/long/opt command -======================================== +Accelerator Variants: *lj/long/coul/long/intel*, *lj/long/coul/long/omp*, *lj/long/coul/long/opt* pair_style lj/long/tip4p/long command ===================================== -pair_style lj/long/tip4p/long/omp command -========================================= +Accelerator Variants: *lj/long/tip4p/long/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 3137a17f73..7ba12c89ba 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth +.. index:: pair_style lj/smooth/omp pair_style lj/smooth command ============================ -pair_style lj/smooth/omp command -================================ +Accelerator Variants: *lj/smooth/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 833a4f035d..b105fc4911 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth/linear +.. index:: pair_style lj/smooth/linear/omp pair_style lj/smooth/linear command =================================== -pair_style lj/smooth/linear/omp command -======================================= +Accelerator Variants: *lj/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 711f2576b3..e83a16c80b 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -1,16 +1,17 @@ .. index:: pair_style lubricate +.. index:: pair_style lubricate/omp +.. index:: pair_style lubricate/poly +.. index:: pair_style lubricate/poly/omp pair_style lubricate command ============================ -pair_style lubricate/omp command -================================ +Accelerator Variants: *lubricate/omp* pair_style lubricate/poly command ================================= -pair_style lubricate/poly/omp command -===================================== +Accelerator Variants: *lubricate/poly/omp* Syntax """""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index f4224ede47..a9382556c5 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -1,4 +1,5 @@ .. index:: pair_style lubricateU +.. index:: pair_style lubricateU/poly pair_style lubricateU command ============================= diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 1b46c51220..84d312e47c 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -1,4 +1,6 @@ .. index:: pair_style lj/mdf +.. index:: pair_style buck/mdf +.. index:: pair_style lennard/mdf pair_style lj/mdf command ========================= diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index bbba66c2b5..b5c94385fa 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -1,10 +1,10 @@ .. index:: pair_style meam/spline +.. index:: pair_style meam/spline/omp pair_style meam/spline command ============================== -pair_style meam/spline/omp command -================================== +Accelerator Variants: *meam/spline/omp* Syntax """""" diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 093eb707ad..1efdfa8b45 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -1,4 +1,7 @@ .. index:: pair_style edpd +.. index:: pair_style mdpd +.. index:: pair_style mdpd/rhosum +.. index:: pair_style tdpd pair_style edpd command ======================= diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index f5b5789315..e26f16fba3 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -1,7 +1,7 @@ .. index:: pair_style mesont/tpm pair_style mesont/tpm command -============================== +============================= Syntax """""" diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index 469817ee5e..e1a34893c9 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -1,10 +1,10 @@ .. index:: pair_style mie/cut +.. index:: pair_style mie/cut/gpu pair_style mie/cut command ========================== -pair_style mie/cut/gpu command -============================== +Accelerator Variants: *mie/cut/gpu* Syntax """""" diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 2b7e9cb903..798df0bf7a 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -1,7 +1,7 @@ .. index:: pair_style mm3/switch3/coulgauss/long pair_style mm3/switch3/coulgauss/long command -============================================== +============================================= Syntax """""" diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b8969c0131..21d0977047 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -1,7 +1,3 @@ -.. index:: pair_modify - -pair_modify command -=================== Syntax """""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 1c8e731bc1..5ede37a916 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -1,25 +1,20 @@ .. index:: pair_style morse +.. index:: pair_style morse/gpu +.. index:: pair_style morse/omp +.. index:: pair_style morse/opt +.. index:: pair_style morse/smooth/linear +.. index:: pair_style morse/smooth/linear/omp +.. index:: pair_style morse/kk pair_style morse command ======================== -pair_style morse/gpu command -============================ - -pair_style morse/omp command -============================ - -pair_style morse/opt command -============================ +Accelerator Variants: *morse/gpu*, *morse/omp*, *morse/opt*, *morse/kk* pair_style morse/smooth/linear command ====================================== -pair_style morse/smooth/linear/omp command -========================================== - -pair_style morse/kk command -=========================== +Accelerator Variants: *morse/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 42a2525195..f6e6652271 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style multi/lucy/rx +.. index:: pair_style multi/lucy/rx/kk pair_style multi/lucy/rx command ================================ -pair_style multi/lucy/rx/kk command -=================================== +Accelerator Variants: *multi/lucy/rx/kk* Syntax """""" diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 7d7648cdc9..d38e21fd15 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -1,22 +1,24 @@ .. index:: pair_style nm/cut +.. index:: pair_style nm/cut/coul/cut +.. index:: pair_style nm/cut/coul/long +.. index:: pair_style nm/cut/omp +.. index:: pair_style nm/cut/coul/cut/omp +.. index:: pair_style nm/cut/coul/long/omp pair_style nm/cut command ========================= +Accelerator Variants: *nm/cut/omp* + pair_style nm/cut/coul/cut command ================================== +Accelerator Variants: *nm/cut/coul/cut/omp* + pair_style nm/cut/coul/long command =================================== -pair_style nm/cut/omp command -============================= - -pair_style nm/cut/coul/cut/omp command -====================================== - -pair_style nm/cut/coul/long/omp command -======================================= +Accelerator Variants: *nm/cut/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index c16e872ccf..4cc57868b4 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -1,4 +1,8 @@ .. index:: pair_style oxdna/excv +.. index:: pair_style oxdna/stk +.. index:: pair_style oxdna/hbond +.. index:: pair_style oxdna/xstk +.. index:: pair_style oxdna/coaxstk pair_style oxdna/excv command ============================= diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index f63bec6a7f..ee01f2f488 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxdna2/excv +.. index:: pair_style oxdna2/stk +.. index:: pair_style oxdna2/hbond +.. index:: pair_style oxdna2/xstk +.. index:: pair_style oxdna2/coaxstk +.. index:: pair_style oxdna2/dh pair_style oxdna2/excv command ============================== diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 05fd27b4a0..831e4d9c4e 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxrna2/excv +.. index:: pair_style oxrna2/stk +.. index:: pair_style oxrna2/hbond +.. index:: pair_style oxrna2/xstk +.. index:: pair_style oxrna2/coaxstk +.. index:: pair_style oxrna2/dh pair_style oxrna2/excv command ============================== diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index de487df9a3..2a1c7f6aa5 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -1,16 +1,19 @@ .. index:: pair_style peri/pmb +.. index:: pair_style peri/pmb/omp +.. index:: pair_style peri/lps +.. index:: pair_style peri/lps/omp +.. index:: pair_style peri/ves +.. index:: pair_style peri/eps pair_style peri/pmb command =========================== -pair_style peri/pmb/omp command -=============================== +Accelerator Variants: *peri/pmb/omp* pair_style peri/lps command =========================== -pair_style peri/lps/omp command -=============================== +Accelerator Variants: *peri/lps/omp* pair_style peri/ves command =========================== diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index 4d4368729e..13ff16d4d3 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -1,13 +1,11 @@ .. index:: pair_style reax/c +.. index:: pair_style reax/c/kk +.. index:: pair_style reax/c/omp pair_style reax/c command ========================= -pair_style reax/c/kk command -============================ - -pair_style reax/c/omp command -============================= +Accelerator Variants: *reax/c/kk*, *reax/c/omp* Syntax """""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 33b40f6776..448af410db 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -1,13 +1,11 @@ .. index:: pair_style resquared +.. index:: pair_style resquared/gpu +.. index:: pair_style resquared/omp pair_style resquared command ============================ -pair_style resquared/gpu command -================================ - -pair_style resquared/omp command -================================ +Accelerator Variants: *resquared/gpu*, *resquared/omp* Syntax """""" diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 02fed36130..541c53d37e 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -11,17 +11,17 @@ pair_style lj/sdk command ========================= -Accelerator Styles: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* +Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* pair_style lj/sdk/coul/long command =================================== -Accelerator Styles: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* +Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* pair_style lj/sdk/coul/msm command ================================== -Accelerator Styles: *lj/sdk/coul/msm/omp* +Accelerator Variants: *lj/sdk/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 9dbd66dcd8..1e33254865 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/tri_surface pair_style smd/tri_surface command -=================================== +================================== Syntax """""" diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 6b3ee7f019..33946d4649 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/ulsph pair_style smd/ulsph command -============================= +============================ Syntax """""" diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 2ba2a9dd58..8aa10f5986 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -1,10 +1,10 @@ .. index:: pair_style snap +.. index:: pair_style snap/kk pair_style snap command ======================= -pair_style snap/kk command -========================== +Accelerator Variants: *snap/kk* Syntax """""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 294868f872..cc024cb6dd 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -1,13 +1,11 @@ .. index:: pair_style soft +.. index:: pair_style soft/gpu +.. index:: pair_style soft/omp pair_style soft command ======================= -pair_style soft/gpu command -=========================== - -pair_style soft/omp command -=========================== +Accelerator Variants: *soft/gpu*, *soft/omp* Syntax """""" diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c86083f1e5..d1bbf3b699 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -1,4 +1,5 @@ .. index:: pair_style spin/dipole/cut +.. index:: pair_style spin/dipole/long pair_style spin/dipole/cut command ================================== diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 5ef01ad10c..1860ed4677 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -1,7 +1,7 @@ .. index:: pair_style spin/magelec pair_style spin/magelec command -================================ +=============================== Syntax """""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4feaeacad0..1b9ceaf0ee 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -1,7 +1,3 @@ -.. index:: pair_style - -pair_style command -================== Syntax """""" diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index b673f652aa..bea417ed3d 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -1,19 +1,13 @@ .. index:: pair_style sw +.. index:: pair_style sw/gpu +.. index:: pair_style sw/intel +.. index:: pair_style sw/kk +.. index:: pair_style sw/omp pair_style sw command ===================== -pair_style sw/gpu command -========================= - -pair_style sw/intel command -=========================== - -pair_style sw/kk command -======================== - -pair_style sw/omp command -========================= +Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp* Syntax """""" diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 1a35cea7fd..39ed690551 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -1,16 +1,12 @@ .. index:: pair_style table +.. index:: pair_style table/gpu +.. index:: pair_style table/kk +.. index:: pair_style table/omp pair_style table command ======================== -pair_style table/gpu command -============================ - -pair_style table/kk command -=========================== - -pair_style table/omp command -============================ +Accelerator Variants: *table/gpu*, *table/kk*, *table/omp* Syntax """""" diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 5545da22ef..9d23a479a3 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style table/rx +.. index:: pair_style table/rx/kk pair_style table/rx command =========================== -pair_style table/rx/kk command -============================== +Accelerator Variants: *table/rx/kk* Syntax """""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 251e12c87a..d9e5d60cd9 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -1,25 +1,20 @@ .. index:: pair_style tersoff +.. index:: pair_style tersoff/table +.. index:: pair_style tersoff/gpu +.. index:: pair_style tersoff/intel +.. index:: pair_style tersoff/kk +.. index:: pair_style tersoff/omp +.. index:: pair_style tersoff/table/omp pair_style tersoff command ========================== +Accelerator Variants: *tersoff/gpu*, *tersoff/intel*, *tersoff/kk*, *tersoff/omp* + pair_style tersoff/table command ================================ -pair_style tersoff/gpu command -============================== - -pair_style tersoff/intel command -================================ - -pair_style tersoff/kk command -============================= - -pair_style tersoff/omp command -============================== - -pair_style tersoff/table/omp command -==================================== +Accelerator Variants: *tersoff/table/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 0426e65f14..7457541c18 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -1,22 +1,19 @@ .. index:: pair_style tersoff/mod +.. index:: pair_style tersoff/mod/c +.. index:: pair_style tersoff/mod/gpu +.. index:: pair_style tersoff/mod/kk +.. index:: pair_style tersoff/mod/omp +.. index:: pair_style tersoff/mod/c/omp pair_style tersoff/mod command ============================== +Accelerator Variants: *tersoff/mod/gpu*, *tersoff/mod/kk*, *tersoff/mod/omp* + pair_style tersoff/mod/c command ================================ -pair_style tersoff/mod/gpu command -================================== - -pair_style tersoff/mod/kk command -================================= - -pair_style tersoff/mod/omp command -================================== - -pair_style tersoff/mod/c/omp command -==================================== +Accelerator Variants: *tersoff/mod/c/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index eff394d9a0..19e77ce8eb 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style tersoff/zbl +.. index:: pair_style tersoff/zbl/gpu +.. index:: pair_style tersoff/zbl/kk +.. index:: pair_style tersoff/zbl/omp pair_style tersoff/zbl command ============================== -pair_style tersoff/zbl/gpu command -================================== - -pair_style tersoff/zbl/kk command -================================= - -pair_style tersoff/zbl/omp command -================================== +Accelerator Variants: *tersoff/zbl/gpu*, *tersoff/zbl/kk*, *tersoff/zbl/omp* Syntax """""" diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 9b05e06cee..a8cf8ee044 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -1,4 +1,6 @@ .. index:: pair_style thole +.. index:: pair_style lj/cut/thole/long +.. index:: pair_style lj/cut/thole/long/omp pair_style thole command ======================== @@ -6,8 +8,7 @@ pair_style thole command pair_style lj/cut/thole/long command ==================================== -pair_style lj/cut/thole/long/omp command -======================================== +Accelerator Variants: *lj/cut/thole/long/omp* Syntax """""" diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index d9b08aaea2..140bb75ee7 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -1,16 +1,12 @@ .. index:: pair_style ufm +.. index:: pair_style ufm/gpu +.. index:: pair_style ufm/omp +.. index:: pair_style ufm/opt pair_style ufm command ====================== -pair_style ufm/gpu command -========================== - -pair_style ufm/omp command -========================== - -pair_style ufm/opt command -========================== +Accelerator Variants: *ufm/gpu*, *ufm/omp*, *ufm/opt* Syntax """""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 0ad6cc3521..aef401ec7c 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -1,22 +1,19 @@ .. index:: pair_style vashishta +.. index:: pair_style vashishta/gpu +.. index:: pair_style vashishta/omp +.. index:: pair_style vashishta/kk +.. index:: pair_style vashishta/table +.. index:: pair_style vashishta/table/omp pair_style vashishta command ============================ -pair_style vashishta/gpu command -================================ - -pair_style vashishta/omp command -================================ - -pair_style vashishta/kk command -=============================== +Accelerator Variants: *vashishta/gpu*, *vashishta/omp*, *vashishta/kk* pair_style vashishta/table command ================================== -pair_style vashishta/table/omp command -====================================== +Accelerator Variants: *vashishta/table/omp* Syntax """""" diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 340c151226..80fb02b47d 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -1,7 +1,3 @@ -.. index:: pair_write - -pair_write command -================== Syntax """""" diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 079c19c3fd..057adbd60f 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -1,16 +1,12 @@ .. index:: pair_style yukawa +.. index:: pair_style yukawa/gpu +.. index:: pair_style yukawa/omp +.. index:: pair_style yukawa/kk pair_style yukawa command ========================= -pair_style yukawa/gpu command -============================= - -pair_style yukawa/omp command -============================= - -pair_style yukawa/kk command -============================ +Accelerator Variants: *yukawa/gpu*, *yukawa/omp*, *yukawa/kk* Syntax """""" diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 78977118a1..4d21d8e8c3 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style yukawa/colloid +.. index:: pair_style yukawa/colloid/gpu +.. index:: pair_style yukawa/colloid/omp pair_style yukawa/colloid command ================================= -pair_style yukawa/colloid/gpu command -===================================== - -pair_style yukawa/colloid/omp command -===================================== +Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/omp* Syntax """""" diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 5c25697484..e01cbf45f2 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style zbl +.. index:: pair_style zbl/gpu +.. index:: pair_style zbl/kk +.. index:: pair_style zbl/omp pair_style zbl command ====================== -pair_style zbl/gpu command -========================== - -pair_style zbl/kk command -========================= - -pair_style zbl/omp command -========================== +Accelerator Variants: *zbl/gpu*, *zbl/kk*, *zbl/omp* Syntax """""" From 98808fb5ff4823cd4dfeb53f5212998e9e7b782a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:04:08 -0400 Subject: [PATCH 18/72] Skip doc files that don't have common file structure --- doc/utils/fixup_headers.py | 43 ++++++++++++++++++++++---------------- 1 file changed, 25 insertions(+), 18 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 884511bd32..73b1fd3112 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 # Utility script to fix headers in doc pages and generate "Accelerator Styles" portion +import os import shutil import re import argparse @@ -16,10 +17,12 @@ for orig_file in args.files: styles = [] headings = {} new_file = f"{orig_file}.tmp" + found_syntax = False with open(orig_file, 'r') as reader, open(new_file, 'w') as writer: for line in reader: if line.startswith("Syntax"): + found_syntax = True break m = index_pattern.match(line) @@ -42,28 +45,32 @@ for orig_file in args.files: headings[style] = [] elif style not in headings[base_name]: headings[base_name].append(style) - - # write new header - for s in styles: - print(f".. index:: {command_type} {s}", file=writer) - print(file=writer) + if found_syntax: + # write new header + for s in styles: + print(f".. index:: {command_type} {s}", file=writer) - for s, variants in headings.items(): - header = f"{command_type} {s} command" - print(header, file=writer) - print("="*len(header), file=writer) print(file=writer) - if len(variants) > 0: - print("Accelerator Variants: ", end="", file=writer) - print(", ".join([f"*{v}*" for v in variants]), file=writer) + for s, variants in headings.items(): + header = f"{command_type} {s} command" + print(header, file=writer) + print("="*len(header), file=writer) print(file=writer) - # write rest of reader - print(line, end="", file=writer) - for line in reader: - print(line, end="", file=writer) + if len(variants) > 0: + print("Accelerator Variants: ", end="", file=writer) + print(", ".join([f"*{v}*" for v in variants]), file=writer) + print(file=writer) - # override original file - shutil.move(new_file, orig_file) + # write rest of reader + print(line, end="", file=writer) + for line in reader: + print(line, end="", file=writer) + + if found_syntax: + # override original file + shutil.move(new_file, orig_file) + else: + os.remove(new_file) From 0c88074525b40474ef8042ef4a3213548e8a63c2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:05:33 -0400 Subject: [PATCH 19/72] Apply header fix to all remaining fix styles docs --- doc/src/fix_ave_histo.rst | 1 + doc/src/fix_bond_create.rst | 1 + doc/src/fix_deform.rst | 4 ++-- doc/src/fix_dpd_energy.rst | 4 ++-- doc/src/fix_dpd_source.rst | 1 + doc/src/fix_drude_transform.rst | 1 + doc/src/fix_enforce2d.rst | 4 ++-- doc/src/fix_eos_table_rx.rst | 4 ++-- doc/src/fix_freeze.rst | 4 ++-- doc/src/fix_gravity.rst | 8 +++----- doc/src/fix_langevin.rst | 4 ++-- doc/src/fix_modify.rst | 4 ---- doc/src/fix_momentum.rst | 5 +++-- doc/src/fix_mvv_dpd.rst | 2 ++ doc/src/fix_nh.rst | 6 +++--- doc/src/fix_nh_eff.rst | 2 ++ doc/src/fix_nh_uef.rst | 1 + doc/src/fix_nph_asphere.rst | 4 ++-- doc/src/fix_nph_sphere.rst | 4 ++-- doc/src/fix_nphug.rst | 4 ++-- doc/src/fix_npt_asphere.rst | 4 ++-- doc/src/fix_npt_sphere.rst | 4 ++-- doc/src/fix_numdiff.rst | 2 +- doc/src/fix_nve.rst | 12 ++++-------- doc/src/fix_nve_asphere.rst | 4 ++-- doc/src/fix_nve_sphere.rst | 8 +++----- doc/src/fix_nvt_asphere.rst | 4 ++-- doc/src/fix_nvt_sllod.rst | 8 +++----- doc/src/fix_nvt_sphere.rst | 4 ++-- doc/src/fix_orient.rst | 1 + doc/src/fix_property_atom.rst | 4 ++-- doc/src/fix_qeq.rst | 4 ++++ doc/src/fix_qeq_comb.rst | 4 ++-- doc/src/fix_qeq_reax.rst | 8 +++----- doc/src/fix_reaxc_bonds.rst | 4 ++-- doc/src/fix_reaxc_species.rst | 4 ++-- doc/src/fix_rigid.rst | 12 ++++++------ doc/src/fix_rx.rst | 4 ++-- doc/src/fix_setforce.rst | 5 +++-- doc/src/fix_shake.rst | 1 + doc/src/fix_shardlow.rst | 4 ++-- doc/src/fix_smd_integrate_ulsph.rst | 2 +- doc/src/fix_sph.rst | 2 +- doc/src/fix_sph_stationary.rst | 2 +- doc/src/fix_temp_csvr.rst | 1 + doc/src/fix_ttm.rst | 1 + doc/src/fix_wall.rst | 9 +++++++-- doc/src/fix_wall_ees.rst | 1 + doc/src/fix_wall_reflect.rst | 4 ++-- 49 files changed, 102 insertions(+), 93 deletions(-) diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 7c4ef88fd6..d50112ac48 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -1,4 +1,5 @@ .. index:: fix ave/histo +.. index:: fix ave/histo/weight fix ave/histo command ===================== diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index d0c7fb985c..34f0d19f8d 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -1,4 +1,5 @@ .. index:: fix bond/create +.. index:: fix bond/create/angle fix bond/create command ======================= diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 70b15f0d79..999a88c4e7 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -1,10 +1,10 @@ .. index:: fix deform +.. index:: fix deform/kk fix deform command ================== -fix deform/kk command -===================== +Accelerator Variants: *deform/kk* Syntax """""" diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 6d510f1825..732f99b516 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -1,10 +1,10 @@ .. index:: fix dpd/energy +.. index:: fix dpd/energy/kk fix dpd/energy command ====================== -fix dpd/energy/kk command -========================= +Accelerator Variants: *dpd/energy/kk* Syntax """""" diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 4373645c84..29bbc92f78 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -1,4 +1,5 @@ .. index:: fix edpd/source +.. index:: fix tdpd/source fix edpd/source command ======================= diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index bda2d25b1f..792b041576 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -1,4 +1,5 @@ .. index:: fix drude/transform/direct +.. index:: fix drude/transform/inverse fix drude/transform/direct command ================================== diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index e92011cb11..7c6ef75089 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -1,10 +1,10 @@ .. index:: fix enforce2d +.. index:: fix enforce2d/kk fix enforce2d command ===================== -fix enforce2d/kk command -======================== +Accelerator Variants: *enforce2d/kk* Syntax """""" diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index bd13398e0a..56bde44d98 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -1,10 +1,10 @@ .. index:: fix eos/table/rx +.. index:: fix eos/table/rx/kk fix eos/table/rx command ======================== -fix eos/table/rx/kk command -=========================== +Accelerator Variants: *eos/table/rx/kk* Syntax """""" diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index f81954ff5d..a7370c7f44 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -1,10 +1,10 @@ .. index:: fix freeze +.. index:: fix freeze/kk fix freeze command ================== -fix freeze/kk command -===================== +Accelerator Variants: *freeze/kk* Syntax """""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 5f06f6d22a..a163eb4ab2 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -1,13 +1,11 @@ .. index:: fix gravity +.. index:: fix gravity/omp +.. index:: fix gravity/kk fix gravity command =================== -fix gravity/omp command -======================= - -fix gravity/kk command -====================== +Accelerator Variants: *gravity/omp*, *gravity/kk* Syntax """""" diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 80f4964242..e31434247f 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -1,10 +1,10 @@ .. index:: fix langevin +.. index:: fix langevin/kk fix langevin command ==================== -fix langevin/kk command -======================= +Accelerator Variants: *langevin/kk* Syntax """""" diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 604b63550c..d6454431c5 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -1,7 +1,3 @@ -.. index:: fix_modify - -fix_modify command -================== Syntax """""" diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index ca6e19005e..393a6a16cd 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -1,10 +1,11 @@ .. index:: fix momentum +.. index:: fix momentum/kk +.. index:: fix momentum/chunk fix momentum command ==================== -fix momentum/kk command -======================= +Accelerator Variants: *momentum/kk* fix momentum/chunk command ========================== diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index c7e9b64c96..d0df1bd0f9 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -1,4 +1,6 @@ .. index:: fix mvv/dpd +.. index:: fix mvv/edpd +.. index:: fix mvv/tdpd fix mvv/dpd command =================== diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 3e23c46e61..84b497dc3f 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -13,17 +13,17 @@ fix nvt command =============== -Accelerator Styles: *nvt/intel*, *nvt/kk*, *nvt/omp* +Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp* fix npt command =============== -Accelerator Styles: *npt/intel*, *npt/kk*, *npt/omp* +Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp* fix nph command =============== -Accelerator Styles: *nph/kk*, *nph/omp* +Accelerator Variants: *nph/kk*, *nph/omp* Syntax """""" diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 4d4d536ac2..3e54ed9765 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -1,4 +1,6 @@ .. index:: fix nvt/eff +.. index:: fix npt/eff +.. index:: fix nph/eff fix nvt/eff command =================== diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 272f84d520..1c1e7a11d2 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -1,4 +1,5 @@ .. index:: fix nvt/uef +.. index:: fix npt/uef fix nvt/uef command =================== diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 2e5dd16c8f..da0510492e 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/asphere +.. index:: fix nph/asphere/omp fix nph/asphere command ======================= -fix nph/asphere/omp command -=========================== +Accelerator Variants: *nph/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index efa6ca38b5..4b76f7252f 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/sphere +.. index:: fix nph/sphere/omp fix nph/sphere command ====================== -fix nph/sphere/omp command -========================== +Accelerator Variants: *nph/sphere/omp* Syntax """""" diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index c46e98fe3e..d55f435d43 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -1,10 +1,10 @@ .. index:: fix nphug +.. index:: fix nphug/omp fix nphug command ================= -fix nphug/omp command -===================== +Accelerator Variants: *nphug/omp* Syntax """""" diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 5537365359..de2289a068 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/asphere +.. index:: fix npt/asphere/omp fix npt/asphere command ======================= -fix npt/asphere/omp command -=========================== +Accelerator Variants: *npt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 4e8188ac0c..7363375ff3 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/sphere +.. index:: fix npt/sphere/omp fix npt/sphere command ====================== -fix npt/sphere/omp command -========================== +Accelerator Variants: *npt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 0c4f731ea0..22c1c59748 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -1,7 +1,7 @@ .. index:: fix numdiff fix numdiff command -==================== +=================== Syntax """""" diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 0026d38e8c..71f8ec300f 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -1,16 +1,12 @@ .. index:: fix nve +.. index:: fix nve/intel +.. index:: fix nve/kk +.. index:: fix nve/omp fix nve command =============== -fix nve/intel command -===================== - -fix nve/kk command -================== - -fix nve/omp command -=================== +Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp* Syntax """""" diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index f1441fdd3c..af80460b32 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nve/asphere +.. index:: fix nve/asphere/intel fix nve/asphere command ======================= -fix nve/asphere/intel command -============================= +Accelerator Variants: *nve/asphere/intel* Syntax """""" diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 59d951782a..0230255b42 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -1,13 +1,11 @@ .. index:: fix nve/sphere +.. index:: fix nve/sphere/omp +.. index:: fix nve/sphere/kk fix nve/sphere command ====================== -fix nve/sphere/omp command -========================== - -fix nve/sphere/kk command -========================= +Accelerator Variants: *nve/sphere/omp*, *nve/sphere/kk* Syntax """""" diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index a08dae765c..bb4139d95f 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/asphere +.. index:: fix nvt/asphere/omp fix nvt/asphere command ======================= -fix nvt/asphere/omp command -=========================== +Accelerator Variants: *nvt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index b5051b8692..ff9a4f0d12 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -1,13 +1,11 @@ .. index:: fix nvt/sllod +.. index:: fix nvt/sllod/intel +.. index:: fix nvt/sllod/omp fix nvt/sllod command ===================== -fix nvt/sllod/intel command -=========================== - -fix nvt/sllod/omp command -========================= +Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index dd4cf9cb3f..8226328cea 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/sphere +.. index:: fix nvt/sphere/omp fix nvt/sphere command ====================== -fix nvt/sphere/omp command -========================== +Accelerator Variants: *nvt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 51edbd48ad..31aa6074d1 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -1,4 +1,5 @@ .. index:: fix orient/fcc +.. index:: fix orient/bcc fix orient/fcc command ====================== diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index eaf246c1a3..7e322777aa 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -1,10 +1,10 @@ .. index:: fix property/atom +.. index:: fix property/atom/kk fix property/atom command ========================= -fix property/atom/kk command -============================ +Accelerator Variants: *property/atom/kk* Syntax """""" diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index f656049e73..56fde059e8 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -1,4 +1,8 @@ .. index:: fix qeq/point +.. index:: fix qeq/shielded +.. index:: fix qeq/slater +.. index:: fix qeq/dynamic +.. index:: fix qeq/fire fix qeq/point command ===================== diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index f70ecb1dd5..74a97720dc 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -1,10 +1,10 @@ .. index:: fix qeq/comb +.. index:: fix qeq/comb/omp fix qeq/comb command ==================== -fix qeq/comb/omp command -======================== +Accelerator Variants: *qeq/comb/omp* Syntax """""" diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 0fd5e78578..47dca86401 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -1,13 +1,11 @@ .. index:: fix qeq/reax +.. index:: fix qeq/reax/kk +.. index:: fix qeq/reax/omp fix qeq/reax command ==================== -fix qeq/reax/kk command -======================= - -fix qeq/reax/omp command -======================== +Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp* Syntax """""" diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 52f0581929..2d0d2d18db 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/bonds +.. index:: fix reax/c/bonds/kk fix reax/c/bonds command ======================== -fix reax/c/bonds/kk command -=========================== +Accelerator Variants: *reax/c/bonds/kk* Syntax """""" diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 275086b52b..9935ecaa3a 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/species +.. index:: fix reax/c/species/kk fix reax/c/species command ========================== -fix reax/c/species/kk command -============================= +Accelerator Variants: *reax/c/species/kk* Syntax """""" diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 8756e72db1..efadc5dd13 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -18,32 +18,32 @@ fix rigid command ================= -Accelerator Styles: *rigid/omp* +Accelerator Variants: *rigid/omp* fix rigid/nve command ===================== -Accelerator Styles: *rigid/nve/omp* +Accelerator Variants: *rigid/nve/omp* fix rigid/nvt command ===================== -Accelerator Styles: *rigid/nvt/omp* +Accelerator Variants: *rigid/nvt/omp* fix rigid/npt command ===================== -Accelerator Styles: *rigid/npt/omp* +Accelerator Variants: *rigid/npt/omp* fix rigid/nph command ===================== -Accelerator Styles: *rigid/nph/omp* +Accelerator Variants: *rigid/nph/omp* fix rigid/small command ======================= -Accelerator Styles: *rigid/small/omp* +Accelerator Variants: *rigid/small/omp* fix rigid/nve/small command =========================== diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 7a3a95f069..c1a1d0950c 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -1,10 +1,10 @@ .. index:: fix rx +.. index:: fix rx/kk fix rx command ============== -fix rx/kk command -================= +Accelerator Variants: *rx/kk* Syntax """""" diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index b417b369e5..406826e5b9 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -1,10 +1,11 @@ .. index:: fix setforce +.. index:: fix setforce/kk +.. index:: fix setforce/spin fix setforce command ==================== -fix setforce/kk command -======================= +Accelerator Variants: *setforce/kk* fix setforce/spin command ========================= diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 5f720d86ea..eb7add7035 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -1,4 +1,5 @@ .. index:: fix shake +.. index:: fix rattle fix shake command ================= diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 3c046dae74..f928044db7 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -1,10 +1,10 @@ .. index:: fix shardlow +.. index:: fix shardlow/kk fix shardlow command ==================== -fix shardlow/kk command -======================= +Accelerator Variants: *shardlow/kk* Syntax """""" diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index f7ba223965..5b4c117452 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -1,7 +1,7 @@ .. index:: fix smd/integrate_ulsph fix smd/integrate_ulsph command -================================ +=============================== Syntax """""" diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 1b482e0252..5ba752debb 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -1,7 +1,7 @@ .. index:: fix sph fix sph command -================ +=============== Syntax """""" diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index 5fa3f1d04d..c86a30b542 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -1,7 +1,7 @@ .. index:: fix sph/stationary fix sph/stationary command -=========================== +========================== Syntax """""" diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 10c92dc2f2..8faa6035cf 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -1,4 +1,5 @@ .. index:: fix temp/csvr +.. index:: fix temp/csld fix temp/csvr command ===================== diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 97cb0cd05b..24bc6f297f 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -1,4 +1,5 @@ .. index:: fix ttm +.. index:: fix ttm/mod fix ttm command =============== diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index d4120ca625..39ff879138 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -1,10 +1,15 @@ .. index:: fix wall/lj93 +.. index:: fix wall/lj93/kk +.. index:: fix wall/lj126 +.. index:: fix wall/lj1043 +.. index:: fix wall/colloid +.. index:: fix wall/harmonic +.. index:: fix wall/morse fix wall/lj93 command ===================== -fix wall/lj93/kk command -======================== +Accelerator Variants: *wall/lj93/kk* fix wall/lj126 command ====================== diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 79f96765f8..2bab8c6056 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -1,4 +1,5 @@ .. index:: fix wall/ees +.. index:: fix wall/region/ees fix wall/ees command ==================== diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 44cde8f3d5..4f014cc628 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -1,10 +1,10 @@ .. index:: fix wall/reflect +.. index:: fix wall/reflect/kk fix wall/reflect command ======================== -fix wall/reflect/kk command -=========================== +Accelerator Variants: *wall/reflect/kk* Syntax """""" From 84e922eff649bff8831d08d02d8a7ce67af55b16 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 11:55:53 -0400 Subject: [PATCH 20/72] Add other styles to fixup_header.py --- doc/utils/fixup_headers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index 73b1fd3112..fb39c59434 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -5,8 +5,8 @@ import shutil import re import argparse -index_pattern = re.compile(r"^.. index:: (fix|pair_style)\s+([a-zA-Z0-9/_]+)$") -pattern = re.compile(r"^(fix|pair_style)\s+([a-zA-Z0-9/_]+)\s+command$") +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)$") +pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') From 549bdd080ccdf65a586aada4d6b3c753b01e4e82 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:37:48 -0400 Subject: [PATCH 21/72] Add kspace_style to fixup_headers.py --- doc/utils/fixup_headers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index fb39c59434..c7fe57bc17 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -5,8 +5,8 @@ import shutil import re import argparse -index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)$") -pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style)\s+([a-zA-Z0-9/_]+)\s+command$") +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") +pattern = re.compile(r"^(compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)\s+command$") parser = argparse.ArgumentParser(description='Fixup headers in docs') parser.add_argument('files', metavar='FILE', nargs='+', help='files to fix') From 286d3866e3bc27bd27b136d2bf775d39b3fac7c5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:42:18 -0400 Subject: [PATCH 22/72] Add style index check in check-styles.py --- doc/utils/check-styles.py | 61 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 60 insertions(+), 1 deletion(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 603f312e9d..45876ea738 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -60,6 +60,7 @@ reader = {} region = {} total = 0 +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") @@ -70,6 +71,26 @@ omp = re.compile("(.+)/omp$") opt = re.compile("(.+)/opt$") removed = re.compile("(.*)Deprecated$") +def load_index_entries_in_file(path): + entries = [] + with open(path, 'r') as reader: + for line in reader: + m = index_pattern.match(line) + if m: + command_type = m.group(1) + style = m.group(2) + entries.append((command_type, style)) + return entries + +def load_index_entries(): + index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(), + 'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()} + rst_files = glob(os.path.join(doc_dir, '*.rst')) + for f in rst_files: + for command_type, style in load_index_entries_in_file(f): + index[command_type].add(style) + return index + def register_style(styles, name, info): if name in styles: for key, value in info.items(): @@ -112,6 +133,24 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set counter += 1 return counter +def check_style_index(name, styles, index): + counter = 0 + for style in styles: + if style not in index and not styles[style]['removed']: + print(f"{name} index entry {style} is missing") + counter += 1 + + for suffix in styles[style]: + if suffix == 'removed': continue + if suffix == 'kokkos': + suffix_style = f"{style}/kk" + else: + suffix_style = f"{style}/{suffix}" + if styles[style][suffix] and suffix_style not in index: + print(f"{name} index entry {suffix_style} is missing") + counter += 1 + return counter + for header in headers: if verbose: print("Checking ", header) with open(header) as f: @@ -207,6 +246,13 @@ Total number of styles (including suffixes): %d""" \ len(fix), len(improper), len(integrate), len(kspace), \ len(minimize), len(pair), len(reader), len(region), total)) +index = load_index_entries() + +total_index = 0 +for command_type, entries in index.items(): + total_index += len(entries) + +print("Total number of style index entries:", total_index) counter = 0 @@ -244,5 +290,18 @@ counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) Date: Wed, 2 Sep 2020 12:43:48 -0400 Subject: [PATCH 23/72] Update headers in angle_*.rst files --- doc/src/angle_charmm.rst | 12 ++++-------- doc/src/angle_class2.rst | 9 ++++----- doc/src/angle_coeff.rst | 4 ---- doc/src/angle_cosine.rst | 8 +++----- doc/src/angle_cosine_delta.rst | 4 ++-- doc/src/angle_cosine_periodic.rst | 4 ++-- doc/src/angle_cosine_shift.rst | 6 +++--- doc/src/angle_cosine_shift_exp.rst | 4 ++-- doc/src/angle_cosine_squared.rst | 4 ++-- doc/src/angle_cross.rst | 2 +- doc/src/angle_dipole.rst | 4 ++-- doc/src/angle_fourier.rst | 4 ++-- doc/src/angle_fourier_simple.rst | 4 ++-- doc/src/angle_harmonic.rst | 12 ++++-------- doc/src/angle_quartic.rst | 4 ++-- doc/src/angle_sdk.rst | 4 ++-- doc/src/angle_style.rst | 4 ---- doc/src/angle_table.rst | 4 ++-- 18 files changed, 39 insertions(+), 58 deletions(-) diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 8410f0f8c0..e557648d9f 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -1,16 +1,12 @@ .. index:: angle_style charmm +.. index:: angle_style charmm/intel +.. index:: angle_style charmm/kk +.. index:: angle_style charmm/omp angle_style charmm command ========================== -angle_style charmm/intel command -================================ - -angle_style charmm/kk command -============================= - -angle_style charmm/omp command -============================== +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* Syntax """""" diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 7d2fdd5d66..bf0305055a 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -1,13 +1,12 @@ .. index:: angle_style class2 +.. index:: angle_style class2/kk +.. index:: angle_style class2/omp +.. index:: angle_style class2/p6 angle_style class2 command ========================== -angle_style class2/kk command -============================= - -angle_style class2/omp command -============================== +Accelerator Variants: *class2/kk*, *class2/omp* angle_style class2/p6 command ============================= diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 07048c1432..873212f3b5 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -1,7 +1,3 @@ -.. index:: angle_coeff - -angle_coeff command -=================== Syntax """""" diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index e39e68b2e1..aea144f7be 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -1,13 +1,11 @@ .. index:: angle_style cosine +.. index:: angle_style cosine/omp +.. index:: angle_style cosine/kk angle_style cosine command ========================== -angle_style cosine/omp command -============================== - -angle_style cosine/kk command -============================= +Accelerator Variants: *cosine/omp*, *cosine/kk* Syntax """""" diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 017b64f8b0..280e6ea2c4 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/delta +.. index:: angle_style cosine/delta/omp angle_style cosine/delta command ================================ -angle_style cosine/delta/omp command -==================================== +Accelerator Variants: *cosine/delta/omp* Syntax """""" diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index aff4ba2322..71c2caa3f0 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/periodic +.. index:: angle_style cosine/periodic/omp angle_style cosine/periodic command =================================== -angle_style cosine/periodic/omp command -======================================= +Accelerator Variants: *cosine/periodic/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 26603e48be..71bda194c7 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift +.. index:: angle_style cosine/shift/omp angle_style cosine/shift command -================================= +================================ -angle_style cosine/shift/omp command -==================================== +Accelerator Variants: *cosine/shift/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index fbdb76aa45..4ae4928751 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift/exp +.. index:: angle_style cosine/shift/exp/omp angle_style cosine/shift/exp command ==================================== -angle_style cosine/shift/exp/omp command -======================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 49ddf59741..4a6a1debe9 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/squared +.. index:: angle_style cosine/squared/omp angle_style cosine/squared command ================================== -angle_style cosine/squared/omp command -====================================== +Accelerator Variants: *cosine/squared/omp* Syntax """""" diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 5769e756c3..3cd1884be0 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -1,7 +1,7 @@ .. index:: angle_style cross angle_style cross command -========================== +========================= Syntax """""" diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 3b4e4f5304..4dd8aadfb8 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -1,10 +1,10 @@ .. index:: angle_style dipole +.. index:: angle_style dipole/omp angle_style dipole command ========================== -angle_style dipole/omp command -============================== +Accelerator Variants: *dipole/omp* Syntax """""" diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index cbe6544271..231f45e808 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier +.. index:: angle_style fourier/omp angle_style fourier command =========================== -angle_style fourier/omp command -=============================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index b36f69cbec..14b4bbcfe9 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier/simple +.. index:: angle_style fourier/simple/omp angle_style fourier/simple command ================================== -angle_style fourier/simple/omp command -====================================== +Accelerator Variants: *fourier/simple/omp* Syntax """""" diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index c6ad93c3ec..06cf1d460b 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -1,16 +1,12 @@ .. index:: angle_style harmonic +.. index:: angle_style harmonic/intel +.. index:: angle_style harmonic/kk +.. index:: angle_style harmonic/omp angle_style harmonic command ============================ -angle_style harmonic/intel command -================================== - -angle_style harmonic/kk command -=============================== - -angle_style harmonic/omp command -================================ +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 71297e60a0..7dfb4b2896 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -1,10 +1,10 @@ .. index:: angle_style quartic +.. index:: angle_style quartic/omp angle_style quartic command =========================== -angle_style quartic/omp command -=============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index f5583d5013..340a3e4de7 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -1,10 +1,10 @@ .. index:: angle_style sdk +.. index:: angle_style sdk/omp angle_style sdk command ======================= -angle_style sdk/omp command -=========================== +Accelerator Variants: *sdk/omp* Syntax """""" diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 91232a6b6c..ba991954ab 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,7 +1,3 @@ -.. index:: angle_style - -angle_style command -=================== Syntax """""" diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index d8d9476620..cad9f5a82f 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -1,10 +1,10 @@ .. index:: angle_style table +.. index:: angle_style table/omp angle_style table command ========================= -angle_style table/omp command -============================= +Accelerator Variants: *table/omp* Syntax """""" From 4e27c47f962fd247219084e0f33b1e177eab34ff Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:52:30 -0400 Subject: [PATCH 24/72] Undo lost headers --- doc/src/angle_coeff.rst | 4 ++++ doc/src/angle_style.rst | 4 ++++ doc/src/fix_modify.rst | 4 ++++ doc/src/pair_coeff.rst | 4 ++++ doc/src/pair_modify.rst | 4 ++++ doc/src/pair_style.rst | 4 ++++ doc/src/pair_write.rst | 4 ++++ doc/utils/fixup_headers.py | 2 +- 8 files changed, 29 insertions(+), 1 deletion(-) diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 873212f3b5..07048c1432 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -1,3 +1,7 @@ +.. index:: angle_coeff + +angle_coeff command +=================== Syntax """""" diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index ba991954ab..91232a6b6c 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,3 +1,7 @@ +.. index:: angle_style + +angle_style command +=================== Syntax """""" diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index d6454431c5..604b63550c 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -1,3 +1,7 @@ +.. index:: fix_modify + +fix_modify command +================== Syntax """""" diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 7c72bb5843..ea62d839ab 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -1,3 +1,7 @@ +.. index:: pair_coeff + +pair_coeff command +================== Syntax """""" diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 21d0977047..b8969c0131 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -1,3 +1,7 @@ +.. index:: pair_modify + +pair_modify command +=================== Syntax """""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1b9ceaf0ee..4feaeacad0 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -1,3 +1,7 @@ +.. index:: pair_style + +pair_style command +================== Syntax """""" diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 80fb02b47d..340c151226 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -1,3 +1,7 @@ +.. index:: pair_write + +pair_write command +================== Syntax """""" diff --git a/doc/utils/fixup_headers.py b/doc/utils/fixup_headers.py index c7fe57bc17..520bec104b 100755 --- a/doc/utils/fixup_headers.py +++ b/doc/utils/fixup_headers.py @@ -69,7 +69,7 @@ for orig_file in args.files: for line in reader: print(line, end="", file=writer) - if found_syntax: + if found_syntax and len(styles) > 0: # override original file shutil.move(new_file, orig_file) else: From f4d2523ce0aca1e2717d77121c49daad3211de09 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:55:18 -0400 Subject: [PATCH 25/72] Update headers in bond_*.rst files --- doc/src/bond_class2.rst | 8 +++----- doc/src/bond_fene.rst | 12 ++++-------- doc/src/bond_fene_expand.rst | 4 ++-- doc/src/bond_gromos.rst | 4 ++-- doc/src/bond_harmonic.rst | 12 ++++-------- doc/src/bond_harmonic_shift.rst | 4 ++-- doc/src/bond_harmonic_shift_cut.rst | 4 ++-- doc/src/bond_morse.rst | 4 ++-- doc/src/bond_nonlinear.rst | 4 ++-- doc/src/bond_oxdna.rst | 2 ++ doc/src/bond_quartic.rst | 4 ++-- doc/src/bond_special.rst | 2 +- doc/src/bond_table.rst | 4 ++-- 13 files changed, 30 insertions(+), 38 deletions(-) diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 41eb2b4e50..aea503738f 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -1,13 +1,11 @@ .. index:: bond_style class2 +.. index:: bond_style class2/omp +.. index:: bond_style class2/kk bond_style class2 command ========================= -bond_style class2/omp command -============================= - -bond_style class2/kk command -============================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 8ec117bf24..0c6a37ca62 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -1,16 +1,12 @@ .. index:: bond_style fene +.. index:: bond_style fene/intel +.. index:: bond_style fene/kk +.. index:: bond_style fene/omp bond_style fene command ======================= -bond_style fene/intel command -============================= - -bond_style fene/kk command -========================== - -bond_style fene/omp command -=========================== +Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp* Syntax """""" diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 5bcb409238..1be06561e9 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -1,10 +1,10 @@ .. index:: bond_style fene/expand +.. index:: bond_style fene/expand/omp bond_style fene/expand command ============================== -bond_style fene/expand/omp command -================================== +Accelerator Variants: *fene/expand/omp* Syntax """""" diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index f09e5761fe..d4eb958ebe 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -1,10 +1,10 @@ .. index:: bond_style gromos +.. index:: bond_style gromos/omp bond_style gromos command ========================= -bond_style gromos/omp command -============================= +Accelerator Variants: *gromos/omp* Syntax """""" diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index eaa1ee7986..e3320f2e19 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -1,16 +1,12 @@ .. index:: bond_style harmonic +.. index:: bond_style harmonic/intel +.. index:: bond_style harmonic/kk +.. index:: bond_style harmonic/omp bond_style harmonic command =========================== -bond_style harmonic/intel command -================================= - -bond_style harmonic/kk command -============================== - -bond_style harmonic/omp command -=============================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index c124bacf0f..469c370969 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift +.. index:: bond_style harmonic/shift/omp bond_style harmonic/shift command ================================= -bond_style harmonic/shift/omp command -===================================== +Accelerator Variants: *harmonic/shift/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index e1b7e990d4..d0f44740b3 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift/cut +.. index:: bond_style harmonic/shift/cut/omp bond_style harmonic/shift/cut command ===================================== -bond_style harmonic/shift/cut/omp command -========================================= +Accelerator Variants: *harmonic/shift/cut/omp* Syntax """""" diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 64fc61298a..f096624ba0 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -1,10 +1,10 @@ .. index:: bond_style morse +.. index:: bond_style morse/omp bond_style morse command ======================== -bond_style morse/omp command -============================ +Accelerator Variants: *morse/omp* Syntax """""" diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 75ab4ad347..77271502ea 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -1,10 +1,10 @@ .. index:: bond_style nonlinear +.. index:: bond_style nonlinear/omp bond_style nonlinear command ============================ -bond_style nonlinear/omp command -================================ +Accelerator Variants: *nonlinear/omp* Syntax """""" diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index ada2f0e1ed..3f52424d49 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -1,4 +1,6 @@ .. index:: bond_style oxdna/fene +.. index:: bond_style oxdna2/fene +.. index:: bond_style oxrna2/fene bond_style oxdna/fene command ============================= diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index d54c19bbd4..8c5b363e54 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -1,10 +1,10 @@ .. index:: bond_style quartic +.. index:: bond_style quartic/omp bond_style quartic command ========================== -bond_style quartic/omp command -============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/bond_special.rst b/doc/src/bond_special.rst index bd93bb644c..d2423c9e23 100644 --- a/doc/src/bond_special.rst +++ b/doc/src/bond_special.rst @@ -1,7 +1,7 @@ .. index:: bond_style special bond_style special command -================================= +========================== Syntax """""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 9f8ebacef0..fedb50355d 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -1,10 +1,10 @@ .. index:: bond_style table +.. index:: bond_style table/omp bond_style table command ======================== -bond_style table/omp command -============================ +Accelerator Variants: *table/omp* Syntax """""" From d01c985febf27f31aeb058515c861ddd3ade151d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:56:24 -0400 Subject: [PATCH 26/72] Update headers in compute_*.rst files --- doc/src/compute_cluster_atom.rst | 2 ++ doc/src/compute_coord_atom.rst | 4 ++-- doc/src/compute_mesont.rst | 2 +- doc/src/compute_orientorder_atom.rst | 4 ++-- doc/src/compute_reduce.rst | 1 + doc/src/compute_smd_ulsph_effm.rst | 2 +- doc/src/compute_sna_atom.rst | 3 +++ doc/src/compute_sph_e_atom.rst | 2 +- doc/src/compute_sph_rho_atom.rst | 2 +- doc/src/compute_sph_t_atom.rst | 2 +- doc/src/compute_stress_atom.rst | 1 + doc/src/compute_stress_mop.rst | 1 + doc/src/compute_tally.rst | 4 ++++ doc/src/compute_temp.rst | 4 ++-- 14 files changed, 23 insertions(+), 11 deletions(-) diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 77149306dc..ab47aed9b3 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -1,4 +1,6 @@ .. index:: compute cluster/atom +.. index:: compute fragment/atom +.. index:: compute aggregate/atom compute cluster/atom command ============================ diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index cbf879b8bd..f3c6f818af 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -1,10 +1,10 @@ .. index:: compute coord/atom +.. index:: compute coord/atom/kk compute coord/atom command ========================== -compute coord/atom/kk command -=================================== +Accelerator Variants: *coord/atom/kk* Syntax """""" diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index bf0ade16c1..44d6054e22 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -1,7 +1,7 @@ .. index:: compute mesont compute mesont command -========================== +====================== Syntax """""" diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index c8ab4d7b9b..2a36fb4cc0 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -1,10 +1,10 @@ .. index:: compute orientorder/atom +.. index:: compute orientorder/atom/kk compute orientorder/atom command ================================ -compute orientorder/atom/kk command -=================================== +Accelerator Variants: *orientorder/atom/kk* Syntax """""" diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index bf7d0dc28c..c7815305c0 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -1,4 +1,5 @@ .. index:: compute reduce +.. index:: compute reduce/region compute reduce command ====================== diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index e6d6b772a0..ff12f9cdac 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -1,7 +1,7 @@ .. index:: compute smd/ulsph/effm compute smd/ulsph/effm command -================================ +============================== Syntax """""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 7e74a1bd61..08b06a32ec 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -1,4 +1,7 @@ .. index:: compute sna/atom +.. index:: compute snad/atom +.. index:: compute snav/atom +.. index:: compute snap compute sna/atom command ======================== diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index 08378c7c99..17591257f2 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/e/atom compute sph/e/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index 975ebf996d..c422a5ecbb 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/rho/atom compute sph/rho/atom command -============================= +============================ Syntax """""" diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 2f8ad12f45..922adfff58 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/t/atom compute sph/t/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 2bdab03bda..16afd49548 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -1,4 +1,5 @@ .. index:: compute stress/atom +.. index:: compute centroid/stress/atom compute stress/atom command =========================== diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 4d0d21cb87..f164a33c26 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -1,4 +1,5 @@ .. index:: compute stress/mop +.. index:: compute stress/mop/profile compute stress/mop command ========================== diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 281425763a..6487618516 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -1,4 +1,8 @@ .. index:: compute force/tally +.. index:: compute heat/flux/tally +.. index:: compute pe/tally +.. index:: compute pe/mol/tally +.. index:: compute stress/tally compute force/tally command =========================== diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index ac11aa155c..a82046367e 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -1,10 +1,10 @@ .. index:: compute temp +.. index:: compute temp/kk compute temp command ==================== -compute temp/kk command -======================= +Accelerator Variants: *temp/kk* Syntax """""" From a0c9c213fd3eded5a61b507a471148edae29e4db Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 12:57:44 -0400 Subject: [PATCH 27/72] Update headers in dihedral_*.rst files --- doc/src/dihedral_charmm.rst | 13 +++++-------- doc/src/dihedral_class2.rst | 8 +++----- doc/src/dihedral_cosine_shift_exp.rst | 4 ++-- doc/src/dihedral_fourier.rst | 8 +++----- doc/src/dihedral_harmonic.rst | 12 ++++-------- doc/src/dihedral_helix.rst | 4 ++-- doc/src/dihedral_multi_harmonic.rst | 4 ++-- doc/src/dihedral_nharmonic.rst | 6 +++--- doc/src/dihedral_opls.rst | 12 ++++-------- doc/src/dihedral_quadratic.rst | 4 ++-- doc/src/dihedral_table.rst | 4 ++-- doc/src/dihedral_zero.rst | 2 +- 12 files changed, 33 insertions(+), 48 deletions(-) diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index bbaaaf2dd4..9588cf8272 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -1,16 +1,13 @@ .. index:: dihedral_style charmm +.. index:: dihedral_style charmm/intel +.. index:: dihedral_style charmm/kk +.. index:: dihedral_style charmm/omp +.. index:: dihedral_style charmmfsw dihedral_style charmm command ============================= -dihedral_style charmm/intel command -=================================== - -dihedral_style charmm/kk command -================================ - -dihedral_style charmm/omp command -================================= +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* dihedral_style charmmfsw command ================================ diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index 907102a4f6..a98cf6b041 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style class2 +.. index:: dihedral_style class2/omp +.. index:: dihedral_style class2/kk dihedral_style class2 command ============================= -dihedral_style class2/omp command -================================= - -dihedral_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 9648bc5387..1f0195df83 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style cosine/shift/exp +.. index:: dihedral_style cosine/shift/exp/omp dihedral_style cosine/shift/exp command ======================================= -dihedral_style cosine/shift/exp/omp command -=========================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index d795488107..f55011c902 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style fourier +.. index:: dihedral_style fourier/intel +.. index:: dihedral_style fourier/omp dihedral_style fourier command ============================== -dihedral_style fourier/intel command -==================================== - -dihedral_style fourier/omp command -================================== +Accelerator Variants: *fourier/intel*, *fourier/omp* Syntax """""" diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index f6e9794d3e..0ee6339ea0 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style harmonic +.. index:: dihedral_style harmonic/intel +.. index:: dihedral_style harmonic/kk +.. index:: dihedral_style harmonic/omp dihedral_style harmonic command =============================== -dihedral_style harmonic/intel command -===================================== - -dihedral_style harmonic/kk command -================================== - -dihedral_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 58738dd7a7..89258cff35 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style helix +.. index:: dihedral_style helix/omp dihedral_style helix command ============================ -dihedral_style helix/omp command -================================ +Accelerator Variants: *helix/omp* Syntax """""" diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index c13d45863f..176d3815dc 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style multi/harmonic +.. index:: dihedral_style multi/harmonic/omp dihedral_style multi/harmonic command ===================================== -dihedral_style multi/harmonic/omp command -========================================= +Accelerator Variants: *multi/harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index e2223382e2..2411903126 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style nharmonic +.. index:: dihedral_style nharmonic/omp dihedral_style nharmonic command -================================= +================================ -dihedral_style nharmonic/omp command -===================================== +Accelerator Variants: *nharmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index a2be0b5b2d..36b1897fce 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style opls +.. index:: dihedral_style opls/intel +.. index:: dihedral_style opls/kk +.. index:: dihedral_style opls/omp dihedral_style opls command =========================== -dihedral_style opls/intel command -================================= - -dihedral_style opls/kk command -============================== - -dihedral_style opls/omp command -=============================== +Accelerator Variants: *opls/intel*, *opls/kk*, *opls/omp* Syntax """""" diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 9c4a707562..dbe680fc82 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style quadratic +.. index:: dihedral_style quadratic/omp dihedral_style quadratic command ================================ -dihedral_style quadratic/omp command -==================================== +Accelerator Variants: *quadratic/omp* Syntax """""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 9ed7249572..ff3e61baee 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style table +.. index:: dihedral_style table/omp dihedral_style table command ============================ -dihedral_style table/omp command -================================ +Accelerator Variants: *table/omp* Syntax """""" diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 3df68edfd5..0f481f917d 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -1,7 +1,7 @@ .. index:: dihedral_style zero dihedral_style zero command -============================ +=========================== Syntax """""" From c812bf7a91b6830e798af64c253307fdb39055a3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:03:03 -0400 Subject: [PATCH 28/72] Update headers in improper_*.rst files --- doc/src/improper_class2.rst | 8 +++----- doc/src/improper_cossq.rst | 4 ++-- doc/src/improper_cvff.rst | 8 +++----- doc/src/improper_fourier.rst | 4 ++-- doc/src/improper_harmonic.rst | 12 ++++-------- doc/src/improper_ring.rst | 4 ++-- doc/src/improper_umbrella.rst | 4 ++-- 7 files changed, 18 insertions(+), 26 deletions(-) diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index eb6b8eab2c..a84e92b090 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -1,13 +1,11 @@ .. index:: improper_style class2 +.. index:: improper_style class2/omp +.. index:: improper_style class2/kk improper_style class2 command ============================= -improper_style class2/omp command -================================= - -improper_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 70885acc28..a6281bc260 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -1,10 +1,10 @@ .. index:: improper_style cossq +.. index:: improper_style cossq/omp improper_style cossq command ============================ -improper_style cossq/omp command -================================ +Accelerator Variants: *cossq/omp* Syntax """""" diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index bde510c3f7..5bd7fdf911 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -1,13 +1,11 @@ .. index:: improper_style cvff +.. index:: improper_style cvff/intel +.. index:: improper_style cvff/omp improper_style cvff command =========================== -improper_style cvff/intel command -================================= - -improper_style cvff/omp command -=============================== +Accelerator Variants: *cvff/intel*, *cvff/omp* Syntax """""" diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 04ce9ba994..84ea97509d 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -1,10 +1,10 @@ .. index:: improper_style fourier +.. index:: improper_style fourier/omp improper_style fourier command ============================== -improper_style fourier/omp command -================================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index e1b78d21db..4f21e48fa9 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -1,16 +1,12 @@ .. index:: improper_style harmonic +.. index:: improper_style harmonic/intel +.. index:: improper_style harmonic/kk +.. index:: improper_style harmonic/omp improper_style harmonic command =============================== -improper_style harmonic/intel command -===================================== - -improper_style harmonic/kk command -================================== - -improper_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index df319396e2..d67c999714 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -1,10 +1,10 @@ .. index:: improper_style ring +.. index:: improper_style ring/omp improper_style ring command =========================== -improper_style ring/omp command -=============================== +Accelerator Variants: *ring/omp* Syntax """""" diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 10981248d9..5d4aa571e1 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -1,10 +1,10 @@ .. index:: improper_style umbrella +.. index:: improper_style umbrella/omp improper_style umbrella command =============================== -improper_style umbrella/omp command -=================================== +Accelerator Variants: *umbrella/omp* Syntax """""" From 28c90a6dea68474297a8b5a3f6eade78c6dfef71 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:40:24 -0400 Subject: [PATCH 29/72] Update index for kspace_style commands --- doc/src/kspace_style.rst | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 5b45b00353..59f5b7f27c 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -1,4 +1,30 @@ -.. index:: kspace_style +.. index:: kspace_style ewald +.. index:: kspace_style ewald/dipole +.. index:: kspace_style ewald/dipole/spin +.. index:: kspace_style ewald/disp +.. index:: kspace_style ewald/omp +.. index:: kspace_style pppm +.. index:: kspace_style pppm/kk +.. index:: kspace_style pppm/omp +.. index:: kspace_style pppm/gpu +.. index:: kspace_style pppm/intel +.. index:: kspace_style pppm/cg +.. index:: kspace_style pppm/dipole +.. index:: kspace_style pppm/dipole/spin +.. index:: kspace_style pppm/disp +.. index:: kspace_style pppm/disp/omp +.. index:: kspace_style pppm/disp/tip4p +.. index:: kspace_style pppm/disp/tip4p/omp +.. index:: kspace_style pppm/disp/intel +.. index:: kspace_style pppm/cg/omp +.. index:: kspace_style pppm/stagger +.. index:: kspace_style pppm/tip4p +.. index:: kspace_style pppm/tip4p/omp +.. index:: kspace_style msm +.. index:: kspace_style msm/omp +.. index:: kspace_style msm/cg +.. index:: kspace_style msm/cg/omp +.. index:: kspace_style scafacos kspace_style command ==================== From e519919caedd58a89976c2d1746f4c1a894ac72e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:48:11 -0400 Subject: [PATCH 30/72] Fix typo --- doc/src/fix_orient_eco.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index bdfab21c9d..58ff38268f 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -1,4 +1,4 @@ -.. index:: fix orient/eco +.. index:: fix orient/eco fix orient/eco command ====================== From 515746063f7177c9d11165aebf5f57f8e59b97b0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:55:27 -0400 Subject: [PATCH 31/72] Fix copy&paste error --- doc/utils/check-styles.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 45876ea738..6dddab82c0 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -299,7 +299,7 @@ counter += check_style_index("fix", fix, index["fix"]) counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) -counter += check_style_index("improper_style", dihedral, index["improper_style"]) +counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) counter += check_style_index("pair_style", pair, index["pair_style"]) From 0f9c46235cec801d597f33bfb0772481613dbf1a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 13:56:17 -0400 Subject: [PATCH 32/72] Add missing index entries --- doc/src/fix_python_invoke.rst | 4 ++++ doc/src/pair_meamc.rst | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 94bad11f00..9ccb24cba1 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -1,5 +1,9 @@ +.. index:: fix python .. index:: fix python/invoke +fix python command +================== + fix python/invoke command ========================= diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 757c4c6712..5f6e3ae984 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -1,5 +1,9 @@ +.. index:: pair_style meam .. index:: pair_style meam/c +pair_style meam command +======================= + pair_style meam/c command ========================= From ac7129b3a920708ac3da73cdfbcae4885d303e83 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 14:02:53 -0400 Subject: [PATCH 33/72] Revert "Add missing index entries" These are intentionally left out from docs --- doc/src/fix_python_invoke.rst | 4 ---- doc/src/pair_meamc.rst | 4 ---- 2 files changed, 8 deletions(-) diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst index 9ccb24cba1..94bad11f00 100644 --- a/doc/src/fix_python_invoke.rst +++ b/doc/src/fix_python_invoke.rst @@ -1,9 +1,5 @@ -.. index:: fix python .. index:: fix python/invoke -fix python command -================== - fix python/invoke command ========================= diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index 5f6e3ae984..757c4c6712 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -1,9 +1,5 @@ -.. index:: pair_style meam .. index:: pair_style meam/c -pair_style meam command -======================= - pair_style meam/c command ========================= From 8def5844c89ef4113ffed754562391f9273d704b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 2 Sep 2020 14:06:35 -0400 Subject: [PATCH 34/72] Skip old styles in check-styles --- doc/utils/check-styles.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 6dddab82c0..f9a7d3e39a 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -133,10 +133,10 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set counter += 1 return counter -def check_style_index(name, styles, index): +def check_style_index(name, styles, index, skip=[]): counter = 0 for style in styles: - if style not in index and not styles[style]['removed']: + if style not in index and not styles[style]['removed'] and style not in skip: print(f"{name} index entry {style} is missing") counter += 1 @@ -146,7 +146,7 @@ def check_style_index(name, styles, index): suffix_style = f"{style}/kk" else: suffix_style = f"{style}/{suffix}" - if styles[style][suffix] and suffix_style not in index: + if styles[style][suffix] and suffix_style not in index and style not in skip: print(f"{name} index entry {suffix_style} is missing") counter += 1 return counter @@ -295,13 +295,13 @@ if counter: counter = 0 counter += check_style_index("compute", compute, index["compute"]) -counter += check_style_index("fix", fix, index["fix"]) +counter += check_style_index("fix", fix, index["fix"], skip=['python']) counter += check_style_index("angle_style", angle, index["angle_style"]) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) -counter += check_style_index("pair_style", pair, index["pair_style"]) +counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam', 'lj/sf']) if counter: print(f"Found {counter} issue(s) with style index") From 6113169a473dc847b8f877855747c26e3c1b754c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 15:26:00 -0400 Subject: [PATCH 35/72] IWYU based include statement cleanup --- src/ASPHERE/compute_erotate_asphere.cpp | 2 +- src/ASPHERE/compute_temp_asphere.cpp | 2 +- src/ASPHERE/fix_nph_asphere.cpp | 2 +- src/ASPHERE/fix_npt_asphere.cpp | 2 +- src/ASPHERE/fix_nvt_asphere.cpp | 4 +-- src/ASPHERE/pair_gayberne.cpp | 4 +-- src/ASPHERE/pair_line_lj.cpp | 2 +- src/ASPHERE/pair_resquared.cpp | 4 +-- src/ASPHERE/pair_tri_lj.cpp | 2 +- src/BODY/compute_body_local.cpp | 2 +- src/BODY/compute_temp_body.cpp | 2 +- src/BODY/fix_nph_body.cpp | 4 +-- src/BODY/fix_npt_body.cpp | 4 +-- src/BODY/fix_nvt_body.cpp | 4 +-- src/BODY/pair_body_nparticle.cpp | 2 +- src/BODY/pair_body_rounded_polygon.cpp | 4 +-- src/BODY/pair_body_rounded_polyhedron.cpp | 4 +-- src/CLASS2/angle_class2.cpp | 4 +-- src/CLASS2/bond_class2.cpp | 4 +-- src/CLASS2/dihedral_class2.cpp | 6 ++-- src/CLASS2/improper_class2.cpp | 6 ++-- src/CLASS2/pair_lj_class2.cpp | 4 +-- src/CLASS2/pair_lj_class2_coul_cut.cpp | 4 +-- src/CLASS2/pair_lj_class2_coul_long.cpp | 4 +-- src/COLLOID/fix_wall_colloid.cpp | 2 +- src/COLLOID/pair_brownian.cpp | 4 +-- src/COLLOID/pair_brownian_poly.cpp | 2 +- src/COLLOID/pair_colloid.cpp | 4 +-- src/COLLOID/pair_lubricate.cpp | 4 +-- src/COLLOID/pair_lubricateU.cpp | 4 +-- src/COLLOID/pair_lubricateU_poly.cpp | 2 +- src/COLLOID/pair_lubricate_poly.cpp | 2 +- src/COMPRESS/dump_atom_gz.cpp | 4 +-- src/COMPRESS/dump_atom_zstd.cpp | 4 +-- src/COMPRESS/dump_cfg_gz.cpp | 4 +-- src/COMPRESS/dump_cfg_zstd.cpp | 4 +-- src/COMPRESS/dump_custom_gz.cpp | 4 +-- src/COMPRESS/dump_custom_zstd.cpp | 4 +-- src/COMPRESS/dump_local_gz.cpp | 4 +-- src/COMPRESS/dump_local_zstd.cpp | 4 +-- src/COMPRESS/dump_xyz_gz.cpp | 4 +-- src/COMPRESS/dump_xyz_zstd.cpp | 4 +-- src/CORESHELL/compute_temp_cs.cpp | 6 ++-- src/DIPOLE/atom_vec_dipole.cpp | 2 +- src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 4 +-- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 4 +-- src/DIPOLE/pair_lj_long_dipole_long.cpp | 4 +-- src/GPU/fix_gpu.cpp | 4 +-- src/GPU/pair_beck_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_gpu.cpp | 2 +- src/GPU/pair_born_gpu.cpp | 2 +- src/GPU/pair_buck_coul_cut_gpu.cpp | 2 +- src/GPU/pair_buck_coul_long_gpu.cpp | 2 +- src/GPU/pair_buck_gpu.cpp | 2 +- src/GPU/pair_colloid_gpu.cpp | 2 +- src/GPU/pair_coul_cut_gpu.cpp | 2 +- src/GPU/pair_coul_debye_gpu.cpp | 2 +- src/GPU/pair_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_coul_long_gpu.cpp | 2 +- src/GPU/pair_dpd_gpu.cpp | 2 +- src/GPU/pair_dpd_tstat_gpu.cpp | 2 +- src/GPU/pair_eam_alloy_gpu.cpp | 4 +-- src/GPU/pair_eam_fs_gpu.cpp | 4 +-- src/GPU/pair_eam_gpu.cpp | 2 +- src/GPU/pair_gauss_gpu.cpp | 2 +- src/GPU/pair_gayberne_gpu.cpp | 2 +- src/GPU/pair_lj96_cut_gpu.cpp | 2 +- src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_gpu.cpp | 2 +- src/GPU/pair_lj_cubic_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_tip4p_long_gpu.cpp | 2 +- src/GPU/pair_lj_expand_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_expand_gpu.cpp | 2 +- src/GPU/pair_lj_gromacs_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_gpu.cpp | 2 +- src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 2 +- src/GPU/pair_mie_cut_gpu.cpp | 2 +- src/GPU/pair_morse_gpu.cpp | 2 +- src/GPU/pair_resquared_gpu.cpp | 2 +- src/GPU/pair_soft_gpu.cpp | 2 +- src/GPU/pair_sw_gpu.cpp | 2 +- src/GPU/pair_table_gpu.cpp | 2 +- src/GPU/pair_tersoff_gpu.cpp | 2 +- src/GPU/pair_tersoff_mod_gpu.cpp | 2 +- src/GPU/pair_tersoff_zbl_gpu.cpp | 2 +- src/GPU/pair_ufm_gpu.cpp | 2 +- src/GPU/pair_vashishta_gpu.cpp | 2 +- src/GPU/pair_yukawa_colloid_gpu.cpp | 2 +- src/GPU/pair_yukawa_gpu.cpp | 2 +- src/GPU/pair_zbl_gpu.cpp | 2 +- src/GRANULAR/fix_freeze.cpp | 2 +- src/GRANULAR/fix_pour.cpp | 4 +-- src/GRANULAR/pair_gran_hooke_history.cpp | 6 ++-- src/GRANULAR/pair_granular.cpp | 6 ++-- src/KIM/pair_kim.cpp | 6 ++-- src/KIM/pair_kim.h | 2 +- src/KOKKOS/angle_charmm_kokkos.cpp | 2 +- src/KOKKOS/angle_class2_kokkos.cpp | 2 +- src/KOKKOS/angle_cosine_kokkos.cpp | 2 +- src/KOKKOS/angle_harmonic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_angle_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_bond_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_charge_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_full_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 +- src/KOKKOS/bond_class2_kokkos.cpp | 2 +- src/KOKKOS/bond_fene_kokkos.cpp | 2 +- src/KOKKOS/bond_harmonic_kokkos.cpp | 2 +- .../compute_orientorder_atom_kokkos.cpp | 2 +- src/KOKKOS/compute_temp_kokkos.cpp | 2 +- src/KOKKOS/dihedral_charmm_kokkos.cpp | 2 +- src/KOKKOS/dihedral_class2_kokkos.cpp | 2 +- src/KOKKOS/dihedral_harmonic_kokkos.cpp | 2 +- src/KOKKOS/dihedral_opls_kokkos.cpp | 2 +- src/KOKKOS/fix_deform_kokkos.cpp | 2 +- src/KOKKOS/fix_momentum_kokkos.cpp | 2 +- src/KOKKOS/fix_nh_kokkos.cpp | 2 +- src/KOKKOS/fix_property_atom_kokkos.cpp | 2 +- src/KOKKOS/fix_rx_kokkos.cpp | 2 +- src/KOKKOS/fix_shardlow_kokkos.cpp | 2 +- src/KOKKOS/fix_wall_reflect_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 4 +-- src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 2 +- src/KOKKOS/pair_reaxc_kokkos.cpp | 2 +- src/KOKKOS/pair_table_rx_kokkos.cpp | 4 +-- src/KSPACE/fix_tune_kspace.cpp | 6 ++-- src/KSPACE/fix_tune_kspace.h | 2 +- src/KSPACE/pair_born_coul_long.cpp | 2 +- src/KSPACE/pair_buck_coul_long.cpp | 4 +-- src/KSPACE/pair_buck_long_coul_long.cpp | 4 +-- src/KSPACE/pair_coul_long.cpp | 4 +-- src/KSPACE/pair_lj_charmm_coul_long.cpp | 2 +- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 2 +- src/KSPACE/pair_lj_cut_coul_long.cpp | 4 +-- src/KSPACE/pair_lj_cut_tip4p_long.cpp | 4 +-- src/KSPACE/pair_lj_long_coul_long.cpp | 6 ++-- src/KSPACE/pair_lj_long_tip4p_long.cpp | 4 +-- src/KSPACE/pair_tip4p_long.cpp | 4 +-- src/MANYBODY/fix_qeq_comb.cpp | 6 ++-- src/MANYBODY/pair_adp.cpp | 6 ++-- src/MANYBODY/pair_airebo.cpp | 6 ++-- src/MANYBODY/pair_atm.cpp | 4 +-- src/MANYBODY/pair_bop.cpp | 6 ++-- src/MANYBODY/pair_comb.cpp | 6 ++-- src/MANYBODY/pair_comb3.cpp | 8 ++--- src/MANYBODY/pair_eam.cpp | 6 ++-- src/MANYBODY/pair_eam_alloy.cpp | 4 +-- src/MANYBODY/pair_eam_cd.cpp | 8 ++--- src/MANYBODY/pair_eam_fs.cpp | 4 +-- src/MANYBODY/pair_eim.cpp | 6 ++-- src/MANYBODY/pair_eim.h | 2 +- src/MANYBODY/pair_gw.cpp | 6 ++-- src/MANYBODY/pair_gw_zbl.cpp | 6 ++-- src/MANYBODY/pair_lcbop.cpp | 4 +-- src/MANYBODY/pair_nb3b_harmonic.cpp | 6 ++-- src/MANYBODY/pair_polymorphic.cpp | 6 ++-- src/MANYBODY/pair_sw.cpp | 6 ++-- src/MANYBODY/pair_tersoff.cpp | 6 ++-- src/MANYBODY/pair_tersoff_mod.cpp | 6 ++-- src/MANYBODY/pair_tersoff_mod_c.cpp | 6 ++-- src/MANYBODY/pair_tersoff_zbl.cpp | 6 ++-- src/MANYBODY/pair_vashishta.cpp | 6 ++-- src/MC/fix_atom_swap.cpp | 2 +- src/MC/fix_bond_break.cpp | 2 +- src/MC/fix_bond_create.cpp | 2 +- src/MC/fix_bond_swap.cpp | 2 +- src/MC/fix_gcmc.cpp | 2 +- src/MC/fix_tfmc.cpp | 2 +- src/MC/fix_widom.cpp | 2 +- src/MC/pair_dsmc.cpp | 6 ++-- src/MISC/compute_msd_nongauss.cpp | 2 +- src/MISC/compute_ti.cpp | 4 +-- src/MISC/dump_xtc.cpp | 2 +- src/MISC/fix_deposit.cpp | 4 +-- src/MISC/fix_efield.cpp | 2 +- src/MISC/fix_evaporate.cpp | 2 +- src/MISC/fix_gld.cpp | 2 +- src/MISC/fix_orient_bcc.cpp | 10 +++--- src/MISC/fix_orient_fcc.cpp | 10 +++--- src/MISC/fix_thermal_conductivity.cpp | 2 +- src/MISC/fix_ttm.cpp | 6 ++-- src/MISC/fix_viscosity.cpp | 2 +- src/MISC/pair_nm_cut.cpp | 4 +-- src/MISC/pair_nm_cut_coul_cut.cpp | 4 +-- src/MISC/pair_nm_cut_coul_long.cpp | 4 +-- src/MLIAP/compute_mliap.cpp | 2 +- src/MLIAP/compute_mliap.h | 2 +- src/MLIAP/pair_mliap.cpp | 4 +-- src/MOLECULE/angle_charmm.cpp | 4 +-- src/MOLECULE/angle_cosine.cpp | 4 +-- src/MOLECULE/angle_cosine_periodic.cpp | 4 +-- src/MOLECULE/angle_cosine_squared.cpp | 4 +-- src/MOLECULE/angle_harmonic.cpp | 4 +-- src/MOLECULE/angle_table.cpp | 8 ++--- src/MOLECULE/atom_vec_template.cpp | 2 +- src/MOLECULE/bond_fene.cpp | 6 ++-- src/MOLECULE/bond_fene_expand.cpp | 4 +-- src/MOLECULE/bond_gromos.cpp | 4 +-- src/MOLECULE/bond_harmonic.cpp | 4 +-- src/MOLECULE/bond_morse.cpp | 4 +-- src/MOLECULE/bond_nonlinear.cpp | 4 +-- src/MOLECULE/bond_quartic.cpp | 4 +-- src/MOLECULE/bond_table.cpp | 8 ++--- src/MOLECULE/dihedral_charmm.cpp | 4 +-- src/MOLECULE/dihedral_charmmfsw.cpp | 4 +-- src/MOLECULE/dihedral_harmonic.cpp | 4 +-- src/MOLECULE/dihedral_helix.cpp | 4 +-- src/MOLECULE/dihedral_multi_harmonic.cpp | 4 +-- src/MOLECULE/dihedral_opls.cpp | 4 +-- src/MOLECULE/fix_cmap.cpp | 8 ++--- src/MOLECULE/improper_cvff.cpp | 4 +-- src/MOLECULE/improper_harmonic.cpp | 4 +-- src/MOLECULE/improper_umbrella.cpp | 4 +-- src/MOLECULE/pair_hbond_dreiding_lj.cpp | 2 +- src/MOLECULE/pair_hbond_dreiding_morse.cpp | 2 +- src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 4 +-- .../pair_lj_charmmfsw_coul_charmmfsh.cpp | 4 +-- src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 4 +-- src/MOLECULE/pair_tip4p_cut.cpp | 4 +-- src/MPIIO/dump_atom_mpiio.cpp | 2 +- src/MPIIO/dump_cfg_mpiio.cpp | 2 +- src/MPIIO/dump_custom_mpiio.cpp | 2 +- src/MPIIO/dump_xyz_mpiio.cpp | 2 +- src/MSCG/fix_mscg.cpp | 4 +-- src/OPT/pair_eam_opt.cpp | 2 +- src/OPT/pair_lj_charmm_coul_long_opt.cpp | 2 +- src/OPT/pair_lj_cut_opt.cpp | 2 +- src/OPT/pair_morse_opt.cpp | 2 +- src/OPT/pair_ufm_opt.cpp | 2 +- src/PERI/fix_peri_neigh.cpp | 2 +- src/PERI/pair_peri_eps.cpp | 6 ++-- src/PERI/pair_peri_lps.cpp | 6 ++-- src/PERI/pair_peri_pmb.cpp | 6 ++-- src/PERI/pair_peri_ves.cpp | 6 ++-- src/POEMS/fix_poems.cpp | 8 ++--- src/PYTHON/pair_python.cpp | 2 +- src/QEQ/fix_qeq.cpp | 4 +-- src/QEQ/fix_qeq_dynamic.cpp | 4 +-- src/QEQ/fix_qeq_fire.cpp | 4 +-- src/QEQ/fix_qeq_slater.cpp | 2 +- src/REPLICA/compute_event_displace.cpp | 2 +- src/REPLICA/fix_hyper_global.cpp | 2 +- src/REPLICA/fix_hyper_local.cpp | 6 ++-- src/REPLICA/fix_neb.cpp | 4 +-- src/RIGID/fix_ehex.cpp | 2 +- src/RIGID/fix_rattle.cpp | 2 +- src/RIGID/fix_rigid.cpp | 8 ++--- src/RIGID/fix_rigid_nh_small.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 8 ++--- src/RIGID/fix_shake.cpp | 6 ++-- src/SHOCK/fix_append_atoms.cpp | 2 +- src/SHOCK/fix_msst.cpp | 6 ++-- src/SNAP/compute_sna_atom.cpp | 2 +- src/SNAP/compute_snad_atom.cpp | 2 +- src/SNAP/compute_snap.cpp | 2 +- src/SNAP/compute_snav_atom.cpp | 2 +- src/SNAP/pair_snap.cpp | 6 ++-- src/SPIN/compute_spin.cpp | 2 +- src/SPIN/fix_langevin_spin.cpp | 2 +- src/SPIN/fix_neb_spin.cpp | 2 +- src/SPIN/fix_precession_spin.cpp | 2 +- src/SPIN/pair_spin_dipole_cut.cpp | 4 +-- src/SPIN/pair_spin_dipole_long.cpp | 4 +-- src/SPIN/pair_spin_dmi.cpp | 4 +-- src/SPIN/pair_spin_exchange.cpp | 4 +-- src/SPIN/pair_spin_magelec.cpp | 4 +-- src/SPIN/pair_spin_neel.cpp | 4 +-- src/SRD/fix_srd.cpp | 2 +- src/SRD/fix_wall_srd.cpp | 2 +- src/USER-AWPMD/fix_nve_awpmd.cpp | 2 +- src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +-- src/USER-BOCS/compute_pressure_bocs.cpp | 6 ++-- src/USER-BOCS/fix_bocs.cpp | 4 +-- src/USER-CGDNA/bond_oxdna_fene.cpp | 4 +-- src/USER-CGDNA/bond_oxrna2_fene.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna2_dh.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_excv.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_hbond.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_stk.cpp | 4 +-- src/USER-CGDNA/pair_oxdna_xstk.cpp | 4 +-- src/USER-CGDNA/pair_oxrna2_excv.cpp | 2 +- src/USER-CGDNA/pair_oxrna2_stk.cpp | 4 +-- src/USER-CGDNA/pair_oxrna2_xstk.cpp | 4 +-- src/USER-CGSDK/angle_sdk.cpp | 4 +-- src/USER-CGSDK/pair_lj_sdk.cpp | 4 +-- src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 4 +-- src/USER-COLVARS/fix_colvars.cpp | 6 ++-- src/USER-DIFFRACTION/compute_saed.cpp | 4 +-- src/USER-DIFFRACTION/compute_xrd.cpp | 4 +-- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 2 +- src/USER-DPD/compute_dpd.cpp | 2 +- src/USER-DPD/fix_eos_table.cpp | 6 ++-- src/USER-DPD/fix_eos_table_rx.cpp | 6 ++-- src/USER-DPD/fix_rx.cpp | 6 ++-- src/USER-DPD/fix_shardlow.cpp | 4 +-- src/USER-DPD/pair_dpd_fdt.cpp | 4 +-- src/USER-DPD/pair_dpd_fdt_energy.cpp | 4 +-- src/USER-DPD/pair_exp6_rx.cpp | 6 ++-- src/USER-DPD/pair_multi_lucy.cpp | 8 ++--- src/USER-DPD/pair_multi_lucy_rx.cpp | 8 ++--- src/USER-DPD/pair_table_rx.cpp | 4 +-- src/USER-DRUDE/compute_temp_drude.cpp | 2 +- src/USER-DRUDE/fix_drude.cpp | 2 +- src/USER-DRUDE/fix_drude_transform.cpp | 2 +- src/USER-DRUDE/fix_langevin_drude.cpp | 2 +- src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 4 +-- src/USER-DRUDE/pair_thole.cpp | 4 +-- src/USER-EFF/compute_ke_atom_eff.cpp | 2 +- src/USER-EFF/compute_ke_eff.cpp | 4 +-- src/USER-EFF/compute_temp_deform_eff.cpp | 4 +-- src/USER-EFF/compute_temp_eff.cpp | 4 +-- src/USER-EFF/compute_temp_region_eff.cpp | 4 +-- src/USER-EFF/fix_langevin_eff.cpp | 4 +-- src/USER-EFF/fix_nh_eff.cpp | 2 +- src/USER-EFF/fix_nve_eff.cpp | 2 +- src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +- src/USER-EFF/fix_temp_rescale_eff.cpp | 2 +- src/USER-EFF/pair_eff_cut.cpp | 6 ++-- src/USER-FEP/compute_fep.cpp | 4 +-- src/USER-FEP/fix_adapt_fep.cpp | 2 +- src/USER-FEP/pair_coul_cut_soft.cpp | 4 +-- src/USER-FEP/pair_coul_long_soft.cpp | 4 +-- .../pair_lj_charmm_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp | 4 +-- .../pair_lj_class2_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_class2_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_soft.cpp | 4 +-- src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp | 4 +-- src/USER-FEP/pair_morse_soft.cpp | 4 +-- src/USER-FEP/pair_tip4p_long_soft.cpp | 4 +-- src/USER-H5MD/dump_h5md.cpp | 2 +- src/USER-INTEL/angle_charmm_intel.cpp | 2 +- src/USER-INTEL/angle_harmonic_intel.cpp | 2 +- src/USER-INTEL/bond_fene_intel.cpp | 2 +- src/USER-INTEL/bond_harmonic_intel.cpp | 2 +- src/USER-INTEL/dihedral_charmm_intel.cpp | 2 +- src/USER-INTEL/dihedral_fourier_intel.cpp | 2 +- src/USER-INTEL/dihedral_harmonic_intel.cpp | 2 +- src/USER-INTEL/dihedral_opls_intel.cpp | 2 +- src/USER-INTEL/fix_intel.cpp | 4 +-- src/USER-INTEL/improper_cvff_intel.cpp | 4 +-- src/USER-INTEL/improper_harmonic_intel.cpp | 4 +-- src/USER-INTEL/pair_airebo_intel.cpp | 2 +- src/USER-INTEL/pair_buck_coul_cut_intel.cpp | 2 +- src/USER-INTEL/pair_buck_coul_long_intel.cpp | 2 +- src/USER-INTEL/pair_eam_alloy_intel.cpp | 4 +-- src/USER-INTEL/pair_eam_fs_intel.cpp | 4 +-- src/USER-INTEL/pair_eam_intel.cpp | 2 +- src/USER-INTEL/pair_sw_intel.cpp | 2 +- src/USER-INTEL/pair_tersoff_intel.cpp | 2 +- src/USER-LB/fix_lb_fluid.cpp | 4 +-- src/USER-LB/fix_lb_momentum.cpp | 4 +-- src/USER-LB/fix_lb_pc.cpp | 2 +- src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 6 ++-- src/USER-MANIFOLD/fix_manifoldforce.cpp | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 2 +- src/USER-MEAMC/pair_meamc.cpp | 10 +++--- src/USER-MEAMC/pair_meamc.h | 2 +- src/USER-MESODPD/atom_vec_edpd.cpp | 2 +- src/USER-MESODPD/atom_vec_tdpd.cpp | 2 +- src/USER-MESODPD/pair_edpd.cpp | 4 +-- src/USER-MESODPD/pair_mdpd.cpp | 4 +-- src/USER-MESODPD/pair_mdpd_rhosum.cpp | 2 +- src/USER-MESODPD/pair_tdpd.cpp | 2 +- src/USER-MESONT/compute_mesont.cpp | 2 +- src/USER-MESONT/pair_mesocnt.cpp | 8 ++--- src/USER-MESONT/pair_mesont_tpm.cpp | 4 +-- src/USER-MGPT/pair_mgpt.cpp | 4 +-- src/USER-MISC/angle_cosine_shift.cpp | 4 +-- src/USER-MISC/angle_cosine_shift_exp.cpp | 4 +-- src/USER-MISC/angle_dipole.cpp | 4 +-- src/USER-MISC/angle_fourier.cpp | 4 +-- src/USER-MISC/angle_fourier_simple.cpp | 4 +-- src/USER-MISC/angle_quartic.cpp | 4 +-- src/USER-MISC/bond_harmonic_shift.cpp | 4 +-- src/USER-MISC/bond_harmonic_shift_cut.cpp | 4 +-- src/USER-MISC/bond_special.cpp | 4 +-- src/USER-MISC/compute_cnp_atom.cpp | 2 +- src/USER-MISC/compute_hma.cpp | 2 +- src/USER-MISC/compute_momentum.cpp | 2 +- src/USER-MISC/compute_pressure_cylinder.cpp | 2 +- src/USER-MISC/compute_stress_mop.cpp | 2 +- src/USER-MISC/compute_stress_mop_profile.cpp | 2 +- src/USER-MISC/compute_temp_rotate.cpp | 2 +- src/USER-MISC/compute_viscosity_cos.cpp | 2 +- src/USER-MISC/dihedral_cosine_shift_exp.cpp | 4 +-- src/USER-MISC/dihedral_fourier.cpp | 4 +-- src/USER-MISC/dihedral_nharmonic.cpp | 4 +-- src/USER-MISC/dihedral_quadratic.cpp | 4 +-- src/USER-MISC/dihedral_spherical.cpp | 4 +-- src/USER-MISC/dihedral_table.cpp | 12 +++---- src/USER-MISC/dihedral_table.h | 2 +- src/USER-MISC/dihedral_table_cut.cpp | 8 ++--- src/USER-MISC/fix_addtorque.cpp | 2 +- src/USER-MISC/fix_ave_correlate_long.cpp | 4 +-- src/USER-MISC/fix_ffl.cpp | 2 +- src/USER-MISC/fix_filter_corotate.cpp | 4 +-- src/USER-MISC/fix_flow_gauss.cpp | 2 +- src/USER-MISC/fix_gle.cpp | 6 ++-- src/USER-MISC/fix_imd.cpp | 2 +- src/USER-MISC/fix_ipi.cpp | 4 +-- src/USER-MISC/fix_momentum_chunk.cpp | 4 +-- src/USER-MISC/fix_momentum_chunk.h | 2 +- src/USER-MISC/fix_npt_cauchy.cpp | 2 +- src/USER-MISC/fix_nvk.cpp | 2 +- src/USER-MISC/fix_orient_eco.cpp | 6 ++-- src/USER-MISC/fix_pafi.cpp | 8 ++--- src/USER-MISC/fix_pimd.cpp | 4 +-- src/USER-MISC/fix_propel_self.cpp | 2 +- src/USER-MISC/fix_rhok.cpp | 2 +- src/USER-MISC/fix_smd.cpp | 2 +- src/USER-MISC/fix_srp.cpp | 2 +- src/USER-MISC/fix_ti_spring.cpp | 2 +- src/USER-MISC/fix_ttm_mod.cpp | 6 ++-- src/USER-MISC/fix_wall_reflect_stochastic.cpp | 2 +- src/USER-MISC/fix_wall_region_ees.cpp | 2 +- src/USER-MISC/improper_cossq.cpp | 4 +-- src/USER-MISC/improper_distance.cpp | 4 +-- src/USER-MISC/improper_fourier.cpp | 4 +-- src/USER-MISC/improper_ring.cpp | 4 +-- src/USER-MISC/pair_agni.cpp | 6 ++-- src/USER-MISC/pair_buck_mdf.cpp | 4 +-- src/USER-MISC/pair_cosine_squared.cpp | 4 +-- src/USER-MISC/pair_coul_diel.cpp | 4 +-- src/USER-MISC/pair_coul_shield.cpp | 2 +- src/USER-MISC/pair_coul_slater_cut.cpp | 2 +- src/USER-MISC/pair_coul_slater_long.cpp | 4 +-- src/USER-MISC/pair_drip.cpp | 6 ++-- src/USER-MISC/pair_e3b.cpp | 2 +- src/USER-MISC/pair_edip.cpp | 6 ++-- src/USER-MISC/pair_edip_multi.cpp | 6 ++-- src/USER-MISC/pair_extep.cpp | 6 ++-- src/USER-MISC/pair_gauss_cut.cpp | 4 +-- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 6 ++-- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 6 ++-- src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 6 ++-- src/USER-MISC/pair_lebedeva_z.cpp | 6 ++-- src/USER-MISC/pair_lennard_mdf.cpp | 4 +-- src/USER-MISC/pair_list.cpp | 4 +-- src/USER-MISC/pair_lj_expand_coul_long.cpp | 4 +-- src/USER-MISC/pair_lj_mdf.cpp | 4 +-- src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 4 +-- src/USER-MISC/pair_local_density.cpp | 8 ++--- src/USER-MISC/pair_meam_spline.cpp | 4 +-- src/USER-MISC/pair_meam_sw_spline.cpp | 4 +-- src/USER-MISC/pair_momb.cpp | 4 +-- src/USER-MISC/pair_morse_smooth_linear.cpp | 4 +-- src/USER-MISC/pair_srp.cpp | 6 ++-- src/USER-MISC/pair_tersoff_table.cpp | 6 ++-- src/USER-MOFFF/angle_class2_p6.cpp | 4 +-- src/USER-MOFFF/angle_cosine_buck6d.cpp | 4 +-- .../improper_inversion_harmonic.cpp | 4 +-- src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 2 +- .../pair_buck6d_coul_gauss_long.cpp | 4 +-- src/USER-MOLFILE/dump_molfile.cpp | 2 +- src/USER-NETCDF/dump_netcdf.cpp | 2 +- src/USER-NETCDF/dump_netcdf_mpiio.cpp | 2 +- src/USER-OMP/fix_nh_asphere_omp.cpp | 2 +- src/USER-OMP/fix_qeq_comb_omp.cpp | 2 +- src/USER-OMP/fix_qeq_reax_omp.cpp | 2 +- src/USER-OMP/fix_rigid_nh_omp.cpp | 2 +- src/USER-OMP/fix_rigid_omp.cpp | 2 +- src/USER-OMP/pair_eam_alloy_omp.cpp | 4 +-- src/USER-OMP/pair_eam_fs_omp.cpp | 4 +-- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 2 +- src/USER-OMP/pair_reaxc_omp.cpp | 2 +- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 4 +-- src/USER-PHONON/fix_phonon.cpp | 2 +- src/USER-PLUMED/fix_plumed.cpp | 4 +-- src/USER-QMMM/fix_qmmm.cpp | 2 +- src/USER-QTB/fix_qbmsst.cpp | 10 +++--- src/USER-QTB/fix_qtb.cpp | 8 ++--- src/USER-QUIP/pair_quip.cpp | 4 +-- src/USER-REACTION/fix_bond_react.cpp | 6 ++-- src/USER-REAXC/fix_qeq_reax.cpp | 2 +- src/USER-REAXC/fix_reaxc_bonds.cpp | 2 +- src/USER-REAXC/fix_reaxc_species.cpp | 4 +-- src/USER-REAXC/pair_reaxc.cpp | 6 ++-- .../pair_sdpd_taitwater_isothermal.cpp | 2 +- src/USER-SMD/compute_smd_vol.cpp | 2 +- src/USER-SMD/fix_smd_adjust_dt.cpp | 4 +-- src/USER-SMD/fix_smd_setvel.cpp | 2 +- .../fix_smd_tlsph_reference_configuration.cpp | 2 +- src/USER-SMD/fix_smd_wall_surface.cpp | 4 +-- src/USER-SMD/pair_smd_hertz.cpp | 6 ++-- src/USER-SMD/pair_smd_tlsph.cpp | 4 +-- .../pair_smd_triangulated_surface.cpp | 6 ++-- src/USER-SMD/pair_smd_ulsph.cpp | 4 +-- src/USER-SMTBQ/pair_smtbq.cpp | 4 +-- src/USER-SPH/pair_sph_heatconduction.cpp | 2 +- src/USER-SPH/pair_sph_idealgas.cpp | 2 +- src/USER-SPH/pair_sph_lj.cpp | 2 +- src/USER-SPH/pair_sph_rhosum.cpp | 2 +- src/USER-SPH/pair_sph_taitwater.cpp | 2 +- src/USER-SPH/pair_sph_taitwater_morris.cpp | 2 +- src/USER-TALLY/compute_force_tally.cpp | 2 +- src/USER-TALLY/compute_heat_flux_tally.cpp | 2 +- src/USER-TALLY/compute_pe_mol_tally.cpp | 2 +- src/USER-TALLY/compute_pe_tally.cpp | 2 +- src/USER-TALLY/compute_stress_tally.cpp | 2 +- src/USER-VTK/dump_vtk.cpp | 2 +- src/USER-VTK/dump_vtk.h | 2 +- src/USER-YAFF/angle_cross.cpp | 4 +-- src/USER-YAFF/angle_mm3.cpp | 4 +-- src/USER-YAFF/bond_mm3.cpp | 4 +-- src/USER-YAFF/improper_distharm.cpp | 4 +-- src/USER-YAFF/improper_sqdistharm.cpp | 4 +-- .../pair_lj_switch3_coulgauss_long.cpp | 4 +-- .../pair_mm3_switch3_coulgauss_long.cpp | 4 +-- src/VORONOI/compute_voronoi_atom.cpp | 2 +- src/angle_deprecated.cpp | 2 -- src/angle_hybrid.cpp | 8 ++--- src/angle_zero.cpp | 7 ++-- src/atom.cpp | 27 +++++++-------- src/atom.h | 16 +++++---- src/atom_map.cpp | 7 ++-- src/atom_vec.cpp | 13 ++++--- src/atom_vec_body.cpp | 15 ++++---- src/atom_vec_ellipsoid.cpp | 12 +++---- src/atom_vec_hybrid.cpp | 6 ++-- src/atom_vec_line.cpp | 12 +++---- src/atom_vec_sphere.cpp | 9 ++--- src/atom_vec_tri.cpp | 14 ++++---- src/balance.cpp | 22 ++++++------ src/bond.cpp | 14 ++++---- src/bond_deprecated.cpp | 5 ++- src/bond_hybrid.cpp | 12 +++---- src/bond_zero.cpp | 9 +++-- src/change_box.cpp | 26 +++++++------- src/comm.cpp | 32 ++++++++--------- src/comm_brick.cpp | 15 ++++---- src/comm_tiled.cpp | 17 +++++----- src/compute.cpp | 17 +++++----- src/compute_adf.cpp | 22 ++++++------ src/compute_aggregate_atom.cpp | 20 +++++------ src/compute_angle.cpp | 6 ++-- src/compute_angmom_chunk.cpp | 11 +++--- src/compute_bond.cpp | 6 ++-- src/compute_chunk_atom.cpp | 28 +++++++-------- src/compute_chunk_spread_atom.cpp | 15 ++++---- src/compute_cluster_atom.cpp | 20 +++++------ src/compute_cna_atom.cpp | 20 +++++------ src/compute_com_chunk.cpp | 11 +++--- src/compute_coord_atom.cpp | 25 +++++++------- src/compute_deprecated.cpp | 3 +- src/compute_dihedral.cpp | 6 ++-- src/compute_dipole_chunk.cpp | 13 +++---- src/compute_displace_atom.cpp | 23 +++++++------ src/compute_erotate_sphere.cpp | 6 ++-- src/compute_fragment_atom.cpp | 14 ++++---- src/compute_global_atom.cpp | 14 ++++---- src/compute_group_group.cpp | 2 +- src/compute_gyration.cpp | 2 +- src/compute_gyration_chunk.cpp | 2 +- src/compute_heat_flux.cpp | 2 +- src/compute_improper.cpp | 2 +- src/compute_inertia_chunk.cpp | 2 +- src/compute_ke.cpp | 2 +- src/compute_msd.cpp | 6 ++-- src/compute_msd_chunk.cpp | 6 ++-- src/compute_omega_chunk.cpp | 2 +- src/compute_orientorder_atom.cpp | 22 ++++++------ src/compute_pair.cpp | 2 +- src/compute_pair_local.cpp | 21 ++++++------ src/compute_pe.cpp | 2 +- src/compute_pressure.cpp | 2 +- src/compute_property_chunk.cpp | 2 +- src/compute_rdf.cpp | 4 +-- src/compute_reduce.cpp | 6 ++-- src/compute_reduce.h | 2 +- src/compute_reduce_chunk.cpp | 6 ++-- src/compute_reduce_region.cpp | 2 +- src/compute_slice.cpp | 15 ++++---- src/compute_temp.cpp | 2 +- src/compute_temp_chunk.cpp | 2 +- src/compute_temp_com.cpp | 2 +- src/compute_temp_deform.cpp | 2 +- src/compute_temp_partial.cpp | 2 +- src/compute_temp_profile.cpp | 2 +- src/compute_temp_ramp.cpp | 2 +- src/compute_temp_region.cpp | 2 +- src/compute_temp_sphere.cpp | 2 +- src/compute_torque_chunk.cpp | 2 +- src/compute_vacf.cpp | 6 ++-- src/compute_vcm_chunk.cpp | 2 +- src/delete_atoms.cpp | 21 +++++------- src/delete_bonds.cpp | 13 +++---- src/deprecated.cpp | 3 +- src/dihedral_deprecated.cpp | 8 ++--- src/dihedral_hybrid.cpp | 4 +-- src/dihedral_zero.cpp | 8 ++--- src/displace_atoms.cpp | 34 +++++++++---------- src/domain.cpp | 30 ++++++++-------- src/domain.h | 4 +-- src/dump.cpp | 6 ++-- src/dump_custom.cpp | 21 +++++------- src/dump_deprecated.cpp | 3 +- src/dump_image.cpp | 4 +-- src/dump_local.cpp | 6 ++-- src/dump_movie.cpp | 2 +- src/fix_adapt.cpp | 4 +-- src/fix_addforce.cpp | 4 +-- src/fix_ave_atom.cpp | 4 +-- src/fix_ave_chunk.cpp | 8 ++--- src/fix_ave_correlate.cpp | 8 ++--- src/fix_ave_histo.cpp | 8 ++--- src/fix_ave_histo_weight.cpp | 2 +- src/fix_ave_time.cpp | 8 ++--- src/fix_aveforce.cpp | 2 +- src/fix_box_relax.cpp | 4 +-- src/fix_controller.cpp | 2 +- src/fix_deprecated.cpp | 4 +-- src/fix_drag.cpp | 2 +- src/fix_dt_reset.cpp | 2 +- src/fix_enforce2d.cpp | 2 +- src/fix_gravity.cpp | 2 +- src/fix_halt.cpp | 6 ++-- src/fix_heat.cpp | 2 +- src/fix_indent.cpp | 2 +- src/fix_langevin.cpp | 4 +-- src/fix_momentum.cpp | 2 +- src/fix_neigh_history.cpp | 2 +- src/fix_nph.cpp | 2 +- src/fix_nph_sphere.cpp | 2 +- src/fix_npt.cpp | 2 +- src/fix_npt_sphere.cpp | 2 +- src/fix_numdiff.cpp | 2 +- src/fix_nve_limit.cpp | 4 +-- src/fix_nvt.cpp | 4 +-- src/fix_nvt_sllod.cpp | 2 +- src/fix_nvt_sphere.cpp | 4 +-- src/fix_press_berendsen.cpp | 2 +- src/fix_print.cpp | 6 ++-- src/fix_property_atom.cpp | 6 ++-- src/fix_restrain.cpp | 4 +-- src/fix_setforce.cpp | 2 +- src/fix_spring_self.cpp | 2 +- src/fix_store_state.cpp | 2 +- src/fix_temp_berendsen.cpp | 4 +-- src/fix_temp_csld.cpp | 4 +-- src/fix_temp_csvr.cpp | 6 ++-- src/fix_temp_rescale.cpp | 4 +-- src/fix_tmd.cpp | 6 ++-- src/fix_vector.cpp | 2 +- src/fix_wall.cpp | 4 +-- src/fix_wall_region.cpp | 2 +- src/improper_deprecated.cpp | 4 +-- src/improper_hybrid.cpp | 4 +-- src/improper_zero.cpp | 2 +- src/lmptype.h | 8 ++--- src/pair_beck.cpp | 4 +-- src/pair_born.cpp | 4 +-- src/pair_born_coul_dsf.cpp | 4 +-- src/pair_born_coul_wolf.cpp | 4 +-- src/pair_buck.cpp | 4 +-- src/pair_buck_coul_cut.cpp | 4 +-- src/pair_coul_cut.cpp | 4 +-- src/pair_coul_debye.cpp | 4 +-- src/pair_coul_dsf.cpp | 4 +-- src/pair_coul_streitz.cpp | 8 ++--- src/pair_coul_wolf.cpp | 4 +-- src/pair_deprecated.cpp | 4 +-- src/pair_dpd.cpp | 4 +-- src/pair_dpd_tstat.cpp | 4 +-- src/pair_gauss.cpp | 4 +-- src/pair_hybrid.cpp | 6 ++-- src/pair_hybrid_overlay.cpp | 2 +- src/pair_lj96_cut.cpp | 4 +-- src/pair_lj_cubic.cpp | 4 +-- src/pair_lj_cut.cpp | 4 +-- src/pair_lj_cut_coul_cut.cpp | 4 +-- src/pair_lj_cut_coul_debye.cpp | 4 +-- src/pair_lj_cut_coul_dsf.cpp | 4 +-- src/pair_lj_cut_coul_wolf.cpp | 4 +-- src/pair_lj_expand.cpp | 4 +-- src/pair_lj_gromacs.cpp | 4 +-- src/pair_lj_gromacs_coul_gromacs.cpp | 4 +-- src/pair_lj_smooth.cpp | 4 +-- src/pair_lj_smooth_linear.cpp | 4 +-- src/pair_mie_cut.cpp | 4 +-- src/pair_morse.cpp | 4 +-- src/pair_soft.cpp | 4 +-- src/pair_table.cpp | 10 +++--- src/pair_ufm.cpp | 4 +-- src/pair_yukawa.cpp | 4 +-- src/pair_zbl.cpp | 2 +- src/pair_zero.cpp | 4 +-- src/region_deprecated.cpp | 4 +-- src/tokenizer.h | 7 ++-- 714 files changed, 1532 insertions(+), 1554 deletions(-) diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index 3cf23b87eb..945b91fbbd 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_asphere.h" -#include + #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 4350678bbd..889563f617 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_asphere.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 0501ea1e8a..6d1727ce45 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index f7f253f40b..064a20d55b 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index e0275d4acf..d439d947bf 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_asphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 064e365dc1..89350dd00f 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gayberne.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -28,7 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index a1c6477542..6397e77f5b 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index a25addaba4..81fb4d4b6c 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_resquared.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 0f840dadf3..cf89cf9d33 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 915407db92..861ffbe4a7 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_body_local.h" -#include + #include #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 4cf9ac5009..18c301678a 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_body.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1e8cc88e7c..f198919ad8 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -17,11 +17,11 @@ #include "fix_nph_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 295777753f..23194bc8ca 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -17,11 +17,11 @@ #include "fix_npt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 458ff1ab14..3cab4416b0 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -17,11 +17,11 @@ #include "fix_nvt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index b3333d4715..ece23d9522 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -23,7 +23,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 9687c28613..fa5a8e57da 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polygon.h" -#include + #include #include #include "math_extra.h" @@ -34,7 +34,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index dfefc318af..d376ac759e 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -21,7 +21,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polyhedron.h" -#include + #include #include #include "atom.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_extra.h" #include "math_const.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 431479b489..eea43480e1 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 2cd63eafcb..a97b06a3c7 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -17,7 +17,7 @@ #include #include "bond_class2.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 44d4902e4a..5be522f2c9 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 662459abb7..0b07a7d60c 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 96b035f83b..bb1dfe0ab3 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -10,7 +10,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 9aca9f048a..8375043ed8 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 5c7c107d02..3b9ef8deaf 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 58593a99b1..61b52a6585 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_colloid.h" -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index d7b2dba14a..786be66c70 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian.h" -#include + #include #include #include "atom.h" @@ -36,7 +36,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index c3eb4f28a5..9c2593ffb1 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 7552d123c3..f95645c613 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_colloid.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4f2a4455a3..867bb91979 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate.h" -#include + #include #include #include "atom.h" @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 4fb1611660..2df1ecaaa6 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 7fd847671e..8483bb0f51 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index e347441cf4..351757e09b 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 6c78ba7910..484175762e 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index a8da9a1a2c..a993f58809 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 2d48e02f3c..18f0fa56d7 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -16,10 +16,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 0f74e2550b..51819772f6 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 35a2d25a2a..fb2b121f7f 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index 395ba51fdc..d0f5335813 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index a346de3127..49a3c3bef2 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 3e658fd070..9393654dd6 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 79d2d20997..cc07b1ce61 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -14,10 +14,10 @@ #include "dump_xyz_gz.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 066609eebb..839e743654 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -20,10 +20,10 @@ #include "dump_xyz_zstd.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index d8f952551d..1b7eb1e43f 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "compute_temp_cs.h" -#include + #include -#include + #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index b6895be301..66de360f6e 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -20,7 +20,7 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 8f91420043..25fed599db 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 73aa628296..67d2e0aa3c 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_long.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index f7c8251e79..86e143626d 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_dipole_long.h" -#include + #include #include #include "math_const.h" @@ -30,7 +30,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 0552d23cdb..15bc42c37e 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -13,7 +13,7 @@ #include "fix_gpu.h" #include -#include + #include "atom.h" #include "force.h" #include "pair.h" @@ -30,7 +30,7 @@ #include "neighbor.h" #include "citeme.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 28386f5fd5..86467f49c0 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_beck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 8bc99a3d49..c27c670f2a 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index 5dd4c3421f..a2524909e5 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4ba28c25aa..cf54b72cf5 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index b5e0edea6d..e9aa951236 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index a5e94389b6..5a5a6d2a36 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index 1a5479ea1d..de9f0d1eba 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 221e178b57..41823fc27e 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 07107750e6..1f7abc06bc 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index a7cafbe75a..39737ab183 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index bacbdbb1a0..34a76c1dff 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 96be67a1fa..40fb359484 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 244941c117..8c05d14aef 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index bcbf7216e2..da59873dd2 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index fcfb20f3ce..185d3a7f94 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index a2e20d016c..d41be6d8c2 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 991c6d900f..33d7178faa 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_tstat_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 08ffaef978..4939537770 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_alloy_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "gpu_extra.h" #include "domain.h" -#include "utils.h" + #include "suffix.h" #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index a82107749b..eb028bc778 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_fs_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -30,7 +30,7 @@ #include "gpu_extra.h" #include "domain.h" #include "suffix.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 1aac379c35..3965f27c67 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_eam_gpu.h" #include #include -#include + #include #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index eb83d5af44..51d4851dc5 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gauss_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 83b24f8774..451799027b 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gayberne_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 7b0d45a437..215998bc88 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj96_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index b08ad5e232..09ed178200 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_charmm_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index 46ecaea9b8..f6d671d95a 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index a7ca661927..fbd6aea08c 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 38f6e1f908..28e74d8f39 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cubic_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 54f0e92bd5..48770d2713 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index e7b1ac5002..45c3cc82a0 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 5d1f4f70be..784c0e379d 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index dff2ba28d4..2a9d431a42 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 2f965d6476..f5987c0ddf 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_msm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 43c2a1e9b7..ac053037d8 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 9416ede516..7de9ae2aa6 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 27924361f2..5656c2e18d 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp index 7c1bb74158..2bd7420e72 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_lj_cut_tip4p_long_gpu.h" #include "atom.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 54eb4d47e6..f13eea51e7 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 32c35420a2..bdfa30b965 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index d7122cb5f3..6d6abdb40d 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_gromacs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index cd76bbd2e9..4054f08523 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 5f07bdbb6c..2016d1db2c 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index a9ddf81bf0..e6834298f3 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sf_dipole_sf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4db07ab79e..60e6e935e8 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_mie_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index fc966f6533..a256f500ce 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_morse_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 0bcabb451c..ca70e3c337 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_resquared_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 48a4f689ff..49c27f515d 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_soft_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 4c4502828d..d544534c9d 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_sw_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index 858a2107dc..4ac674aa94 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_table_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index d7b1ef5dd5..885dd73d9e 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 1b35045902..35edd9ea22 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_mod_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index ae50552f14..73251ee726 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_zbl_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 2b4cc2269f..fe6adfef12 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -20,7 +20,7 @@ #include "pair_ufm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index ccd2773130..868b8de0c0 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_vashishta_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index c3439e3306..3c7b2f5ba7 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index b9b9d6e0a4..8147609f45 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index d0cbfa1d7c..0472d9b7c1 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -19,7 +19,7 @@ #include "lmptype.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 1df5c9d0a8..dd68aa032f 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_freeze.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 879f48e023..d449bb5614 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_pour.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index a8cd808411..68a7803f4b 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_gran_hooke_history.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 88a9fe36f0..ee0eb2ad77 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -18,10 +18,10 @@ ----------------------------------------------------------------------- */ #include "pair_granular.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 69586b55d6..3422f93f3a 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -56,8 +56,8 @@ ------------------------------------------------------------------------- */ #include "pair_kim.h" #include -#include -#include + + #include #include "atom.h" #include "comm.h" @@ -68,7 +68,7 @@ #include "update.h" #include "memory.h" #include "domain.h" -#include "utils.h" + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 1f2c8c8599..0361f2351e 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -65,7 +65,7 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" -#include + extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 288e5a475b..14850525ef 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_charmm_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index ebb016b31b..4406f51f83 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 960988b3b5..7ba634cd13 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_cosine_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index bc08ff4b65..2e5831ef07 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "angle_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e9fee6d8f6..e9c101eb79 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 7a66dc753a..c76af73420 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 157f194125..47e77c33b3 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 8f468b8e46..183bdb94e4 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 5319744c22..b112605859 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 5d5833af07..89275c7067 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 0cc609f91c..34a246008d 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -20,7 +20,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index b0fca4e316..dceedc8e60 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -16,7 +16,7 @@ #include "comm_kokkos.h" #include "domain.h" #include "atom_masks.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 7832d6f9b0..6a4d94dc14 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index b1099d0fa6..569498f664 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "memory_kokkos.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 88504608f6..5481a41806 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index e6aa27649f..9d2200dd90 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_fene_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index ee1b58c91f..9239a4191b 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "bond_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index b17434d09a..7d635dbeb7 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -17,7 +17,7 @@ #include "compute_orientorder_atom_kokkos.h" #include -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 0e7fe25540..7e4d3ad6ae 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 0d8256f306..c25ab18c60 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_charmm_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 371af44e9a..df60ebd1e4 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_class2_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 408fa276e4..0acd61222e 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_harmonic_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 309d617f0a..70beae918a 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -17,7 +17,7 @@ #include "dihedral_opls_kokkos.h" #include -#include + #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 05eb1c22f6..5d8430d337 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -17,7 +17,7 @@ #include "fix_deform_kokkos.h" #include -#include + #include #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9c9d6cb1cd..1821b6dadd 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 96e9663712..8cd58b0927 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -17,7 +17,7 @@ #include "fix_nh_kokkos.h" #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index ff374b885f..d6afae3ec2 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 38968bdd35..18bc4225a7 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -27,7 +27,7 @@ #include "comm.h" #include "domain.h" #include "kokkos.h" -#include "utils.h" + #include // DBL_EPSILON diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 75964f4829..9be4321ff2 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -35,7 +35,7 @@ #include "fix_shardlow_kokkos.h" #include -#include + #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index a5bd6e6e6c..c581edb123 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_kokkos.h" -#include + #include #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 28cf65c8d8..280e47b771 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index da49414892..a4828c00aa 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 2e2c3ef04e..035bf87cec 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -17,7 +17,7 @@ #include "pair_exp6_rx_kokkos.h" #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_request.h" #include "atom_kokkos.h" #include "kokkos.h" -#include "utils.h" + #ifdef _OPENMP #include diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index 1f2ad404bb..9c75f3abe8 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -17,7 +17,7 @@ #include "atom.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index d0fe11285a..bf8518e3c3 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -17,7 +17,7 @@ #include "pair_reaxc_kokkos.h" #include -#include + #include #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 26aa4373cc..09e38e6387 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx_kokkos.h" -#include + #include #include #include "kokkos.h" @@ -33,7 +33,7 @@ #include "kokkos_few.h" #include "kokkos.h" #include "modify.h" -#include "utils.h" + #include using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 45c8a35971..3288f15ff7 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -19,7 +19,7 @@ #include #include #include -#include + #include "comm.h" #include "update.h" #include "force.h" @@ -32,8 +32,8 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" -#include "utils.h" -#include "fmt/format.h" + + #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 339f79626f..3e4db40344 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -21,7 +21,7 @@ FixStyle(tune/kspace,FixTuneKspace) #define LMP_FIX_TUNE_KSPACE_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 4742e4c48c..a05a6a282b 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index f589dfaa90..8d15a6480a 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_long.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 3552e8bb86..a845ddd1d2 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -31,7 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 60187ce901..2520da2654 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index ff52720a08..261e93fbc9 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index b10cdf2b08..9df9862c11 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index ef25055a76..7fd8a72559 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index 426ec00e55..a62c1bd55b 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 7b7a065e22..b6727c2c99 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -33,8 +33,8 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index c71fee8206..8f17bda008 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index ee7d4fed1b..54973c69c2 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index b8bbba73da..54169d08d7 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb.h" -#include + #include #include #include "pair_comb.h" @@ -30,8 +30,8 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 74fd03e080..ff30ac7b1e 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_adp.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 6d783545f7..50b5b7d953 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -23,7 +23,7 @@ #include "pair_airebo.h" #include #include -#include + #include "atom.h" #include "neighbor.h" #include "force.h" @@ -34,10 +34,10 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 60905fd2ff..2a69e70b81 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_atm.h" -#include + #include #include "atom.h" #include "citeme.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 5b080c9f0e..28389cb59f 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -36,7 +36,7 @@ #include #include #include -#include + #include "atom.h" #include "neighbor.h" #include "neigh_request.h" @@ -45,10 +45,10 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 6b8d4e428e..a27aaef4ab 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -19,9 +19,9 @@ ------------------------------------------------------------------------- */ #include "pair_comb.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 385e3ca35d..eea2fca927 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_comb3.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,10 +33,10 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 159ba55a29..999384ea2f 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 3e33d40ee4..193134c24c 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_eam_alloy.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 4f5041090f..dc36c73272 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam_cd.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "memory.h" #include "error.h" #include "tokenizer.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index fbe6bee529..78d7f4646d 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_eam_fs.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index cdd928788b..a17947b7fe 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_eim.h" -#include + #include #include #include "atom.h" @@ -26,10 +26,10 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 1266ffd242..75f8ea6bea 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -21,7 +21,7 @@ PairStyle(eim,PairEIM) #define LMP_PAIR_EIM_H #include "pair.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 0928d14696..051c30f873 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_gw.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index 1a2bf5eb5d..dc33ab20a9 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_gw_zbl.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -27,7 +27,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 56ef70d8f9..d2e478b37d 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lcbop.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index dc537a7b58..0a197a1576 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_nb3b_harmonic.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 502580719a..4c8ebaf8ad 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_polymorphic.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index f6b5a803d2..da6f7c1623 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_sw.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -28,7 +28,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index c57740963f..95212b23ab 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,7 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index d1ab6f2034..b02545fb2b 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index ff8916cdcd..325e9ac677 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod_c.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 141cb45964..4c967b4ebb 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -29,7 +29,7 @@ #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 815854a34b..63765234b3 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 53338f08dc..f786179aa4 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_atom_swap.h" -#include + #include #include #include diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 833a071694..8a7cd20b0f 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_break.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 9603fc1583..a2c2eee2c5 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_create.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 82b27d490f..270a497772 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_swap.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f286ab6807..fc306696ed 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_gcmc.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index cf327dc2e1..b855c0b79e 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_tfmc.h" -#include + #include #include #include diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 7f6f7ae1bd..a87ead64a7 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_widom.h" #include "atom.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 30c66a671f..c00f5dcbff 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dsmc.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "domain.h" #include "update.h" #include "random_mars.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index 6123bf49af..7f4e6b1f3c 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_msd_nongauss.h" -#include + #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 286770017c..d8be8679c6 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_ti.h" -#include + #include #include "atom.h" #include "update.h" @@ -27,7 +27,7 @@ #include "input.h" #include "variable.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index fbd56b9096..9f2bbfe424 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -24,7 +24,7 @@ #include "dump_xtc.h" #include -#include + #include #include #include "domain.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 7d9766c57c..32e836f31d 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_deposit.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 0dc0be4947..bd2f9acfb9 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_efield.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 153de8851b..6396d139a0 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_evaporate.h" -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index c4ff1ebeba..75642b632f 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_gld.h" -#include + #include #include #include "atom.h" diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 3141f6496c..ab9a921d3e 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -21,9 +21,9 @@ #include "fix_orient_bcc.h" #include #include -#include -#include -#include + + + #include "atom.h" #include "update.h" #include "respa.h" @@ -36,8 +36,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index bcba14c355..bcbdcfabc5 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -18,9 +18,9 @@ #include "fix_orient_fcc.h" #include #include -#include -#include -#include + + + #include "atom.h" #include "update.h" #include "respa.h" @@ -33,8 +33,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index 7eec60be8b..115045db81 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_thermal_conductivity.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 24f988a76d..2d38f3c6c6 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index b8c04132ea..9c021c5ca8 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_viscosity.h" -#include + #include #include #include "atom.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index e2e6f40857..4fc1fb0628 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index efc84f22b5..4a18680415 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 79b1ebae66..576637c593 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MLIAP/compute_mliap.cpp b/src/MLIAP/compute_mliap.cpp index 134994f829..aad28c7bb1 100644 --- a/src/MLIAP/compute_mliap.cpp +++ b/src/MLIAP/compute_mliap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" diff --git a/src/MLIAP/compute_mliap.h b/src/MLIAP/compute_mliap.h index 5602ace89b..1172111247 100644 --- a/src/MLIAP/compute_mliap.h +++ b/src/MLIAP/compute_mliap.h @@ -21,7 +21,7 @@ ComputeStyle(mliap,ComputeMLIAP) #define LMP_COMPUTE_MLIAP_H #include "compute.h" -#include + namespace LAMMPS_NS { diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index f2e042141c..d74a1820cc 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include + #include -#include + #include #include "mliap_data.h" #include "mliap_model_linear.h" diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 117056ac58..6cd550384d 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_charmm.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 732843f412..0288a61d83 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 2ec59bfb1e..1a05edc20b 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index ac276511a2..5fb40b54c9 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 02bab37a8a..eb5e48ec9b 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 83e4485d48..100b75cb0a 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "angle_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,10 +28,10 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 97d4c865ba..514250d058 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -20,7 +20,7 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 9617894a9a..b2271d45fc 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene.h" -#include + #include #include #include "atom.h" @@ -22,8 +22,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index eec8c14872..676d5f6871 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene_expand.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4e20a2711d..89b3830cb5 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_gromos.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 773a4ee12a..28100512a8 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 38d8d6a45f..49074e1cdc 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_morse.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 1733ffc670..63b640730a 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_nonlinear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index c89ac552ae..c8d182e4ff 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 2724d4f20c..5cc91ceae0 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "bond_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,10 +26,10 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 71c9f586a3..11422e0820 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index d4956b42bd..408be8ef99 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmmfsw.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 403bafd23e..55e2f25006 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index ce31a12ed3..40e026c2f1 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_helix.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index a3c76b91ee..963304da80 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_multi_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 151986ca3f..fe05dc7c3d 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index ddf035070b..2de6dd4183 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -28,9 +28,9 @@ ------------------------------------------------------------------------- */ #include "fix_cmap.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -41,8 +41,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index d819642bb1..90cf3eee39 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_cvff.h" -#include + #include #include "atom.h" #include "comm.h" @@ -21,7 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 2af1126876..6327ea8b06 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 1f2da63486..7b2c4e0b09 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_umbrella.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 69ea81a017..6d9c851422 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 8d6dfc7d68..422da8d827 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index f09f9a483a..dea6bd6251 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index e646392e0e..31083312a9 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmmfsw_coul_charmmfsh.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index b23195086c..b5ed255789 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index bea8acbcbc..8d8f5ec78e 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_cut.h" -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 9d15e8b1a8..62d940af37 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_atom_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index bca19e58c8..e05b7bf317 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_cfg_mpiio.h" #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3f9c09738e..b623df82d0 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_custom_mpiio.h" #include -#include + #include #include "domain.h" #include "input.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index d1b2d5079a..139245e4b0 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_xyz_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index 9c9e415be5..29d6d550e4 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_mscg.h" -#include + #include -#include + #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index e6b6fb72f4..82510e8177 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -21,7 +21,7 @@ #include "pair_eam_opt.h" #include -#include + #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index 3dc6bdb6b4..a7fbfb823a 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -20,7 +20,7 @@ #include "pair_lj_charmm_coul_long_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 3b3a19a9e8..a31f521ecc 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_opt.h" -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index 1d2e226777..89d254ee04 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -20,7 +20,7 @@ #include "pair_morse_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index d824d82e6c..2cb5323745 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm_opt.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 022eb0bab6..2950381197 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_peri_neigh.h" -#include + #include #include "pair_peri_lps.h" #include "pair_peri_ves.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 5e3a514b61..b3986e75fa 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_eps.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -33,7 +33,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index e73e2eff67..101a6d0bd9 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_lps.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index cf751885d6..c5f893dd32 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "pair_peri_pmb.h" -#include + #include #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -33,7 +33,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 138584123a..dca80cc6fd 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_peri_ves.h" -#include + #include #include -#include + #include "atom.h" #include "domain.h" #include "lattice.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "update.h" using namespace LAMMPS_NS; diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index b0b1287717..12dc59c286 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include "fix_poems.h" -#include + #include #include -#include + #include "workspace.h" #include "atom.h" #include "domain.h" @@ -34,8 +34,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index d0650bcb51..c59ba5eb5f 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -17,7 +17,7 @@ #include "pair_python.h" #include // IWYU pragma: keep -#include + #include #include "atom.h" #include "force.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index ba4932a485..5cadce617f 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index a2cc683b56..7f50736b18 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_dynamic.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 265528a089..6dcc5e9cdc 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_fire.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 4f5369eb87..327a9c5b3a 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -17,7 +17,7 @@ #include "fix_qeq_slater.h" #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index e130f85f5f..d7abcb62b8 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_event_displace.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 16c37fcb77..f104d14c2f 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_global.h" -#include + #include #include #include "atom.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 9e3ce9b00d..e57419022c 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_local.h" -#include + #include #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -30,7 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 93689eb7f9..76953b6c2c 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_neb.h" -#include + #include #include -#include + #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 03119d304e..03b79cc750 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "fix_ehex.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index ff31ab9755..436b2191ff 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_rattle.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 761b957292..f74cce8233 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid.h" -#include + #include -#include + #include #include "math_extra.h" #include "atom.h" @@ -35,8 +35,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5b75640549..d1204e2bbc 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh_small.h" -#include + #include #include #include "math_extra.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 01dd9e889e..85cadc826e 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_small.h" -#include + #include -#include + #include #include #include "math_extra.h" @@ -39,8 +39,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index d6603cd7b6..ee88f57341 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_shake.h" -#include + #include #include #include @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index b5b586bc7f..509e45202c 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_append_atoms.h" -#include + #include #include #include "atom.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 986b1323e8..3930133221 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_msst.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "domain.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 1e85441d1f..37b82b86f0 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -13,7 +13,7 @@ #include "compute_sna_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 1376193070..bb546708b8 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snad_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp index eb18b7274e..ca989a75b4 100644 --- a/src/SNAP/compute_snap.cpp +++ b/src/SNAP/compute_snap.cpp @@ -13,7 +13,7 @@ #include "compute_snap.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 066fc56c11..dd562cac5c 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snav_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 48014592ed..cb1a71aa45 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_snap.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "sna.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 94eff27f53..281100740a 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 6df9dd4af2..82bf83ac10 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -34,7 +34,7 @@ #include "random_mars.h" #include "respa.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 110cfb58d8..0b2e86e465 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_neb_spin.h" -#include + #include #include #include "universe.h" diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 9a33f0d61d..cbb367e438 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_precession_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 5573d914b7..4da05c57cb 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_cut.h" -#include + #include #include #include "atom.h" @@ -35,7 +35,7 @@ #include "modify.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 4188bb214c..605370f7f1 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "modify.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index b4b3fcb6f5..0a5bde2c9f 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dmi.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index b82dca3dcc..a932aa5c54 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_exchange.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 50cd1fe54a..65a2904228 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_magelec.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 4468e157b4..ceb487d378 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "pair_spin_neel.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "memory.h" #include "modify.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index ca0bdbac0a..688522c1bd 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_srd.h" -#include + #include #include #include "math_extra.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 8b9ea6fb79..461dc5f5ad 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_srd.h" -#include + #include #include "fix.h" #include "domain.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 2aa2e7680b..178f0f42de 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -22,7 +22,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include "utils.h" + #include "TCP/wpmd_split.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 4d812852db..18704deb0b 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_awpmd_cut.h" -#include + #include #include #include @@ -32,7 +32,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "logexc.h" #include "vector_3.h" diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 39da9fc23b..4af2356e1a 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,10 +16,10 @@ #include "compute_pressure_bocs.h" -#include + #include #include -#include + #include "angle.h" #include "atom.h" @@ -28,7 +28,7 @@ #include "domain.h" #include "error.h" #include "fix.h" -#include "fmt/format.h" + #include "force.h" #include "improper.h" #include "kspace.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index c61a37388b..6f7962c83f 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -17,7 +17,7 @@ #include "fix_bocs.h" #include -#include + #include #include @@ -29,7 +29,7 @@ #include "domain.h" #include "error.h" #include "fix_deform.h" -#include "fmt/format.h" + #include "force.h" #include "group.h" #include "irregular.h" diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index cc70f2fb31..c9540bf0c0 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna_fene.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp index bdddccda87..152961f290 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "bond_oxrna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 32ee0ed145..60c1c8788f 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_coaxstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 04aaf82ccb..7d2c8aa2c2 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_dh.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 87f58857bb..17ba194030 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_coaxstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 22ed310003..33005046b7 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_excv.h" -#include + #include #include #include "mf_oxdna.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index df952d0ff2..88c5dc5e36 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_hbond.h" -#include + #include #include #include "mf_oxdna.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index fa9204ed86..bf52d61182 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_stk.h" -#include + #include #include #include @@ -26,7 +26,7 @@ #include "neighbor.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 7845451daf..87de92e0e0 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_xstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp index 3c0194d636..ec93ce592e 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -16,7 +16,7 @@ #include #include -#include + #include #include "pair_oxrna2_excv.h" diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index 1b6c577a19..d38ccb86ab 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -16,7 +16,7 @@ #include #include -#include + #include #include "pair_oxrna2_stk.h" #include "mf_oxdna.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index 11c2f2b9b1..f3f65b695e 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxrna2_xstk.h" -#include + #include #include #include "mf_oxdna.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index d535baeda5..6f97d2104f 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "angle_sdk.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index cf478e85fb..8185e24876 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index cd02c7f9e1..42f1ff3ce7 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index f9e071a0b3..fc575c2e79 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -25,11 +25,11 @@ ------------------------------------------------------------------------- */ #include "fix_colvars.h" -#include -#include + + #include #include -#include + #include #include diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 5dd47b28bd..677bf62a25 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -17,9 +17,9 @@ #include "omp_compat.h" #include "compute_saed.h" -#include + #include -#include + #include #include "math_const.h" #include "compute_saed_consts.h" diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index e75546b548..0dac7aca5e 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -18,9 +18,9 @@ #include "omp_compat.h" #include "compute_xrd.h" -#include + #include -#include + #include #include "math_const.h" #include "compute_xrd_consts.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 0a018338a4..08833db224 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_saed_vtk.h" -#include + #include #include #include "update.h" diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 0ef7868164..97e12d5cb4 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_dpd.h" -#include + #include "atom.h" #include "update.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 69e5336945..7134eaca22 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table.h" -#include -#include + + #include #include "atom.h" #include "error.h" #include "force.h" #include "memory.h" -#include "utils.h" + #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index d728f7e987..c220d84a57 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table_rx.h" -#include -#include + + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "comm.h" #include "modify.h" -#include "utils.h" + #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index ced7283ef4..d974d12473 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_rx.h" -#include -#include + + #include #include #include // DBL_EPSILON @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "math_special.h" #include "pair_dpd_fdt_energy.h" -#include "utils.h" + #include // std::vector<> #include // std::max diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 18c86976ac..e533140dd6 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -34,7 +34,7 @@ ------------------------------------------------------------------------- */ #include "fix_shardlow.h" -#include + #include #include #include @@ -54,7 +54,7 @@ #include "pair_dpd_fdt_energy.h" #include "npair_half_bin_newton_ssa.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 876d76a42f..c988f4205c 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 3686bcb7e9..9231ab7ba3 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt_energy.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 839d22b50b..666a1b0ea9 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_exp6_rx.h" -#include + #include -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "fix.h" diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index f9074d5c05..ceb5c78eaf 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy.h" #include "atom.h" @@ -33,9 +33,9 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 90f6dc6170..d769d94783 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy_rx.h" #include "atom.h" @@ -33,11 +33,11 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 56c3e28c46..f791107f1d 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index a12c248680..b806b4434b 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_drude.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 080408459c..313ac249d7 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_drude.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 4128c508d6..bdccaaebc8 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -13,7 +13,7 @@ /** Fix Drude Transform ******************************************************/ #include "fix_drude_transform.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index e865e9cd29..da74510821 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_drude.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 875b4a9cba..461f972885 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_thole_long.h" -#include + #include #include #include "fix_drude.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "domain.h" diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 882fd047a9..281317c076 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_thole.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "fix.h" #include "fix_drude.h" #include "domain.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index c943366f1b..001e1d4c43 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "compute_ke_atom_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index 3e277fc66c..d1781b75f7 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include + + #include "compute_ke_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index dcf7e86234..90e25ca3c8 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_deform_eff.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index e9295ea680..174f032b83 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "compute_temp_eff.h" -#include -#include + + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index b27699cde9..c95cf0de2d 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 5158d7c681..3966bc7b98 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include "fix_langevin_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 034233732e..9fdbc6a0bf 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,7 +15,7 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index ea719c91c0..f32a45fd46 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "fix_nve_eff.h" #include "atom.h" #include "force.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 0ebbf04d64..02a463b3ba 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -13,7 +13,7 @@ #include #include -#include + #include "fix_nvt_sllod_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index e2163990bd..a013270049 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_temp_rescale_eff.h" #include "atom.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index b9b442ed2a..f4e7af6584 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include #include "pair_eff_cut.h" #include "pair_eff_inline.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index 488a85fc20..ff1e303a30 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -18,7 +18,7 @@ #include "compute_fep.h" #include #include -#include + #include "comm.h" #include "update.h" #include "atom.h" @@ -34,7 +34,7 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index f88f2b6c40..2f97b5a0e3 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index fd5141525c..b0a099a56f 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 39e06ddd60..80173f3f0f 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index f9149c8fb8..e13b98329f 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index f1aa99b416..bfd5a630f6 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 19c41f04cb..e027a30185 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index 3c1869da08..0cd1fc9e87 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 4a92a6fcef..a18256f98a 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 56cf31b9d3..4b3fae77b3 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 2ab677c454..786715d6c9 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 35342f68d8..18f8db5021 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 904799e1d3..85a30a5414 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index fa130a9dc6..9578befd37 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 0c07e844cb..e9daf71867 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include #include "ch5md.h" diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index 9275e82f1c..b6e0b0dac5 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "angle_charmm_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 49a71038da..6d3deee9ba 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "angle_harmonic_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 5c58e7bf10..072800db42 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "bond_fene_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 8bf0a82218..1ddb424a7b 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include "bond_harmonic_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index 61fc1dfbd5..ddfa0c1228 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_charmm_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index fb8051474e..cd62012255 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_fourier_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index f6c4ea0fde..dd8c3d98db 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_harmonic_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 79a8874a72..ef48f7e8ee 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_opls_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 7bd510b189..b3649be7c8 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -29,10 +29,10 @@ #include "timer.h" #include "universe.h" #include "update.h" -#include "utils.h" + #include -#include + #include #include diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 4562c63cdb..4dcdb34b69 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include -#include + #include "improper_cvff_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index fc5cf08c52..c63dfc9567 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include -#include + #include "improper_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index c1e4a5374a..8b7ff71603 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -19,7 +19,7 @@ #pragma offload_attribute(push, target(mic)) #endif #include -#include + #include #include #include diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 4ad4398fbe..a67db0ad32 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_cut_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 150cfd3ee0..d0cb1837c9 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_long_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 31430e4bf7..b979d2dcdf 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_alloy_intel.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index c5804922f6..a1c71d9c21 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_fs_intel.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 994f0d3910..d27a019532 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_eam_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 32afcbf8a9..b8ac84bc3c 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -26,7 +26,7 @@ #endif #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 8784029320..75f5f85f2d 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_tersoff_intel.h" #include "atom.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 8ad3dbe33e..204a9c073b 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -18,8 +18,8 @@ #include "fix_lb_fluid.h" #include -#include -#include + + #include #include #include diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index 10fffed018..0a307790d5 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include "fix_lb_momentum.h" -#include -#include + + #include #include "atom.h" #include "group.h" diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index d61692419a..2c7e8dbf47 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -26,7 +26,7 @@ #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" -#include + #include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 9cc03591fa..f714e31719 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "fix_lb_rigid_pc_sphere.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 41074903bd..b016dd8ecb 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_manifoldforce.h" // For stuff -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 2baa2944ae..b3122a68d4 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -33,7 +33,7 @@ #include "fix_nve_manifold_rattle.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index f40df56c19..6f674c9f45 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_meamc.h" -#include -#include + + #include -#include + #include "meam.h" #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 21e44e7ff2..9cbda8f6ad 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -22,7 +22,7 @@ PairStyle(meam,PairMEAMC) #define LMP_PAIR_MEAMC_H #include "pair.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index d08a626fad..c3fae823ea 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -21,7 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/atom_vec_tdpd.cpp b/src/USER-MESODPD/atom_vec_tdpd.cpp index f50fe168d6..63b88f921d 100644 --- a/src/USER-MESODPD/atom_vec_tdpd.cpp +++ b/src/USER-MESODPD/atom_vec_tdpd.cpp @@ -16,7 +16,7 @@ #include "atom.h" #include "update.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp index 60a437a47c..9c2e74b882 100644 --- a/src/USER-MESODPD/pair_edpd.cpp +++ b/src/USER-MESODPD/pair_edpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_edpd.h" -#include + #include #include #include @@ -31,7 +31,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd.cpp b/src/USER-MESODPD/pair_mdpd.cpp index 755008f443..88b6724a03 100644 --- a/src/USER-MESODPD/pair_mdpd.cpp +++ b/src/USER-MESODPD/pair_mdpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp index bfbc6f7c82..def61dea8f 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.cpp +++ b/src/USER-MESODPD/pair_mdpd_rhosum.cpp @@ -29,7 +29,7 @@ #include "memory.h" #include "error.h" #include "neighbor.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_tdpd.cpp b/src/USER-MESODPD/pair_tdpd.cpp index face9221d9..65a518c07e 100644 --- a/src/USER-MESODPD/pair_tdpd.cpp +++ b/src/USER-MESODPD/pair_tdpd.cpp @@ -29,7 +29,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/compute_mesont.cpp b/src/USER-MESONT/compute_mesont.cpp index 397b071a1b..96792c8988 100644 --- a/src/USER-MESONT/compute_mesont.cpp +++ b/src/USER-MESONT/compute_mesont.cpp @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/USER-MESONT/pair_mesocnt.cpp index 4af8a99d6f..96d53bd41a 100644 --- a/src/USER-MESONT/pair_mesocnt.cpp +++ b/src/USER-MESONT/pair_mesocnt.cpp @@ -20,9 +20,9 @@ #include #include -#include + #include -#include + #include "atom.h" #include "comm.h" @@ -33,8 +33,8 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-MESONT/pair_mesont_tpm.cpp b/src/USER-MESONT/pair_mesont_tpm.cpp index 9fb0f604c8..6d8c8126ae 100644 --- a/src/USER-MESONT/pair_mesont_tpm.cpp +++ b/src/USER-MESONT/pair_mesont_tpm.cpp @@ -16,7 +16,7 @@ #include "pair_mesont_tpm.h" #include "export_mesont.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -29,7 +29,7 @@ #include #include #include -#include + #include #include #include diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index e7ab62608a..070e3cb61e 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_mgpt.h" -#include + #include -#include + #include #include diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index 2ed1a85672..a986cb8322 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index fb1cc0a4e6..52bfe751f1 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 6e449fe472..336638f25d 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_dipole.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 5f34be8d65..907ee973bd 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index cddc07da90..8894f7b4c9 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index c84739ac91..93f45f9562 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index dd2c1a1524..5889400b97 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 2cbfa01c0a..86e6263f93 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift_cut.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.cpp b/src/USER-MISC/bond_special.cpp index ebbdcb1899..a956468497 100644 --- a/src/USER-MISC/bond_special.cpp +++ b/src/USER-MISC/bond_special.cpp @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "bond_special.h" #include "atom.h" @@ -25,7 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index fdce944034..52656ec9d6 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_cnp_atom.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index ccecf43aaf..02c697a786 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -45,7 +45,7 @@ https://doi.org/10.1103/PhysRevE.92.043303 #include #include -#include + #include "compute_hma.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index 541b52d9c0..f1c35993e3 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,6 +1,6 @@ #include "compute_momentum.h" -#include + #include "atom.h" #include "error.h" #include "update.h" diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 8346bd3410..6cf375dd19 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure_cylinder.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index 1e42a9df02..c733c929ba 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop.h" -#include + #include #include diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 022840166f..323aee851e 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop_profile.h" -#include + #include #include diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 94c6115186..c333357a93 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_rotate.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/USER-MISC/compute_viscosity_cos.cpp index 7311f991cc..12e1991d54 100644 --- a/src/USER-MISC/compute_viscosity_cos.cpp +++ b/src/USER-MISC/compute_viscosity_cos.cpp @@ -15,7 +15,7 @@ Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com) ------------------------------------------------------------------------- */ -#include + #include "compute_viscosity_cos.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 1b3afb13eb..7c131682fa 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index e897e58649..066447f92d 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index 0ff62320e4..bde8d84070 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_nharmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index d91c237838..deafc8391f 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_quadratic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 1cfb756127..a33452dbe1 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_spherical.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 37410ba085..aebe468905 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,12 +17,12 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ -#include + #include #include -#include + #include -#include + #include // IWYU pragma: keep #include // IWYU pragma: keep @@ -33,12 +33,12 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "dihedral_table.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 8a397b20f2..a8d1f8f8bb 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -24,7 +24,7 @@ DihedralStyle(table,DihedralTable) #ifndef LMP_DIHEDRAL_TABLE_H #define LMP_DIHEDRAL_TABLE_H #include "dihedral.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 2a5b46a4f1..f8a2f02596 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -17,12 +17,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_table_cut.h" -#include + #include #include -#include + #include -#include + #include // IWYU pragma: keep #include // IWYU pragma: keep @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 4583d76e09..ed796280e7 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_addtorque.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index abfa751d15..1f2022d520 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate_long.h" -#include + #include -#include + #include #include #include "update.h" diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 4460c55183..fb111c1f27 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_ffl.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 18fd784861..86650cd50d 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_filter_corotate.h" -#include + #include #include #include -#include + #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 2463e18b40..23e61641d8 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_flow_gauss.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 30e62c7eb9..f4776c3d6c 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_gle.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -29,7 +29,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index af4a517269..4264126c26 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,7 +58,7 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include + #include #if defined(_MSC_VER) || defined(__MINGW32__) diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index b1d07eef41..b8045a9ff1 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_ipi.h" -#include + #include #include "atom.h" #include "force.h" @@ -45,7 +45,7 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include + #include #include #include diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/USER-MISC/fix_momentum_chunk.cpp index 0ed5e1f877..3df632eb30 100644 --- a/src/USER-MISC/fix_momentum_chunk.cpp +++ b/src/USER-MISC/fix_momentum_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_chunk.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "error.h" #include "force.h" #include "modify.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/USER-MISC/fix_momentum_chunk.h index 5e056f2494..5007e38c69 100644 --- a/src/USER-MISC/fix_momentum_chunk.h +++ b/src/USER-MISC/fix_momentum_chunk.h @@ -21,7 +21,7 @@ FixStyle(momentum/chunk,FixMomentumChunk) #define LMP_FIX_MOMENTUM_CHUNK_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/USER-MISC/fix_npt_cauchy.cpp index 221886d388..9361d9ebd6 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/USER-MISC/fix_npt_cauchy.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_npt_cauchy.h" #include "math_extra.h" diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 410a269f8c..f0fbddf18d 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_nvk.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 4e97cac3f9..a9abf7baf7 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_orient_eco.h" -#include + #include #include #include "atom.h" @@ -33,8 +33,8 @@ #include "pair.h" #include "respa.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 33407aec44..222369f572 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -19,10 +19,10 @@ #include "fix_pafi.h" -#include + #include #include -#include + #include "math_extra.h" #include "atom.h" #include "force.h" @@ -35,9 +35,9 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 8de31f19b3..5be9bf162b 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "fix_pimd.h" -#include + #include #include -#include + #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index 0a40177993..b17ee55f94 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -21,7 +21,7 @@ #include #include -#include + #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 612352aae1..0771122bfd 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ #include "fix_rhok.h" -#include + #include #include diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index d110637b3c..baee8a5699 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index d61e7f1ee1..1bd6957997 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_srp.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index ef7c4c0296..34c667a9e2 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "fix_ti_spring.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 8c37b19e8b..c12019528c 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm_mod.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "error.h" #include "citeme.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 8afc506804..7da818732e 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -18,7 +18,7 @@ #include "fix_wall_reflect_stochastic.h" #include -#include + #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 3a8323d58d..a8d6ea9424 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region_ees.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 09cf7cf2c6..5714931215 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_cossq.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 8ea58b23b3..476cf8ab43 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_distance.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 3bdbc7bc68..85f7809a02 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 4102a250dd..c85e4850c8 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -37,7 +37,7 @@ ------------------------------------------------------------------------- */ #include "improper_ring.h" -#include + #include #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 764ccc587f..0a00c914c7 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_agni.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -31,7 +31,7 @@ #include "citeme.h" #include "math_special.h" #include "math_const.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 6a4575c6e4..9ef96f1188 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_mdf.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 8e400d23ed..57dd55c593 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -16,7 +16,7 @@ #include "pair_cosine_squared.h" #include -#include + #include #include "atom.h" #include "comm.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index 14fbd374b6..5a3e12f1a5 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_diel.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 883796de1b..44ab555b02 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -28,7 +28,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/USER-MISC/pair_coul_slater_cut.cpp index 194ff664b3..6b1af9a42f 100644 --- a/src/USER-MISC/pair_coul_slater_cut.cpp +++ b/src/USER-MISC/pair_coul_slater_cut.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_coul_slater_cut.h" #include "atom.h" diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/USER-MISC/pair_coul_slater_long.cpp index d801d0342f..0fbd56f811 100644 --- a/src/USER-MISC/pair_coul_slater_long.cpp +++ b/src/USER-MISC/pair_coul_slater_long.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_coul_slater_long.h" #include "atom.h" @@ -31,7 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index cc890f8c94..7b56caa205 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_drip.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 2b58e4b1f8..a7ed0fcaad 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_e3b.h" -#include + #include #include #include diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index bb9c742212..6ccaded35d 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "pair_edip.h" -#include + #include #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -35,7 +35,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index 90a3502eae..4a81a41a26 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_edip_multi.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 8f8d539679..0db7f8739a 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_extep.h" -#include + #include -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 38d4c4d4c2..c9601c416e 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 62101d0e80..671dcb309d 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_ilp_graphene_hbn.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index fb1da5dab8..9f986fa101 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -22,9 +22,9 @@ #include "pair_kolmogorov_crespi_full.h" #include -#include + #include -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index f02423e952..7ce6f8652a 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_kolmogorov_crespi_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index 5a84882cd9..b8f9e5c38f 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -23,9 +23,9 @@ ------------------------------------------------------------------------- */ #include "pair_lebedeva_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index 6faa599d2c..31d32db505 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lennard_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index c553e671cb..a93e0a81af 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 20081fa1e1..92e869e58c 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index 22f20a690e..baa0e233f2 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index 6a92602683..ab845e69d5 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sf_dipole_sf.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "update.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 8ad9793f98..3b76bd8482 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -18,11 +18,11 @@ ------------------------------------------------------------------------- */ #include "pair_local_density.h" -#include + #include -#include + #include -#include + #include "atom.h" #include "force.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "error.h" #include "domain.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 6091b95837..4d9b3866b7 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -33,7 +33,7 @@ #include "pair_meam_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -43,7 +43,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 34cbe82581..0a8aae233a 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -25,7 +25,7 @@ #include "pair_meam_sw_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -35,7 +35,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 534f4acff5..d534284b57 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_momb.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 399723e0c5..9f895800df 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_smooth_linear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 9926318597..150895108e 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -26,9 +26,9 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ #include "pair_srp.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -44,7 +44,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "thermo.h" #include "output.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 4df172a001..1f5cfddff1 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -32,7 +32,7 @@ #include "force.h" #include "comm.h" #include "memory.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index aa56ababe1..7ef134405d 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2_p6.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 0f49882e83..1bede58751 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_buck6d.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 0ecc60ecc1..bbe6e48a35 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "improper_inversion_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 28fc955448..0de5423d30 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -29,7 +29,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 20bf7fa049..c6ba832fff 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck6d_coul_gauss_long.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index d9d8ec3c97..e0e92f9339 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_molfile.h" -#include + #include #include #include "domain.h" diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index bb85dfb784..f936de6d02 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_NETCDF) #include -#include + #include #include #include "dump_netcdf.h" diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 8747bbea25..19b0632922 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_PNETCDF) #include -#include + #include #include #include "dump_netcdf_mpiio.h" diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index 9c7317bebd..f097e93be2 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include -#include + #include #include "math_extra.h" #include "fix_nh_asphere_omp.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index b0573dfa97..5b2ee88420 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb_omp.h" -#include + #include #include #include "pair_comb.h" diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index a10d3127a9..ef0f918cbf 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -32,7 +32,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_omp.h" -#include + #include #include "pair_reaxc.h" #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 63084fcc9e..f53fcf63bc 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include "fix_rigid_nh_omp.h" -#include + #include #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 9f78f6dc26..62f853d23b 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include "fix_rigid_omp.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 3e0e423f3d..f0823204c0 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_alloy_omp.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 76e9840a5c..89590bb3e6 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "pair_eam_fs_omp.h" #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 72a7d5f16a..fb579fb980 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -19,7 +19,7 @@ #include "pair_lj_cut_thole_long_omp.h" #include #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 73b1373fad..08efb73aab 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,7 +34,7 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index 005cd427a9..d1d808307a 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -18,7 +18,7 @@ #include #include -#include + #include #include "pair_tersoff_zbl_omp.h" #include "atom.h" @@ -30,7 +30,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 17325b062a..382eabe82d 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,7 +23,7 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include + #include #include #include "fix_phonon.h" diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 3a52bbaaa1..b7a29c7bc9 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "atom.h" @@ -33,7 +33,7 @@ #include "compute.h" #include "modify.h" #include "pair.h" -#include "utils.h" + #include "timer.h" #include "plumed/wrapper/Plumed.h" diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index f1a34d9538..9f07030004 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ -#include + #include #include "fix_qmmm.h" #include "atom.h" diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b590e1ae9a..034738023c 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_qbmsst.h" -#include + #include #include -#include -#include + + #include "atom.h" #include "force.h" #include "update.h" @@ -34,8 +34,8 @@ #include "error.h" #include "kspace.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 80c0efddab..3f29229beb 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_qtb.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 64c56cb0e6..5511efe681 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -16,10 +16,10 @@ Aidan Thompson (Sandia, athomps@sandia.gov) ------------------------------------------------------------------------- */ -#include + #include #include -#include + #include #include "pair_quip.h" #include "atom.h" diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 99d016f1a0..0370d83fdc 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -16,10 +16,10 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ #include "fix_bond_react.h" -#include + #include #include -#include + #include "update.h" #include "modify.h" #include "respa.h" @@ -43,7 +43,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "error.h" #include "input.h" #include "variable.h" -#include "fmt/format.h" + #include "superpose3d.h" #include diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 433fd82bcd..4a61cfa03b 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax.h" -#include + #include #include #include "pair_reaxc.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 5c57fed261..c0ffd4c17e 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 74692f1c9b..ec03ab1808 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_species.h" -#include -#include + + #include #include "fix_ave_atom.h" #include "atom.h" diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index e0888e8514..c38257ae30 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc.h" -#include + #include -#include + #include #include #include "atom.h" @@ -39,7 +39,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index b215e8d278..9d52ee2250 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -30,7 +30,7 @@ #include "error.h" #include "domain.h" #include "update.h" -#include "utils.h" + #ifndef USE_ZEST #include "random_mars.h" #endif diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index eb1f144275..5999dfaa5d 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "compute_smd_vol.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index ab6dd5ef5c..b5dab3d3a1 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -23,8 +23,8 @@ ------------------------------------------------------------------------- */ #include "fix_smd_adjust_dt.h" -#include -#include + + #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 895e5b1a25..90589f3044 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -24,7 +24,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd_setvel.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index 4ade21a6fd..3e63de08f3 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -25,7 +25,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd_tlsph_reference_configuration.h" -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index ba3a324d56..c61fe14353 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_smd_wall_surface.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 67fda5f18d..8d3c06d5e6 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_hertz.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -40,7 +40,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1ba4b37520..25301685a7 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -23,10 +23,10 @@ ------------------------------------------------------------------------- */ #include "pair_smd_tlsph.h" -#include + #include #include -#include + #include #include #include "fix_smd_tlsph_reference_configuration.h" diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index 9243883719..8ccba562e2 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_triangulated_surface.h" -#include + #include -#include + #include #include #include "atom.h" @@ -41,7 +41,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index ecd0d5f4ec..e9cf256c3c 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -23,10 +23,10 @@ ------------------------------------------------------------------------- */ #include "pair_smd_ulsph.h" -#include + #include #include -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index f6ecd40bb6..875d254ac9 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -39,9 +39,9 @@ ------------------------------------------------------------------------- */ #include "pair_smtbq.h" -#include + #include -#include + #include #include #include diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 7bb06c14d9..fb8c928f2d 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -19,7 +19,7 @@ #include "error.h" #include "neigh_list.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index c80e2b4725..5480ff8e4c 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 4004e41574..eb76d800c8 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index c70cc7cd83..429d4199a4 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "update.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index 6455c1e8be..c0051201d0 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 7a6188da69..497aea293b 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 9d15fbc441..d010b004d5 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_force_tally.h" -#include + #include #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 350bc4b4b6..1a2dd36285 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index ce647a04c3..835d1e80bd 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_mol_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index edfa49b1b1..ef7c13fed2 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 1ea096e286..2a0cbc8e4b 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_stress_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 72ed2640d8..59dba0d90d 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "dump_vtk.h" #include "atom.h" diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h index e8de87f11c..b9db1f88cb 100644 --- a/src/USER-VTK/dump_vtk.h +++ b/src/USER-VTK/dump_vtk.h @@ -27,7 +27,7 @@ DumpStyle(vtk,DumpVTK) #include "dump_custom.h" #include #include -#include + #include #include diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 9c925d2365..c45af1d198 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cross.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 38a2cea3aa..34de772672 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index 39f238f1ab..f5d5fed946 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index e9b454bdb9..37039b27e4 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_distharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index af5086917a..ddc4d78c93 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_sqdistharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 2cbf01f7b7..98fd317794 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 52bcf20b9b..e1ee0e0b98 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mm3_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index bda4299a68..be77b8457b 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_voronoi_atom.h" -#include + #include #include #include diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index fb3f90ec28..7c2426739d 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include "angle_deprecated.h" -#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index d0a1d29e65..56590d6757 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "angle_hybrid.h" -#include -#include -#include + #include "atom.h" #include "neighbor.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index eb9cbf1ea2..e087b774e0 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "angle_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom.cpp b/src/atom.cpp index f4c93db459..6fff15d11f 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,31 +12,28 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include -#include -#include -#include -#include #include "style_atom.h" + #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "comm.h" -#include "neighbor.h" -#include "force.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "group.h" #include "input.h" -#include "variable.h" -#include "molecule.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "molecule.h" +#include "neighbor.h" +#include "update.h" +#include "variable.h" + +#include +#include #ifdef LMP_USER_INTEL #include "neigh_request.h" diff --git a/src/atom.h b/src/atom.h index 4dac15d758..21b9c06f8c 100644 --- a/src/atom.h +++ b/src/atom.h @@ -15,16 +15,20 @@ #define LMP_ATOM_H #include "pointers.h" + #include #include -#include namespace LAMMPS_NS { + // forward declaration + + class AtomVec; + class Atom : protected Pointers { public: char *atom_style; - class AtomVec *avec; + AtomVec *avec; enum{DOUBLE,INT,BIGINT}; // atom counts @@ -273,12 +277,12 @@ class Atom : protected Pointers { void add_peratom_vary(const char *, void *, int, int *, void *, int collength=0); void create_avec(const std::string &, int, char **, int); - virtual class AtomVec *new_avec(const std::string &, int, int &); + virtual AtomVec *new_avec(const std::string &, int, int &); void init(); void setup(); - class AtomVec *style_match(const char *); + AtomVec *style_match(const char *); void modify_params(int, char **); void tag_check(); void tag_extend(); @@ -296,8 +300,8 @@ class Atom : protected Pointers { void data_angles(int, char *, int *, tagint, int); void data_dihedrals(int, char *, int *, tagint, int); void data_impropers(int, char *, int *, tagint, int); - void data_bonus(int, char *, class AtomVec *, tagint); - void data_bodies(int, char *, class AtomVec *, tagint); + void data_bonus(int, char *, AtomVec *, tagint); + void data_bodies(int, char *, AtomVec *, tagint); void data_fix_compute_variable(int, int); virtual void allocate_type_arrays(); diff --git a/src/atom_map.cpp b/src/atom_map.cpp index c23aeec83c..02b97a1134 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include + #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 261b068997..4a00e5852b 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -12,20 +12,19 @@ ------------------------------------------------------------------------- */ #include "atom_vec.h" -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" -#include "modify.h" +#include "error.h" #include "fix.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 10cbb9c841..871f40084d 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include -#include -#include "my_pool_chunk.h" #include "style_body.h" -#include "body.h" + #include "atom.h" -#include "domain.h" -#include "modify.h" +#include "body.h" +#include "error.h" #include "fix.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index dc2760c5f9..c22111f48c 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_ellipsoid.h" -#include -#include "math_extra.h" + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index db593dcee0..5c37be4aa4 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid.h" -#include + #include "atom.h" #include "comm.h" -#include "memory.h" #include "error.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index af768f9943..88dcb8c2fa 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_line.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 03f417b1d0..03412a11cc 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere.h" -#include + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" -#include "error.h" -#include "utils.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index d5b48b9540..e391a73215 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -12,18 +12,18 @@ ------------------------------------------------------------------------- */ #include "atom_vec_tri.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/balance.cpp b/src/balance.cpp index 168d7f59a4..af8d904812 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -19,28 +19,26 @@ // #define BALANCE_DEBUG 1 #include "balance.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "rcb.h" -#include "irregular.h" #include "domain.h" -#include "force.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix_store.h" #include "imbalance.h" #include "imbalance_group.h" -#include "imbalance_time.h" #include "imbalance_neigh.h" #include "imbalance_store.h" +#include "imbalance_time.h" #include "imbalance_var.h" +#include "irregular.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "rcb.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/bond.cpp b/src/bond.cpp index 12659fd8aa..1f953bbd19 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -12,20 +12,18 @@ ------------------------------------------------------------------------- */ #include "bond.h" -#include -#include -#include + #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" +#include "memory.h" #include "neighbor.h" #include "suffix.h" -#include "atom_masks.h" -#include "memory.h" -#include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 0d91f73ea7..5422ab35f6 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "bond_deprecated.h" -#include + #include "bond_hybrid.h" #include "comm.h" -#include "force.h" #include "error.h" -#include "utils.h" +#include "force.h" using namespace LAMMPS_NS; diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 2fe9f7d388..b42683c300 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "bond_hybrid.h" -#include -#include -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 8053c5531d..71146ec4d6 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "bond_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/change_box.cpp b/src/change_box.cpp index 5fe4eb8a06..1bd3fe733f 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -12,22 +12,20 @@ ------------------------------------------------------------------------- */ #include "change_box.h" -#include + +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "group.h" +#include "irregular.h" +#include "lattice.h" +#include "modify.h" +#include "output.h" + #include #include -#include "atom.h" -#include "modify.h" -#include "fix.h" -#include "domain.h" -#include "lattice.h" -#include "comm.h" -#include "irregular.h" -#include "output.h" -#include "group.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/comm.cpp b/src/comm.cpp index 7e603f2104..24a5d050d4 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -12,31 +12,29 @@ ------------------------------------------------------------------------- */ #include "comm.h" -#include -#include -#include -#include "universe.h" + +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "modify.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" #include "domain.h" -#include "output.h" #include "dump.h" -#include "group.h" -#include "procmap.h" -#include "irregular.h" -#include "accelerator_kokkos.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "irregular.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "procmap.h" +#include "universe.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include #ifdef _OPENMP #include diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index c5ec8b35f4..37a4f0ae3d 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -16,19 +16,20 @@ ------------------------------------------------------------------------- */ #include "comm_brick.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "pair.h" -#include "domain.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" #include "error.h" +#include "fix.h" #include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 9f0169568d..48c9680d2f 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -17,19 +17,20 @@ ------------------------------------------------------------------------- */ #include "comm_tiled.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "pair.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute.cpp b/src/compute.cpp index 208b93730e..4cde9ff567 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute.h" + +#include "atom_masks.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "group.h" +#include "memory.h" +#include "modify.h" + #include #include -#include "domain.h" -#include "force.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 0bd329079a..5d55f1fbbb 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_adf.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "utils.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6e28a94388..6b6f376b4c 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -16,23 +16,23 @@ ------------------------------------------------------------------------- */ #include "compute_aggregate_atom.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "pair.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index fc72a58453..e3e44efbbb 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_angle.h" -#include + #include "angle.h" -#include "update.h" -#include "force.h" #include "angle_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 05ea963b82..6c9f1d65a2 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_angmom_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 5cc947c764..503582bc65 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_bond.h" -#include + #include "bond.h" -#include "update.h" -#include "force.h" #include "bond_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index ae041c1997..d0044410d8 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,29 +14,27 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include "compute_chunk_atom.h" -#include -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "force.h" +#include "comm.h" #include "domain.h" -#include "region.h" -#include "lattice.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "comm.h" #include "group.h" #include "input.h" -#include "variable.h" +#include "lattice.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 579b194b9f..953ae3a8cb 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_chunk_spread_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "compute.h" #include "compute_chunk_atom.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 021665a647..8086ef3f41 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -12,22 +12,22 @@ ------------------------------------------------------------------------- */ #include "compute_cluster_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 8bbe2c15d0..e9b6f16990 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_cna_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index c39911214c..8398311a05 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_com_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index be2f9c39bd..cb919d3a83 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -12,22 +12,23 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom.h" -#include -#include -#include "compute_orientorder_atom.h" + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "pair.h" #include "comm.h" +#include "compute_orientorder_atom.h" +#include "error.h" +#include "force.h" #include "group.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 2419e5bc8b..4b7e3dae3c 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index e50903104a..8853887f18 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_dihedral.h" -#include -#include "update.h" -#include "force.h" + #include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 3790da2035..361ee36c18 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_dipole_chunk.h" -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" #include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index b20dd3bec3..4b194cfab1 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -12,19 +12,20 @@ ------------------------------------------------------------------------- */ #include "compute_displace_atom.h" + +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "fix_store.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + #include #include -#include "atom.h" -#include "update.h" -#include "group.h" -#include "domain.h" -#include "modify.h" -#include "fix_store.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 2a8588f061..447b28b51a 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_sphere.h" -#include + #include "atom.h" -#include "update.h" -#include "force.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 664e2fa9ec..db003c93e7 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "compute_fragment_atom.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "modify.h" -#include "force.h" -#include "group.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 0c0e34fa0c..b3e4f88bf3 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_global_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index c8876daeef..ca0483fce9 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_group_group.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index bce0c0de85..81876109c4 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration.h" -#include + #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 5677ce4b6a..ad0520bc01 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration_chunk.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 7b607bd4db..15a17949eb 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 181771dcfb..3721dbfd48 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_improper.h" -#include + #include "update.h" #include "force.h" #include "improper.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index be980a08ee..65de1d7bb5 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_inertia_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index c6ba478dcb..e673f7fe53 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_ke.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 930f979bf0..d23c389ab6 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index dda921ef42..b0e2520f99 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd_chunk.h" -#include + #include -#include + #include "atom.h" #include "group.h" #include "update.h" @@ -24,7 +24,7 @@ #include "fix_store.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 327c64493f..4151b2cdb8 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_omega_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index ade9f7615e..84ae20e92a 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -17,22 +17,22 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 054a50bed4..7ace5615a7 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pair.h" -#include + #include #include #include "update.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 2018d929f3..e41221f70b 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "compute_pair_local.h" + +#include "atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + #include #include -#include -#include "atom.h" -#include "update.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 379de0f9de..d9ed312328 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 4712c83461..b57b53f522 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 579c7cae3f..c27cfc4096 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_property_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 920228e056..a28223b3a7 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_rdf.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "memory.h" #include "error.h" #include "comm.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index d4730c1de0..b024b4365c 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "domain.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce.h b/src/compute_reduce.h index 9701f0e61e..00c1a9a6b9 100644 --- a/src/compute_reduce.h +++ b/src/compute_reduce.h @@ -20,7 +20,7 @@ ComputeStyle(reduce,ComputeReduce) #ifndef LMP_COMPUTE_REDUCE_H #define LMP_COMPUTE_REDUCE_H -#include "compute.h" +#include "compute.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index cd64c8cb1b..6e8aa48410 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_chunk.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 9074124a61..8153618a88 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_region.h" -#include + #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 6ff462258f..ca4b735d6e 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_slice.h" -#include -#include -#include -#include "update.h" -#include "modify.h" + +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 402b84bb4b..6af5d2b86c 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 6274ac4292..54f0529006 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index dc12e8f6db..f69eaadf2b 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_com.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 7d81a84bc4..b50962a2c6 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_deform.h" -#include + #include #include "domain.h" #include "atom.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index c78e830c95..85e51d2a5d 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_partial.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c2ef1d5c11..eacca87e19 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_profile.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 187ea2454c..3874c1f286 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_ramp.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 4c0b925eb6..74955da421 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_region.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 786ef523ad..6ef3038d68 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_sphere.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 35eef8fe10..c0b648418b 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_torque_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index ec19137a0e..635c3e4161 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_vacf.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index b0a8dbeee7..6651110e77 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_vcm_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 7dcc4748e9..8baee645cf 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -12,33 +12,30 @@ ------------------------------------------------------------------------- */ #include "delete_atoms.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "molecule.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" #include "group.h" -#include "region.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "random_mars.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "region.h" +#include #include -#include +#include using namespace LAMMPS_NS; diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index f08c94a273..b8ec5f7883 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "delete_bonds.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "group.h" #include "special.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/deprecated.cpp b/src/deprecated.cpp index dc0ab400d4..ab9cc8cf44 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "deprecated.h" -#include + #include "comm.h" #include "error.h" #include "input.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 1709f7d3d7..91ef3e8e9e 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_deprecated.h" -#include -#include "dihedral_hybrid.h" + #include "comm.h" -#include "force.h" +#include "dihedral_hybrid.h" #include "error.h" -#include "utils.h" +#include "force.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 8f41b30d56..61e0fdc72a 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 59167ca30e..9570590c09 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_zero.h" -#include + #include "atom.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index a30ac2c2b2..018288d470 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,30 +12,28 @@ ------------------------------------------------------------------------- */ #include "displace_atoms.h" -#include -#include -#include + #include "atom.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "comm.h" -#include "irregular.h" -#include "group.h" -#include "math_const.h" -#include "random_park.h" -#include "force.h" -#include "input.h" -#include "variable.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "irregular.h" +#include "lattice.h" +#include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/domain.cpp b/src/domain.cpp index 81de88d1ee..f54df1f382 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,30 +16,28 @@ ------------------------------------------------------------------------- */ #include "domain.h" -#include -#include -#include -#include -#include "style_region.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "kspace.h" -#include "update.h" -#include "modify.h" +#include "comm.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "region.h" +#include "force.h" +#include "kspace.h" #include "lattice.h" -#include "comm.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" #include "output.h" +#include "region.h" +#include "style_region.h" #include "thermo.h" #include "universe.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/domain.h b/src/domain.h index 58b935ce01..f3c8026e72 100644 --- a/src/domain.h +++ b/src/domain.h @@ -14,10 +14,10 @@ #ifndef LMP_DOMAIN_H #define LMP_DOMAIN_H +#include "pointers.h" + #include #include -#include -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump.cpp b/src/dump.cpp index 0698a84e81..ecb87b79fd 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,21 +12,21 @@ ------------------------------------------------------------------------- */ #include "dump.h" -#include -#include + #include "atom.h" #include "irregular.h" #include "update.h" #include "domain.h" #include "group.h" #include "output.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "compute.h" #include "memory.h" #include "error.h" +#include + using namespace LAMMPS_NS; #if defined(LMP_QSORT) diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 3b0594a2cb..167d88789c 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -12,25 +12,22 @@ ------------------------------------------------------------------------- */ #include "dump_custom.h" -#include -#include -#include + #include "atom.h" -#include "force.h" -#include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "modify.h" #include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "group.h" +#include "input.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "region.h" #include "update.h" #include "variable.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index 822bed7832..ed8336eebc 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "dump_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dump_image.cpp b/src/dump_image.cpp index ea9fb612cb..96a338950b 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dump_image.h" -#include + #include #include #include @@ -35,7 +35,7 @@ #include "math_extra.h" #include "error.h" #include "memory.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 666a7773bd..6f824e5559 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "dump_local.h" -#include + #include -#include + #include "modify.h" #include "fix.h" #include "compute.h" @@ -24,7 +24,7 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 4966310470..a37341a15c 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index c07b225f9d..dba4fde077 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -30,8 +30,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d5c1bbef29..08025b8392 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_addforce.h" -#include + #include -#include + #include "atom.h" #include "atom_masks.h" #include "update.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index a8d78f14e7..838d2487b2 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_ave_atom.h" -#include + #include #include "atom.h" #include "update.h" @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index dd753ddc2d..18fb335279 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_chunk.h" -#include -#include + + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 293b7fc296..92a01932e7 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -18,8 +18,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate.h" -#include -#include + + #include #include #include "update.h" @@ -30,8 +30,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 091ec19fff..790fb9a1d4 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_histo.h" -#include -#include + + #include #include #include "atom.h" @@ -25,8 +25,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 4b86681153..5e93df0313 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -15,7 +15,7 @@ Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ #include "fix_ave_histo_weight.h" -#include + #include #include "fix.h" #include "atom.h" diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 4cc8cc3d3d..e83a3f60f5 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_time.h" -#include -#include + + #include #include #include "update.h" @@ -28,8 +28,8 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index b5b2527e25..7b8dc28cb3 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_aveforce.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 39760e9479..5fd9ef190e 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -18,7 +18,7 @@ #include "fix_box_relax.h" #include #include -#include + #include "atom.h" #include "domain.h" #include "update.h" @@ -29,7 +29,7 @@ #include "compute.h" #include "error.h" #include "math_extra.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 4b12c393cb..190a8bcd7d 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_controller.h" -#include + #include #include "force.h" #include "update.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index d3ceb69ea0..877eac0524 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 5b74b75fcd..25e21c5ee1 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_drag.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 8fb4f0cdfc..360f0d2998 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_dt_reset.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 7dd8c08204..be2a74d81b 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -19,7 +19,7 @@ #include "modify.h" #include "respa.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 82b8311968..88ce2faaad 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_gravity.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index cf39ba61e2..39591cd5f1 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_halt.h" -#include + #include #include -#include + #include "update.h" #include "force.h" #include "input.h" @@ -26,7 +26,7 @@ #include "comm.h" #include "timer.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 7fbdd24b4c..e2eb399322 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_heat.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index dcddad95b2..f42e0a527b 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_indent.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 81c186c703..9d0b5f28f1 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin.h" -#include + #include #include #include "math_extra.h" @@ -38,7 +38,7 @@ #include "memory.h" #include "error.h" #include "group.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index c1056d2b16..4af2ed3961 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_momentum.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index d951a924fe..43415a6ef5 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history.h" -#include + #include #include "my_page.h" #include "atom.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 9251ce384e..f4ff71d3a3 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -13,7 +13,7 @@ #include "fix_nph.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index cf2298f5f8..b49eb0c5c5 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 6949ead1d6..f6ec24991b 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -13,7 +13,7 @@ #include "fix_npt.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index e38d88fadd..1bd879c786 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_numdiff.cpp b/src/fix_numdiff.cpp index f6d064b794..145d60e8df 100644 --- a/src/fix_numdiff.cpp +++ b/src/fix_numdiff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_numdiff.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 83a6af5d0c..ed79c6b21b 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_nve_limit.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7868693b69..f7a53cf382 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -13,11 +13,11 @@ #include "fix_nvt.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index ccf7aaecaf..3cc88772d7 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -26,7 +26,7 @@ #include "fix_deform.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 40c3ba19e3..7c4159455f 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_sphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index a430130fe4..a90bf86c56 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -14,7 +14,7 @@ #include "fix_press_berendsen.h" #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 8964a9ba82..017ae48925 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_print.h" -#include + #include #include "update.h" #include "input.h" @@ -21,8 +21,8 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 374d0069fd..07108721c4 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom.h" -#include + #include #include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 305ee0ea26..4f675bf7bf 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_restrain.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 1a3158ed4c..329edbd6ef 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_setforce.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index fef7e2086c..112b675826 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_spring_self.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 60a1a70037..e18317ba03 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_store_state.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 5016b8c343..ec2965d072 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -13,7 +13,7 @@ #include "fix_temp_berendsen.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 5a7b9a04db..cf7e9e9fe2 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -17,7 +17,7 @@ #include "fix_temp_csld.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -31,7 +31,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 72e4dd635d..c620905102 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_temp_csvr.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index e575d72f7f..b5cb9c9a1b 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -13,7 +13,7 @@ #include "fix_temp_rescale.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 98fb373075..12e36d890e 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_tmd.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 48f14f5e2f..8af098d66f 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_vector.h" -#include + #include #include "update.h" #include "force.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 0c343938ab..e2237d074d 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall.h" -#include + #include #include "input.h" #include "variable.h" @@ -23,7 +23,7 @@ #include "respa.h" #include "error.h" #include "force.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index e60b3b4aad..76b2cd11fa 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region.h" -#include + #include #include #include "atom.h" diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 0c1a45603e..431cc03997 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_deprecated.h" -#include + #include "improper_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index ce0f36539f..096e0c3614 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index f269f8bf03..11c9257ec9 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/lmptype.h b/src/lmptype.h index e2e7a88a42..e0e081dd12 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -42,10 +42,10 @@ #define __STDC_FORMAT_MACROS #endif -#include -#include -#include -#include +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export // grrr - IBM Power6 does not provide this def in their system header files diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index a858f87910..87aa0bab5f 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_beck.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/pair_born.cpp b/src/pair_born.cpp index ca0ab9a17b..5b0d3a6562 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 1a6b12a345..e4617b5c4b 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_dsf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 4c51b0bb9f..30fe8fcde9 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 91071fccb1..1abdbcc68b 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 6141205db0..9fac17aede 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index d19374b5d9..67c471a5e3 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 2a3def0d4f..2093718245 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_coul_debye.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 2f1a834060..ee124c7f59 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index efe8d46017..f98b84417a 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_coul_streitz.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -30,8 +30,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + #include "potential_file_reader.h" using namespace LAMMPS_NS; diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index e94c4abb73..e3079dcaf6 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 75cb7efcdf..046726892e 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "pair_deprecated.h" -#include + #include "pair_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 613ad90cc3..d0d9b98fc9 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 3f3f05f7f5..dd0e144953 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_tstat.h" -#include + #include #include "atom.h" #include "update.h" @@ -21,7 +21,7 @@ #include "comm.h" #include "random_mars.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index d8b8e36b8c..6732296764 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 693ed7fa24..0b1882f12b 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -13,7 +13,7 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid.h" -#include + #include #include #include "atom.h" @@ -26,9 +26,9 @@ #include "memory.h" #include "error.h" #include "respa.h" -#include "utils.h" + #include "suffix.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index dc8ac65dd4..e85973ed6a 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -17,7 +17,7 @@ #include "atom.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index c60908e8cf..a4ba3b8585 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj96_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 833c954330..b6c91cafe2 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cubic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index fedf029fb8..bd42801f3b 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index a11de35c53..669d48c860 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 2d4b0bbe98..3ddb898c8f 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_debye.h" -#include + #include #include "atom.h" #include "neigh_list.h" #include "force.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index 2d9368a0ca..952a140039 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index c6fa33f03c..749cc9e6a9 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 1063d05672..3f711e2a15 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index b7e3516ec3..0818c60f31 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 37837b695f..005bc44061 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs_coul_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 5c6bc671f9..a53d703b8b 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 14646f19f2..3697208d42 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth_linear.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index f838d96145..7447e143f7 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mie_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index cbfaccab2c..efcc1aa811 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 4d3702313e..f3dd139b69 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 4aec954c38..1711465ffa 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_table.h" -#include + #include -#include + #include -#include + #include "atom.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index fd700e9886..50cc87cf96 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index b746204892..6429492346 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa.h" -#include + #include #include "atom.h" #include "force.h" @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index d78c156935..68c63c9806 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + // From J.F. Zeigler, J. P. Biersack and U. Littmark, // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index f08d919f83..b34e0b2b82 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -16,14 +16,14 @@ ------------------------------------------------------------------------- */ #include "pair_zero.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index afbe9e4189..137c167ab9 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/tokenizer.h b/src/tokenizer.h index eb19c4421b..2db9870866 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -18,10 +18,11 @@ #ifndef LMP_TOKENIZER_H #define LMP_TOKENIZER_H -#include -#include #include "lmptype.h" -#include + +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export namespace LAMMPS_NS { From 1421817276e3107042e0432b07e69a96b77bec94 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 17:54:29 -0400 Subject: [PATCH 36/72] remove redundant includes --- src/atom.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 6fff15d11f..ccd93401fb 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -14,8 +14,6 @@ #include "atom.h" #include "style_atom.h" -#include "atom_vec.h" -#include "atom_vec_ellipsoid.h" #include "comm.h" #include "compute.h" #include "domain.h" From d5027c125c5df6f73153ad735a64b4c610433637 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 17:54:57 -0400 Subject: [PATCH 37/72] rename fmt() macro to logfmt() to avoid clashes with fmtlib --- lib/awpmd/ivutils/include/logexc.h | 2 +- lib/awpmd/systems/interact/TCP/wpmd.cpp | 22 +- lib/awpmd/systems/interact/TCP/wpmd_split.cpp | 376 +++++++++--------- lib/awpmd/systems/interact/TCP/wpmd_split.h | 4 +- src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +- 5 files changed, 204 insertions(+), 204 deletions(-) diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 80942f60bf..7bf6125bc6 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -273,7 +273,7 @@ public: }; /// format a string -const char *fmt(const char *format,...); +const char *logfmt(const char *format,...); /// macros with common usage #define LOGFATAL(code,text,lineinfo) ((lineinfo) ? ::message(vblFATAL,(code)," %s at %s:%d",(text),__FILE__,__LINE__) : \ diff --git a/lib/awpmd/systems/interact/TCP/wpmd.cpp b/lib/awpmd/systems/interact/TCP/wpmd.cpp index 1e53f3141c..660d7c21d7 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd.cpp @@ -170,7 +170,7 @@ int AWPMD::set_pbc(const Vector_3P pcell, int pbc_){ int AWPMD::set_electrons(int s, int n, Vector_3P x, Vector_3P v, double* w, double* pw, double mass, double *q) { if(s < 0 || s > 1) - return LOGERR(-1,fmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); norm_matrix_state[s] = NORM_UNDEFINED; nwp[s]=ne[s]=n; @@ -363,20 +363,20 @@ int AWPMD::interaction(int flag, Vector_3P fi, Vector_3P fe_x, //3. inverting the overlap matrix int info=0; if(nes){ - /*FILE *f1=fopen(fmt("matrO_%d.d",s),"wt"); + /*FILE *f1=fopen(logfmt("matrO_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);8*/ - + ZPPTRF("L",&nes,Y[s].arr,&info); // analyze return code here if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); ZPPTRI("L",&nes,Y[s].arr,&info); if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); - - /*f1=fopen(fmt("matrY_%d.d",s),"wt"); + + /*f1=fopen(logfmt("matrY_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);*/ } @@ -758,7 +758,7 @@ void AWPMD::norm_factorize(int s) { int nes8 = ne[s]*8, info; DGETRF(&nes8, &nes8, Norm[s].arr, &nes8, &ipiv[0], &info); if(info < 0) - LOGERR(info,fmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_FACTORIZED; } @@ -773,7 +773,7 @@ void AWPMD::norm_invert(int s) { DGETRI(&nes8, Norm[s].arr, &nes8, &ipiv[0], (double*)IDD.arr, &IDD_size, &info); // use IDD for work storage if(info < 0) - LOGERR(info,fmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_INVERTED; } @@ -829,7 +829,7 @@ int AWPMD::step(double dt){ //e gets current electronic coordinates int AWPMD::get_electrons(int spin, Vector_3P x, Vector_3P v, double* w, double* pw, double mass){ if(spin<0 || spin >1) - return -1; // invalid spin: return LOGERR(-1,fmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); + return -1; // invalid spin: return LOGERR(-1,logfmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); if(mass<0) mass=me; for(int i=0;i 1) - return LOGERR(-1,fmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); // calculating the total n nvar[s]=0; @@ -68,22 +68,22 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* norm_matrix_state[s] = NORM_UNDEFINED; ne[s]=nel; wp[s].resize(n); - + split_c[s].resize(n); split_c[s].assign(c,c+n); - - + + nspl[s].resize(nel); nspl[s].assign(splits,splits+nel); partition1[s].clear(); for(int i=0;i0){ // width PBC, keeping the width are within [0,Lextra] w[i]=fmod(w[i],Lextra); @@ -107,7 +107,7 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* else qe[s].assign(nwp[s],-1); - + return 1; } @@ -121,40 +121,40 @@ void AWPMD_split::eterm_deriv(int ic1,int s1,int c1, int j1,int ic2,int s2, int cdouble ck(split_c[s2][ic2+k2][0],split_c[s2][ic2+k2][1]); int indw1=8*ic1, indw2=8*ic2; int indn1=(nvar[s1]/10)*8+2*ic1, indn2=(nvar[s2]/10)*8+2*ic2; - cdouble part_jk=conj(cj)*ck; + cdouble part_jk=conj(cj)*ck; int M= 1; //(j1==k2 ? 1 : 2); // over a_k_re - E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); + E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); // over a_k_im - E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); + E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); // over a_j_re - E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); // over a_j_im - E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); for(int i=0;i<3;i++){ // over b_k_re - E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); // over b_k_im - E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); // over b_j_re - E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); // over b_j_im - E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); } // over ck_re - E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); + E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); // over ck_im E_der[s2][indn2+2*k2+1]+=M*real(pref*i_unit*conj(cj)*o.I0*v); // over cj_re - E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); + E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); // over cj_im - E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); - + E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); + double t= -M*real(pref*part_jk*o.I0*v); // nonlocal terms: TODO: make a separate global loop for summation of nonlocal terms for(int j=0;j -mu, v -> -v !!! } - - + + for(int k1=j1+1;k1(E_der[s1].begin()+indw1,(double *)&fe_x[iv1+k1],(double *)&fe_p[iv1+k1],&fe_w[iv1+k1],&fe_pw[iv1+k1], 1./one_h); @@ -341,14 +341,14 @@ void AWPMD_split::get_el_forces(int flag, Vector_3P fe_x, ic1+=nspl[s1][c1]; // incrementing block1 wp address iv1+=nspl[s1][c1]; // incrementing global variable address } - } + } } } //e same as interaction, but using Hartee factorization (no antisymmetrization) -int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, +int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, Vector_3P fe_p, double *fe_w, double *fe_pw, Vector_2P fe_c){ - + // resize arrays if needed enum APPROX tmp=HARTREE; swap(tmp,approx); // do not need large matrices @@ -358,39 +358,39 @@ int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, // clearing forces clear_forces(flag,fi,fe_x,fe_p,fe_w,fe_pw,fe_c); // calculate block norms and (optionally) derivatives - calc_norms(flag); + calc_norms(flag); Eee = Ew = 0.; for(int s1=0;s1<2;s1++){ Ee[s1]=0.; Eei[s1]=0.; int ic1=0; // starting index of the wp for current electron - + for(int c1=0;c1 1) - return LOGERR(-1,fmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); s_add=s; spl_add=0; return ne[s_add]; diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 18704deb0b..d492cd082d 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -237,7 +237,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) etmap[etag[i]].push_back(i); } else - error->all(FLERR,fmt("Invalid spin value (%d) for particle %d !",spin[i],i)); + error->all(FLERR,logfmt("Invalid spin value (%d) for particle %d !",spin[i],i)); } // ion force vector Vector_3 *fi=NULL; @@ -254,7 +254,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) for(size_t k=0;kall(FLERR,fmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); + error->all(FLERR,logfmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); double m= atom->mass ? atom->mass[type[i]] : force->e_mass; Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]); Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]); From 4a10111ceda7f4de0727f3dcefa9d9f0e94522d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:42:19 -0400 Subject: [PATCH 38/72] add iwyu target to CMake configuration --- cmake/CMakeLists.txt | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index cc4c1cc905..8fd862e857 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -249,6 +249,27 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") endif() endif() +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if (IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -p ${CMAKE_BINARY_DIR} + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") mark_as_advanced(ENABLE_SANITIZER) set(ENABLE_SANITIZER_VALUES none address leak thread undefined) @@ -293,7 +314,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) endif() endif() - find_package(JPEG QUIET) option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) if(WITH_JPEG) From 5e429b8212dea8f435da1944338f843a66b4e4f8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:42:41 -0400 Subject: [PATCH 39/72] update include conventions and refer to the new CMake build target --- doc/include-file-conventions.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index ea4e07eb59..87b9eba8df 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -93,7 +93,8 @@ Include files should be included in this order: * the header matching the implementation (`some_class.h` for file `some_class.cpp`) * mpi.h (only if needed) * LAMMPS local headers (preferably in alphabetical order) -* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* system and library headers (anything that is using angular brackets; preferably in alphabetical order) +* conditional include statements (i.e. anything bracketed with ifdefs) ### Special Cases and Exceptions @@ -111,12 +112,10 @@ those headers. The [Include What You Use tool](https://include-what-you-use.org/) can be used to provide supporting information about compliance with -the rules listed here. There are some limitations and the IWYU tool -may give incorrect advice. The tools is activated by setting the -CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the -path of the `include-what-you-use` command. When activated, the -tool will be run after each compilation and provide suggestions for -which include files should be added or removed. +the rules listed here. Through setting `-DENABLE_IWYU=on` when running +CMake, a custom build target is added that will enable recording +the compilation commands and then run the `iwyu_tool` using the +recorded compilation commands information when typing `make iwyu`. ## Legacy Code From b741a07a34f22f68c320e3f949d19e76cf092ef3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:43:03 -0400 Subject: [PATCH 40/72] document IWYU analysis custom build target --- doc/src/Build_development.rst | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index cd432dddcb..eebde77b4d 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -28,6 +28,40 @@ variable VERBOSE set to 1: ---------- +.. _iwyu_processing: + +Report missing and unneeded '#include' statements +------------------------------------------------- + +The conventions for how and when to use and order include statements in +LAMMPS are `documented in a separate file `_ +(also included in the source code distribution). To assist with following +these conventions one can use the `Include What You Use tool `_. +This is still under development and for large and complex projects like LAMMPS +there are some false positives, so suggested changes need to be verified manually. +It is recommended to use at least version 0.14, which has much fewer incorrect +reports than earlier versions. + +The necessary steps to generate the report can be enabled via a +CMake variable: + +.. code-block:: bash + + -D ENABLE_IWYU=value # value = no (default) or yes + +This will check if the required binary (include-what-you-use or iwyu) +and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can +be found in the path. The analysis can then be started with: + +.. code-block:: bash + + make iwyu + +This may first run some compilation, as the analysis is dependent +on recording all commands required to do the compilation. + +---------- + .. _sanitizer: Address, Undefined Behavior, and Thread Sanitizer Support From 79584c842dfa99127bc990903dd8cf13a635cc8d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 18:44:12 -0400 Subject: [PATCH 41/72] add false positive --- doc/utils/sphinx-config/false_positives.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a9f976c3fd..586e14da88 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1355,6 +1355,7 @@ iva Ivanov Ivector Iw +iwyu ixcm ixx Ixx From 4ba6a4f958e2e0cb864e310631a9c3d28b82aa1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 21:43:20 -0400 Subject: [PATCH 42/72] have clang-style output for easier parsing in compilation mode in emacs --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 8fd862e857..1d67bfde37 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,7 +260,7 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -p ${CMAKE_BINARY_DIR} + ${IWYU_TOOL} -o clang -p ${CMAKE_BINARY_DIR} WORKING_DIRECTORY ${CMAKE_BINARY_DIR} COMMENT "Running IWYU") add_dependencies(iwyu lammps) From f88f4cd60e22a9e62994602221d38f177042fdb4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 21:44:04 -0400 Subject: [PATCH 43/72] more include file updates --- .../pair_lj_charmm_coul_charmm_intel.cpp | 8 ++- src/atom.cpp | 2 +- src/atom_vec_body.cpp | 2 +- src/atom_vec_hybrid.cpp | 4 +- src/create_atoms.cpp | 32 ++++----- src/create_bonds.cpp | 22 +++--- src/domain.cpp | 5 +- src/dump_local.cpp | 13 ++-- src/dump_movie.cpp | 4 +- src/error.cpp | 13 ++-- src/error.h | 1 - src/finish.cpp | 20 +++--- src/fix.cpp | 13 ++-- src/fix_addforce.cpp | 15 ++--- src/fix_ave_atom.cpp | 13 ++-- src/fix_ave_correlate.cpp | 17 ++--- src/fix_ave_histo.cpp | 19 +++--- src/fix_ave_time.cpp | 17 ++--- src/fix_aveforce.cpp | 12 ++-- src/fix_controller.cpp | 12 ++-- src/fix_drag.cpp | 10 +-- src/fix_external.cpp | 9 +-- src/fix_gravity.cpp | 20 +++--- src/fix_group.cpp | 21 +++--- src/fix_halt.cpp | 22 +++--- src/fix_indent.cpp | 14 ++-- src/fix_lineforce.cpp | 11 +-- src/fix_momentum.cpp | 8 +-- src/fix_nh_sphere.cpp | 11 +-- src/fix_nve_sphere.cpp | 11 +-- src/fix_planeforce.cpp | 11 +-- src/fix_print.cpp | 14 ++-- src/fix_read_restart.cpp | 2 +- src/fix_recenter.cpp | 15 +++-- src/fix_respa.cpp | 5 +- src/fix_setforce.cpp | 14 ++-- src/fix_spring.cpp | 13 ++-- src/fix_spring_chunk.cpp | 15 +++-- src/fix_spring_rg.cpp | 11 +-- src/fix_spring_self.cpp | 10 +-- src/fix_store.cpp | 7 +- src/fix_store_state.cpp | 20 +++--- src/fix_vector.cpp | 14 ++-- src/fix_viscous.cpp | 9 +-- src/fix_wall.cpp | 11 ++- src/fix_wall_reflect.cpp | 15 +++-- src/fix_wall_region.cpp | 12 ++-- src/force.cpp | 36 +++++----- src/force.h | 2 +- src/group.cpp | 31 ++++----- src/group.h | 2 +- src/image.cpp | 16 ++--- src/imbalance_group.cpp | 5 +- src/imbalance_neigh.cpp | 10 ++- src/imbalance_store.cpp | 5 +- src/imbalance_time.cpp | 6 +- src/imbalance_var.cpp | 10 +-- src/improper_zero.cpp | 10 +-- src/info.cpp | 32 +++++---- src/info.h | 2 +- src/input.cpp | 67 +++++++++---------- src/input.h | 2 +- src/irregular.cpp | 9 +-- src/kspace.cpp | 22 +++--- src/kspace_deprecated.cpp | 3 +- src/lammps.cpp | 15 ++--- 66 files changed, 416 insertions(+), 448 deletions(-) diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index ff8a9869b7..2078e5277b 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -12,19 +12,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_charmm_coul_charmm_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "group.h" #include "memory.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" #include "suffix.h" + +#include +#include + using namespace LAMMPS_NS; #define LJ_T typename IntelBuffers::vec4_t diff --git a/src/atom.cpp b/src/atom.cpp index ccd93401fb..864c7af638 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #include "comm.h" #include "compute.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 871f40084d..608c803e20 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include "style_body.h" +#include "style_body.h" // IWYU pragma: keep #include "atom.h" #include "body.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 5c37be4aa4..7a8c73570d 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -595,7 +595,7 @@ void AtomVecHybrid::build_styles() nallstyles = 0; #define ATOM_CLASS #define AtomStyle(key,Class) nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS @@ -609,7 +609,7 @@ void AtomVecHybrid::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index b121edb5b2..7e84e9cce0 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -16,31 +16,27 @@ ------------------------------------------------------------------------- */ #include "create_atoms.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" -#include "irregular.h" -#include "modify.h" -#include "force.h" -#include "special.h" #include "domain.h" -#include "lattice.h" -#include "region.h" -#include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" -#include "math_const.h" #include "error.h" +#include "input.h" +#include "irregular.h" +#include "lattice.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" +#include "modify.h" +#include "molecule.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "special.h" +#include "variable.h" -#include -#include "utils.h" -#include "fmt/format.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 4261d9f766..9e3eb65801 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -18,21 +18,19 @@ ------------------------------------------------------------------------- */ #include "create_bonds.h" -#include -#include -#include + #include "atom.h" -#include "domain.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "comm.h" -#include "group.h" -#include "special.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "force.h" +#include "group.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "special.h" + +#include using namespace LAMMPS_NS; diff --git a/src/domain.cpp b/src/domain.cpp index f54df1f382..984c735a20 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "domain.h" +#include "style_region.h" // IWYU pragma: keep #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "molecule.h" #include "output.h" #include "region.h" -#include "style_region.h" #include "thermo.h" #include "universe.h" #include "update.h" @@ -106,7 +106,8 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) #define REGION_CLASS #define RegionStyle(key,Class) \ (*region_map)[#key] = ®ion_creator; -#include "style_region.h" +#include "style_region.h" // IWYU pragma: keep + #undef RegionStyle #undef REGION_CLASS } diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 6f824e5559..a71166ec57 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -13,18 +13,15 @@ #include "dump_local.h" -#include - -#include "modify.h" -#include "fix.h" #include "compute.h" #include "domain.h" -#include "update.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index a37341a15c..5f6d0b80d7 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "dump_movie.h" -#include + #include "comm.h" -#include "force.h" #include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/error.cpp b/src/error.cpp index 7458f816c0..0ea218887f 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -12,16 +12,11 @@ ------------------------------------------------------------------------- */ #include "error.h" -#include -#include -#include -#include -#include "universe.h" -#include "output.h" -#include "input.h" + #include "accelerator_kokkos.h" -#include "utils.h" -#include "fmt/format.h" +#include "input.h" +#include "output.h" +#include "universe.h" #if defined(LAMMPS_EXCEPTIONS) #include "update.h" diff --git a/src/error.h b/src/error.h index 40c1559464..dedebc4148 100644 --- a/src/error.h +++ b/src/error.h @@ -15,7 +15,6 @@ #define LMP_ERROR_H #include "pointers.h" -#include #ifdef LAMMPS_EXCEPTIONS #include "exceptions.h" diff --git a/src/finish.cpp b/src/finish.cpp index 51f886b5db..7990a3c141 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "finish.h" -#include -#include -#include -#include + #include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "timer.h" #include "universe.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 549208a0ce..03313739a1 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix.h" + +#include "atom.h" +#include "atom_masks.h" +#include "error.h" +#include "group.h" +#include "memory.h" + #include #include -#include "atom.h" -#include "group.h" -#include "force.h" -#include "atom_masks.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index 08025b8392..0983728ea9 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -13,20 +13,19 @@ #include "fix_addforce.h" -#include - #include "atom.h" #include "atom_masks.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index 838d2487b2..da009c55d5 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -13,17 +13,16 @@ #include "fix_ave_atom.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 92a01932e7..031dfc26bf 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -19,19 +19,16 @@ #include "fix_ave_correlate.h" +#include "compute.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" #include #include -#include "update.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" - - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 790fb9a1d4..3a9346498f 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -13,20 +13,17 @@ #include "fix_ave_histo.h" +#include "atom.h" +#include "compute.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" #include #include -#include "atom.h" -#include "update.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" - - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index e83a3f60f5..9c493b9846 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -17,19 +17,16 @@ #include "fix_ave_time.h" +#include "compute.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" #include #include -#include "update.h" -#include "force.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" - - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 7b8dc28cb3..00ec0d67ba 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -13,17 +13,17 @@ #include "fix_aveforce.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 190a8bcd7d..92fd42f3db 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -13,14 +13,14 @@ #include "fix_controller.h" -#include -#include "force.h" -#include "update.h" -#include "modify.h" #include "compute.h" -#include "input.h" -#include "variable.h" #include "error.h" +#include "input.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 25e21c5ee1..2400014569 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -13,14 +13,14 @@ #include "fix_drag.h" -#include -#include #include "atom.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 5d810ff38b..1db7e15295 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_external.h" -#include + #include "atom.h" -#include "update.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 88ce2faaad..6dff937385 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -13,18 +13,18 @@ #include "fix_gravity.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "input.h" +#include "math_const.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + #include #include -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "respa.h" -#include "modify.h" -#include "input.h" -#include "variable.h" -#include "math_const.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 5e2a12c988..bb51fafa12 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -12,20 +12,21 @@ ------------------------------------------------------------------------- */ #include "fix_group.h" -#include -#include "group.h" -#include "update.h" + #include "atom.h" -#include "force.h" #include "comm.h" #include "domain.h" -#include "region.h" -#include "modify.h" -#include "respa.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "region.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 39591cd5f1..f8222e3ece 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -13,21 +13,19 @@ #include "fix_halt.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "input.h" +#include "modify.h" +#include "neighbor.h" +#include "timer.h" +#include "update.h" +#include "variable.h" + #include #include -#include "update.h" -#include "force.h" -#include "input.h" -#include "variable.h" -#include "atom.h" -#include "neighbor.h" -#include "modify.h" -#include "comm.h" -#include "timer.h" -#include "error.h" - - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index f42e0a527b..ae58f27913 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -17,18 +17,18 @@ #include "fix_indent.h" -#include -#include #include "atom.h" -#include "input.h" -#include "variable.h" #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 0287c8c0db..cacec13302 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_lineforce.h" + +#include "atom.h" +#include "error.h" +#include "respa.h" +#include "update.h" + #include #include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 4af2ed3961..259099e07c 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -13,13 +13,13 @@ #include "fix_momentum.h" -#include -#include #include "atom.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index 1ff3fc2d4d..d60798e007 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "fix_nh_sphere.h" -#include -#include + #include "atom.h" -#include "atom_vec.h" +#include "domain.h" #include "error.h" #include "force.h" -#include "domain.h" -#include "math_vector.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index c0fea17c2b..87fba3eca3 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_nve_sphere.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "atom_vec.h" -#include "force.h" #include "error.h" -#include "math_vector.h" +#include "force.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 9434a4b348..2e3bcadd69 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_planeforce.h" + +#include "atom.h" +#include "error.h" +#include "respa.h" +#include "update.h" + #include #include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 017ae48925..78fceea184 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -13,16 +13,14 @@ #include "fix_print.h" -#include -#include "update.h" -#include "input.h" -#include "modify.h" -#include "variable.h" -#include "memory.h" #include "error.h" -#include "force.h" - +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index c1c0150177..2e10b15ffa 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_read_restart.h" + #include "atom.h" #include "memory.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 8997e4b805..3f9eec9ee4 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -16,18 +16,19 @@ ------------------------------------------------------------------------- */ #include "fix_recenter.h" -#include -#include + #include "atom.h" -#include "group.h" -#include "update.h" +#include "comm.h" #include "domain.h" +#include "error.h" +#include "group.h" #include "lattice.h" #include "modify.h" -#include "comm.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 459b30c1b2..b116f8ccac 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_respa.h" -#include + #include "atom.h" -#include "force.h" #include "memory.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 329edbd6ef..229890c5df 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -13,18 +13,18 @@ #include "fix_setforce.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 1bd76f5c55..2d695add26 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -16,14 +16,15 @@ ------------------------------------------------------------------------- */ #include "fix_spring.h" + +#include "atom.h" +#include "error.h" +#include "group.h" +#include "respa.h" +#include "update.h" + #include #include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "force.h" -#include "group.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 778a6f0c43..d8de88bd63 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_spring_chunk.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "respa.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index e3ba935340..5715e7eb88 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -17,15 +17,16 @@ ------------------------------------------------------------------------- */ #include "fix_spring_rg.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "group.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "group.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 112b675826..8e7b3eb925 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -17,14 +17,14 @@ #include "fix_spring_self.h" -#include #include "atom.h" -#include "update.h" #include "domain.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 8ce94fb54a..3eb2075250 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_store.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index e18317ba03..fd4563b7ad 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -13,19 +13,19 @@ #include "fix_store_state.h" -#include #include "atom.h" -#include "domain.h" -#include "update.h" -#include "group.h" -#include "modify.h" #include "compute.h" -#include "fix.h" -#include "input.h" -#include "variable.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "force.h" +#include "fix.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 8af098d66f..6bcdfe948e 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -13,15 +13,15 @@ #include "fix_vector.h" -#include -#include "update.h" -#include "force.h" -#include "modify.h" #include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 7d532d832d..08649280d8 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_viscous.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index e2237d074d..cb822f1090 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -13,17 +13,16 @@ #include "fix_wall.h" -#include -#include "input.h" -#include "variable.h" #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 061083e55c..227ef66564 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "force.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" +#include "input.h" +#include "lattice.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 76b2cd11fa..fc3735cfbf 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -13,16 +13,16 @@ #include "fix_wall_region.h" -#include -#include #include "atom.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_const.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/force.cpp b/src/force.cpp index 10b82afabe..8eef7a4224 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -12,31 +12,29 @@ ------------------------------------------------------------------------- */ #include "force.h" -#include -#include -#include -#include -#include "style_bond.h" -#include "style_angle.h" -#include "style_dihedral.h" -#include "style_improper.h" -#include "style_pair.h" -#include "style_kspace.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep + +#include "angle.h" #include "atom.h" +#include "bond.h" +#include "bond_hybrid.h" #include "comm.h" +#include "dihedral.h" +#include "error.h" +#include "improper.h" +#include "kspace.h" #include "pair.h" #include "pair_hybrid.h" #include "pair_hybrid_overlay.h" -#include "bond.h" -#include "bond_hybrid.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/force.h b/src/force.h index d7824ea90e..999e9650aa 100644 --- a/src/force.h +++ b/src/force.h @@ -15,8 +15,8 @@ #define LMP_FORCE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/group.cpp b/src/group.cpp index 2377f028bd..ee96c20f47 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -12,30 +12,27 @@ ------------------------------------------------------------------------- */ #include "group.h" -#include -#include -#include -#include -#include -#include "domain.h" + #include "atom.h" -#include "force.h" #include "comm.h" -#include "region.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "output.h" -#include "input.h" -#include "variable.h" +#include "domain.h" #include "dump.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "input.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "output.h" +#include "region.h" +#include "variable.h" +#include +#include #include +#include using namespace LAMMPS_NS; @@ -538,7 +535,7 @@ void Group::assign(int narg, char **arg) void Group::assign(const std::string &groupcmd) { - std::vector args = utils::split_words(groupcmd); + auto args = utils::split_words(groupcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/group.h b/src/group.h index b9a5c27140..39c446d119 100644 --- a/src/group.h +++ b/src/group.h @@ -15,8 +15,8 @@ #define LMP_GROUP_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/image.cpp b/src/image.cpp index 56d9bc301a..755be587d8 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "image.h" -#include -#include -#include -#include -#include "math_extra.h" -#include "random_mars.h" -#include "math_const.h" + #include "error.h" -#include "force.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" +#include "random_mars.h" + +#include +#include +#include #ifdef LAMMPS_JPEG #include diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index 72b1028791..b7be70dd25 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -12,12 +12,11 @@ ------------------------------------------------------------------------- */ #include "imbalance_group.h" + #include "atom.h" +#include "error.h" #include "force.h" #include "group.h" -#include "error.h" -#include -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 0beb62bdb4..70d5580b9c 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "imbalance_neigh.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "error.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 919d1f3f61..2661b57b25 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "imbalance_store.h" -#include + #include "atom.h" #include "error.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index 99e549e90e..438728ef3e 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "imbalance_time.h" -#include + #include "atom.h" -#include "force.h" -#include "timer.h" #include "error.h" -#include "fmt/format.h" +#include "timer.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index d1a76ed9f7..a2c940789e 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "imbalance_var.h" -#include -#include + #include "atom.h" +#include "error.h" #include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 11c9257ec9..3da38a890c 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_zero.h" -#include -#include "atom.h" -#include "force.h" -#include "memory.h" -#include "error.h" +#include "atom.h" +#include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/info.cpp b/src/info.cpp index fbe43442f0..79ba9f7a45 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -17,39 +17,37 @@ ------------------------------------------------------------------------- */ #include "info.h" -#include -#include -#include -#include -#include -#include -#include + #include "accelerator_kokkos.h" +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" #include "compute.h" +#include "dihedral.h" #include "domain.h" #include "dump.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "group.h" +#include "improper.h" #include "input.h" #include "modify.h" #include "neighbor.h" #include "output.h" +#include "pair.h" +#include "pair_hybrid.h" #include "region.h" #include "universe.h" -#include "variable.h" #include "update.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "variable.h" + +#include +#include +#include +#include +#include #ifdef _WIN32 #define PSAPI_VERSION 1 diff --git a/src/info.h b/src/info.h index 5a379eaa78..65690ab28e 100644 --- a/src/info.h +++ b/src/info.h @@ -21,7 +21,7 @@ CommandStyle(info,Info) #define LMP_INFO_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/input.cpp b/src/input.cpp index c74232648c..84abaf141f 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,45 +12,44 @@ ------------------------------------------------------------------------- */ #include "input.h" -#include + +#include "accelerator_kokkos.h" +#include "angle.h" +#include "atom.h" +#include "atom_vec.h" +#include "bond.h" +#include "comm.h" +#include "comm_brick.h" +#include "comm_tiled.h" +#include "compute.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "kspace.h" +#include "memory.h" +#include "min.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "special.h" +#include "style_command.h" +#include "thermo.h" +#include "timer.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + #include #include #include #include -#include #include -#include "style_command.h" -#include "universe.h" -#include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "comm_brick.h" -#include "comm_tiled.h" -#include "group.h" -#include "domain.h" -#include "output.h" -#include "thermo.h" -#include "force.h" -#include "pair.h" -#include "min.h" -#include "modify.h" -#include "compute.h" -#include "fix.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "update.h" -#include "neighbor.h" -#include "special.h" -#include "timer.h" -#include "variable.h" -#include "accelerator_kokkos.h" -#include "error.h" -#include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include #ifdef _WIN32 #include diff --git a/src/input.h b/src/input.h index 48caa13fde..b8ffb276f9 100644 --- a/src/input.h +++ b/src/input.h @@ -15,8 +15,8 @@ #define LMP_INPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/irregular.cpp b/src/irregular.cpp index 2213b37d55..f6de6947bd 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "irregular.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" +#include "domain.h" #include "fix.h" #include "memory.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; diff --git a/src/kspace.cpp b/src/kspace.cpp index 2485db67b8..e51cc54c97 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -12,21 +12,19 @@ ------------------------------------------------------------------------- */ #include "kspace.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "comm.h" -#include "force.h" -#include "pair.h" -#include "memory.h" #include "atom_masks.h" -#include "error.h" -#include "suffix.h" +#include "comm.h" #include "domain.h" -#include "fmt/format.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "pair.h" +#include "suffix.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 5dc2b50e2b..16e9ff6abb 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "kspace_deprecated.h" -#include + #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/lammps.cpp b/src/lammps.cpp index ded9d93167..b6c8450a4d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,13 +12,7 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include -#include -#include -#include -#include -#include -#include + #include "style_angle.h" // IWYU pragma: keep #include "style_atom.h" // IWYU pragma: keep #include "style_bond.h" // IWYU pragma: keep @@ -54,8 +48,11 @@ #include "version.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include +#include #include "lmpinstalledpkgs.h" #include "lmpgitversion.h" From 203e42073a08aa4e8b9efccd064af3b956b9a508 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:14 -0400 Subject: [PATCH 44/72] fix compilation error --- lib/awpmd/ivutils/src/logexc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/awpmd/ivutils/src/logexc.cpp b/lib/awpmd/ivutils/src/logexc.cpp index d29745fda1..7e82af0f65 100644 --- a/lib/awpmd/ivutils/src/logexc.cpp +++ b/lib/awpmd/ivutils/src/logexc.cpp @@ -16,7 +16,7 @@ message_logger &message_logger::global(){ message_logger *message_logger::glogp=NULL; stdfile_logger default_log("",0,stdout,stderr,vblALLBAD|vblMESS1,vblFATAL,1); -const char *fmt(const char *format,...){ +const char *logfmt(const char *format,...){ va_list args; va_start(args,format); static char buff[1024]; From 71d111ccd9cd355d1a4d6fe3b59510919a12ddd1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:30 -0400 Subject: [PATCH 45/72] get rid of 'using namespace std;' --- src/info.cpp | 57 ++++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 28 deletions(-) diff --git a/src/info.cpp b/src/info.cpp index 79ba9f7a45..87161e9ca5 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -103,6 +103,8 @@ static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES | DUMP_STYLES | COMMAND_STYLES; } +using namespace LAMMPS_NS; + static const char *varstyles[] = { "index", "loop", "world", "universe", "uloop", "string", "getenv", "file", "atomfile", "format", "equal", "atom", "vector", "python", "internal", "(unknown)"}; @@ -114,17 +116,15 @@ static const char *commlayout[] = { "uniform", "nonuniform", "irregular" }; static const char bstyles[] = "pfsm"; -using namespace LAMMPS_NS; -using namespace std; +template +static void print_columns(FILE *fp, std::map *styles); template -static void print_columns(FILE* fp, map * styles); +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check); template -static bool find_style(const LAMMPS * lmp, map * styles, const string & name, bool suffix_check); - -template -static vector get_style_names(map * styles); +static std::vector get_style_names(std::map *styles); /* ---------------------------------------------------------------------- */ @@ -355,7 +355,7 @@ void Info::command(int narg, char **arg) if (flags & COMM) { int major,minor; - string version = get_mpi_info(major,minor); + std::string version = get_mpi_info(major,minor); fmt::print(out,"\nCommunication information:\n" "MPI library level: MPI v{}.{}\n" @@ -947,7 +947,7 @@ bool Info::is_defined(const char *category, const char *name) return false; } -bool Info::has_style(const string & category, const string & name) +bool Info::has_style(const std::string &category, const std::string &name) { if ( category == "atom" ) { return find_style(lmp, atom->avec_map, name, false); @@ -981,7 +981,7 @@ bool Info::has_style(const string & category, const string & name) return false; } -vector Info::get_available_styles(const string & category) +std::vector Info::get_available_styles(const std::string &category) { if ( category == "atom" ) { return get_style_names(atom->avec_map); @@ -1012,13 +1012,13 @@ vector Info::get_available_styles(const string & category) } else if( category == "command" ) { return get_style_names(input->command_map); } - return vector(); + return std::vector(); } template -static vector get_style_names(map * styles) +static std::vector get_style_names(std::map *styles) { - vector names; + std::vector names; names.reserve(styles->size()); for(auto const& kv : *styles) { @@ -1031,7 +1031,8 @@ static vector get_style_names(map * styles) } template -static bool find_style(const LAMMPS* lmp, map * styles, const string & name, bool suffix_check) +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check) { if (styles->find(name) != styles->end()) { return true; @@ -1039,13 +1040,13 @@ static bool find_style(const LAMMPS* lmp, map * styles, const if (suffix_check && lmp->suffix_enable) { if (lmp->suffix) { - string name_w_suffix = name + "/" + lmp->suffix; + std::string name_w_suffix = name + "/" + lmp->suffix; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } } if (lmp->suffix2) { - string name_w_suffix = name + "/" + lmp->suffix2; + std::string name_w_suffix = name + "/" + lmp->suffix2; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } @@ -1055,7 +1056,7 @@ static bool find_style(const LAMMPS* lmp, map * styles, const } template -static void print_columns(FILE* fp, map * styles) +static void print_columns(FILE *fp, std::map *styles) { if (styles->empty()) { fprintf(fp, "\nNone"); @@ -1064,8 +1065,8 @@ static void print_columns(FILE* fp, map * styles) // std::map keys are already sorted int pos = 80; - for(typename map::iterator it = styles->begin(); it != styles->end(); ++it) { - const string & style_name = it->first; + for(typename std::map::iterator it = styles->begin(); it != styles->end(); ++it) { + const std::string &style_name = it->first; // skip "secret" styles if (isupper(style_name[0])) continue; @@ -1147,9 +1148,9 @@ bool Info::has_package(const char * package_name) { /* ---------------------------------------------------------------------- */ #define _INFOBUF_SIZE 256 -string Info::get_os_info() +std::string Info::get_os_info() { - string buf; + std::string buf; #if defined(_WIN32) DWORD fullversion,majorv,minorv,buildv=0; @@ -1189,9 +1190,9 @@ string Info::get_os_info() return buf; } -string Info::get_compiler_info() +std::string Info::get_compiler_info() { - string buf; + std::string buf; #if __clang__ buf = fmt::format("Clang C++ {}", __VERSION__); #elif __INTEL_COMPILER @@ -1206,7 +1207,7 @@ string Info::get_compiler_info() return buf; } -string Info::get_openmp_info() +std::string Info::get_openmp_info() { #if !defined(_OPENMP) @@ -1241,7 +1242,7 @@ string Info::get_openmp_info() #endif } -string Info::get_mpi_vendor() { +std::string Info::get_mpi_vendor() { #if defined(MPI_STUBS) return "MPI STUBS"; #elif defined(OPEN_MPI) @@ -1261,7 +1262,7 @@ string Info::get_mpi_vendor() { #endif } -string Info::get_mpi_info(int &major, int &minor) +std::string Info::get_mpi_info(int &major, int &minor) { int len; #if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS) @@ -1277,10 +1278,10 @@ string Info::get_mpi_info(int &major, int &minor) char *ptr = strchr(version+80,'\n'); if (ptr) *ptr = '\0'; } - return string(version); + return std::string(version); } -string Info::get_cxx_info() +std::string Info::get_cxx_info() { #if __cplusplus > 201703L return "newer than C++17"; From 7b8fe97a88eadbe8fd32d94ed0f9c043a71fe1c5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:51:42 -0400 Subject: [PATCH 46/72] remove trailing whitespace --- doc/src/Build_development.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index eebde77b4d..bed5f31a13 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -59,7 +59,7 @@ be found in the path. The analysis can then be started with: This may first run some compilation, as the analysis is dependent on recording all commands required to do the compilation. - + ---------- .. _sanitizer: From 45f80f4f067bae3c5b3c05c40b4c78aa61444e2e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 22:52:22 -0400 Subject: [PATCH 47/72] more include file updates found by iwyu --- src/atom.cpp | 1 + src/body.h | 2 +- src/compute_orientorder_atom.cpp | 1 - src/compute_pressure.cpp | 19 ++++++++-------- src/domain.h | 3 ++- src/lattice.cpp | 16 ++++++-------- src/library.cpp | 38 +++++++++++++++----------------- src/memory.cpp | 3 +-- src/min_cg.cpp | 7 +++--- src/min_fire_old.cpp | 9 ++++---- src/min_hftn.cpp | 9 ++++---- src/min_linesearch.cpp | 9 ++++---- src/min_quickmin.cpp | 9 ++++---- src/min_sd.cpp | 6 +++-- src/minimize.cpp | 10 ++++----- src/modify.cpp | 26 +++++++++++----------- src/modify.h | 13 ++++++----- 17 files changed, 94 insertions(+), 87 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 864c7af638..90dce44764 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "atom.h" +#include "atom_vec.h" #include "style_atom.h" // IWYU pragma: keep #include "comm.h" diff --git a/src/body.h b/src/body.h index 1c742d3e65..c9c289792e 100644 --- a/src/body.h +++ b/src/body.h @@ -15,7 +15,7 @@ #define LMP_BODY_H #include "pointers.h" -#include "atom_vec_body.h" +#include "atom_vec_body.h" // IWYU pragma: keep namespace LAMMPS_NS { diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 84ae20e92a..7323b6ef01 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -36,7 +36,6 @@ using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; #ifdef DBL_EPSILON #define MY_EPSILON (10.0*DBL_EPSILON) diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index b57b53f522..90e4f9b39c 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -13,22 +13,23 @@ #include "compute_pressure.h" -#include +#include "angle.h" #include "atom.h" -#include "update.h" +#include "bond.h" +#include "dihedral.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "error.h" +#include "modify.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/domain.h b/src/domain.h index f3c8026e72..d807463bf3 100644 --- a/src/domain.h +++ b/src/domain.h @@ -20,6 +20,7 @@ #include namespace LAMMPS_NS { + class Region; class Domain : protected Pointers { public: @@ -90,7 +91,7 @@ class Domain : protected Pointers { int nregion; // # of defined Regions int maxregion; // max # list can hold - class Region **regions; // list of defined Regions + Region **regions; // list of defined Regions int copymode; enum{NO_REMAP,X_REMAP,V_REMAP}; diff --git a/src/lattice.cpp b/src/lattice.cpp index f41c32d239..68f3e7abe1 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -12,17 +12,15 @@ ------------------------------------------------------------------------- */ #include "lattice.h" + +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" +#include "update.h" + #include #include -#include -#include "update.h" -#include "domain.h" -#include "comm.h" -#include "force.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/library.cpp b/src/library.cpp index 30d52aefe5..3f37aecd7a 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -16,33 +16,31 @@ #include "library.h" #include -#include -#include -#include -#include -#include "universe.h" -#include "atom_vec.h" + #include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "compute.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "fix.h" +#include "fix_external.h" +#include "force.h" #include "group.h" +#include "info.h" #include "input.h" -#include "variable.h" +#include "memory.h" #include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "output.h" #include "thermo.h" -#include "compute.h" -#include "fix.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "info.h" -#include "fix_external.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" diff --git a/src/memory.cpp b/src/memory.cpp index 6211687a7a..bbbc233bbf 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "memory.h" -#include + #include "error.h" -#include "fmt/format.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) #ifndef LMP_INTEL_NO_TBB diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 46da4bfa5b..511b16cef8 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_cg.h" -#include -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_fire_old.cpp b/src/min_fire_old.cpp index bd76b2d1fc..6efd00a4b8 100644 --- a/src/min_fire_old.cpp +++ b/src/min_fire_old.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_fire_old.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 63432aab63..909f0b0689 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -18,17 +18,18 @@ ------------------------------------------------------------------------- */ #include "min_hftn.h" -#include -#include -#include + #include "atom.h" #include "error.h" #include "fix_minimize.h" #include "modify.h" #include "output.h" #include "pair.h" -#include "update.h" #include "timer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index a7a10dcd51..7226f61614 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -22,15 +22,16 @@ ------------------------------------------------------------------------- */ #include "min_linesearch.h" -#include -#include + #include "atom.h" -#include "modify.h" #include "fix_minimize.h" -#include "pair.h" +#include "modify.h" #include "output.h" +#include "pair.h" #include "thermo.h" +#include + using namespace LAMMPS_NS; // ALPHA_MAX = max alpha allowed to avoid long backtracks diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 5e7643bf3b..025e80b95d 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_quickmin.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index d973ec1c82..5868acbe48 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -12,11 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_sd.h" -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/minimize.cpp b/src/minimize.cpp index 0146390763..451412ecc8 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "minimize.h" + #include "domain.h" -#include "update.h" -#include "min.h" -#include "finish.h" -#include "timer.h" #include "error.h" -#include "force.h" +#include "finish.h" +#include "min.h" +#include "timer.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/modify.cpp b/src/modify.cpp index 96335946ae..c88d52b623 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "modify.h" -#include -#include #include "style_compute.h" #include "style_fix.h" + #include "atom.h" #include "comm.h" -#include "fix.h" #include "compute.h" -#include "group.h" -#include "update.h" #include "domain.h" -#include "region.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "fix.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -947,7 +947,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) void Modify::add_fix(const std::string &fixcmd, int trysuffix) { - std::vector args = utils::split_words(fixcmd); + auto args = utils::split_words(fixcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { @@ -1249,7 +1249,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) void Modify::add_compute(const std::string &computecmd, int trysuffix) { - std::vector args = utils::split_words(computecmd); + auto args = utils::split_words(computecmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/modify.h b/src/modify.h index 05eebc7e14..4c3db0a1b9 100644 --- a/src/modify.h +++ b/src/modify.h @@ -15,11 +15,14 @@ #define LMP_MODIFY_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { + class Compute; + class Fix; + class Modify : protected Pointers { friend class Info; friend class FixSRP; @@ -27,7 +30,6 @@ class Modify : protected Pointers { friend class RespaOMP; public: - int nfix,maxfix; int n_initial_integrate,n_post_integrate,n_pre_exchange; int n_pre_neighbor,n_post_neighbor; int n_pre_force,n_pre_reverse,n_post_force; @@ -41,11 +43,12 @@ class Modify : protected Pointers { int nfix_restart_global; // stored fix global info from restart file int nfix_restart_peratom; // stored fix peratom info from restart file - class Fix **fix; // list of fixes + int nfix,maxfix; + Fix **fix; // list of fixes int *fmask; // bit mask for when each fix is applied - int ncompute,maxcompute; // list of computes - class Compute **compute; + int ncompute,maxcompute; + Compute **compute; // list of computes Modify(class LAMMPS *); virtual ~Modify(); From 047c14d17c055118258013b85b0797d0bac1800e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 23:41:16 -0400 Subject: [PATCH 48/72] tweak iwyu target. generate file with custom mappings --- cmake/CMakeLists.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 1d67bfde37..f541ad7025 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,10 +260,14 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_BINARY_DIR} - WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp COMMENT "Running IWYU") add_dependencies(iwyu lammps) + # generate file with additional mappings + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + " { include: [ \"\", private, \"\", public ] },\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" "and the iwyu-tool/iwyu_tool script installed in your PATH") From a4a1f7e8484ce075048428ad6dd2f869b49e5efe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 2 Sep 2020 23:42:08 -0400 Subject: [PATCH 49/72] more IWYU cleanup --- src/force.cpp | 2 -- src/force.h | 42 +++++++++++++++++++-------------- src/imbalance_group.cpp | 1 - src/input.cpp | 2 -- src/min.cpp | 36 ++++++++++++++-------------- src/min_fire.cpp | 17 ++++++------- src/ntopo.cpp | 6 ++--- src/ntopo_angle_all.cpp | 4 ++-- src/ntopo_angle_partial.cpp | 4 ++-- src/ntopo_angle_template.cpp | 4 ++-- src/ntopo_bond_all.cpp | 4 ++-- src/ntopo_bond_partial.cpp | 4 ++-- src/ntopo_bond_template.cpp | 4 ++-- src/ntopo_dihedral_all.cpp | 4 ++-- src/ntopo_dihedral_partial.cpp | 4 ++-- src/ntopo_dihedral_template.cpp | 4 ++-- src/ntopo_improper_all.cpp | 4 ++-- src/ntopo_improper_partial.cpp | 4 ++-- src/ntopo_improper_template.cpp | 4 ++-- src/output.cpp | 28 ++++++++++------------ src/output.h | 6 +++-- src/pair.cpp | 32 ++++++++++++------------- src/pair_coul_streitz.cpp | 17 +++++++------ src/pair_hybrid_overlay.cpp | 6 ++--- src/pair_zero.cpp | 3 +-- src/potential_file_reader.cpp | 14 ++++------- src/potential_file_reader.h | 5 ++-- src/procmap.cpp | 16 ++++++------- src/rcb.cpp | 5 ++-- src/read_data.cpp | 33 +++++++++++++------------- src/read_dump.cpp | 19 +++++++-------- src/read_restart.cpp | 35 +++++++++++++-------------- src/reader.cpp | 6 ++--- src/reader_native.cpp | 14 +++++++---- src/reader_native.h | 3 +-- src/table_file_reader.cpp | 9 +++---- 36 files changed, 195 insertions(+), 210 deletions(-) diff --git a/src/force.cpp b/src/force.cpp index 8eef7a4224..701113d7ef 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -31,9 +31,7 @@ #include "pair.h" #include "pair_hybrid.h" #include "pair_hybrid_overlay.h" -#include "update.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/force.h b/src/force.h index 999e9650aa..1302e20f12 100644 --- a/src/force.h +++ b/src/force.h @@ -19,6 +19,12 @@ #include namespace LAMMPS_NS { + class Angle; + class Bond; + class Dihedral; + class Improper; + class KSpace; + class Pair; class Force : protected Pointers { public: @@ -47,23 +53,23 @@ class Force : protected Pointers { int newton,newton_pair,newton_bond; // Newton's 3rd law settings - class Pair *pair; + Pair *pair; char *pair_style; char *pair_restart; - class Bond *bond; + Bond *bond; char *bond_style; - class Angle *angle; + Angle *angle; char *angle_style; - class Dihedral *dihedral; + Dihedral *dihedral; char *dihedral_style; - class Improper *improper; + Improper *improper; char *improper_style; - class KSpace *kspace; + KSpace *kspace; char *kspace_style; typedef Pair *(*PairCreator)(LAMMPS *); @@ -102,29 +108,29 @@ class Force : protected Pointers { void setup(); void create_pair(const std::string &, int); - class Pair *new_pair(const std::string &, int, int &); - class Pair *pair_match(const std::string &, int, int nsub=0); + Pair *new_pair(const std::string &, int, int &); + Pair *pair_match(const std::string &, int, int nsub=0); char *pair_match_ptr(Pair *); void create_bond(const std::string &, int); - class Bond *new_bond(const std::string &, int, int &); - class Bond *bond_match(const std::string &); + Bond *new_bond(const std::string &, int, int &); + Bond *bond_match(const std::string &); void create_angle(const std::string &, int); - class Angle *new_angle(const std::string &, int, int &); - class Angle *angle_match(const std::string &); + Angle *new_angle(const std::string &, int, int &); + Angle *angle_match(const std::string &); void create_dihedral(const std::string &, int); - class Dihedral *new_dihedral(const std::string &, int, int &); - class Dihedral *dihedral_match(const std::string &); + Dihedral *new_dihedral(const std::string &, int, int &); + Dihedral *dihedral_match(const std::string &); void create_improper(const std::string &, int); - class Improper *new_improper(const std::string &, int, int &); - class Improper *improper_match(const std::string &); + Improper *new_improper(const std::string &, int, int &); + Improper *improper_match(const std::string &); void create_kspace(const std::string &, int); - class KSpace *new_kspace(const std::string &, int, int &); - class KSpace *kspace_match(const std::string &, int); + KSpace *new_kspace(const std::string &, int, int &); + KSpace *kspace_match(const std::string &, int); void store_style(char *&, const std::string &, int); void set_special(int, char **); diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index b7be70dd25..f604f150b5 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -15,7 +15,6 @@ #include "atom.h" #include "error.h" -#include "force.h" #include "group.h" using namespace LAMMPS_NS; diff --git a/src/input.cpp b/src/input.cpp index 84abaf141f..1cb7893871 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -25,7 +25,6 @@ #include "dihedral.h" #include "domain.h" #include "error.h" -#include "fix.h" #include "force.h" #include "group.h" #include "improper.h" @@ -44,7 +43,6 @@ #include "update.h" #include "variable.h" -#include #include #include #include diff --git a/src/min.cpp b/src/min.cpp index 0bf0445525..6bcb4b4e2e 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -20,32 +20,32 @@ ------------------------------------------------------------------------- */ #include "min.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize.h" -#include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" +#include "compute.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "thermo.h" -#include "timer.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "thermo.h" +#include "timer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 53bedfbb6c..b7225a1a5a 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -16,21 +16,18 @@ Erik Bitzek, FAU Erlangen-Nuernberg ------------------------------------------------------------------------- */ -#include #include "min_fire.h" -#include "universe.h" + #include "atom.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "variable.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "neighbor.h" -#include "comm.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index ca63b85328..d4ddcc7fc0 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "ntopo.h" -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 71521e6891..21ac894d92 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c72073718e..583339ed11 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index d6303a0ad4..17e17ca462 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 9fac01bdba..20ec5aa290 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 138f8f4330..9b5914b2c8 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index a651715320..88a31460d9 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 81193605c1..bcfe8ce712 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 855fa800b6..31a78c5c48 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 06fac50400..0d2a9451e0 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index e839e9161b..53f229a86a 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index c4c6ec3177..8fc619c9e4 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 060ba173fd..bd19d5877c 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/output.cpp b/src/output.cpp index 16d2fa54a0..9b091f89a2 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -12,27 +12,25 @@ ------------------------------------------------------------------------- */ #include "output.h" -#include -#include -#include #include "style_dump.h" + #include "atom.h" -#include "neighbor.h" -#include "input.h" -#include "variable.h" #include "comm.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "thermo.h" -#include "modify.h" -#include "force.h" #include "dump.h" -#include "write_restart.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "thermo.h" +#include "update.h" +#include "variable.h" +#include "write_restart.h" + +#include using namespace LAMMPS_NS; diff --git a/src/output.h b/src/output.h index 1bf4128ee0..06be7b244a 100644 --- a/src/output.h +++ b/src/output.h @@ -15,11 +15,13 @@ #define LMP_OUTPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { +class Dump; + class Output : protected Pointers { public: bigint next; // next timestep for any kind of output @@ -39,7 +41,7 @@ class Output : protected Pointers { bigint *last_dump; // last timestep each snapshot was output char **var_dump; // variable name for dump frequency int *ivar_dump; // variable index for dump frequency - class Dump **dump; // list of defined Dumps + Dump **dump; // list of defined Dumps int restart_flag; // 1 if any restart files are written int restart_flag_single; // 1 if single restart files are written diff --git a/src/pair.cpp b/src/pair.cpp index e003ef740a..d869bbe8d8 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,28 +16,26 @@ ------------------------------------------------------------------------- */ #include "pair.h" -#include + +#include "atom.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "kspace.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" +#include "suffix.h" +#include "update.h" + #include // IWYU pragma: keep #include // IWYU pragma: keep #include #include #include -#include -#include "atom.h" -#include "neighbor.h" -#include "domain.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "compute.h" -#include "suffix.h" -#include "atom_masks.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" -#include "update.h" -#include "utils.h" -#include "fmt/format.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index f98b84417a..e538275b3c 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -17,22 +17,21 @@ #include "pair_coul_streitz.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" - - +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index e85973ed6a..34c4cfe418 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid_overlay.h" -#include -#include + #include "atom.h" -#include "force.h" #include "error.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index b34e0b2b82..976bb1ba33 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -17,13 +17,12 @@ #include "pair_zero.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" +#include using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 62658a9ac5..a71d7944d6 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -15,17 +15,13 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" #include "potential_file_reader.h" -#include "update.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "comm.h" +#include "error.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 9094d3957a..57aa827638 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -18,14 +18,13 @@ #ifndef LMP_POTENTIAL_FILE_READER_H #define LMP_POTENTIAL_FILE_READER_H -#include - #include "pointers.h" #include "tokenizer.h" -#include "text_file_reader.h" namespace LAMMPS_NS { + class TextFileReader; + class PotentialFileReader : protected Pointers { protected: TextFileReader *reader; diff --git a/src/procmap.cpp b/src/procmap.cpp index 1741e351fe..f80af9330e 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,18 +16,18 @@ ------------------------------------------------------------------------- */ #include "procmap.h" -#include + +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "math_extra.h" +#include "memory.h" +#include "universe.h" + #include #include #include -#include #include -#include "universe.h" -#include "comm.h" -#include "domain.h" -#include "math_extra.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 2cc70a2de9..03c99560b3 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "rcb.h" -#include -#include + #include "irregular.h" #include "memory.h" +#include + using namespace LAMMPS_NS; #define MYHUGE 1.0e30 diff --git a/src/read_data.cpp b/src/read_data.cpp index 7224ac89ea..7cdb768dd2 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -16,34 +16,33 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_data.h" -#include -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "molecule.h" -#include "group.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "domain.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" -#include "special.h" #include "irregular.h" -#include "error.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "molecule.h" +#include "pair.h" +#include "special.h" +#include "update.h" + +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/read_dump.cpp b/src/read_dump.cpp index fbafb4ca84..eb58d3e3ff 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -20,22 +20,19 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_dump.h" -#include -#include -#include -#include "reader.h" -#include "style_reader.h" + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "force.h" -#include "irregular.h" +#include "domain.h" #include "error.h" +#include "irregular.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "reader.h" +#include "style_reader.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 157992bce3..dcab9f834c 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -12,31 +12,30 @@ ------------------------------------------------------------------------- */ #include "read_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "comm.h" -#include "irregular.h" -#include "update.h" -#include "modify.h" -#include "fix_read_restart.h" -#include "group.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_read_restart.h" +#include "force.h" +#include "group.h" #include "improper.h" +#include "irregular.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "pair.h" #include "special.h" #include "universe.h" -#include "mpiio.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #include "lmprestart.h" diff --git a/src/reader.cpp b/src/reader.cpp index 2a6e4bf90c..8230fa3ed3 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "reader.h" -#include + #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 9b93c78000..8ebab4b349 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -12,13 +12,17 @@ ------------------------------------------------------------------------- */ #include "reader_native.h" + +#include "atom.h" +#include "error.h" +#include "memory.h" +#include "tokenizer.h" +#include "utils.h" + #include #include -#include "atom.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/reader_native.h b/src/reader_native.h index 6456dc275a..d1c8433016 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -23,9 +23,8 @@ ReaderStyle(native,ReaderNative) #define LMP_READER_NATIVE_H #include "reader.h" -#include + #include -#include namespace LAMMPS_NS { diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index 525db24961..917aea7d49 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -15,14 +15,11 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "error.h" #include "table_file_reader.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "error.h" +#include "text_file_reader.h" +#include "tokenizer.h" using namespace LAMMPS_NS; From 9925122cea69079293b3bb5789f9c6fdabdc452c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:22:09 -0400 Subject: [PATCH 50/72] more IWYU updates --- src/tokenizer.cpp | 4 +++- src/universe.cpp | 12 +++++------- src/update.cpp | 8 ++++---- src/update.h | 2 +- src/utils.cpp | 12 ++++++------ src/variable.cpp | 45 ++++++++++++++++++++----------------------- src/variable.h | 1 - src/velocity.cpp | 28 +++++++++++++-------------- src/verlet.cpp | 24 +++++++++++------------ src/write_coeff.cpp | 25 ++++++++++++------------ src/write_data.h | 1 - src/write_dump.cpp | 11 ++++++----- src/write_restart.cpp | 40 ++++++++++++++++++-------------------- src/write_restart.h | 1 - 14 files changed, 103 insertions(+), 111 deletions(-) diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index eadff698cb..33a81db748 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -17,7 +17,9 @@ #include "tokenizer.h" #include "utils.h" -#include +#include +#include + #include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index e920270c1e..acb5100337 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -12,16 +12,14 @@ ------------------------------------------------------------------------- */ #include "universe.h" -#include -#include -#include -#include -#include "version.h" + #include "error.h" #include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "version.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/update.cpp b/src/update.cpp index a1c712c354..399584473c 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -15,8 +15,8 @@ #include #include "integrate.h" #include "min.h" -#include "style_integrate.h" -#include "style_minimize.h" +#include "style_integrate.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep #include "neighbor.h" #include "force.h" #include "modify.h" @@ -61,7 +61,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define INTEGRATE_CLASS #define IntegrateStyle(key,Class) \ (*integrate_map)[#key] = &integrate_creator; -#include "style_integrate.h" +#include "style_integrate.h" // IWYU pragma: keep #undef IntegrateStyle #undef INTEGRATE_CLASS @@ -70,7 +70,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define MINIMIZE_CLASS #define MinimizeStyle(key,Class) \ (*minimize_map)[#key] = &minimize_creator; -#include "style_minimize.h" +#include "style_minimize.h" // IWYU pragma: keep #undef MinimizeStyle #undef MINIMIZE_CLASS diff --git a/src/update.h b/src/update.h index e70325a498..558719f4cc 100644 --- a/src/update.h +++ b/src/update.h @@ -15,8 +15,8 @@ #define LMP_UPDATE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/utils.cpp b/src/utils.cpp index 45bd629c19..c3a6d1e480 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,20 +12,20 @@ ------------------------------------------------------------------------- */ #include "utils.h" -#include -#include -#include -#include "lammps.h" + #include "comm.h" #include "compute.h" #include "error.h" #include "fix.h" #include "memory.h" #include "modify.h" -#include "tokenizer.h" #include "text_file_reader.h" +#include "tokenizer.h" #include "update.h" -#include "fmt/format.h" + +#include +#include +#include #if defined(__linux__) #include // for readlink diff --git a/src/variable.cpp b/src/variable.cpp index d16987984f..8d4416dfa7 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -12,36 +12,33 @@ ------------------------------------------------------------------------- */ #include "variable.h" -#include -#include -#include -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "group.h" -#include "domain.h" #include "comm.h" -#include "region.h" -#include "modify.h" #include "compute.h" -#include "input.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "force.h" -#include "output.h" -#include "thermo.h" -#include "random_mars.h" -#include "math_const.h" -#include "lmppython.h" -#include "memory.h" +#include "group.h" #include "info.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "input.h" +#include "lmppython.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "output.h" +#include "random_mars.h" +#include "region.h" +#include "thermo.h" +#include "universe.h" +#include "update.h" + +#include +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/variable.h b/src/variable.h index f5ea11c0b4..efffacc7bb 100644 --- a/src/variable.h +++ b/src/variable.h @@ -15,7 +15,6 @@ #define LMP_VARIABLE_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 140a396926..eafa98cb7c 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "velocity.h" -#include -#include + #include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" -#include "force.h" -#include "modify.h" -#include "fix.h" +#include "comm.h" #include "compute.h" #include "compute_temp.h" -#include "random_park.h" -#include "group.h" -#include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" +#include "fix.h" +#include "group.h" +#include "input.h" +#include "lattice.h" +#include "memory.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/verlet.cpp b/src/verlet.cpp index 97c5f918b5..a7b9ba4c22 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -12,26 +12,26 @@ ------------------------------------------------------------------------- */ #include "verlet.h" -#include -#include -#include "neighbor.h" -#include "domain.h" -#include "comm.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "timer.h" -#include "error.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 612f5bb123..121a2ed1fd 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -12,22 +12,21 @@ ------------------------------------------------------------------------- */ #include "write_coeff.h" -#include -#include -#include -#include -#include "pair.h" -#include "bond.h" + #include "angle.h" -#include "dihedral.h" -#include "improper.h" +#include "bond.h" #include "comm.h" -#include "force.h" -#include "universe.h" -#include "error.h" +#include "dihedral.h" #include "domain.h" -#include "utils.h" -#include "fmt/format.h" +#include "error.h" +#include "force.h" +#include "improper.h" +#include "pair.h" +#include "universe.h" + +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/write_data.h b/src/write_data.h index e94e7f5595..a4e71c9cda 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -21,7 +21,6 @@ CommandStyle(write_data,WriteData) #define LMP_WRITE_DATA_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 9b257b9ab0..56839a2f5e 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "write_dump.h" -#include -#include #include "style_dump.h" + +#include "comm.h" #include "dump.h" #include "dump_image.h" -#include "comm.h" -#include "update.h" #include "error.h" -#include "utils.h" +#include "update.h" + +#include + using namespace LAMMPS_NS; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 22e993c37c..256d7a377e 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "write_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "update.h" -#include "neighbor.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "universe.h" #include "comm.h" -#include "output.h" -#include "thermo.h" -#include "mpiio.h" -#include "memory.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "thermo.h" +#include "universe.h" +#include "update.h" + +#include #include "lmprestart.h" diff --git a/src/write_restart.h b/src/write_restart.h index 5056f50636..a4a606482e 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -21,7 +21,6 @@ CommandStyle(write_restart,WriteRestart) #define LMP_WRITE_RESTART_H #include "pointers.h" -#include namespace LAMMPS_NS { From baa79bd1c453a90d1e958cc04105e5782b1fca24 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:22:28 -0400 Subject: [PATCH 51/72] add another iwyu-mapping entry --- cmake/CMakeLists.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f541ad7025..87c70e4483 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -267,6 +267,8 @@ if(ENABLE_IWYU) file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp " { include: [ \"\", private, \"\", public ] },\n") + file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + " { include: [ \"\", public, \"\", public ] },\n") file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" From c2cf19bdd49e57398b41b5e9fa5e780b25c69d3d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:32:57 -0400 Subject: [PATCH 52/72] fixes for file readers --- src/MANYBODY/pair_airebo.cpp | 20 ++++++++++---------- src/MANYBODY/pair_bop.cpp | 20 ++++++++++---------- src/MANYBODY/pair_comb3.cpp | 19 +++++++++---------- src/MANYBODY/pair_sw.cpp | 12 ++++++------ src/MANYBODY/pair_tersoff.cpp | 23 +++++++++++------------ 5 files changed, 46 insertions(+), 48 deletions(-) diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 50b5b7d953..7ab2eaa27b 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -21,23 +21,23 @@ ------------------------------------------------------------------------- */ #include "pair_airebo.h" -#include -#include #include "atom.h" -#include "neighbor.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "my_page.h" +#include "error.h" +#include "force.h" #include "math_special.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 28389cb59f..cf7268ab62 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -33,22 +33,22 @@ ------------------------------------------------------------------------- */ #include "pair_bop.h" -#include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index eea2fca927..265d30c6f7 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -19,24 +19,23 @@ #include "pair_comb3.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "my_page.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "group.h" #include "math_const.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index da6f7c1623..4e010d816c 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -17,20 +17,20 @@ #include "pair_sw.h" -#include - -#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" - -#include "tokenizer.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 95212b23ab..a654922182 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -17,23 +17,22 @@ #include "pair_tersoff.h" -#include - -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" -#include "potential_file_reader.h" - +#include "force.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "potential_file_reader.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; From c7c4297cfc45ececef10a927ad04c29f0e23c582 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 00:51:58 -0400 Subject: [PATCH 53/72] update include handling for commands --- src/neighbor.cpp | 49 +++++++++++++++++---------------- src/read_data.cpp | 1 - src/reader_native.cpp | 2 -- src/reader_xyz.cpp | 5 ++-- src/region.cpp | 17 ++++++------ src/region_block.cpp | 7 ++--- src/region_cone.cpp | 7 ++--- src/region_cylinder.cpp | 13 ++++----- src/region_intersect.cpp | 5 ++-- src/region_plane.cpp | 5 ++-- src/region_prism.cpp | 7 ++--- src/region_sphere.cpp | 11 ++++---- src/region_union.cpp | 5 ++-- src/replicate.cpp | 16 +++++------ src/rerun.cpp | 13 ++++----- src/reset_atom_ids.cpp | 18 ++++++------- src/reset_mol_ids.cpp | 12 ++++----- src/respa.cpp | 31 +++++++++++---------- src/run.cpp | 13 ++++----- src/set.cpp | 34 +++++++++++------------ src/special.cpp | 16 +++++------ src/table_file_reader.cpp | 1 - src/text_file_reader.cpp | 9 +++---- src/text_file_reader.h | 2 +- src/thermo.cpp | 57 +++++++++++++++++++-------------------- src/write_data.cpp | 34 +++++++++++------------ 26 files changed, 191 insertions(+), 199 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index c9b16f67a0..66ab92496a 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -16,38 +16,37 @@ ------------------------------------------------------------------------- */ #include "neighbor.h" -#include -#include -#include -#include "neigh_list.h" -#include "neigh_request.h" -#include "nbin.h" -#include "nstencil.h" -#include "npair.h" -#include "ntopo.h" -#include "style_nbin.h" -#include "style_nstencil.h" -#include "style_npair.h" -#include "style_ntopo.h" + #include "atom.h" #include "atom_vec.h" +#include "citeme.h" #include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix.h" #include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "nbin.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "npair.h" +#include "nstencil.h" +#include "ntopo.h" +#include "output.h" #include "pair.h" #include "pair_hybrid.h" -#include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" -#include "update.h" #include "respa.h" -#include "output.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "style_nbin.h" +#include "style_npair.h" +#include "style_nstencil.h" +#include "style_ntopo.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/read_data.cpp b/src/read_data.cpp index 7cdb768dd2..2a6801b3a5 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -40,7 +40,6 @@ #include "special.h" #include "update.h" -#include #include #include diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 8ebab4b349..8931c569ff 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -17,10 +17,8 @@ #include "error.h" #include "memory.h" #include "tokenizer.h" -#include "utils.h" #include -#include #include #include diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index ad8cb0cc6e..5350e01117 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "reader_xyz.h" -#include + #include "memory.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region.cpp b/src/region.cpp index 8a6ec3305a..15b6fee272 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "region.h" + +#include "domain.h" +#include "error.h" +#include "input.h" +#include "lattice.h" +#include "math_extra.h" +#include "update.h" +#include "variable.h" + #include #include -#include "update.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" -#include "math_extra.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/region_block.cpp b/src/region_block.cpp index e06c05d1a7..2204f2e6a4 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "region_block.h" -#include -#include "force.h" + #include "domain.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 400fb07229..d669008e93 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_cone.h" -#include -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index dc1584a96b..f7676a3d74 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "region_cylinder.h" + +#include "domain.h" +#include "error.h" +#include "input.h" +#include "update.h" +#include "variable.h" + #include #include -#include "update.h" -#include "domain.h" -#include "input.h" -#include "variable.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 4096657d30..a61e2556b0 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_intersect.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_plane.cpp b/src/region_plane.cpp index bf12f3cd91..4895c1f081 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_plane.h" -#include + #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 5d7c5bce1f..af270cc47f 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_prism.h" -#include + #include "domain.h" -#include "force.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 44db951fde..4256af4213 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "region_sphere.h" + +#include "error.h" +#include "input.h" +#include "update.h" +#include "variable.h" + #include #include -#include "update.h" -#include "input.h" -#include "variable.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/region_union.cpp b/src/region_union.cpp index 30f563df2c..677f1022f9 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_union.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/replicate.cpp b/src/replicate.cpp index 9c915d08c0..374d7113b2 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "replicate.h" -#include -#include + +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "domain.h" #include "comm.h" -#include "special.h" -#include "accelerator_kokkos.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "memory.h" +#include "special.h" + +#include using namespace LAMMPS_NS; diff --git a/src/rerun.cpp b/src/rerun.cpp index a63fd1ea55..51c0f6fdb2 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "rerun.h" -#include -#include "read_dump.h" + #include "domain.h" -#include "update.h" +#include "error.h" +#include "finish.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" +#include "read_dump.h" #include "timer.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 526de60cba..0b7cf9879f 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ #include "reset_atom_ids.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" -#include "fix.h" -#include "special.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "special.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index a6cfb69185..0d9fe55e07 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -16,17 +16,15 @@ ------------------------------------------------------------------------- */ #include "reset_mol_ids.h" -#include + #include "atom.h" -#include "domain.h" #include "comm.h" +#include "compute_chunk_atom.h" +#include "compute_fragment_atom.h" +#include "domain.h" +#include "error.h" #include "group.h" #include "modify.h" -#include "compute_fragment_atom.h" -#include "compute_chunk_atom.h" -#include "utils.h" -#include "error.h" -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/respa.cpp b/src/respa.cpp index 1dcc4b898a..c970c63a19 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -16,30 +16,29 @@ ------------------------------------------------------------------------- */ #include "respa.h" -#include -#include -#include "neighbor.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "comm.h" -#include "fix.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "fix_respa.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" -#include "fix_respa.h" -#include "timer.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "pair_hybrid.h" -#include "fmt/format.h" +#include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/run.cpp b/src/run.cpp index 91e2db5c6b..166955d6ac 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "run.h" -#include + #include "domain.h" -#include "update.h" -#include "force.h" +#include "error.h" +#include "finish.h" +#include "input.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" -#include "input.h" #include "timer.h" -#include "error.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/set.cpp b/src/set.cpp index b4a82e5c72..3b2cd44ad0 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "set.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "domain.h" -#include "region.h" -#include "group.h" #include "comm.h" -#include "force.h" -#include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" -#include "math_const.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" #include "modify.h" -#include "utils.h" -#include "fmt/format.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/special.cpp b/src/special.cpp index 3780fab5c0..eb74f534f7 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -12,18 +12,16 @@ ------------------------------------------------------------------------- */ #include "special.h" -#include -#include "atom.h" -#include "atom_vec.h" -#include "force.h" -#include "comm.h" -#include "modify.h" -#include "fix.h" + #include "accelerator_kokkos.h" // IWYU pragma: export +#include "atom.h" #include "atom_masks.h" +#include "atom_vec.h" +#include "comm.h" +#include "fix.h" +#include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index 917aea7d49..50843c119e 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -17,7 +17,6 @@ #include "table_file_reader.h" -#include "error.h" #include "text_file_reader.h" #include "tokenizer.h" diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 1e1e5e2ec1..3c63bba5fb 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -15,14 +15,11 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" -#include "utils.h" #include "text_file_reader.h" -#include "tokenizer.h" + #include "fmt/format.h" +#include "tokenizer.h" +#include "utils.h" #include diff --git a/src/text_file_reader.h b/src/text_file_reader.h index b64407701f..e74a285961 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -19,8 +19,8 @@ #define LMP_TEXT_FILE_READER_H #include -#include #include + #include "tokenizer.h" namespace LAMMPS_NS diff --git a/src/thermo.cpp b/src/thermo.cpp index 96de72b4ab..787b0cdda8 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -16,37 +16,36 @@ // before lmptype.h can set flags to insure it is done correctly #include "thermo.h" -#include + +#include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" +#include "compute.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "input.h" +#include "kspace.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "timer.h" +#include "tokenizer.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + #include #include -#include "atom.h" -#include "update.h" -#include "comm.h" -#include "domain.h" -#include "universe.h" -#include "lattice.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "output.h" -#include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" -#include "fmt/format.h" -#include "tokenizer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/write_data.cpp b/src/write_data.cpp index d549d8bf77..53d277b723 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -12,29 +12,27 @@ ------------------------------------------------------------------------- */ #include "write_data.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "update.h" -#include "modify.h" -#include "fix.h" -#include "domain.h" -#include "universe.h" #include "comm.h" -#include "output.h" -#include "thermo.h" -#include "memory.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "fix.h" +#include "force.h" +#include "improper.h" +#include "memory.h" +#include "modify.h" +#include "output.h" +#include "pair.h" +#include "thermo.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; From 55704368d0f0ccc785579b574707cfd1d9c6a57e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 01:45:05 -0400 Subject: [PATCH 54/72] include updates for commonly used packages --- src/BODY/body_nparticle.cpp | 15 +++++------ src/BODY/body_rounded_polygon.cpp | 14 +++++----- src/BODY/body_rounded_polyhedron.cpp | 15 +++++------ src/BODY/compute_body_local.cpp | 8 +++--- src/COLLOID/fix_wall_colloid.cpp | 1 - src/COMPRESS/dump_atom_zstd.cpp | 4 +-- src/COMPRESS/dump_cfg_zstd.cpp | 6 ++--- src/COMPRESS/dump_custom_zstd.cpp | 4 +-- src/COMPRESS/dump_xyz_zstd.cpp | 3 +-- src/DIPOLE/atom_vec_dipole.cpp | 11 +++----- src/KSPACE/ewald.cpp | 14 +++++----- src/KSPACE/ewald_dipole.cpp | 16 +++++------- src/KSPACE/ewald_dipole_spin.cpp | 16 +++++------- src/KSPACE/ewald_disp.cpp | 22 ++++++++-------- src/KSPACE/fft3d_wrap.cpp | 2 +- src/KSPACE/fix_tune_kspace.cpp | 20 +++++++-------- src/KSPACE/gridcomm.cpp | 8 +++--- src/KSPACE/msm.cpp | 20 +++++++-------- src/KSPACE/pppm.cpp | 35 ++++++++++++------------- src/KSPACE/pppm_cg.cpp | 16 +++++------- src/KSPACE/pppm_dipole_spin.cpp | 19 ++++++-------- src/KSPACE/pppm_disp.cpp | 32 +++++++++++------------ src/KSPACE/remap_wrap.cpp | 2 +- src/MANYBODY/pair_bop.cpp | 1 - src/MANYBODY/pair_eam_alloy.cpp | 9 +++---- src/MANYBODY/pair_eam_fs.cpp | 9 +++---- src/MANYBODY/pair_eim.cpp | 20 +++++++-------- src/MANYBODY/pair_gw_zbl.cpp | 19 ++++++-------- src/MANYBODY/pair_sw.cpp | 1 - src/MANYBODY/pair_tersoff.cpp | 1 - src/MANYBODY/pair_tersoff_mod.cpp | 13 ++++------ src/MANYBODY/pair_tersoff_mod_c.cpp | 13 ++++------ src/MANYBODY/pair_tersoff_zbl.cpp | 15 +++++------ src/MC/fix_widom.cpp | 38 +++++++++++++--------------- src/MC/pair_dsmc.cpp | 10 +++----- src/MISC/fix_deposit.cpp | 25 +++++++++--------- src/MISC/fix_oneway.cpp | 5 ++-- src/MISC/fix_orient_bcc.cpp | 24 ++++++++---------- src/MISC/fix_viscosity.cpp | 8 +++--- src/MLIAP/mliap_data.cpp | 21 +++++---------- src/MLIAP/mliap_descriptor.cpp | 5 ---- src/reader_native.cpp | 1 - 42 files changed, 234 insertions(+), 307 deletions(-) diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index a99c025e1f..e63d50f814 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -12,16 +12,15 @@ ------------------------------------------------------------------------- */ #include "body_nparticle.h" -#include -#include -#include "my_pool_chunk.h" -#include "math_extra.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" -#include "memory.h" +#include "atom_vec_body.h" #include "error.h" -#include "fmt/format.h" +#include "math_extra.h" +#include "memory.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 349ad957c2..c43484dca2 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polygon.h" -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" #include "domain.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index cb84517b6f..18fd65c1dd 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polyhedron.h" -#include -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 861ffbe4a7..cf570d71a3 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -13,14 +13,14 @@ #include "compute_body_local.h" -#include #include "atom.h" #include "atom_vec_body.h" #include "body.h" -#include "update.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 61b52a6585..ef5bfb72e1 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -19,7 +19,6 @@ #include #include "atom.h" -#include "atom_vec.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index a993f58809..8fb08db3c8 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -17,12 +17,12 @@ #ifdef LAMMPS_ZSTD -#include "dump_atom_zstd.h" #include "domain.h" +#include "dump_atom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 51819772f6..5948a3f83e 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #ifdef LAMMPS_ZSTD -#include "dump_cfg_zstd.h" + #include "atom.h" #include "domain.h" +#include "dump_cfg_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index d0f5335813..c7ede3b38c 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -17,12 +17,12 @@ #ifdef LAMMPS_ZSTD -#include "dump_custom_zstd.h" #include "domain.h" +#include "dump_custom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 839e743654..eb0600f34b 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -19,12 +19,11 @@ #include "dump_xyz_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) : diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 66de360f6e..4193b5c6a8 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_dipole.h" -#include -#include "atom.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" -#include "error.h" +#include "atom.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 4aa95318db..6133df398f 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -19,19 +19,17 @@ ------------------------------------------------------------------------- */ #include "ewald.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 1921b8dc55..33d21b416e 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index bdbb737de8..94cacd3a75 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -16,21 +16,19 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole_spin.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index b616b2ae5d..546ac472c9 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -16,23 +16,21 @@ ------------------------------------------------------------------------- */ #include "ewald_disp.h" -#include -#include -#include -#include -#include "math_vector.h" -#include "math_const.h" -#include "math_special.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_special.h" +#include "math_vector.h" +#include "memory.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index 507b23d27d..d0e3a2b50c 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fft3d_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 3288f15ff7..c205f9de05 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -16,24 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_tune_kspace.h" -#include -#include -#include #include "comm.h" -#include "update.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "info.h" #include "kspace.h" -#include "pair.h" -#include "error.h" -#include "memory.h" -#include "timer.h" -#include "neighbor.h" #include "modify.h" -#include "compute.h" - +#include "neighbor.h" +#include "pair.h" +#include "timer.h" +#include "update.h" +#include +#include +#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index 4024670b9f..0f899d31cf 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "gridcomm.h" -#include + #include "comm.h" -#include "kspace.h" -#include "irregular.h" -#include "memory.h" #include "error.h" +#include "irregular.h" +#include "kspace.h" +#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 00bdac53db..d0f4d38686 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "msm.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" - +#include "force.h" +#include "gridcomm.h" #include "math_const.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 9ce8ded7dd..41ffec4f3b 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -19,28 +19,25 @@ ------------------------------------------------------------------------- */ #include "pppm.h" -#include -#include -#include -#include -#include "atom.h" -#include "comm.h" -#include "gridcomm.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" +#include "gridcomm.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" +#include "remap_wrap.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index fa5235d6eb..b319014c78 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "pppm_cg.h" -#include -#include -#include + #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "neighbor.h" -#include "memory.h" +#include "gridcomm.h" #include "math_const.h" +#include "memory.h" +#include "neighbor.h" #include "remap.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 4e33c11793..595c257331 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -16,22 +16,19 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole_spin.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" -#include "update.h" -#include "utils.h" -#include "fmt/format.h" - +#include "force.h" +#include "gridcomm.h" #include "math_const.h" +#include "memory.h" +#include "pair.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index fba3f27938..a484751a81 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -17,26 +17,24 @@ ------------------------------------------------------------------------- */ #include "pppm_disp.h" -#include -#include -#include -#include -#include "math_const.h" -#include "atom.h" -#include "comm.h" -#include "gridcomm.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" + #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" #include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "fft3d_wrap.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" +#include "remap_wrap.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 7929cd053c..4aaaa1329e 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "remap_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index cf7268ab62..e7c2f64672 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -46,7 +46,6 @@ #include "text_file_reader.h" #include "tokenizer.h" -#include #include #include diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 193134c24c..d30f46aa36 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -17,15 +17,14 @@ #include "pair_eam_alloy.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 78d7f4646d..dd45d12da3 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -17,15 +17,14 @@ #include "pair_eam_fs.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index a17947b7fe..cb5a95faa2 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -17,19 +17,17 @@ #include "pair_eim.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "tokenizer.h" + #include #include -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "tokenizer.h" -#include "potential_file_reader.h" - using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index dc33ab20a9..ee3bebda13 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -18,20 +18,17 @@ #include "pair_gw_zbl.h" -#include - -#include -#include "atom.h" -#include "update.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" -#include "potential_file_reader.h" - #include "math_const.h" +#include "memory.h" +#include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 4e010d816c..2deb45ac75 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -26,7 +26,6 @@ #include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" -#include "text_file_reader.h" #include "tokenizer.h" #include diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index a654922182..c08c722e5f 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -28,7 +28,6 @@ #include "neigh_request.h" #include "neighbor.h" #include "potential_file_reader.h" -#include "text_file_reader.h" #include "tokenizer.h" #include diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index b02545fb2b..ea40125ce4 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -18,19 +18,16 @@ #include "pair_tersoff_mod.h" -#include - -#include -#include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" - -#include "tokenizer.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 325e9ac677..6a6497afae 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -17,17 +17,14 @@ #include "pair_tersoff_mod_c.h" -#include - -#include -#include "atom.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 4c967b4ebb..fad89195b2 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -18,20 +18,17 @@ #include "pair_tersoff_zbl.h" -#include - -#include -#include "atom.h" -#include "update.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" #include "math_const.h" #include "math_special.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index a87ead64a7..d7fdf69b86 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -15,38 +15,36 @@ Contributing author: Evangelos Voyiatzis (Royal DSM) ------------------------------------------------------------------------- */ -#include - -#include #include "fix_widom.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" -#include "domain.h" -#include "region.h" -#include "random_park.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "thermo.h" -#include "output.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" -#include +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace std; using namespace LAMMPS_NS; diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index c00f5dcbff..588d57f324 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -17,18 +17,16 @@ #include "pair_dsmc.h" -#include -#include #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "domain.h" -#include "update.h" #include "random_mars.h" +#include "update.h" - +#include using namespace LAMMPS_NS; diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 32e836f31d..7ee6fce1b9 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -13,25 +13,24 @@ #include "fix_deposit.h" -#include -#include #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "domain.h" -#include "lattice.h" -#include "region.h" -#include "random_park.h" -#include "math_extra.h" -#include "math_const.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "lattice.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" +#include "random_park.h" +#include "region.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index d2bef7cb9b..1ca24a5906 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_oneway.h" -#include + #include "atom.h" #include "domain.h" #include "error.h" -#include "force.h" #include "region.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index ab9a921d3e..cc22a509ba 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -19,25 +19,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_bcc.h" -#include -#include - - #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "force.h" -#include "math_const.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" - +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 9c021c5ca8..5dcd2d291d 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -18,13 +18,13 @@ #include "fix_viscosity.h" -#include -#include #include "atom.h" #include "domain.h" -#include "modify.h" #include "error.h" -#include "force.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MLIAP/mliap_data.cpp b/src/MLIAP/mliap_data.cpp index 7bffd8ec3b..28f9a988d8 100644 --- a/src/MLIAP/mliap_data.cpp +++ b/src/MLIAP/mliap_data.cpp @@ -11,24 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "mliap_data.h" -#include "mliap_model_linear.h" -#include "mliap_model_quadratic.h" -#include "mliap_descriptor_snap.h" -#include "compute_mliap.h" + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" #include "memory.h" -#include "error.h" +#include "mliap_descriptor.h" +#include "mliap_model.h" +#include "neigh_list.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_descriptor.cpp b/src/MLIAP/mliap_descriptor.cpp index d654b33008..63d4241e01 100644 --- a/src/MLIAP/mliap_descriptor.cpp +++ b/src/MLIAP/mliap_descriptor.cpp @@ -12,14 +12,9 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor.h" -#include "atom.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -#define MAXLINE 1024 -#define MAXWORD 3 /* ---------------------------------------------------------------------- */ diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 8931c569ff..19e53f3efe 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -20,7 +20,6 @@ #include #include -#include using namespace LAMMPS_NS; From 88ddfa4eb05d20786204c58a5ce43228881046b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 04:39:23 -0400 Subject: [PATCH 55/72] more IWYU cleanup in packages --- src/KIM/kim_init.cpp | 23 ++-- src/KIM/kim_interactions.cpp | 19 ++-- src/KIM/kim_param.cpp | 15 ++- src/KIM/kim_property.cpp | 15 +-- src/KIM/kim_query.cpp | 14 +-- src/KIM/kim_units.cpp | 2 + src/KIM/pair_kim.h | 1 - src/MLIAP/mliap_descriptor_snap.cpp | 19 ++-- src/MLIAP/mliap_model.cpp | 12 +- src/MLIAP/mliap_model_linear.h | 2 +- src/MLIAP/pair_mliap.cpp | 18 +-- src/MOLECULE/atom_vec_template.cpp | 11 +- src/MPIIO/dump_cfg_mpiio.cpp | 5 +- src/MPIIO/restart_mpiio.cpp | 3 +- src/PERI/atom_vec_peri.cpp | 7 +- src/PERI/pair_peri_eps.cpp | 28 +++-- src/PERI/pair_peri_lps.cpp | 23 ++-- src/PERI/pair_peri_pmb.cpp | 27 ++--- src/PERI/pair_peri_ves.cpp | 23 ++-- src/PYTHON/fix_python_invoke.cpp | 9 +- src/PYTHON/fix_python_move.cpp | 8 +- src/PYTHON/pair_python.cpp | 19 ++-- src/PYTHON/python_compat.h | 2 + src/PYTHON/python_impl.cpp | 16 +-- src/REPLICA/compute_event_displace.cpp | 8 +- src/REPLICA/fix_event_hyper.cpp | 1 + src/REPLICA/fix_neb.cpp | 25 ++-- src/REPLICA/hyper.cpp | 35 +++--- src/REPLICA/neb.cpp | 28 +++-- src/REPLICA/prd.cpp | 43 ++++--- src/REPLICA/tad.cpp | 32 +++--- src/REPLICA/temper.cpp | 23 ++-- src/USER-CGDNA/bond_oxrna2_fene.cpp | 2 - src/USER-CGDNA/fix_nve_dotc_langevin.cpp | 13 ++- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 23 ++-- src/USER-CGDNA/pair_oxdna2_dh.cpp | 19 ++-- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 23 ++-- src/USER-CGDNA/pair_oxdna_excv.cpp | 21 ++-- src/USER-CGDNA/pair_oxdna_hbond.cpp | 21 ++-- src/USER-CGDNA/pair_oxdna_xstk.cpp | 23 ++-- src/USER-CGDNA/pair_oxrna2_excv.cpp | 4 +- src/USER-CGDNA/pair_oxrna2_stk.cpp | 28 ++--- src/USER-CGDNA/pair_oxrna2_xstk.cpp | 23 ++-- src/USER-CGSDK/pair_lj_sdk.h | 1 - src/USER-MEAMC/meam_dens_init.cpp | 6 +- src/USER-MEAMC/meam_force.cpp | 7 +- src/USER-MEAMC/meam_funcs.cpp | 2 + src/USER-MEAMC/meam_impl.cpp | 4 +- src/USER-MEAMC/meam_setup_done.cpp | 6 +- src/USER-MEAMC/meam_setup_global.cpp | 2 + src/USER-MEAMC/meam_setup_param.cpp | 5 + src/USER-MISC/bond_special.cpp | 18 ++- src/USER-MISC/bond_special.h | 1 - src/USER-MISC/compute_hma.cpp | 33 +++--- src/USER-MISC/compute_viscosity_cos.cpp | 5 +- src/USER-MISC/dihedral_spherical.cpp | 9 +- src/USER-MISC/dihedral_table.cpp | 107 +++++++----------- src/USER-MISC/fix_accelerate_cos.cpp | 8 +- src/USER-MISC/fix_ave_correlate_long.cpp | 19 ++-- src/USER-MISC/fix_electron_stopping.cpp | 21 ++-- src/USER-MISC/fix_flow_gauss.cpp | 10 +- src/USER-MISC/fix_imd.cpp | 7 +- src/USER-MISC/fix_momentum_chunk.cpp | 7 +- src/USER-MISC/fix_orient_eco.cpp | 6 +- src/USER-MISC/fix_pafi.cpp | 85 ++++++-------- src/USER-MISC/fix_propel_self.cpp | 16 +-- src/USER-MISC/fix_rhok.cpp | 11 +- src/USER-MISC/fix_smd.cpp | 10 +- src/USER-MISC/fix_srp.cpp | 20 ++-- src/USER-MISC/fix_ti_spring.cpp | 14 +-- src/USER-MISC/fix_wall_ees.cpp | 5 +- src/USER-MISC/fix_wall_reflect_stochastic.cpp | 10 +- src/USER-MISC/fix_wall_region_ees.cpp | 12 +- src/USER-MISC/pair_agni.cpp | 20 ++-- src/USER-MISC/pair_cosine_squared.cpp | 13 +-- src/USER-MISC/pair_coul_slater_cut.cpp | 13 +-- src/USER-MISC/pair_coul_slater_long.cpp | 16 +-- src/USER-MISC/pair_local_density.cpp | 20 ++-- src/USER-MISC/temper_npt.cpp | 23 ++-- src/USER-SMD/atom_vec_smd.cpp | 5 +- src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 12 +- src/USER-SMD/compute_smd_tlsph_shape.cpp | 12 +- src/USER-SMD/compute_smd_tlsph_strain.cpp | 12 +- .../compute_smd_tlsph_strain_rate.cpp | 12 +- 84 files changed, 610 insertions(+), 731 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 5e3bd934a9..684108be71 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -57,24 +57,19 @@ ------------------------------------------------------------------------- */ #include "kim_init.h" -#include "fix_store_kim.h" -#include "kim_units.h" -#include -#include -#include -#include -#include "error.h" -#include "atom.h" + +#include "citeme.h" #include "comm.h" #include "domain.h" -#include "modify.h" -#include "update.h" -#include "universe.h" +#include "error.h" +#include "fix_store_kim.h" #include "input.h" +#include "kim_units.h" +#include "modify.h" +#include "universe.h" #include "variable.h" -#include "citeme.h" -#include "utils.h" -#include "fmt/format.h" + +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index a91c615d09..5f45dd34dc 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -57,23 +57,18 @@ ------------------------------------------------------------------------- */ #include "kim_interactions.h" -#include -#include -#include -#include -#include -#include "error.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_store_kim.h" +#include "input.h" #include "modify.h" #include "update.h" -#include "universe.h" -#include "input.h" -#include "variable.h" -#include "utils.h" -#include "fix_store_kim.h" -#include "fmt/format.h" + +#include +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index 6df8c075dc..ae4ca9b13d 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -56,19 +56,18 @@ ------------------------------------------------------------------------- */ #include "kim_param.h" -#include "fix_store_kim.h" -#include "pair_kim.h" -#include -#include -#include -#include + #include "comm.h" #include "error.h" +#include "fix_store_kim.h" +#include "force.h" #include "input.h" #include "modify.h" +#include "pair_kim.h" #include "variable.h" -#include "force.h" -#include "fmt/format.h" + +#include +#include extern "C" { diff --git a/src/KIM/kim_property.cpp b/src/KIM/kim_property.cpp index 643e0da47b..95a1274859 100644 --- a/src/KIM/kim_property.cpp +++ b/src/KIM/kim_property.cpp @@ -53,21 +53,18 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ -#if LMP_PYTHON -#define PY_SSIZE_T_CLEAN -#include -#endif - #include "kim_property.h" #include "comm.h" -#include "input.h" -#include "variable.h" -#include "utils.h" #include "error.h" +#include "input.h" #include "lmppython.h" +#include "variable.h" -#include +#if LMP_PYTHON +#define PY_SSIZE_T_CLEAN +#include // IWYU pragma: export +#endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 4a1db9450d..ec13210665 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -56,24 +56,22 @@ ------------------------------------------------------------------------- */ #include "kim_query.h" -#include "fix_store_kim.h" -#include -#include -#include -#include + #include "comm.h" #include "error.h" +#include "fix_store_kim.h" +#include "info.h" #include "input.h" #include "modify.h" #include "variable.h" #include "version.h" -#include "info.h" -#include "fmt/format.h" + +#include +#include #if defined(LMP_KIM_CURL) #include #include -#include #endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index c0c1aee07c..77dbad6f1d 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -57,6 +57,8 @@ #include #include #include +#include + using namespace std; namespace diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 0361f2351e..0c2e8d2684 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -66,7 +66,6 @@ PairStyle(kim,PairKIM) class KIM_API_model; #include "pair.h" - extern "C" { #include "KIM_SimulatorHeaders.h" } diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index fd1bf18330..5f0ee33c8c 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" -#include "mliap_data.h" -#include -#include -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "utils.h" -#include "sna.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" +#include "mliap_data.h" +#include "pair_mliap.h" +#include "sna.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index b8ad1913a0..ac82a671d4 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -12,17 +12,13 @@ ------------------------------------------------------------------------- */ #include "mliap_model.h" -#include "pair_mliap.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "utils.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model_linear.h b/src/MLIAP/mliap_model_linear.h index 67ba0985a2..326407faa8 100644 --- a/src/MLIAP/mliap_model_linear.h +++ b/src/MLIAP/mliap_model_linear.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class MLIAPModelLinear : public MLIAPModel { public: - MLIAPModelLinear(LAMMPS*, char* = NULL); + MLIAPModelLinear(LAMMPS*, char* = nullptr); ~MLIAPModelLinear(); virtual int get_nparams(); virtual int get_gamma_nnz(class MLIAPData*); diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index d74a1820cc..4c6d906787 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -11,22 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_mliap.h" -#include - -#include #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" + #include "atom.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 514250d058..ead8de7cb5 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_template.h" -#include "atom.h" -#include "molecule.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" -#include "error.h" +#include "atom.h" +#include "error.h" +#include "molecule.h" using namespace LAMMPS_NS; diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index e05b7bf317..6d5fc3da8e 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -17,15 +17,16 @@ #include "omp_compat.h" #include "dump_cfg_mpiio.h" -#include -#include #include "atom.h" #include "domain.h" #include "update.h" #include "memory.h" #include "error.h" +#include +#include + #ifdef LMP_USER_IO_TIMER #include #include diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 66c7d8a417..b2caa411e3 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "restart_mpiio.h" -#include -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 5ce74575ba..ada25431c8 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "atom_vec_peri.h" -#include -#include + #include "atom.h" #include "citeme.h" -#include "memory.h" #include "error.h" +#include +#include + using namespace LAMMPS_NS; static const char cite_peri_package[] = diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index b3986e75fa..0e5760ac8d 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -17,24 +17,22 @@ #include "pair_peri_eps.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_peri_neigh.h" +#include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" + #include #include -#include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "force.h" -#include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" - - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 101a6d0bd9..b60f28d9f1 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -17,23 +17,20 @@ #include "pair_peri_lps.h" -#include -#include - #include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "force.h" -#include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" +#include "domain.h" #include "error.h" - +#include "fix_peri_neigh.h" +#include "force.h" +#include "lattice.h" #include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index c5f893dd32..5d6973a915 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -17,23 +17,20 @@ #include "pair_peri_pmb.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_peri_neigh.h" +#include "force.h" +#include "lattice.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" + #include #include -#include - -#include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "force.h" -#include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index dca80cc6fd..93c980702b 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -17,24 +17,21 @@ #include "pair_peri_ves.h" -#include -#include - #include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "force.h" -#include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" +#include "domain.h" #include "error.h" - +#include "fix_peri_neigh.h" +#include "force.h" +#include "lattice.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 767c22c496..8966d9a9db 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_invoke.h" -#include // IWYU pragma: keep -#include -#include "force.h" -#include "update.h" + #include "error.h" #include "lmppython.h" #include "python_compat.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index be63b851a2..53bde5e804 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,12 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_move.h" -#include // IWYU pragma: keep -#include -#include "lmppython.h" + #include "error.h" +#include "lmppython.h" #include "python_compat.h" +#include +#include // IWYU pragma: export + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index c59ba5eb5f..074de2f39a 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,17 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_python.h" -#include // IWYU pragma: keep + +#include "atom.h" +#include "error.h" +#include "force.h" +#include "lmppython.h" +#include "memory.h" +#include "neigh_list.h" +#include "python_compat.h" +#include "update.h" #include -#include "atom.h" -#include "force.h" -#include "memory.h" -#include "update.h" -#include "neigh_list.h" -#include "lmppython.h" -#include "error.h" -#include "python_compat.h" +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/PYTHON/python_compat.h b/src/PYTHON/python_compat.h index 175d797ffa..effac81cef 100644 --- a/src/PYTHON/python_compat.h +++ b/src/PYTHON/python_compat.h @@ -14,6 +14,8 @@ #ifndef LMP_PYTHON_COMPAT_H #define LMP_PYTHON_COMPAT_H +#include + // Wrap API changes between Python 2 and 3 using macros #if PY_MAJOR_VERSION == 2 #define PY_INT_FROM_LONG(X) PyInt_FromLong(X) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index b54abe28b0..cb35cba85a 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) + Contributing authors: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ #include "python_impl.h" -#include -#include -#include // IWYU pragma: keep -#include "force.h" -#include "input.h" -#include "variable.h" -#include "memory.h" + #include "error.h" +#include "input.h" +#include "memory.h" #include "python_compat.h" +#include "variable.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index d7abcb62b8..531f488e60 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -17,15 +17,15 @@ #include "compute_event_displace.h" -#include #include "atom.h" #include "domain.h" -#include "modify.h" -#include "fix_event.h" #include "error.h" -#include "force.h" +#include "fix_event.h" +#include "modify.h" #include "update.h" +#include + using namespace LAMMPS_NS; #define INVOKED_SCALAR 1 diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index ddbe10adc9..ba784cc3e9 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_event_hyper.h" + #include "comm.h" #include "error.h" #include "update.h" diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 76953b6c2c..b2981afa01 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -18,21 +18,20 @@ #include "fix_neb.h" -#include -#include - +#include "atom.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" #include "universe.h" #include "update.h" -#include "atom.h" -#include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "group.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "math_const.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 1e78326fbd..6c4cba4ab8 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -12,28 +12,25 @@ ------------------------------------------------------------------------- */ #include "hyper.h" -#include -#include -#include -#include "update.h" -#include "domain.h" -#include "region.h" -#include "integrate.h" -#include "min.h" -#include "force.h" -#include "neighbor.h" -#include "modify.h" + #include "compute_event_displace.h" -#include "fix_hyper.h" -#include "fix_event_hyper.h" -#include "output.h" +#include "domain.h" #include "dump.h" -#include "finish.h" -#include "timer.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "finish.h" +#include "fix_event_hyper.h" +#include "fix_hyper.h" +#include "integrate.h" +#include "memory.h" +#include "min.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "region.h" +#include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 34b5cf40fe..2d1dd6eea7 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "neb.h" -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb.h" +#include "math_const.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 796cf01681..cdb1eb9b02 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -16,32 +16,29 @@ ------------------------------------------------------------------------- */ #include "prd.h" -#include -#include -#include + +#include "atom.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix_event_prd.h" +#include "integrate.h" +#include "memory.h" +#include "min.h" +#include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "timer.h" #include "universe.h" #include "update.h" -#include "atom.h" -#include "domain.h" -#include "region.h" -#include "comm.h" #include "velocity.h" -#include "integrate.h" -#include "min.h" -#include "neighbor.h" -#include "modify.h" -#include "compute.h" -#include "fix.h" -#include "fix_event_prd.h" -#include "force.h" -#include "random_park.h" -#include "random_mars.h" -#include "output.h" -#include "finish.h" -#include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index fba753d602..db74b63c35 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -16,28 +16,28 @@ ------------------------------------------------------------------------- */ #include "tad.h" -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" -#include "domain.h" -#include "integrate.h" -#include "min.h" -#include "neighbor.h" -#include "modify.h" -#include "neb.h" #include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix_event_tad.h" #include "fix_store.h" #include "force.h" -#include "output.h" -#include "finish.h" -#include "timer.h" +#include "integrate.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "min.h" +#include "modify.h" +#include "neb.h" +#include "neighbor.h" +#include "output.h" +#include "timer.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index a7ad4c068b..0cce389bf0 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -16,22 +16,23 @@ ------------------------------------------------------------------------- */ #include "temper.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix.h" +#include "force.h" #include "integrate.h" #include "modify.h" -#include "compute.h" -#include "force.h" -#include "fix.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp index 152961f290..2dee1224d3 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -14,8 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include - #include "bond_oxrna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index 66871fa64e..17b1fb7b42 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -16,16 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_nve_dotc_langevin.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "random_mars.h" #include "error.h" +#include "math_extra.h" +#include "random_mars.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 60c1c8788f..662d55c590 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna2_coaxstk.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 7d2c8aa2c2..f23ca4fbf7 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -16,18 +16,17 @@ #include "pair_oxdna2_dh.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" + #include #include -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 17ba194030..f1d425a0b3 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna_coaxstk.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 33005046b7..ad96186b6b 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -16,19 +16,18 @@ #include "pair_oxdna_excv.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 88c5dc5e36..7987210d7a 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -16,19 +16,18 @@ #include "pair_oxdna_hbond.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 87de92e0e0..1751499683 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxdna_xstk.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp index ec93ce592e..af9fdaaaa1 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -14,11 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_oxrna2_excv.h" #include -#include "pair_oxrna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index d38ccb86ab..fd02946134 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -14,26 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_oxrna2_stk.h" -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" +#include "atom.h" #include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neighbor.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index f3f65b695e..673ef1c9a3 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -16,20 +16,19 @@ #include "pair_oxrna2_xstk.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + #include #include -#include "mf_oxdna.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -#include "atom_vec_ellipsoid.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/USER-CGSDK/pair_lj_sdk.h index ef0263c06b..11c123a72c 100644 --- a/src/USER-CGSDK/pair_lj_sdk.h +++ b/src/USER-CGSDK/pair_lj_sdk.h @@ -27,7 +27,6 @@ PairStyle(lj/sdk,PairLJSDK) #include "pair.h" namespace LAMMPS_NS { -class LAMMPS; class PairLJSDK : public Pair { public: diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 39e3ff9467..dcaa5866de 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,7 +1,9 @@ #include "meam.h" -#include -#include "memory.h" + #include "math_special.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 2b6832e155..df1f8f9a1d 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,10 +1,11 @@ #include "meam.h" -#include -#include + #include "math_special.h" -using namespace LAMMPS_NS; +#include +#include +using namespace LAMMPS_NS; void MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl, diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 706075ffd0..0a632bc40a 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -16,7 +16,9 @@ ------------------------------------------------------------------------- */ #include "meam.h" + #include "math_special.h" + #include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index 0a0b95e14a..a546aa0c7f 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,9 +16,11 @@ ------------------------------------------------------------------------- */ #include "meam.h" -#include + #include "memory.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 25f1bb9e81..f493d9dcac 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,9 +1,11 @@ #include "meam.h" + +#include "math_special.h" +#include "memory.h" + #include #include #include -#include "math_special.h" -#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 60264b87cb..c5f3115249 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,5 +1,7 @@ #include "meam.h" + #include + using namespace LAMMPS_NS; template diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp index f0e04ff1c0..ea76ee896c 100644 --- a/src/USER-MEAMC/meam_setup_param.cpp +++ b/src/USER-MEAMC/meam_setup_param.cpp @@ -1,5 +1,10 @@ + #include "meam.h" + +#include "math_const.h" #include +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/bond_special.cpp b/src/USER-MISC/bond_special.cpp index a956468497..87671655b1 100644 --- a/src/USER-MISC/bond_special.cpp +++ b/src/USER-MISC/bond_special.cpp @@ -13,19 +13,15 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "bond_special.h" -#include "atom.h" -#include "neighbor.h" -#include "domain.h" -#include "comm.h" -#include "force.h" -#include "pair.h" -#include "memory.h" -#include "error.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.h b/src/USER-MISC/bond_special.h index 389990b1d7..d5e360ca53 100644 --- a/src/USER-MISC/bond_special.h +++ b/src/USER-MISC/bond_special.h @@ -22,7 +22,6 @@ BondStyle(special,BondSpecial) #ifndef LMP_BOND_SPECIAL_H #define LMP_BOND_SPECIAL_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index 02c697a786..f2ccf2694d 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -43,33 +43,30 @@ properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015 https://doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ -#include -#include - #include "compute_hma.h" -#include "atom.h" -#include "update.h" -#include "force.h" -#include "pair.h" -#include "bond.h" + #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" #include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "group.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "kspace.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "modify.h" #include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" -#include - +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/USER-MISC/compute_viscosity_cos.cpp index 12e1991d54..dae93a8d81 100644 --- a/src/USER-MISC/compute_viscosity_cos.cpp +++ b/src/USER-MISC/compute_viscosity_cos.cpp @@ -15,17 +15,18 @@ Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com) ------------------------------------------------------------------------- */ - #include "compute_viscosity_cos.h" + #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index a33452dbe1..15bb458c48 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -19,20 +19,19 @@ #include "dihedral_spherical.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index aebe468905..91a8642b10 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,33 +17,24 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ - -#include -#include - -#include - -#include // IWYU pragma: keep -#include // IWYU pragma: keep +#include "dihedral_table.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "dihedral_table.h" - -#include "tokenizer.h" -#include "table_file_reader.h" - - +#include "force.h" #include "math_const.h" #include "math_extra.h" +#include "memory.h" +#include "neighbor.h" +#include "table_file_reader.h" +#include "tokenizer.h" + +#include +#include +#include // IWYU pragma: keep -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; @@ -829,28 +820,20 @@ void DihedralTable::coeff(int narg, char **arg) // --- and resolve issues with periodicity --- if (tb->ninput < 2) { - string err_msg; - err_msg = string("Invalid dihedral table length (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); - } - else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { - string err_msg; - err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); + error->one(FLERR,fmt::format("Invalid dihedral table length ({}).", + arg[2])); + } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { + error->one(FLERR,fmt::format("Invalid dihedral spline table length. " + "(Try linear)\n ({}).",arg[2])); } // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { if (tb->phifile[i] >= tb->phifile[i+1]) { - stringstream i_str; - i_str << i+1; - string err_msg = - string("Dihedral table values are not increasing (") + - string(arg[2]) + string(", ")+i_str.str()+string("th entry)"); + auto err_msg = fmt::format("Dihedral table values are not increasing " + "({}, {}th entry)",arg[2],i+1); if (i==0) - err_msg += string("\n(This is probably a mistake with your table format.)\n"); + err_msg += std::string("\n(This is probably a mistake with your table format.)\n"); error->all(FLERR,err_msg); } } @@ -859,20 +842,13 @@ void DihedralTable::coeff(int narg, char **arg) double philo = tb->phifile[0]; double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { - if ((phihi - philo) >= 360) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 360 degrees (") - +string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } - } - else { - if ((phihi - philo) >= MY_2PI) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 2*PI radians (") - + string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } + if ((phihi - philo) >= 360) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " + "degrees ({}).",arg[2])); + } else { + if ((phihi - philo) >= MY_2PI) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " + "radians ({}).",arg[2])); } // convert phi from degrees to radians @@ -940,10 +916,9 @@ void DihedralTable::coeff(int narg, char **arg) // Optional: allow the user to print out the interpolated spline tables if (me == 0) { - if (!checkU_fname.empty()) - { - ofstream checkU_file; - checkU_file.open(checkU_fname, ios::out); + if (!checkU_fname.empty()) { + std::ofstream checkU_file; + checkU_file.open(checkU_fname, std::ios::out); for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double u = tb->e[i]; @@ -953,12 +928,10 @@ void DihedralTable::coeff(int narg, char **arg) } checkU_file.close(); } - if (!checkF_fname.empty()) - { - ofstream checkF_file; - checkF_file.open(checkF_fname, ios::out); - for (int i=0; i < tablength; i++) - { + if (!checkF_fname.empty()) { + std::ofstream checkF_file; + checkF_file.open(checkF_fname, std::ios::out); + for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double f; if ((tabstyle == SPLINE) && (tb->f_unspecified)) { @@ -973,8 +946,7 @@ void DihedralTable::coeff(int narg, char **arg) // To be nice and report something, I do the same thing here.) cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi); f = -dU_dphi; - } - else + } else // Otherwise we calculated the tb->f[] array. Report its contents. f = tb->f[i]; if (tb->use_degrees) { @@ -991,8 +963,7 @@ void DihedralTable::coeff(int narg, char **arg) // store ptr to table in tabindex int count = 0; - for (int i = ilo; i <= ihi; i++) - { + for (int i = ilo; i <= ihi; i++) { tabindex[i] = ntables; //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported setflag[i] = 1; @@ -1213,7 +1184,7 @@ void DihedralTable::spline_table(Table *tb) } // for (int i=0; ininput; i++) if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { - string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); + std::string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); error->all(FLERR, msg); } @@ -1319,7 +1290,7 @@ void DihedralTable::param_extract(Table *tb, char *line) ValueTokenizer values(line); while (values.has_next()) { - std::string word = values.next_string(); + auto word = values.next_string(); if (word == "N") { tb->ninput = values.next_int(); } @@ -1342,10 +1313,8 @@ void DihedralTable::param_extract(Table *tb, char *line) //else if (word == "EQ") { // tb->theta0 = values.next_double(); //} - else { - string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word); - error->one(FLERR,err_msg); - } + else error->one(FLERR,fmt::format("Invalid keyword in dihedral angle " + "table parameters ({})", word)); } } catch (TokenizerException & e) { error->one(FLERR, e.what()); diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/USER-MISC/fix_accelerate_cos.cpp index 17d6e9ad94..4e84b47ac3 100644 --- a/src/USER-MISC/fix_accelerate_cos.cpp +++ b/src/USER-MISC/fix_accelerate_cos.cpp @@ -16,15 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_accelerate_cos.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" #include "force.h" #include "math_const.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index 1f2022d520..d92789f03f 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -23,19 +23,18 @@ #include "fix_ave_correlate_long.h" -#include +#include "citeme.h" +#include "compute.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include "variable.h" +#include #include #include -#include "update.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index bf97066275..952ffe7584 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -17,21 +17,22 @@ ------------------------------------------------------------------------- */ #include "fix_electron_stopping.h" -#include -#include -#include "mpi.h" + #include "atom.h" -#include "update.h" -#include "domain.h" -#include "region.h" -#include "force.h" -#include "fix.h" -#include "memory.h" #include "comm.h" +#include "domain.h" #include "error.h" -#include "neighbor.h" +#include "fix.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 23e61641d8..d603e37671 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -18,15 +18,15 @@ #include "fix_flow_gauss.h" -#include #include "atom.h" -#include "force.h" -#include "group.h" -#include "update.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "citeme.h" +#include "group.h" #include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 4264126c26..7c3fac9c33 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -48,16 +48,15 @@ negotiate an appropriate license for such distribution." ------------------------------------------------------------------------- */ #include "fix_imd.h" + #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" -#include "force.h" #include "error.h" #include "group.h" #include "memory.h" - +#include "respa.h" +#include "update.h" #include diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/USER-MISC/fix_momentum_chunk.cpp index 3df632eb30..fcd6d47922 100644 --- a/src/USER-MISC/fix_momentum_chunk.cpp +++ b/src/USER-MISC/fix_momentum_chunk.cpp @@ -13,18 +13,17 @@ #include "fix_momentum_chunk.h" -#include -#include #include "atom.h" #include "compute.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" #include "modify.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index a9abf7baf7..5f1582d580 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -17,12 +17,9 @@ #include "fix_orient_eco.h" -#include -#include #include "atom.h" #include "citeme.h" #include "comm.h" -#include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -34,7 +31,8 @@ #include "respa.h" #include "update.h" - +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 222369f572..1ac0ffb188 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -20,24 +20,21 @@ #include "fix_pafi.h" -#include -#include - -#include "math_extra.h" #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "respa.h" +#include "citeme.h" #include "comm.h" #include "compute.h" -#include "random_mars.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" -#include "citeme.h" - +#include +#include using namespace LAMMPS_NS; @@ -61,7 +58,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), random(NULL), computename(NULL), + Fix(lmp, narg, arg), computename(NULL), random(NULL), h(NULL), step_respa(NULL) { if (lmp->citeme) lmp->citeme->add(cite_fix_pafi_package); @@ -122,15 +119,15 @@ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : } force_flag = 0; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i=0; i<6; i++) { + for (int i=0; i<6; i++) { proj[i] = 0.0; proj_all[i] = 0.0; } - for(int i=0; i<5; i++) { + for (int i=0; i<5; i++) { results[i] = 0.0; results_all[i] = 0.0; } @@ -208,14 +205,14 @@ void FixPAFI::setup(int vflag) void FixPAFI::min_setup(int vflag) { - if( utils::strmatch(update->minimize_style,"^fire")==0 && + if (utils::strmatch(update->minimize_style,"^fire")==0 && utils::strmatch(update->minimize_style,"^quickmin")==0 ) error->all(FLERR,"fix pafi requires a damped dynamics minimizer"); min_post_force(vflag); } -void FixPAFI::post_force(int vflag) +void FixPAFI::post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; @@ -236,24 +233,20 @@ void FixPAFI::post_force(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -293,7 +286,7 @@ void FixPAFI::post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -345,7 +338,7 @@ void FixPAFI::post_force(int vflag) if (od_flag == 0) { for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += -gamma * mass_f * mass_f * v[i][0]; @@ -361,7 +354,7 @@ void FixPAFI::post_force(int vflag) for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += sqrtD * h[i][0] * mass_f; @@ -378,13 +371,12 @@ void FixPAFI::post_force(int vflag) }; -void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) +void FixPAFI::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // set force to desired value on requested level, 0.0 on other levels if (ilevel == ilevel_respa) post_force(vflag); else { - double **x = atom->x; double **f = atom->f; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -396,38 +388,31 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) } }; -void FixPAFI::min_post_force(int vflag) +void FixPAFI::min_post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; double **f = atom->f; - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -464,7 +449,7 @@ void FixPAFI::min_post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -519,7 +504,7 @@ double FixPAFI::compute_vector(int n) -void FixPAFI::initial_integrate(int vflag) +void FixPAFI::initial_integrate(int /*vflag*/) { double dtfm; @@ -539,11 +524,11 @@ void FixPAFI::initial_integrate(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -559,7 +544,7 @@ void FixPAFI::initial_integrate(int vflag) proj[1] += v[i][2] * path[i][5]; // v.n } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -651,11 +636,11 @@ void FixPAFI::final_integrate() PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -665,7 +650,7 @@ void FixPAFI::final_integrate() proj[0] += f[i][1] * path[i][4]; // f.n proj[0] += f[i][2] * path[i][5]; // f.n } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -710,7 +695,7 @@ void FixPAFI::final_integrate() /* ---------------------------------------------------------------------- */ -void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -724,7 +709,7 @@ void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixPAFI::final_integrate_respa(int ilevel, int iloop) +void FixPAFI::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index b17ee55f94..e17ef4652f 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -19,25 +19,15 @@ #include "fix_propel_self.h" -#include -#include - - #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "citeme.h" -#include "comm.h" #include "error.h" -#include "force.h" -#include "group.h" #include "math.h" #include "math_const.h" #include "math_extra.h" -#include "math_vector.h" -#include "modify.h" -#include "random_mars.h" -#include "respa.h" -#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 0771122bfd..b088a86661 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -15,17 +15,16 @@ #include "fix_rhok.h" -#include -#include - #include "atom.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "math_const.h" #include "respa.h" #include "update.h" -#include "citeme.h" -#include "math_const.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index baee8a5699..0dace284a9 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -18,16 +18,16 @@ #include "fix_smd.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" #include "group.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index 1bd6957997..97bf1fb07b 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -17,18 +17,18 @@ #include "fix_srp.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" + #include #include -#include "atom.h" -#include "force.h" -#include "domain.h" -#include "modify.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "neighbor.h" -#include "atom_vec.h" -#include "modify.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 34c667a9e2..bc10b5284c 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -20,15 +20,15 @@ #include "fix_ti_spring.h" -#include #include "atom.h" -#include "update.h" -#include "domain.h" -#include "respa.h" -#include "memory.h" -#include "error.h" #include "citeme.h" -#include "force.h" +#include "domain.h" +#include "error.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index bd7e230472..c4be8b9f1b 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_wall_ees.h" -#include + #include "math_extra.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 7da818732e..9a8454b017 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -17,19 +17,17 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_stochastic.h" -#include #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" #include "force.h" #include "lattice.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" -#include "error.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index a8d6ea9424..dfb11d6467 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -17,17 +17,17 @@ #include "fix_wall_region_ees.h" -#include -#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_extra.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 0a00c914c7..41f9bc9531 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -17,21 +17,19 @@ #include "pair_agni.h" -#include - -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" #include "citeme.h" -#include "math_special.h" +#include "comm.h" +#include "error.h" #include "math_const.h" +#include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 57dd55c593..1203cea5f2 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -15,22 +15,17 @@ ------------------------------------------------------------------------- */ #include "pair_cosine_squared.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/USER-MISC/pair_coul_slater_cut.cpp index 6b1af9a42f..5e799178c9 100644 --- a/src/USER-MISC/pair_coul_slater_cut.cpp +++ b/src/USER-MISC/pair_coul_slater_cut.cpp @@ -15,18 +15,15 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_coul_slater_cut.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "neigh_list.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/USER-MISC/pair_coul_slater_long.cpp index 0fbd56f811..0c94254f48 100644 --- a/src/USER-MISC/pair_coul_slater_long.cpp +++ b/src/USER-MISC/pair_coul_slater_long.cpp @@ -15,23 +15,19 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_coul_slater_long.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 3b76bd8482..f8b813ef0b 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -19,21 +19,17 @@ #include "pair_local_density.h" -#include - -#include - #include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "domain.h" #include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index e4cab277c1..69f4559cac 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -18,22 +18,23 @@ ------------------------------------------------------------------------- */ #include "temper_npt.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix.h" +#include "force.h" #include "integrate.h" #include "modify.h" -#include "compute.h" -#include "force.h" -#include "fix.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 670783a3d7..81a43ff7f3 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -23,9 +23,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_smd.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 09aeeea74a..81792355e0 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -23,14 +23,16 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_defgrad.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index ba1a9306ef..a3727871de 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -23,16 +23,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_shape.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index f0061bf7a1..db51ca4125 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -24,16 +24,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_strain.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp index 895a973f6a..577dc0e40f 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -23,17 +23,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_smd_tlsph_strain_rate.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace LAMMPS_NS; From 27203304d60f04fa26732b4a0071766e9809db8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 09:47:48 -0400 Subject: [PATCH 56/72] USER-INTEL include handling cleanup --- src/USER-INTEL/improper_cvff_intel.cpp | 16 +++---- src/USER-INTEL/improper_harmonic_intel.cpp | 15 ++++--- src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 10 ++--- src/USER-INTEL/npair_full_bin_intel.cpp | 7 ++- .../npair_half_bin_newton_intel.cpp | 7 ++- .../npair_half_bin_newton_tri_intel.cpp | 7 ++- .../npair_halffull_newton_intel.cpp | 12 +++-- src/USER-INTEL/npair_intel.h | 1 + src/USER-INTEL/npair_skip_intel.cpp | 14 +++--- src/USER-INTEL/pair_airebo_intel.cpp | 44 +++++++++---------- src/USER-INTEL/pair_airebo_morse_intel.cpp | 1 - src/USER-INTEL/pair_buck_intel.cpp | 16 +++---- src/USER-INTEL/pair_eam_alloy_intel.cpp | 12 +++-- src/USER-INTEL/pair_eam_fs_intel.cpp | 12 +++-- src/USER-INTEL/pair_eam_intel.cpp | 16 +++---- .../pair_lj_charmm_coul_charmm_intel.cpp | 1 + .../pair_lj_cut_coul_long_intel.cpp | 9 ++-- .../pair_lj_long_coul_long_intel.cpp | 9 +--- src/USER-INTEL/pair_sw_intel.cpp | 28 ++++++------ src/USER-INTEL/pppm_disp_intel.cpp | 12 ++--- src/USER-INTEL/pppm_intel.cpp | 13 +++--- 21 files changed, 121 insertions(+), 141 deletions(-) diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 4dcdb34b69..ba5ff79cd5 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include - #include "improper_cvff_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index c63dfc9567..8da3c67022 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -15,22 +15,23 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "improper_harmonic_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 00b032d495..bd4a95f774 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost_intel.h" -#include "neighbor.h" -#include "nstencil.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" -#include "domain.h" -#include "molecule.h" #include "error.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp index 4ef84be75f..c4433ba16c 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp index 799ba2b57b..55bac4cdb7 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp index 1f859cb5f1..d5384904e5 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp index 8248f2257a..dd11802797 100644 --- a/src/USER-INTEL/npair_halffull_newton_intel.cpp +++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp @@ -16,16 +16,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" -#include "modify.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" #include "error.h" +#include "modify.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index 6d4e01462f..e040a1d8f3 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -15,6 +15,7 @@ #define LMP_NPAIR_INTEL_H #include "npair.h" +#include "domain.h" #include "fix_intel.h" #if defined(_OPENMP) diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp index fa202d5da1..df09829c86 100644 --- a/src/USER-INTEL/npair_skip_intel.cpp +++ b/src/USER-INTEL/npair_skip_intel.cpp @@ -16,17 +16,15 @@ ------------------------------------------------------------------------- */ #include "npair_skip_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" -#include "modify.h" -#include "molecule.h" -#include "neigh_request.h" -#include "domain.h" -#include "my_page.h" #include "error.h" +#include "modify.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 8b7ff71603..6b576220fe 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -15,41 +15,37 @@ Contributing author: Markus Hohnerbach (RWTH) ------------------------------------------------------------------------- */ -#ifdef __INTEL_OFFLOAD -#pragma offload_attribute(push, target(mic)) -#endif -#include +#include "pair_airebo_intel.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" -#include -#include -#include -#include // requires C++-11 #include -#include -#include "lmptype.h" +#include +#include + #include "intel_preprocess.h" #include "intel_intrinsics_airebo.h" + #ifdef __INTEL_OFFLOAD #pragma offload_attribute(pop) #endif +#ifdef __INTEL_OFFLOAD +#pragma offload_attribute(push, target(mic)) +#endif + #if defined(_OPENMP) #include #endif -#include "pair_airebo_intel.h" -#include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "group.h" -#include "kspace.h" -#include "modify.h" -#include "suffix.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/USER-INTEL/pair_airebo_morse_intel.cpp index f68e299fa0..a99ab913ba 100644 --- a/src/USER-INTEL/pair_airebo_morse_intel.cpp +++ b/src/USER-INTEL/pair_airebo_morse_intel.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_intel.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index b21ce13a34..bb5b44d260 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -15,20 +15,20 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_buck_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "error.h" #include "math_const.h" #include "memory.h" -#include "suffix.h" -#include "force.h" #include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index b979d2dcdf..084714daf4 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_alloy_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index a1c71d9c21..8786c0d782 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_fs_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index d27a019532..561621a388 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -15,22 +15,22 @@ Contributing authors: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_eam_intel.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "suffix.h" +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 2078e5277b..c8e4a3d0ef 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" #include "modify.h" diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index 243c7f577d..34ab97fd35 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -12,20 +12,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "group.h" #include "kspace.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp index 8b9670f419..533252d018 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp @@ -15,21 +15,16 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_lj_long_coul_long_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "kspace.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" - using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index b8ac84bc3c..4ec2af40b0 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -17,6 +17,19 @@ #include "pair_sw_intel.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "neighbor.h" +#include "suffix.h" + +#include + #ifdef _LMP_INTEL_OFFLOAD #pragma offload_attribute(push,target(mic)) #endif @@ -25,21 +38,6 @@ #pragma offload_attribute(pop) #endif -#include - -#include -#include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "modify.h" -#include "suffix.h" #ifdef LMP_USE_AVXCD #include "intel_simd.h" diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 270299b4c5..1149c9b2c3 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -15,23 +15,23 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_disp_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 26af974086..d596df4490 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -18,23 +18,24 @@ W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; From f67bd8eb5d4ffd536052bd77917f253abd4c7c6c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 10:22:08 -0400 Subject: [PATCH 57/72] more KOKKOS, USER-OMP, and USER-INTEL include file cleanup --- src/KOKKOS/angle_charmm_kokkos.cpp | 9 ++--- src/KOKKOS/angle_class2_kokkos.cpp | 9 ++--- src/KOKKOS/angle_cosine_kokkos.cpp | 9 ++--- src/KOKKOS/angle_harmonic_kokkos.cpp | 9 ++--- src/KOKKOS/atom_kokkos.h | 2 +- src/KOKKOS/atom_vec_angle_kokkos.cpp | 10 ++--- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 10 ++--- src/KOKKOS/atom_vec_bond_kokkos.cpp | 10 ++--- src/KOKKOS/atom_vec_charge_kokkos.cpp | 10 ++--- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 11 +++--- src/KOKKOS/atom_vec_kokkos.cpp | 4 +- src/KOKKOS/atom_vec_kokkos.h | 3 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 10 ++--- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 11 +++--- src/KOKKOS/bond_class2_kokkos.cpp | 9 ++--- src/KOKKOS/bond_fene_kokkos.cpp | 10 ++--- src/KOKKOS/bond_harmonic_kokkos.cpp | 10 ++--- src/KOKKOS/comm_kokkos.cpp | 21 ++++++----- src/KOKKOS/comm_tiled_kokkos.cpp | 16 +------- src/KOKKOS/compute_coord_atom_kokkos.cpp | 20 ++++------ .../compute_orientorder_atom_kokkos.cpp | 22 +++++------ src/KOKKOS/compute_temp_kokkos.cpp | 13 +++---- src/KOKKOS/dihedral_charmm_kokkos.cpp | 15 ++++---- src/KOKKOS/dihedral_class2_kokkos.cpp | 15 ++++---- src/KOKKOS/dihedral_harmonic_kokkos.cpp | 15 ++++---- src/KOKKOS/dihedral_opls_kokkos.cpp | 15 ++++---- src/KOKKOS/domain_kokkos.h | 2 +- src/KOKKOS/fft3d_kokkos.cpp | 9 ++--- src/KOKKOS/fix_deform_kokkos.cpp | 29 +++++++-------- src/KOKKOS/fix_gravity_kokkos.cpp | 11 +++--- src/KOKKOS/fix_langevin_kokkos.cpp | 19 +++++----- src/KOKKOS/fix_minimize_kokkos.cpp | 3 +- src/KOKKOS/fix_momentum_kokkos.cpp | 5 +-- src/KOKKOS/fix_neigh_history_kokkos.cpp | 4 +- src/KOKKOS/fix_nh_kokkos.cpp | 35 ++++++++---------- src/KOKKOS/fix_nph_kokkos.cpp | 4 +- src/KOKKOS/fix_npt_kokkos.cpp | 4 +- src/KOKKOS/fix_nve_kokkos.cpp | 11 ++---- src/KOKKOS/fix_nvt_kokkos.cpp | 6 ++- src/KOKKOS/fix_property_atom_kokkos.cpp | 9 ++--- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 16 ++++---- src/KOKKOS/fix_reaxc_bonds_kokkos.cpp | 11 +++--- src/KOKKOS/fix_setforce_kokkos.cpp | 5 ++- src/KOKKOS/fix_wall_reflect_kokkos.cpp | 15 +++----- src/KOKKOS/gridcomm_kokkos.cpp | 9 ++--- src/KOKKOS/kokkos.cpp | 16 ++++---- src/KOKKOS/memory_kokkos.h | 2 +- src/KOKKOS/min_kokkos.cpp | 37 +++++++++---------- src/KOKKOS/min_linesearch_kokkos.cpp | 5 ++- src/KOKKOS/nbin_kokkos.cpp | 7 +--- src/KOKKOS/neigh_bond_kokkos.cpp | 20 +++++----- src/KOKKOS/neigh_list_kokkos.cpp | 2 - src/KOKKOS/neigh_list_kokkos.h | 3 +- src/KOKKOS/neighbor_kokkos.cpp | 35 +++++++++--------- src/KOKKOS/neighbor_kokkos.h | 3 +- src/KOKKOS/npair_halffull_kokkos.cpp | 13 +++---- src/KOKKOS/npair_skip_kokkos.cpp | 6 +-- src/KOKKOS/pair_kokkos.h | 2 +- src/KOKKOS/pair_reaxc_kokkos.cpp | 16 ++++---- src/KOKKOS/pair_vashishta_kokkos.cpp | 21 ++++++----- src/KOKKOS/pppm_kokkos.cpp | 30 +++++++-------- src/KOKKOS/remap_kokkos.cpp | 6 +-- src/USER-INTEL/angle_charmm_intel.cpp | 15 ++++---- src/USER-INTEL/angle_harmonic_intel.cpp | 15 ++++---- src/USER-INTEL/bond_fene_intel.cpp | 14 ++++--- src/USER-INTEL/bond_harmonic_intel.cpp | 15 ++++---- src/USER-INTEL/dihedral_fourier_intel.cpp | 18 ++++----- src/USER-INTEL/dihedral_harmonic_intel.cpp | 18 ++++----- src/USER-INTEL/dihedral_opls_intel.cpp | 18 ++++----- src/USER-INTEL/fix_intel.cpp | 9 +---- src/USER-INTEL/fix_nh_intel.cpp | 4 +- src/USER-INTEL/fix_nve_asphere_intel.cpp | 10 ++--- src/USER-INTEL/fix_nvt_sllod_intel.cpp | 15 ++++---- src/USER-INTEL/intel_buffers.cpp | 2 +- src/USER-INTEL/nbin_intel.cpp | 6 +-- src/USER-INTEL/npair_intel.cpp | 8 ++-- src/USER-OMP/reaxc_forces_omp.cpp | 11 ++++-- src/USER-OMP/reaxc_init_md_omp.cpp | 4 +- src/USER-OMP/reaxc_multi_body_omp.cpp | 8 ++-- src/USER-OMP/reaxc_torsion_angles_omp.cpp | 4 +- src/USER-OMP/reaxc_valence_angles_omp.cpp | 9 +++-- 81 files changed, 442 insertions(+), 490 deletions(-) diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 14850525ef..59ccac92ce 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 4406f51f83..bfa0f81a1d 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_class2_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 7ba634cd13..cf93bfbde5 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index 2e5831ef07..3a8878d222 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index ce480f6f9d..6eebbad661 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "atom.h" +#include "atom.h" // IWYU pragma: export #include "kokkos_type.h" #ifndef LMP_ATOM_KOKKOS_H diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e9c101eb79..662f09fe5a 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_angle_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index c76af73420..995985b29d 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_atomic_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 47e77c33b3..db56d58dff 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 183bdb94e4..9846d2f4f8 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_charge_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 34a246008d..7c7f3c9826 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid_kokkos.h" -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "modify.h" +#include using namespace LAMMPS_NS; @@ -1177,7 +1178,7 @@ void AtomVecHybridKokkos::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index dceedc8e60..9e39f53733 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "atom_masks.h" - using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index 7d8796b1ae..d414101966 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -14,7 +14,8 @@ #ifndef LMP_ATOM_VEC_KOKKOS_H #define LMP_ATOM_VEC_KOKKOS_H -#include "atom_vec.h" +#include "atom_vec.h" // IWYU pragma: export + #include "kokkos_type.h" #include diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 6a4d94dc14..7e3cdbf5e3 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_molecular_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" -#include "fix.h" -#include "atom_masks.h" -#include "memory_kokkos.h" #include "error.h" - +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 569498f664..6b62014e4a 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -12,27 +12,26 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" #include "memory.h" -#include "error.h" #include "memory_kokkos.h" +#include "modify.h" +#include using namespace LAMMPS_NS; +using namespace MathConst; #define DELTA 10 -static const double MY_PI = 3.14159265358979323846; // pi - /* ---------------------------------------------------------------------- */ AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 5481a41806..07712df203 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -16,16 +16,15 @@ ------------------------------------------------------------------------- */ #include "bond_class2_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index 9d2200dd90..1ee82476b2 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "bond_fene_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 9239a4191b..20b8778463 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_kokkos.h" -#include #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; - /* ---------------------------------------------------------------------- */ template diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 8f865f6459..51ba6bbdb2 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -12,23 +12,24 @@ ------------------------------------------------------------------------- */ #include "comm_kokkos.h" -#include "kokkos.h" + #include "atom.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" #include "atom_vec_kokkos.h" -#include "domain.h" -#include "atom_masks.h" -#include "error.h" -#include "memory_kokkos.h" -#include "force.h" -#include "pair.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" -#include "output.h" -#include "modify.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "kokkos.h" #include "kokkos_base.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index a29d9f63b3..88d3d1ac8c 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -12,22 +12,10 @@ ------------------------------------------------------------------------- */ #include "comm_tiled_kokkos.h" -#include -#include "comm_brick.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" -#include "output.h" -#include "dump.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_coord_atom_kokkos.cpp b/src/KOKKOS/compute_coord_atom_kokkos.cpp index 90bd151b2d..c1f9324942 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.cpp +++ b/src/KOKKOS/compute_coord_atom_kokkos.cpp @@ -12,22 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom_kokkos.h" -#include -#include -#include "compute_orientorder_atom_kokkos.h" + #include "atom_kokkos.h" -#include "update.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute_orientorder_atom_kokkos.h" +#include "error.h" +#include "memory_kokkos.h" #include "modify.h" -#include "neighbor_kokkos.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" -#include "group.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index 7d635dbeb7..6e35dfd94f 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -16,23 +16,19 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom_kokkos.h" -#include -#include #include "atom_kokkos.h" -#include "update.h" -#include "modify.h" -#include "neighbor_kokkos.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "math_const.h" #include "atom_masks.h" #include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor_kokkos.h" +#include "pair.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 7e4d3ad6ae..5e60d62be1 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -13,15 +13,14 @@ #include "compute_temp_kokkos.h" -#include #include "atom_kokkos.h" -#include "update.h" -#include "force.h" -#include "domain.h" -#include "comm.h" -#include "group.h" -#include "error.h" #include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index c25ab18c60..88b5e1344d 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -16,19 +16,18 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "kokkos.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "kokkos.h" +#include "neighbor_kokkos.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index df60ebd1e4..156a13c2ec 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" -#include "force.h" -#include "update.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 0acd61222e..d4855b10c1 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" -#include "force.h" -#include "update.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 70beae918a..42874936f9 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" -#include "force.h" -#include "update.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index eccc36a021..3bfdeb708b 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_DOMAIN_KOKKOS_H #define LMP_DOMAIN_KOKKOS_H -#include "domain.h" +#include "domain.h" // IWYU pragma: export #include "kokkos_type.h" #include "kokkos_few.h" diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index e49d780040..ff95998e4e 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -14,16 +14,13 @@ /* ---------------------------------------------------------------------- Contributing authors: Stan Moore (SNL), Sam Mish (U.C. Davis) ------------------------------------------------------------------------- */ - -#include -#include -#include -#include #include "fft3d_kokkos.h" -#include "remap_kokkos.h" + #include "error.h" #include "kokkos.h" +#include "remap_kokkos.h" +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 5d8430d337..87d860b5ae 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -16,23 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_deform_kokkos.h" -#include + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "domain_kokkos.h" +#include "error.h" +#include "force.h" +#include "input.h" +#include "irregular.h" +#include "kspace.h" +#include "math_const.h" +#include "modify.h" +#include "update.h" +#include "variable.h" #include -#include "atom_kokkos.h" -#include "update.h" -#include "comm.h" -#include "irregular.h" -#include "domain_kokkos.h" -#include "lattice.h" -#include "force.h" -#include "modify.h" -#include "math_const.h" -#include "kspace.h" -#include "input.h" -#include "variable.h" -#include "error.h" -#include "atom_masks.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp index 4f8b57365e..7d413a1d57 100644 --- a/src/KOKKOS/fix_gravity_kokkos.cpp +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_gravity_kokkos.h" -#include "atom_masks.h" -#include "modify.h" -#include "input.h" -#include "variable.h" -#include "update.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" +#include "input.h" +#include "modify.h" +#include "update.h" +#include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 44ae18f9a9..dadf9e4c8b 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -12,21 +12,22 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_kokkos.h" -#include -#include "atom_masks.h" + #include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "group.h" -#include "update.h" -#include "error.h" -#include "memory_kokkos.h" -#include "compute.h" -#include "comm.h" -#include "modify.h" #include "input.h" -#include "region.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp index e7b10dbb8e..13b9cb02a7 100644 --- a/src/KOKKOS/fix_minimize_kokkos.cpp +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_minimize_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" #include "memory_kokkos.h" -#include "atom_masks.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 1821b6dadd..be486bf752 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -13,16 +13,15 @@ #include "fix_momentum_kokkos.h" -#include #include "atom_kokkos.h" #include "atom_masks.h" -#include "domain.h" #include "domain_kokkos.h" #include "group.h" #include "error.h" -#include "force.h" #include "kokkos_few.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index a43c5ef458..d1f3f66327 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history_kokkos.h" + #include "atom_kokkos.h" #include "error.h" #include "memory_kokkos.h" +#include "modify.h" #include "neigh_list_kokkos.h" #include "pair_kokkos.h" -#include "comm.h" -#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 8cd58b0927..a2985502bb 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -16,27 +16,24 @@ ------------------------------------------------------------------------- */ #include "fix_nh_kokkos.h" -#include + +#include "atom.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute.h" +#include "domain_kokkos.h" +#include "error.h" +#include "fix_deform.h" +#include "force.h" +#include "irregular.h" +#include "kspace.h" +#include "memory_kokkos.h" +#include "neighbor.h" +#include "update.h" #include -#include "math_extra.h" -#include "atom.h" -#include "force.h" -#include "group.h" -#include "comm.h" -#include "neighbor.h" -#include "irregular.h" -#include "modify.h" -#include "fix_deform.h" -#include "compute.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" -#include "domain_kokkos.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "atom_kokkos.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index d667e29221..7efcb150bd 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nph_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 47b3da4efe..5b73eee4d7 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_npt_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index da0a326d5d..beabc55727 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_kokkos.h" -#include -#include -#include "atom_masks.h" + #include "atom_kokkos.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" +#include "atom_masks.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 013095abc0..6e69582617 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_kokkos.h" -#include + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index d6afae3ec2..185e7445b2 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -13,13 +13,12 @@ #include "fix_property_atom_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "update.h" #include "atom_masks.h" +#include "error.h" +#include "memory_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 8c007586a9..eac044da28 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -17,21 +17,21 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_kokkos.h" -#include -#include "kokkos.h" + #include "atom.h" -#include "atom_masks.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "kokkos.h" +#include "memory_kokkos.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "integrate.h" -#include "memory_kokkos.h" -#include "error.h" -#include "pair_reaxc_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 3a706ece83..f98ab0314c 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds_kokkos.h" + #include "atom.h" -#include "pair_reaxc_kokkos.h" -#include "force.h" -#include "compute.h" -#include "memory_kokkos.h" -#include "error.h" -#include "reaxc_defs.h" #include "atom_masks.h" +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "pair_reaxc_kokkos.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index da516f5ba2..a11e8b4bd4 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_setforce_kokkos.h" -#include + #include "atom_kokkos.h" #include "update.h" #include "modify.h" @@ -24,7 +24,8 @@ #include "error.h" #include "atom_masks.h" #include "kokkos_base.h" -#include "region.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index c581edb123..046c97c12b 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -13,19 +13,14 @@ #include "fix_wall_reflect_kokkos.h" -#include #include "atom_kokkos.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" -#include "error.h" -#include "force.h" #include "atom_masks.h" +#include "input.h" +#include "modify.h" +#include "update.h" +#include "variable.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 5f32c5b4ae..909e3c8544 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "gridcomm_kokkos.h" -#include + #include "comm.h" -#include "kspace.h" #include "irregular.h" -#include "memory_kokkos.h" -#include "error.h" -#include "kokkos_base_fft.h" #include "kokkos.h" +#include "kokkos_base_fft.h" +#include "kspace.h" +#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index b5e6174528..79fd0685b0 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "kokkos.h" -#include -#include + +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neighbor_kokkos.h" + #include -#include #include #include #include -#include "lammps.h" -#include "force.h" -#include "neighbor_kokkos.h" -#include "neigh_list_kokkos.h" -#include "error.h" -#include "memory_kokkos.h" #ifdef KOKKOS_ENABLE_CUDA diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h index 39d30ac785..83e8b9ec7c 100644 --- a/src/KOKKOS/memory_kokkos.h +++ b/src/KOKKOS/memory_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_MEMORY_KOKKOS_H #define LMP_MEMORY_KOKKOS_H -#include "memory.h" +#include "memory.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index e5f22411f6..032538fe60 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -16,32 +16,31 @@ ------------------------------------------------------------------------- */ #include "min_kokkos.h" -#include -#include -#include -#include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize_kokkos.h" -#include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" + #include "angle.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "bond.h" +#include "comm.h" +#include "compute.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize_kokkos.h" +#include "force.h" #include "improper.h" +#include "kokkos.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "kokkos.h" -#include "atom_masks.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index cb07c7db86..3c94f07233 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "min_linesearch_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "modify.h" #include "fix_minimize_kokkos.h" @@ -27,6 +26,8 @@ #include "error.h" #include "atom_masks.h" +#include + using namespace LAMMPS_NS; // ALPHA_MAX = max alpha allowed to avoid long backtracks diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index 89a69dc633..158a87796e 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "nbin_kokkos.h" -#include "neighbor.h" + #include "atom_kokkos.h" -#include "group.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "update.h" -#include "error.h" -#include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index bf9234e17c..021dcc7a1c 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -16,22 +16,22 @@ ------------------------------------------------------------------------- */ #include "neigh_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" #include "domain_kokkos.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "memory_kokkos.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "memory_kokkos.h" -#include "error.h" -#include "modify.h" -#include "fix.h" -#include -#include "atom_masks.h" -#include "domain.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; #define BONDDELTA 10000 diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 14591f8246..7db78e38d2 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "neigh_list_kokkos.h" -#include "atom.h" -#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index edd775f7f9..8ae873036b 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -15,7 +15,8 @@ #define LMP_NEIGH_LIST_KOKKOS_H #include "pointers.h" -#include "neigh_list.h" + +#include "neigh_list.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index 4d0cf7ea3a..b21a7cb1ee 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -12,25 +12,26 @@ ------------------------------------------------------------------------- */ #include "neighbor_kokkos.h" -#include "atom_kokkos.h" -#include "pair.h" -#include "fix.h" -#include "neigh_request.h" -#include "memory_kokkos.h" -#include "update.h" -#include "atom_masks.h" -#include "error.h" -#include "kokkos.h" -#include "force.h" -#include "bond.h" + #include "angle.h" -#include "dihedral.h" -#include "improper.h" -#include "style_nbin.h" -#include "style_nstencil.h" -#include "style_npair.h" -#include "style_ntopo.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "improper.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neigh_request.h" +#include "pair.h" +#include "style_nbin.h" +#include "style_npair.h" +#include "style_nstencil.h" +#include "style_ntopo.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 3829502c0d..304fe8f1da 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -14,11 +14,10 @@ #ifndef LMP_NEIGHBOR_KOKKOS_H #define LMP_NEIGHBOR_KOKKOS_H -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: export #include "neigh_list_kokkos.h" #include "neigh_bond_kokkos.h" #include "kokkos_type.h" -#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/npair_halffull_kokkos.cpp b/src/KOKKOS/npair_halffull_kokkos.cpp index b109010935..ca9c14b29d 100644 --- a/src/KOKKOS/npair_halffull_kokkos.cpp +++ b/src/KOKKOS/npair_halffull_kokkos.cpp @@ -12,15 +12,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_kokkos.h" -#include "neighbor.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" +#include "domain.h" +#include "neigh_list_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index 13080a9580..81f78844d3 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" +#include "neigh_list_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index ffafdf7f17..396a5f2d48 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -19,7 +19,7 @@ #define LMP_PAIR_KOKKOS_H #include "Kokkos_Macros.hpp" -#include "pair.h" +#include "pair.h" // IWYU pragma: export #include "neighbor_kokkos.h" #include "neigh_list_kokkos.h" #include "Kokkos_Vectorization.hpp" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index bf8518e3c3..3a7359df93 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -16,25 +16,23 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_kokkos.h" -#include -#include -#include "kokkos.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list_kokkos.h" +#include "kokkos.h" #include "math_const.h" #include "math_special.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_request.h" +#include "neighbor.h" #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" +#include + #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index f5489c0e0c..b5dd43f12a 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -16,20 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_kokkos.h" -#include -#include -#include "kokkos.h" -#include "pair_kokkos.h" + #include "atom_kokkos.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" +#include "force.h" +#include "kokkos.h" +#include "math_const.h" #include "memory_kokkos.h" #include "neigh_list_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "math_const.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 2eea527947..4a795833fb 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -16,26 +16,22 @@ ------------------------------------------------------------------------- */ #include "pppm_kokkos.h" -#include -#include -#include "atom_kokkos.h" -#include "comm.h" -#include "gridcomm_kokkos.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "domain.h" -#include "fft3d_kokkos.h" -#include "remap_kokkos.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "kokkos.h" -#include "utils.h" -#include "fmt/format.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "domain.h" +#include "error.h" +#include "fft3d_kokkos.h" +#include "force.h" +#include "gridcomm_kokkos.h" +#include "kokkos.h" #include "math_const.h" #include "math_special_kokkos.h" +#include "memory_kokkos.h" +#include "pair.h" +#include "remap_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index d496db05e2..af87ba3644 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "remap_kokkos.h" -#include "pack_kokkos.h" + #include "error.h" +#include "pack_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index b6e0b0dac5..7aad7f754a 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "angle_charmm_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 6d3deee9ba..290f7320b1 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "angle_harmonic_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 072800db42..6b458aeefb 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -15,19 +15,21 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "bond_fene_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 1ddb424a7b..84d94b8f3d 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -15,19 +15,20 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - #include "bond_harmonic_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index cd62012255..67b82b62bf 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_fourier_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "update.h" -#include "error.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index dd8c3d98db..ea9bc33c57 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_harmonic_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "update.h" -#include "error.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index ef48f7e8ee..fa8fd53def 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" - -#include #include "dihedral_opls_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "update.h" -#include "error.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index b3649be7c8..eacbc7ddcc 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -16,8 +16,8 @@ Anupama Kurpad (Intel) - Host Affinitization ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_intel.h" + #include "comm.h" #include "error.h" #include "force.h" @@ -25,17 +25,10 @@ #include "neigh_request.h" #include "pair.h" #include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "timer.h" -#include "universe.h" #include "update.h" - #include -#include -#include - #ifdef _LMP_INTEL_OFFLOAD #ifndef INTEL_OFFLOAD_NOAFFINITY #include diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index a072e823a4..2122bfd370 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "fix_nh_intel.h" + #include "atom.h" -#include "compute.h" #include "domain.h" #include "error.h" #include "force.h" -#include "kspace.h" #include "memory.h" #include "modify.h" #include "neighbor.h" @@ -29,7 +28,6 @@ #include #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 7eeb8a1635..55e51227f4 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -15,18 +15,16 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere_intel.h" -#include "math_extra_intel.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" +#include "error.h" #include "force.h" +#include "math_extra_intel.h" +#include "memory.h" #include "neighbor.h" #include "update.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index f5a5dabfb1..4382542710 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -11,18 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_intel.h" -#include "math_extra.h" + #include "atom.h" +#include "compute.h" #include "domain.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 04791dee78..dc5b0fad5a 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -12,8 +12,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "intel_buffers.h" + #include "force.h" #include "memory.h" diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 78c6246389..4a046bc845 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include "nbin_intel.h" + #include "atom.h" -#include "group.h" #include "comm.h" -#include "domain.h" +#include "error.h" +#include "group.h" #include "modify.h" #include "update.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index f7a233efc9..9aae0d27b7 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -15,13 +15,13 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "npair_intel.h" + #include "comm.h" #include "domain.h" -#include "timer.h" #include "modify.h" -#include "npair_intel.h" -#include "nstencil.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index ee4670fe59..ce38cb0544 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,13 +26,11 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_forces_omp.h" -#include -#include + #include "fix_omp.h" -#include "reaxc_defs.h" #include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" @@ -44,6 +42,11 @@ #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" +#include +#include + +#include "omp_compat.h" + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index b0cf4a5fb8..fd216844eb 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_init_md_omp.h" -#include + #include "reaxc_defs.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" @@ -38,6 +38,8 @@ #include "error.h" #include "fmt/format.h" +#include + // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); extern int Init_System(reax_system*, control_params*, char*); diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 5f4b6d4eb0..57c056fff7 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -27,14 +27,16 @@ ----------------------------------------------------------------------*/ #include "reaxc_multi_body_omp.h" -#include -#include + #include "fix_omp.h" -#include #include "pair_reaxc_omp.h" + #include "reaxc_defs.h" #include "reaxc_list.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index 68bacb7202..7d567b259c 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_torsion_angles_omp.h" -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 104fadbbae..f9117d3a53 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -27,11 +27,10 @@ ----------------------------------------------------------------------*/ #include "reaxc_valence_angles_omp.h" -#include -#include -#include "pair_reaxc_omp.h" -#include "fix_omp.h" + #include "error.h" +#include "fix_omp.h" +#include "pair_reaxc_omp.h" #include "reaxc_defs.h" #include "reaxc_types.h" @@ -39,6 +38,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif From 05c7cfe59f09f76b3ce4ac22e98bde3df3969bde Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 11:16:32 -0400 Subject: [PATCH 58/72] more include updates for USER-OMP --- src/USER-OMP/ewald_omp.cpp | 12 ++++++------ src/USER-OMP/improper_fourier_omp.cpp | 16 +++++++++------- src/USER-OMP/improper_ring_omp.cpp | 11 ++++++----- src/USER-OMP/msm_cg_omp.cpp | 17 +++++++---------- src/USER-OMP/msm_omp.cpp | 7 ++++--- src/USER-OMP/pppm_cg_omp.cpp | 14 ++++++++------ src/USER-OMP/pppm_disp_tip4p_omp.cpp | 13 ++++++++----- src/USER-OMP/pppm_omp.cpp | 10 +++++----- src/USER-OMP/pppm_tip4p_omp.cpp | 13 +++++++------ src/USER-OMP/respa_omp.cpp | 24 ++++++++++++------------ src/USER-OMP/thr_data.h | 2 +- 11 files changed, 73 insertions(+), 66 deletions(-) diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index ec8d708da2..d5480d2a9f 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,18 +15,18 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "ewald_omp.h" -#include -#include + #include "atom.h" #include "comm.h" #include "force.h" -#include "memory.h" -#include "timer.h" #include "math_const.h" - +#include "memory.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index 0671bdc375..3763465e79 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -15,18 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "improper_fourier_omp.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "timer.h" -#include "force.h" -#include "update.h" #include "error.h" - +#include "force.h" +#include "neighbor.h" #include "suffix.h" +#include "timer.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 4ba67aab70..51ea5e5198 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,17 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "improper_ring_omp.h" -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "timer.h" #include "force.h" #include "math_special.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 524850eb63..93904fd8f8 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,24 +16,21 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_cg_omp.h" -#include -#include -#include -#include #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" #include "force.h" -#include "neighbor.h" +#include "gridcomm.h" #include "memory.h" +#include "neighbor.h" #include "thr_omp.h" -#include "timer.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 2689226725..783ebb40f1 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -15,14 +15,15 @@ Contributing authors: Axel Kohlmeyer (Temple U), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_omp.h" -#include + #include "comm.h" #include "domain.h" #include "error.h" -#include "timer.h" +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 31098d2675..86997713ef 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,22 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_cg_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 7da4257e07..93b7a87a61 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,21 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index e3e46f4de0..7065588526 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,19 +15,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 8bd9805f01..936f3cf31c 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,11 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" @@ -27,12 +24,16 @@ #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index b5e5293aa4..b8d0af5c86 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,25 +15,25 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "respa_omp.h" -#include "neighbor.h" -#include "comm.h" -#include "atom.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "bond.h" + #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" -#include "error.h" -#include "timer.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" +#include "update.h" +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 4853d6dbbf..4b87357101 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,7 +18,7 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#include "timer.h" +#include "timer.h" // IWYU pragma: export namespace LAMMPS_NS { From 93d0358ebc5e91428bb686ace66713c0275bb4b6 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 3 Sep 2020 11:36:02 -0600 Subject: [PATCH 59/72] cmake: use static iwyu-extra-map.imp --- cmake/CMakeLists.txt | 9 +-------- cmake/iwyu/iwyu-extra-map.imp | 4 ++++ 2 files changed, 5 insertions(+), 8 deletions(-) create mode 100644 cmake/iwyu/iwyu-extra-map.imp diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 87c70e4483..9fff73f49e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -260,16 +260,9 @@ if(ENABLE_IWYU) if (IWYU_EXE AND IWYU_TOOL) add_custom_target( iwyu - ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp COMMENT "Running IWYU") add_dependencies(iwyu lammps) - # generate file with additional mappings - file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "[\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp - " { include: [ \"\", private, \"\", public ] },\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp - " { include: [ \"\", public, \"\", public ] },\n") - file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/iwyu-extra-map.imp "]\n") else() message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" "and the iwyu-tool/iwyu_tool script installed in your PATH") diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp new file mode 100644 index 0000000000..8985998704 --- /dev/null +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -0,0 +1,4 @@ +[ + { include: [ "", private, "", public ] } + { include: [ "", public, "", public ] } +] From 390c6ba1061d5461995f905c78af7418c9dd368c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Sep 2020 15:28:07 -0400 Subject: [PATCH 60/72] rechecking some corefiles with IWYU after the many updates --- src/comm.cpp | 8 ++++---- src/finish.cpp | 6 +++--- src/group.cpp | 1 + src/lammps.cpp | 6 +++--- src/molecule.cpp | 15 +++++++-------- src/molecule.h | 2 +- src/output.cpp | 4 ++-- src/read_dump.cpp | 4 ++-- src/reader_native.cpp | 1 - src/reset_mol_ids.cpp | 2 ++ src/reset_mol_ids.h | 1 - src/timer.cpp | 8 +++----- src/universe.cpp | 1 - 13 files changed, 28 insertions(+), 31 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 24a5d050d4..7b351e12fc 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -14,20 +14,20 @@ #include "comm.h" #include "accelerator_kokkos.h" -#include "atom.h" +#include "atom.h" // IWYU pragma: keep #include "atom_vec.h" #include "bond.h" #include "compute.h" -#include "domain.h" +#include "domain.h" // IWYU pragma: keep #include "dump.h" #include "error.h" #include "fix.h" #include "force.h" #include "group.h" #include "irregular.h" -#include "memory.h" +#include "memory.h" // IWYU pragma: keep #include "modify.h" -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: keep #include "output.h" #include "pair.h" #include "procmap.h" diff --git a/src/finish.cpp b/src/finish.cpp index 7990a3c141..3bfe3a7bbf 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -20,13 +20,13 @@ #include "error.h" #include "force.h" #include "kspace.h" -#include "memory.h" +#include "memory.h" // IWYU pragma: keep #include "min.h" #include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" -#include "neighbor.h" -#include "timer.h" +#include "neighbor.h" // IWYU pragma: keep +#include "timer.h" // IWYU pragma: keep #include "universe.h" #include "update.h" diff --git a/src/group.cpp b/src/group.cpp index ee96c20f47..a2e20a6ab1 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -33,6 +33,7 @@ #include #include #include +#include using namespace LAMMPS_NS; diff --git a/src/lammps.cpp b/src/lammps.cpp index b6c8450a4d..4d643c327c 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -30,12 +30,12 @@ #include "universe.h" #include "input.h" #include "info.h" -#include "atom.h" +#include "atom.h" // IWYU pragma: keep #include "update.h" -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: keep #include "comm.h" #include "comm_brick.h" -#include "domain.h" +#include "domain.h" // IWYU pragma: keep #include "force.h" #include "modify.h" #include "group.h" diff --git a/src/molecule.cpp b/src/molecule.cpp index 18f5c38992..0d81f49a50 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -12,23 +12,22 @@ ------------------------------------------------------------------------- */ #include "molecule.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" -#include "force.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" #include "tokenizer.h" +#include +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 256 diff --git a/src/molecule.h b/src/molecule.h index d752be3f81..5a3fa5a327 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -15,7 +15,7 @@ #define LMP_ONE_MOLECULE_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/output.cpp b/src/output.cpp index 9b091f89a2..6c90198de4 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "output.h" -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep #include "atom.h" #include "comm.h" @@ -79,7 +79,7 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp) #define DUMP_CLASS #define DumpStyle(key,Class) \ (*dump_map)[#key] = &dump_creator; -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep #undef DumpStyle #undef DUMP_CLASS } diff --git a/src/read_dump.cpp b/src/read_dump.cpp index eb58d3e3ff..10218fe617 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -29,7 +29,7 @@ #include "irregular.h" #include "memory.h" #include "reader.h" -#include "style_reader.h" +#include "style_reader.h" // IWYU pragma: keep #include "update.h" #include @@ -243,7 +243,7 @@ void ReadDump::setup_reader(int narg, char **arg) for (int i = 0; i < nreader; i++) \ readers[i] = new Class(lmp); \ } -#include "style_reader.h" +#include "style_reader.h" // IWYU pragma: keep #undef READER_CLASS // unrecognized style diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 19e53f3efe..e0f0d7792b 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -13,7 +13,6 @@ #include "reader_native.h" -#include "atom.h" #include "error.h" #include "memory.h" #include "tokenizer.h" diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index 0d9fe55e07..ad2caad656 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -26,6 +26,8 @@ #include "group.h" #include "modify.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index 9d2dd24bc8..fbb6fceb03 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -21,7 +21,6 @@ CommandStyle(reset_mol_ids,ResetMolIDs) #define LMP_RESET_MOL_IDS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/timer.cpp b/src/timer.cpp index b9124978a9..adf143b4ae 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -12,13 +12,11 @@ ------------------------------------------------------------------------- */ #include "timer.h" -#include -#include -#include + #include "comm.h" #include "error.h" -#include "force.h" -#include "utils.h" + +#include #ifdef _WIN32 #include diff --git a/src/universe.cpp b/src/universe.cpp index acb5100337..838313665e 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -14,7 +14,6 @@ #include "universe.h" #include "error.h" -#include "force.h" #include "memory.h" #include "version.h" From 508b49c976303738e812de845ae3d6c5623e65cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 00:45:41 -0400 Subject: [PATCH 61/72] add missing comma --- cmake/iwyu/iwyu-extra-map.imp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index 8985998704..8f6af087b4 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -1,4 +1,4 @@ [ - { include: [ "", private, "", public ] } - { include: [ "", public, "", public ] } + { include: [ "", private, "", public ] }, + { include: [ "", public, "", public ] }, ] From 2e0af2fdcead01067edf54f10af585b4b78f03ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 00:46:23 -0400 Subject: [PATCH 62/72] some more second pass cleanup --- src/KIM/kim_init.h | 1 - src/KIM/kim_interactions.h | 1 - src/KIM/kim_param.h | 1 - src/KIM/kim_query.h | 1 - src/KOKKOS/min_linesearch_kokkos.cpp | 11 +++++---- src/KSPACE/pppm_dipole.cpp | 25 +++++++++------------ src/MANYBODY/pair_polymorphic.cpp | 19 ++++++++-------- src/MANYBODY/pair_polymorphic.h | 1 - src/MC/fix_widom.cpp | 1 - src/MC/fix_widom.h | 1 - src/MLIAP/mliap_data.cpp | 2 -- src/USER-MISC/fix_accelerate_cos.cpp | 2 ++ src/USER-MISC/fix_propel_self.cpp | 1 + src/USER-MISC/fix_wall_reflect_stochastic.h | 1 - src/USER-MISC/pair_local_density.cpp | 1 - src/potential_file_reader.h | 2 +- src/text_file_reader.h | 5 ++--- src/tokenizer.cpp | 4 ++-- 18 files changed, 33 insertions(+), 47 deletions(-) diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 3311d4e13d..8fa3247b22 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -66,7 +66,6 @@ CommandStyle(kim_init,KimInit) #define LMP_KIM_INIT_H #include "pointers.h" -#include // Forward declaration. typedef struct KIM_Model KIM_Model; diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 414c7b39d5..071e5b284f 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -66,7 +66,6 @@ CommandStyle(kim_interactions,KimInteractions) #define LMP_KIM_INTERACTIONS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h index a4e26451f2..e4fc5ce59a 100644 --- a/src/KIM/kim_param.h +++ b/src/KIM/kim_param.h @@ -65,7 +65,6 @@ CommandStyle(kim_param, KimParam) #define LMP_KIM_PARAM_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 6888f911f4..e1c49ed71d 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -64,7 +64,6 @@ CommandStyle(kim_query,KimQuery) #define LMP_KIM_QUERY_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index 3c94f07233..4306a5bd3b 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -18,13 +18,12 @@ #include "min_linesearch_kokkos.h" #include "atom_kokkos.h" -#include "modify.h" -#include "fix_minimize_kokkos.h" -#include "pair.h" -#include "output.h" -#include "thermo.h" -#include "error.h" #include "atom_masks.h" +#include "error.h" +#include "fix_minimize_kokkos.h" +#include "output.h" +#include "pair.h" +#include "thermo.h" #include diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 1a87c81bee..1b7d325326 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -16,26 +16,23 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" -#include "memory.h" #include "error.h" -#include "update.h" -#include "utils.h" -#include "fmt/format.h" - +#include "fft3d_wrap.h" +#include "force.h" +#include "gridcomm.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "pair.h" +#include "remap_wrap.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 4c8ebaf8ad..0f7fd7a1c7 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -18,20 +18,19 @@ #include "pair_polymorphic.h" -#include - -#include #include "atom.h" -#include "neighbor.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" - -#include "tokenizer.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 18956699d7..2593905b22 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,7 +22,6 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include -#include namespace LAMMPS_NS { diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index d7fdf69b86..94b2481742 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -20,7 +20,6 @@ #include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "bond.h" #include "comm.h" #include "compute.h" diff --git a/src/MC/fix_widom.h b/src/MC/fix_widom.h index 05060e76ac..19102e4f4a 100644 --- a/src/MC/fix_widom.h +++ b/src/MC/fix_widom.h @@ -20,7 +20,6 @@ FixStyle(widom,FixWidom) #ifndef LMP_FIX_WIDOM_H #define LMP_FIX_WIDOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MLIAP/mliap_data.cpp b/src/MLIAP/mliap_data.cpp index 28f9a988d8..a7e50012cb 100644 --- a/src/MLIAP/mliap_data.cpp +++ b/src/MLIAP/mliap_data.cpp @@ -19,8 +19,6 @@ #include "mliap_model.h" #include "neigh_list.h" -#include - using namespace LAMMPS_NS; MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in, diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/USER-MISC/fix_accelerate_cos.cpp index 4e84b47ac3..4c15685556 100644 --- a/src/USER-MISC/fix_accelerate_cos.cpp +++ b/src/USER-MISC/fix_accelerate_cos.cpp @@ -23,6 +23,8 @@ #include "force.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index e17ef4652f..522c2eb4a5 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -27,6 +27,7 @@ #include "math_extra.h" #include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/USER-MISC/fix_wall_reflect_stochastic.h index 0568dc8ae5..558ad7d084 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.h +++ b/src/USER-MISC/fix_wall_reflect_stochastic.h @@ -20,7 +20,6 @@ FixStyle(wall/reflect/stochastic,FixWallReflectStochastic) #ifndef LMP_FIX_WALL_REFLECT_STOCHASTIC_H #define LMP_FIX_WALL_REFLECT_STOCHASTIC_H -#include "random_mars.h" #include "fix_wall_reflect.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index f8b813ef0b..404f6e2db1 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -28,7 +28,6 @@ #include "neigh_list.h" #include "neighbor.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 57aa827638..d3befca282 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -18,7 +18,7 @@ #ifndef LMP_POTENTIAL_FILE_READER_H #define LMP_POTENTIAL_FILE_READER_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #include "tokenizer.h" namespace LAMMPS_NS diff --git a/src/text_file_reader.h b/src/text_file_reader.h index e74a285961..65af0a08d9 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -18,11 +18,10 @@ #ifndef LMP_TEXT_FILE_READER_H #define LMP_TEXT_FILE_READER_H -#include -#include - #include "tokenizer.h" +#include + namespace LAMMPS_NS { class TextFileReader { diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index 33a81db748..3b172181a2 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -17,11 +17,11 @@ #include "tokenizer.h" #include "utils.h" +#include "fmt/format.h" + #include #include -#include "fmt/format.h" - using namespace LAMMPS_NS; TokenizerException::TokenizerException(const std::string & msg, const std::string & token){ From d0691d0a5d7291379293e3a3b45671c5a21458ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 01:32:15 -0400 Subject: [PATCH 63/72] add mapping for Eigen3 includes --- cmake/iwyu/iwyu-extra-map.imp | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index 8f6af087b4..a6d88cf571 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -1,4 +1,5 @@ [ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, + { include: [ "@", private, "", public ] }, ] From fc3d9fee5e4aeae2dc6ba04d1ee5fce475b59581 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 01:32:52 -0400 Subject: [PATCH 64/72] more USER-OMP updates --- src/USER-OMP/angle_charmm_omp.cpp | 2 +- src/USER-OMP/angle_class2_omp.cpp | 2 +- src/USER-OMP/angle_cosine_delta_omp.cpp | 2 +- src/USER-OMP/angle_cosine_omp.cpp | 2 +- src/USER-OMP/angle_cosine_periodic_omp.cpp | 2 +- src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/angle_cosine_shift_omp.cpp | 2 +- src/USER-OMP/angle_cosine_squared_omp.cpp | 2 +- src/USER-OMP/angle_dipole_omp.cpp | 2 +- src/USER-OMP/angle_fourier_omp.cpp | 2 +- src/USER-OMP/angle_fourier_simple_omp.cpp | 2 +- src/USER-OMP/angle_harmonic_omp.cpp | 2 +- src/USER-OMP/angle_quartic_omp.cpp | 2 +- src/USER-OMP/angle_sdk_omp.cpp | 2 +- src/USER-OMP/angle_table_omp.cpp | 2 +- src/USER-OMP/bond_class2_omp.cpp | 2 +- src/USER-OMP/bond_fene_expand_omp.cpp | 2 +- src/USER-OMP/bond_fene_omp.cpp | 2 +- src/USER-OMP/bond_gromos_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_omp.cpp | 2 +- src/USER-OMP/bond_morse_omp.cpp | 2 +- src/USER-OMP/bond_nonlinear_omp.cpp | 2 +- src/USER-OMP/bond_quartic_omp.cpp | 2 +- src/USER-OMP/bond_table_omp.cpp | 2 +- src/USER-OMP/dihedral_charmm_omp.cpp | 2 +- src/USER-OMP/dihedral_class2_omp.cpp | 2 +- .../dihedral_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/dihedral_fourier_omp.cpp | 2 +- src/USER-OMP/dihedral_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_helix_omp.cpp | 2 +- src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_nharmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_opls_omp.cpp | 2 +- src/USER-OMP/dihedral_quadratic_omp.cpp | 2 +- src/USER-OMP/dihedral_table_omp.cpp | 2 +- src/USER-OMP/fix_omp.cpp | 9 ++++---- src/USER-OMP/fix_rigid_nh_omp.cpp | 2 +- src/USER-OMP/fix_rigid_small_omp.cpp | 2 +- src/USER-OMP/improper_class2_omp.cpp | 2 +- src/USER-OMP/improper_cossq_omp.cpp | 2 +- src/USER-OMP/improper_cvff_omp.cpp | 2 +- src/USER-OMP/improper_fourier_omp.cpp | 2 +- src/USER-OMP/improper_harmonic_omp.cpp | 2 +- src/USER-OMP/improper_umbrella_omp.cpp | 2 +- src/USER-OMP/msm_cg_omp.cpp | 3 +++ src/USER-OMP/pair_adp_omp.cpp | 10 ++++----- src/USER-OMP/pair_airebo_morse_omp.cpp | 2 -- src/USER-OMP/pair_airebo_omp.cpp | 10 ++++----- src/USER-OMP/pair_beck_omp.cpp | 2 +- src/USER-OMP/pair_born_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_born_coul_msm_omp.cpp | 10 +++++---- src/USER-OMP/pair_born_coul_wolf_omp.cpp | 2 +- src/USER-OMP/pair_born_omp.cpp | 2 +- src/USER-OMP/pair_brownian_omp.cpp | 21 +++++++++---------- src/USER-OMP/pair_brownian_poly_omp.cpp | 20 +++++++++--------- src/USER-OMP/pair_buck_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_buck_coul_msm_omp.cpp | 10 +++++---- src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 14 ++++++------- src/USER-OMP/pair_buck_omp.cpp | 2 +- src/USER-OMP/pair_colloid_omp.cpp | 11 +++++----- src/USER-OMP/pair_comb_omp.cpp | 12 ++++++----- src/USER-OMP/pair_coul_cut_omp.cpp | 2 +- src/USER-OMP/pair_coul_debye_omp.cpp | 2 +- src/USER-OMP/pair_coul_dsf_omp.cpp | 2 +- src/USER-OMP/pair_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_coul_msm_omp.cpp | 10 +++++---- src/USER-OMP/pair_coul_wolf_omp.cpp | 2 +- src/USER-OMP/pair_dpd_omp.cpp | 2 +- src/USER-OMP/pair_dpd_tstat_omp.cpp | 11 +++++----- src/USER-OMP/pair_gauss_omp.cpp | 9 ++++---- src/USER-OMP/pair_gayberne_omp.cpp | 17 +++++++-------- src/USER-OMP/pair_lj96_cut_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 10 +++++---- src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_class2_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_class2_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cubic_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp | 13 ++++++------ src/USER-OMP/pair_lj_cut_coul_long_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 10 +++++---- src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_cut_omp.cpp | 7 +++---- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 2 +- src/USER-OMP/pair_lj_expand_omp.cpp | 9 ++++---- .../pair_lj_gromacs_coul_gromacs_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_gromacs_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 11 +++++----- src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 15 ++++++------- src/USER-OMP/pair_lj_smooth_linear_omp.cpp | 9 ++++---- src/USER-OMP/pair_lj_smooth_omp.cpp | 9 ++++---- src/USER-OMP/pair_lubricate_omp.cpp | 19 ++++++++--------- src/USER-OMP/pair_lubricate_poly_omp.cpp | 18 +++++++--------- src/USER-OMP/pair_morse_omp.cpp | 9 ++++---- src/USER-OMP/pair_reaxc_omp.cpp | 2 +- src/USER-OMP/pair_resquared_omp.cpp | 10 ++++----- src/USER-OMP/pair_soft_omp.cpp | 9 ++++---- src/USER-OMP/pair_table_omp.cpp | 8 +++---- src/USER-OMP/pair_ufm_omp.cpp | 9 ++++---- src/USER-OMP/pair_yukawa_colloid_omp.cpp | 9 ++++---- src/USER-OMP/pair_yukawa_omp.cpp | 9 ++++---- src/USER-OMP/pair_zbl_omp.cpp | 9 ++++---- src/USER-OMP/pppm_disp_omp.cpp | 13 ++++++------ src/USER-OMP/thr_omp.cpp | 2 +- 108 files changed, 338 insertions(+), 305 deletions(-) diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 6933afdcd9..abc23367b1 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index 09ee59d5af..b33b1c2e2f 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index ca5afe1449..0c209d3fe5 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 48fdd9ba60..cbeb10e08c 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index a0e45fe131..b59046031a 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 21019336b3..4870e6a3bb 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 1e6d712b62..bec65caf6d 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6df1e028a0..dced90a967 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index 26d8a7817e..cea707161f 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -23,7 +23,7 @@ #include "error.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b6ddea3ff9..ec9236902c 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 992acf7c99..774f06f809 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 0cfc6f95af..5c81e3cba4 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index a774edb8c4..d6e9285f11 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e0bc021f1b..45d6c83aa1 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -20,7 +20,7 @@ #include #include "atom.h" #include "neighbor.h" -#include "timer.h" + #include "comm.h" #include "force.h" #include "lj_sdk_common.h" diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index 1af60f85f6..f67d340176 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 06edf46024..9c52bdb281 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index 5f3dd48841..38df4f50da 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index ebf5afdc57..5dde355a76 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index d4d2d25601..012737f77d 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index 9160ee7023..e8f17d5eae 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 7a6c616e4a..61a60fa995 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 19f0a08510..50b4ed98a7 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index 90318c8faf..51586370f5 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 809950f2b7..720d660eae 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index 0efaa10e37..bc1ae96ac9 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index f503bcab26..3ccc65441a 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index afd3071434..8454dc1004 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 49b8659e2f..cf65d735a6 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index cea22adf1b..5d9164d3b3 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 756931774a..be19a6d958 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index d1f511954e..3d51a4db43 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 5289fc2c62..5209fac23a 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index edf8a20899..a6e0ab66d6 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index bf51a01713..4604771912 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 8814d3f3f0..ff0f6bb12b 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index e61c5f0d85..5ffb8d64f2 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index bf5332a1c1..c18d5fb4c0 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -23,7 +23,7 @@ #include "domain.h" #include "neighbor.h" #include "force.h" -#include "timer.h" + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 47757c4ec3..f3c86a7746 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -16,7 +16,9 @@ OpenMP based threading support for LAMMPS ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "fix_omp.h" +#include "thr_data.h" + #include "atom.h" #include "comm.h" #include "error.h" @@ -25,10 +27,6 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "timer.h" - -#include "fix_omp.h" -#include "thr_data.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -39,6 +37,7 @@ #include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index f53fcf63bc..9038efec13 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -31,7 +31,7 @@ #include "kspace.h" #include "modify.h" #include "update.h" -#include "timer.h" + #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 227b0e1f8a..f720dd617e 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -24,7 +24,7 @@ #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" -#include "timer.h" + #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 8927980951..05fc8e4475 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 72d76e8c42..e2a43c58c4 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index e9ff4bfc73..715819cfb9 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index 3763465e79..93dfb9bc99 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -23,7 +23,7 @@ #include "force.h" #include "neighbor.h" #include "suffix.h" -#include "timer.h" + #include "update.h" #include diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 8bef42bf23..6bb76871b2 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index bf466afb19..0c9befade6 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 93904fd8f8..c42aa8e0c1 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -31,6 +31,9 @@ #include #include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 63a539c93c..97d94e5513 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -12,19 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_adp_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/USER-OMP/pair_airebo_morse_omp.cpp index 5d5ac0b885..6977842af2 100644 --- a/src/USER-OMP/pair_airebo_morse_omp.cpp +++ b/src/USER-OMP/pair_airebo_morse_omp.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_omp.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 25d6c35174..77dd874076 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -12,19 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_airebo_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" +#include "math_special.h" #include "memory.h" #include "my_page.h" -#include "math_special.h" -#include "neighbor.h" #include "neigh_list.h" +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index bb41334153..01e33dc5c5 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_special.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index 7f92ab6734..b410c998e1 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index eec1765859..4adba396e8 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index ffa069ec4e..9bc6507c6a 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index aaac28d07c..e74f0139c1 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index ca28fa14bb..b7b82c3dac 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,26 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "variable.h" -#include "random_mars.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" - -#include "fix_wall.h" - +#include "neigh_list.h" +#include "random_mars.h" #include "suffix.h" +#include "update.h" +#include "variable.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 939bc223eb..4d8b457281 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,25 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" - #include "math_const.h" #include "math_special.h" - +#include "neigh_list.h" +#include "random_mars.h" #include "suffix.h" +#include "update.h" +#include "variable.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 1be2b7272f..264073a07e 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index b26243b19a..631a1ee61d 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index a2e34b9a1b..71b1540e8c 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -11,18 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -#include "omp_compat.h" -#include -#include "math_vector.h" #include "pair_buck_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" #include "force.h" - +#include "math_vector.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index fc85d79c81..bddacaf5b5 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index cce588f516..94325232fc 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_special.h" - +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 8912cbc243..9a0155d6d3 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -12,19 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_comb_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "group.h" -#include "force.h" #include "memory.h" #include "my_page.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; #define MAXNEIGH 24 diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 69eb9ac0f3..57b821cb8b 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index c22f7340c4..1bb8676998 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index ddcc8dbeb0..3a8db45634 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index 6c9b9d034d..92cb51f7a4 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index 32a657e286..e907d63eb1 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index d0f6fdb125..71e8148a50 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index f3a1c29a70..6e3da77cbe 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "update.h" #include "random_mars.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index 06e80274bd..823367109b 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_dpd_tstat_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" #include "random_mars.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 103a766614..3e5777e4ec 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index f0fd60a309..991c72a9be 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gayberne_omp.h" -#include "math_extra.h" -#include "atom.h" -#include "comm.h" -#include "atom_vec_ellipsoid.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "force.h" +#include "math_extra.h" +#include "neigh_list.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index adf0aac9b2..5aeec25d13 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj96_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index 437bd183ed..56cf0a68dd 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index 0000e63cda..a39ef0aa81 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 59a6841c9e..63fb4fe529 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index 480e2adae0..f618f7f423 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index 2b91e10cfa..39cc320e44 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 778c25393d..27f6132491 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cubic_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index d560b803f1..2f46e0bfe7 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 79754e704b..82031f91ab 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_debye_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index ec69a1a1ca..7ab6f31b3f 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_dsf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - -#include "suffix.h" #include "math_const.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index 618986389c..c7b6de8022 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index 58e5cee0c2..0e6d11327a 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index 7d5d25c39b..2cc915a435 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_dipole_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 3e7e92de21..2aa71026e3 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index fb579fb980..9296050173 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -32,7 +32,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "timer.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index 70b5e436fa..89077ba6af 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_expand_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 0f0a8de2ff..26a6e979b4 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_coul_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index ea2c9e8f55..3082091539 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index e74f487129..d869d91d09 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "math_vector.h" #include "force.h" -#include "neighbor.h" +#include "math_vector.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index 9c8de110d7..af24e93a41 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -12,20 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_tip4p_long_omp.h" + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "math_vector.h" -#include "force.h" -#include "neighbor.h" +#include "domain.h" #include "error.h" +#include "force.h" #include "memory.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index 497c2c3a43..2c0c028189 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index bdb9b3141e..0b4ea4e5f8 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 9db4239587..827fae8e44 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -12,24 +12,23 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lubricate_omp.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" #include "math_const.h" - +#include "neigh_list.h" +#include "neighbor.h" #include "suffix.h" +#include "variable.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index dc143a3160..feb110194f 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,24 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lubricate_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" #include "math_const.h" - +#include "neigh_list.h" #include "suffix.h" +#include "variable.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 1f566dbd42..48687781ef 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 08efb73aab..dfc1f428eb 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -48,7 +48,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "timer.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index 557d212531..689ff297e5 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -12,18 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_resquared_omp.h" -#include "math_extra.h" + #include "atom.h" #include "comm.h" -#include "atom_vec_ellipsoid.h" #include "force.h" -#include "neighbor.h" +#include "math_extra.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index 85425974cc..f733b5106f 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index 2546bfdc9a..f5fbabccab 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index 605d6dd2c6..e1c2ff457e 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -14,16 +14,17 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_ufm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index e6ac3fa9fb..227ec0744f 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index f222876cb5..347575e283 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 284ebbf09c..9679a00b24 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_zbl_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairZBLConstants; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index aad77cffc7..96a2cc282e 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,23 +16,24 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index c086f6d6b5..6e096defa8 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "modify.h" #include "neighbor.h" -#include "timer.h" + #include "thr_omp.h" From bb7447363cd00147c0b3288de48b3ec90d11a77b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 07:22:39 -0400 Subject: [PATCH 65/72] more include cleanup and IWYU tweaks --- src/KIM/kim_param.cpp | 1 - src/KIM/pair_kim.cpp | 13 ++++----- src/MISC/fix_orient_fcc.cpp | 24 +++++++--------- src/MLIAP/mliap_model.cpp | 1 - src/SPIN/min_spin.cpp | 16 +++++------ src/SPIN/min_spin_cg.cpp | 19 ++++++------- src/SPIN/min_spin_lbfgs.cpp | 18 ++++++------ src/SPIN/neb_spin.cpp | 29 +++++++++----------- src/SPIN/pair_spin_dipole_cut.cpp | 11 +++----- src/SPIN/pair_spin_dipole_long.cpp | 11 +++----- src/SPIN/pair_spin_dmi.cpp | 9 ++---- src/SPIN/pair_spin_exchange.cpp | 9 ++---- src/SPIN/pair_spin_magelec.cpp | 9 ++---- src/SPIN/pair_spin_neel.cpp | 9 ++---- src/SRD/fix_wall_srd.cpp | 12 ++++---- src/USER-ATC/fix_atc.cpp | 18 ++++-------- src/USER-ATC/fix_atc.h | 1 - src/USER-AWPMD/atom_vec_wavepacket.cpp | 5 ++-- src/USER-AWPMD/pair_awpmd_cut.cpp | 23 ++++++++-------- src/USER-BOCS/compute_pressure_bocs.cpp | 9 ++---- src/USER-COLVARS/fix_colvars.cpp | 15 ++++------ src/USER-COLVARS/fix_colvars.h | 1 - src/USER-COLVARS/group_ndx.cpp | 5 ++-- src/USER-COLVARS/ndx_group.cpp | 8 +++--- src/USER-DIFFRACTION/compute_saed.cpp | 22 +++++++-------- src/USER-DIFFRACTION/compute_xrd.cpp | 24 ++++++++-------- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 13 ++++----- src/USER-DPD/fix_eos_cv.cpp | 2 +- src/USER-DPD/fix_eos_table.cpp | 4 +-- src/USER-DPD/fix_shardlow.cpp | 23 ++++++++-------- src/USER-DPD/pair_dpd_fdt.cpp | 13 ++++----- src/USER-DPD/pair_dpd_fdt_energy.cpp | 13 ++++----- src/USER-EFF/atom_vec_electron.cpp | 5 ++-- src/USER-EFF/fix_nh_eff.cpp | 2 +- src/USER-MANIFOLD/fix_manifoldforce.cpp | 13 ++++----- src/USER-MANIFOLD/manifold_gaussian_bump.cpp | 2 ++ src/USER-MEAMC/meam.h | 16 ++++++++++- src/USER-MEAMC/meam_dens_final.cpp | 12 ++++++++ src/USER-MEAMC/meam_dens_init.cpp | 12 ++++++++ src/USER-MEAMC/meam_force.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_done.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_global.cpp | 12 ++++++++ src/USER-MEAMC/meam_setup_param.cpp | 12 ++++++++ src/USER-MESODPD/atom_vec_edpd.cpp | 15 ++++------ src/USER-MESODPD/compute_tdpd_cc_atom.cpp | 11 ++++---- src/USER-MESODPD/fix_edpd_source.cpp | 7 +++-- src/USER-MESODPD/fix_tdpd_source.cpp | 7 +++-- src/USER-MESODPD/pair_mdpd_rhosum.cpp | 8 +++--- src/USER-MISC/fix_propel_self.cpp | 1 - 49 files changed, 291 insertions(+), 258 deletions(-) diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index ae4ca9b13d..6f4ac5cc21 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -57,7 +57,6 @@ #include "kim_param.h" -#include "comm.h" #include "error.h" #include "fix_store_kim.h" #include "force.h" diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 3422f93f3a..7ed70972c5 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -55,21 +55,20 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ #include "pair_kim.h" -#include - -#include #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "memory.h" -#include "domain.h" -#include "error.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index bcbdcfabc5..f391eab91e 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -16,25 +16,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_fcc.h" -#include -#include - - #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "force.h" -#include "math_const.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" - +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index ac82a671d4..b731e1c9f8 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -13,7 +13,6 @@ #include "mliap_model.h" -#include "atom.h" #include "comm.h" #include "error.h" #include "memory.h" diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index df7fc71f8b..f36f11f2a9 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -18,17 +18,17 @@ ------------------------------------------------------------------------- */ #include "min_spin.h" -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "output.h" -#include "timer.h" #include "error.h" #include "math_const.h" +#include "output.h" +#include "timer.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index a658713d1b..4b8b745419 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -21,25 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_cg.h" -#include "universe.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index f92fc69e04..40029b7e71 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -21,24 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_lbfgs.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 96808b7f10..a89ca403ce 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -22,29 +22,26 @@ ------------------------------------------------------------------------- */ #include "neb_spin.h" -#include -#include -#include -#include -#include "citeme.h" -#include "force.h" -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" +#include "citeme.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb_spin.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4da05c57cb..b27c9736b2 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -23,19 +23,16 @@ #include "pair_spin_dipole_cut.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 605370f7f1..d4b1b8e43e 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -18,20 +18,17 @@ #include "pair_spin_dipole_long.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 0a5bde2c9f..e27f9fad7d 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -23,18 +23,15 @@ #include "pair_spin_dmi.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "fix.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index a932aa5c54..27da47dd0f 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -23,18 +23,15 @@ #include "pair_spin_exchange.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 65a2904228..2242cf985d 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -23,18 +23,15 @@ #include "pair_spin_magelec.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index ceb487d378..33ea904c0c 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -23,18 +23,15 @@ #include "pair_spin_neel.h" -#include -#include #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 461dc5f5ad..8ffd764447 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -13,17 +13,17 @@ #include "fix_wall_srd.h" -#include -#include "fix.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix.h" #include "input.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" #include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 2165132856..dd02676466 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -12,23 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_atc.h" -#include -#include -#include -#include "fix_nve.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "pointers.h" #include "comm.h" +#include "error.h" #include "group.h" +#include "neigh_request.h" +#include "neighbor.h" #include "ATC_Method.h" -#include "ATC_Transfer.h" #include "ATC_TransferKernel.h" #include "ATC_TransferPartitionOfUnity.h" #include "ATC_CouplingEnergy.h" @@ -37,6 +29,8 @@ #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; using std::string; diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index 2512c658db..5bf26f6eaa 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -8,7 +8,6 @@ FixStyle(atc,FixATC) #define FIX_ATC_H #include "fix.h" -#include "pointers.h" // access to lammps pointers namespace ATC { class ATC_Method; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 0d11e983ad..46b239be08 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -16,9 +16,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_wavepacket.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index d492cd082d..5e23b7fc69 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -17,28 +17,29 @@ #include "pair_awpmd_cut.h" -#include -#include -#include -#include #include "atom.h" -#include "update.h" -#include "min.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" +#include "min.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" - +#include "neighbor.h" +#include "update.h" #include "logexc.h" #include "vector_3.h" #include "TCP/wpmd.h" #include "TCP/wpmd_split.h" +#include +#include +#include +#include +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 4af2356e1a..a4b8de84bd 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,11 +16,6 @@ #include "compute_pressure_bocs.h" - -#include -#include - - #include "angle.h" #include "atom.h" #include "bond.h" @@ -28,15 +23,15 @@ #include "domain.h" #include "error.h" #include "fix.h" - #include "force.h" #include "improper.h" #include "kspace.h" -#include "memory.h" #include "modify.h" #include "pair.h" #include "update.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index fc575c2e79..fcbfb58456 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -26,28 +26,25 @@ #include "fix_colvars.h" - -#include -#include - -#include -#include - #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "respa.h" #include "universe.h" #include "update.h" -#include "citeme.h" #include "colvarproxy_lammps.h" #include "colvarmodule.h" +#include +#include +#include +#include + static const char colvars_pub[] = "fix colvars command:\n\n" "@Article{fiorin13,\n" diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index 2486446f35..fff61ce218 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" -#include class colvarproxy_lammps; diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 1e37e2de9c..07a8ac2d5c 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,12 +17,11 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index feab2f22b2..bab1592b1e 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,13 +17,13 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" + +#include using namespace LAMMPS_NS; #define BUFLEN 4096 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 677bf62a25..d16fbf2876 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,23 +15,23 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_saed.h" -#include - -#include -#include "math_const.h" -#include "compute_saed_consts.h" #include "atom.h" -#include "comm.h" -#include "update.h" -#include "domain.h" -#include "group.h" #include "citeme.h" -#include "memory.h" +#include "comm.h" +#include "compute_saed_consts.h" +#include "domain.h" #include "error.h" +#include "group.h" +#include "math_const.h" +#include "memory.h" +#include "update.h" +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index 0dac7aca5e..b48de49c81 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,23 +16,23 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_xrd.h" +#include "compute_xrd_consts.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "math_const.h" +#include "memory.h" +#include "update.h" #include - #include -#include "math_const.h" -#include "compute_xrd_consts.h" -#include "atom.h" -#include "comm.h" -#include "update.h" -#include "domain.h" -#include "group.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 08833db224..39382264c4 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -18,17 +18,16 @@ #include "fix_saed_vtk.h" -#include -#include -#include "update.h" -#include "modify.h" #include "compute.h" #include "compute_saed.h" -#include "memory.h" -#include "error.h" -#include "force.h" #include "domain.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index bd0e334ffc..db9b877b1c 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_eos_cv.h" + #include "atom.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 7134eaca22..57cfe03dc8 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -17,13 +17,11 @@ #include "fix_eos_table.h" - -#include #include "atom.h" #include "error.h" -#include "force.h" #include "memory.h" +#include #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index e533140dd6..c4480a0373 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -35,26 +35,25 @@ #include "fix_shardlow.h" -#include -#include -#include #include "atom.h" -#include "force.h" -#include "update.h" -#include "error.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "npair.h" -#include "memory.h" -#include "domain.h" -#include "modify.h" +#include "npair_half_bin_newton_ssa.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "npair_half_bin_newton_ssa.h" -#include "citeme.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index c988f4205c..1d3d952e9f 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -17,20 +17,19 @@ #include "pair_dpd_fdt.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 9231ab7ba3..b843e4601a 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -17,20 +17,19 @@ #include "pair_dpd_fdt_energy.h" -#include -#include #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 0912fb0498..65923d2e75 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_electron.h" -#include + #include "atom.h" #include "citeme.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 9fdbc6a0bf..d5b574510c 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -17,8 +17,8 @@ #include "fix_nh_eff.h" + #include "atom.h" -#include "atom_vec.h" #include "error.h" #include "domain.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index b016dd8ecb..732ba0909e 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -13,16 +13,15 @@ #include "fix_manifoldforce.h" // For stuff -#include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "force.h" - #include "manifold.h" #include "manifold_factory.h" // For constructing manifold +#include "atom.h" +#include "error.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index b9b7ae7279..ef26999295 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -3,6 +3,8 @@ #include "comm.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index b4f8fd341b..b974ce5bc8 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,9 +1,23 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MEAM_H #define LMP_MEAM_H +#include "math_const.h" // IWYU pragma: export + #include #include -#include "math_const.h" #define maxelt 5 diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index fe9e74ca7c..02c461e6b7 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index dcaa5866de..7a5ee7a651 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index df1f8f9a1d..eba4f79ea9 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index f493d9dcac..ddbb40310c 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include "math_special.h" diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index c5f3115249..93b866a14f 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" #include diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp index ea76ee896c..f2c44504de 100644 --- a/src/USER-MEAMC/meam_setup_param.cpp +++ b/src/USER-MEAMC/meam_setup_param.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index c3fae823ea..1542c73604 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -12,16 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_edpd.h" -#include -#include "atom.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "update.h" -#include "memory.h" -#include "error.h" +#include "atom.h" +#include "error.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp index bc02c93e1a..7e9d5eb29e 100644 --- a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp +++ b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp @@ -11,15 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_tdpd_cc_atom.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/fix_edpd_source.cpp b/src/USER-MESODPD/fix_edpd_source.cpp index 9d31e5f410..c84f2f29a2 100644 --- a/src/USER-MESODPD/fix_edpd_source.cpp +++ b/src/USER-MESODPD/fix_edpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_edpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/fix_tdpd_source.cpp b/src/USER-MESODPD/fix_tdpd_source.cpp index 7c19d78b1f..440c5055fb 100644 --- a/src/USER-MESODPD/fix_tdpd_source.cpp +++ b/src/USER-MESODPD/fix_tdpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_tdpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp index def61dea8f..2f25177b0a 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.cpp +++ b/src/USER-MESODPD/pair_mdpd_rhosum.cpp @@ -20,16 +20,16 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd_rhosum.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index 522c2eb4a5..1b0d780c69 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -22,7 +22,6 @@ #include "atom.h" #include "atom_vec_ellipsoid.h" #include "error.h" -#include "math.h" #include "math_const.h" #include "math_extra.h" From 63e5ca53ef2cec88c38f4742c45de6c2cf7d8d55 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:00:38 -0400 Subject: [PATCH 66/72] add iwyu mappings for gtest and gmock --- cmake/iwyu/iwyu-extra-map.imp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index a6d88cf571..c212cc56dd 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -2,4 +2,6 @@ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, { include: [ "@", private, "", public ] }, + { include: [ "@\"gtest/.*\"", private, "\"gtest/gtest.h\"", public ] }, + { include: [ "@\"gmock/.*\"", private, "\"gmock/gmock.h\"", public ] }, ] From 91a87b745f7567d074a6eff918db7e7133c85245 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:01:11 -0400 Subject: [PATCH 67/72] final second round IWYU cleanup --- src/USER-MOLFILE/molfile_interface.cpp | 4 +-- src/USER-MOLFILE/reader_molfile.cpp | 13 ++++--- src/USER-OMP/fix_nh_asphere_omp.cpp | 10 ++---- src/USER-OMP/fix_rigid_nh_omp.cpp | 12 +++---- src/USER-OMP/pair_agni_omp.cpp | 18 +++++----- src/USER-OMP/pair_buck_coul_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 1 + src/USER-OMP/pair_coul_cut_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_coul_diel_omp.cpp | 9 ++--- src/USER-OMP/pair_coul_long_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_eam_alloy_omp.cpp | 12 +++---- src/USER-OMP/pair_eam_fs_omp.cpp | 12 +++---- src/USER-OMP/pair_eam_omp.cpp | 11 +++--- src/USER-OMP/pair_edip_omp.cpp | 9 +++-- src/USER-OMP/pair_eim_omp.cpp | 11 +++--- src/USER-OMP/pair_gauss_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp | 14 ++++---- .../pair_hbond_dreiding_morse_omp.cpp | 14 ++++---- ...air_lj_charmm_coul_charmm_implicit_omp.cpp | 7 ++-- .../pair_lj_charmm_coul_charmm_omp.cpp | 9 ++--- .../pair_lj_charmm_coul_long_soft_omp.cpp | 9 ++--- .../pair_lj_cut_coul_cut_soft_omp.cpp | 9 ++--- .../pair_lj_cut_coul_long_soft_omp.cpp | 9 ++--- src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp | 13 +++---- src/USER-OMP/pair_lj_cut_soft_omp.cpp | 7 ++-- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 12 +++---- src/USER-OMP/pair_lj_cut_thole_long_omp.h | 1 - src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 1 + src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp | 12 +++---- src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 12 +++---- src/USER-OMP/pair_lj_sdk_omp.cpp | 12 +++---- src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 9 ++--- src/USER-OMP/pair_lubricate_omp.cpp | 1 - src/USER-OMP/pair_meam_spline_omp.cpp | 13 ++++--- src/USER-OMP/pair_morse_smooth_linear_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 9 ++--- src/USER-OMP/pair_nm_cut_omp.cpp | 9 ++--- src/USER-OMP/pair_peri_lps_omp.cpp | 20 +++++------ src/USER-OMP/pair_peri_pmb_omp.cpp | 16 ++++----- src/USER-OMP/pair_sw_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_mod_c_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_mod_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_omp.cpp | 8 ++--- src/USER-OMP/pair_tersoff_table_omp.cpp | 11 +++--- src/USER-OMP/pair_tersoff_zbl_omp.cpp | 15 +++----- src/USER-OMP/pair_vashishta_omp.cpp | 8 ++--- src/USER-OMP/pair_vashishta_table_omp.cpp | 8 ++--- src/USER-OMP/reaxc_bond_orders_omp.cpp | 7 ++-- src/USER-OMP/reaxc_bond_orders_omp.h | 1 - src/USER-OMP/reaxc_forces_omp.cpp | 3 +- src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp | 7 ++-- src/USER-OMP/reaxc_init_md_omp.h | 2 ++ src/USER-OMP/reaxc_nonbonded_omp.cpp | 4 +-- src/USER-PHONON/dynamical_matrix.cpp | 27 +++++++------- src/USER-PHONON/third_order.cpp | 29 ++++++++------- src/USER-PTM/ptm_deformation_gradient.h | 4 ++- src/USER-REACTION/fix_bond_react.cpp | 35 ++++++++++--------- .../pair_sdpd_taitwater_isothermal.cpp | 15 ++++---- .../fix_smd_move_triangulated_surface.cpp | 13 +++---- src/USER-SMD/fix_smd_setvel.cpp | 16 ++++----- src/USER-SMD/fix_smd_wall_surface.cpp | 15 ++++---- src/USER-SMD/pair_smd_ulsph.cpp | 20 +++++------ src/USER-SMD/smd_material_models.cpp | 5 +-- src/USER-SPH/atom_vec_sph.cpp | 5 +-- src/USER-SPH/pair_sph_rhosum.cpp | 9 +++-- 66 files changed, 335 insertions(+), 350 deletions(-) diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 798beaee09..90a5781fff 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "molfile_interface.h" +#include "molfile_plugin.h" #include #include -#include #include #include #include @@ -31,8 +31,6 @@ #include #endif -#include "molfile_plugin.h" - #if vmdplugin_ABIVERSION < 16 #error "unsupported VMD molfile plugin ABI version" #endif diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 292a451a87..d26a4d4ba0 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "reader_molfile.h" -#include -#include -#include "comm.h" -#include "memory.h" -#include "error.h" - #include "molfile_interface.h" -#include "math_const.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; typedef MolfileInterface MFI; using namespace MathConst; diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index f097e93be2..26cad769ec 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -15,19 +15,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include - -#include -#include "math_extra.h" #include "fix_nh_asphere_omp.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "compute.h" -#include "group.h" -#include "memory.h" #include "error.h" +#include "math_extra.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 9038efec13..d56b633bd0 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_rigid_nh_omp.h" -#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -29,18 +27,20 @@ #include "error.h" #include "force.h" #include "kspace.h" +#include "math_const.h" +#include "math_extra.h" #include "modify.h" +#include "rigid_const.h" #include "update.h" +#include +#include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "math_extra.h" -#include "math_const.h" -#include "rigid_const.h" - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index b61bf52e4e..de6903aab9 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -12,21 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include // requires C++-11 #include "pair_agni_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_special.h" #include "math_const.h" - +#include "math_special.h" +#include "neigh_list.h" #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index 4154c1281c..1c433f8083 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index 71b1540e8c..00ab1c248c 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -21,6 +21,7 @@ #include "suffix.h" #include +#include #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index 89222903ec..f8b3a36e39 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index 656cdc9421..62f2580426 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_diel_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index ff3267fb38..28ba13d5cf 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index f0823204c0..c7559420bc 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_alloy_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 89590bb3e6..66a7581c21 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include - -#include #include "pair_eam_fs_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" - -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 60ae65def5..e6ba299a4d 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eam_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 0e59674b0e..864ff68f7a 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_edip_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" using namespace LAMMPS_NS; +#include + +#include "omp_compat.h" #define GRIDDENSITY 8000 #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index 02b765a956..74b460a788 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eim_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index 6d5344701d..a453915738 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index bb8bbcc984..338eb52453 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_lj_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 4ad3a8f057..5094d5c193 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_morse_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index f357fd9068..3ff02b6109 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_implicit_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index 55227e2e10..77caf63f18 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index b32f108098..e19632dc7e 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index 1c88600e7a..03f0852b06 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index ce84ba01c3..6e804bd8ae 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 4111c5b22c..0e9a333121 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_wolf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - -#include "suffix.h" #include "math_const.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 5064c4705e..406c5f41d9 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 9296050173..b921c8f1c1 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,25 +15,21 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lj_cut_thole_long_omp.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "fix_drude.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "error.h" +#include "neigh_list.h" #include "suffix.h" +#include +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/USER-OMP/pair_lj_cut_thole_long_omp.h index dc64c5c3a2..212f3c4e2e 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.h @@ -20,7 +20,6 @@ PairStyle(lj/cut/thole/long/omp,PairLJCutTholeLongOMP) #ifndef LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H #define LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H -#include "pair.h" #include "pair_lj_cut_thole_long.h" #include "thr_omp.h" diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index d869d91d09..cdd62ff96e 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -22,6 +22,7 @@ #include "suffix.h" #include +#include #include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index 4ad082cde1..4a53f2c083 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -12,18 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_long_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - -#include "lj_sdk_common.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 4871356b18..4b89375b5b 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -13,19 +13,19 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_msm_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - -#include "lj_sdk_common.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index 9f0671c61c..d5146c6798 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -13,18 +13,18 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - -#include "lj_sdk_common.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 1adaf93953..8828b40b98 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sf_dipole_sf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 827fae8e44..caf5a11124 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -22,7 +22,6 @@ #include "input.h" #include "math_const.h" #include "neigh_list.h" -#include "neighbor.h" #include "suffix.h" #include "variable.h" diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index 19fb09dd7b..782371e843 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_meam_spline_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index f2ab417028..220fb9481d 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -13,16 +13,17 @@ Most code borrowed from pair_morse_omp.cpp ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index 4326434450..1cfe576a32 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index 970b383f7e..d9e1231827 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index a937668fdd..a232da1a90 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index cf29b5cab8..9bf707ad91 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -12,24 +12,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_lps_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" - +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 1990b46fe5..28df45b67f 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -12,23 +12,23 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_pmb_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index ebe501ff8e..c2eb4cb156 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_sw_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 5e1e6b1b0e..83baa56e44 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -12,16 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_c_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index aa90b88375..ab2f07322d 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -12,16 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index 34dbfb73b6..a367749978 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index a0a7f4c810..8321ad9d9f 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index d1d808307a..7bb3814549 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -16,26 +16,19 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include - -#include #include "pair_tersoff_zbl_omp.h" -#include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" #include "memory.h" #include "error.h" - #include "tokenizer.h" #include "potential_file_reader.h" - #include "math_const.h" #include "math_special.h" + +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 425a06c296..0637fe3dfc 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index 36c86a8995..9650a57e72 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_table_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index d581819e00..85a77370fa 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -27,8 +27,8 @@ ----------------------------------------------------------------------*/ #include "reaxc_bond_orders_omp.h" -#include -#include +#include "reaxc_bond_orders.h" + #include "fix_omp.h" #include "reaxc_defs.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,9 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h index 36be3337ad..2027a8628e 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.h +++ b/src/USER-OMP/reaxc_bond_orders_omp.h @@ -30,7 +30,6 @@ #define __BOND_ORDERS_OMP_H_ #include "reaxc_types.h" -#include "reaxc_bond_orders.h" void Add_dBond_to_ForcesOMP( reax_system*, int, int, storage*, reax_list** ); void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int, diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index ce38cb0544..ad6ea35eb8 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -28,6 +28,7 @@ #include "reaxc_forces_omp.h" +#include "error.h" #include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" @@ -45,8 +46,6 @@ #include #include -#include "omp_compat.h" - #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 22d9df7702..029062470d 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,10 +26,8 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_hydrogen_bonds_omp.h" -#include -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" @@ -38,6 +36,9 @@ #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_init_md_omp.h b/src/USER-OMP/reaxc_init_md_omp.h index 8416a768cf..45478ec632 100644 --- a/src/USER-OMP/reaxc_init_md_omp.h +++ b/src/USER-OMP/reaxc_init_md_omp.h @@ -31,6 +31,8 @@ #include "reaxc_types.h" +#include + void InitializeOMP( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); #endif diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index 564088880a..3c3ca12575 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -27,17 +27,17 @@ ----------------------------------------------------------------------*/ #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index adfcf6adb5..238aa7c96e 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -2,28 +2,29 @@ // Created by charlie sievers on 6/21/18. // -#include -#include -#include #include "dynamical_matrix.h" -#include "atom.h" -#include "domain.h" -#include "comm.h" -#include "error.h" -#include "group.h" -#include "force.h" -#include "memory.h" -#include "bond.h" + #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "memory.h" #include "modify.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" +#include "update.h" + +#include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index 6e09710833..e15b82fbab 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -3,29 +3,28 @@ // #include "third_order.h" -#include -#include -#include -#include "atom.h" -#include "domain.h" -#include "comm.h" -#include "error.h" -#include "group.h" -#include "force.h" -#include "memory.h" -#include "bond.h" + #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "math_special.h" +#include "memory.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" -#include "math_special.h" +#include "update.h" + +#include #include -#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h index 546efab437..6c686431f6 100644 --- a/src/USER-PTM/ptm_deformation_gradient.h +++ b/src/USER-PTM/ptm_deformation_gradient.h @@ -10,9 +10,11 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #ifndef PTM_DEFORMATION_GRADIENT_H #define PTM_DEFORMATION_GRADIENT_H -#include #include "ptm_constants.h" +#include +#include + namespace ptm { void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 0370d83fdc..5d57b74056 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -17,35 +17,36 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "fix_bond_react.h" -#include -#include - -#include "update.h" -#include "modify.h" -#include "respa.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" +#include "citeme.h" #include "comm.h" #include "domain.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "reset_mol_ids.h" -#include "molecule.h" +#include "error.h" +#include "force.h" #include "group.h" -#include "citeme.h" +#include "input.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "input.h" +#include "modify.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "random_mars.h" +#include "reset_mol_ids.h" +#include "respa.h" +#include "update.h" #include "variable.h" #include "superpose3d.h" +#include +#include +#include + #include using namespace LAMMPS_NS; diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index 9d52ee2250..bf2fc73b01 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -19,18 +19,19 @@ ------------------------------------------------------------------------- */ #include "pair_sdpd_taitwater_isothermal.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "update.h" +#include + #ifndef USE_ZEST #include "random_mars.h" #endif diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index 2aa6f980ed..e0e76a18fb 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -23,15 +23,16 @@ ------------------------------------------------------------------------- */ #include "fix_smd_move_triangulated_surface.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "update.h" + #include #include #include -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "update.h" -#include "error.h" -#include "math_const.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 90589f3044..d3e71f0e50 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -25,17 +25,17 @@ #include "fix_smd_setvel.h" -#include #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index c61fe14353..10f248c39f 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -17,16 +17,15 @@ #include "fix_smd_wall_surface.h" -#include - -#include #include "atom.h" -#include "domain.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" #include "atom_vec.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index e9cf256c3c..3a6cdf5d2f 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -24,23 +24,21 @@ #include "pair_smd_ulsph.h" -#include -#include - -#include #include "atom.h" -#include "domain.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include "smd_kernels.h" #include "smd_material_models.h" #include "smd_math.h" -#include "smd_kernels.h" +#include "update.h" + +#include +#include using namespace SMD_Kernels; using namespace std; diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 096600df52..942b6a8cab 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -22,12 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "smd_material_models.h" + +#include "math_special.h" + #include #include -#include #include #include -#include "math_special.h" #include diff --git a/src/USER-SPH/atom_vec_sph.cpp b/src/USER-SPH/atom_vec_sph.cpp index 2811c57e6c..93ca2b60a7 100644 --- a/src/USER-SPH/atom_vec_sph.cpp +++ b/src/USER-SPH/atom_vec_sph.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sph.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 429d4199a4..3d3065f839 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "pair_sph_rhosum.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" #include "update.h" -#include "domain.h" - using namespace LAMMPS_NS; From 2d802411e99ee55b1a392bf52e2a43a35e0cc916 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:03:53 -0400 Subject: [PATCH 68/72] remove pointless stringstream abuse --- src/USER-PHONON/third_order.cpp | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index e15b82fbab..e7997d6397 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -169,13 +169,11 @@ void ThirdOrder::options(int narg, char **arg) if (narg < 0) error->all(FLERR,"Illegal third_order command"); int iarg = 0; const char *filename = "third_order.dat"; - std::stringstream fss; while (iarg < narg) { if (strcmp(arg[iarg],"file") == 0) { if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command"); - fss << arg[iarg + 1]; - filename = fss.str().c_str(); + filename = arg[iarg + 1]; file_flag = 1; iarg += 2; } else if (strcmp(arg[iarg],"binary") == 0) { From d6ba95bed6b982df025cbb219a8adb985e0ef5f1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 08:05:59 -0400 Subject: [PATCH 69/72] minor tweaks --- src/MLIAP/compute_mliap.cpp | 1 - src/USER-OMP/pair_airebo_omp.cpp | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/MLIAP/compute_mliap.cpp b/src/MLIAP/compute_mliap.cpp index aad28c7bb1..956cb0196f 100644 --- a/src/MLIAP/compute_mliap.cpp +++ b/src/MLIAP/compute_mliap.cpp @@ -22,7 +22,6 @@ #include "update.h" #include "modify.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "force.h" #include "pair.h" diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 77dd874076..837734d6e4 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -21,6 +21,7 @@ #include "memory.h" #include "my_page.h" #include "neigh_list.h" +#include "suffix.h" #include @@ -29,7 +30,6 @@ #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathSpecial; From f541647d44332b94a0133ebef721dd89e83b1560 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:23:20 -0400 Subject: [PATCH 70/72] some more IWYU tweaks --- src/fix_nh.h | 2 +- src/main.cpp | 4 +++- src/min.h | 2 +- src/neigh_list.h | 2 +- src/reader_xyz.cpp | 2 -- tools/msi2lmp/src/WriteDataFile.c | 1 - tools/msi2lmp/src/msi2lmp.c | 1 - tools/msi2lmp/src/msi2lmp.h | 2 +- 8 files changed, 7 insertions(+), 9 deletions(-) diff --git a/src/fix_nh.h b/src/fix_nh.h index 624b0c8bb4..f137ecbe55 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_NH_H #define LMP_FIX_NH_H -#include "fix.h" +#include "fix.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/main.cpp b/src/main.cpp index 9fb084aaea..d705db4e5b 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -12,9 +12,11 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include #include "input.h" +#include +#include + #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include #endif diff --git a/src/min.h b/src/min.h index b23c9b6670..1db196a55e 100644 --- a/src/min.h +++ b/src/min.h @@ -14,7 +14,7 @@ #ifndef LMP_MIN_H #define LMP_MIN_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/neigh_list.h b/src/neigh_list.h index 501188a724..c26b008136 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -14,7 +14,7 @@ #ifndef LMP_NEIGH_LIST_H #define LMP_NEIGH_LIST_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 5350e01117..8a2f7a3989 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -20,8 +20,6 @@ #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; #define MAXLINE 1024 // max line length in dump file diff --git a/tools/msi2lmp/src/WriteDataFile.c b/tools/msi2lmp/src/WriteDataFile.c index c03eba71c5..a6f1615809 100644 --- a/tools/msi2lmp/src/WriteDataFile.c +++ b/tools/msi2lmp/src/WriteDataFile.c @@ -3,7 +3,6 @@ */ #include "msi2lmp.h" -#include "Forcefield.h" #include diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index efc929639a..b5e9a96293 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -151,7 +151,6 @@ #include #include -#include /* global variables */ diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index c9b1984444..af7978d181 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -34,7 +34,7 @@ * compatibility with the obsolete LAMMPS version written in Fortran 90. */ -# include +#include /* IWYU pragma: export */ #define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018" From 255bf2f8fd1dbdc66e06a3132f18ff95dca56d96 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:41:57 -0400 Subject: [PATCH 71/72] update iwyu custom mapping file --- cmake/iwyu/iwyu-extra-map.imp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp index c212cc56dd..4fadea73fb 100644 --- a/cmake/iwyu/iwyu-extra-map.imp +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -2,6 +2,6 @@ { include: [ "", private, "", public ] }, { include: [ "", public, "", public ] }, { include: [ "@", private, "", public ] }, - { include: [ "@\"gtest/.*\"", private, "\"gtest/gtest.h\"", public ] }, - { include: [ "@\"gmock/.*\"", private, "\"gmock/gmock.h\"", public ] }, + { include: [ "@", private, "\"gtest/gtest.h\"", public ] }, + { include: [ "@", private, "\"gmock/gmock.h\"", public ] }, ] From f19ce32bf56aa81a3b488c2f6a6227b668bb7704 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 4 Sep 2020 09:42:11 -0400 Subject: [PATCH 72/72] a few more small tweaks --- unittest/formats/test_atom_styles.cpp | 1 + unittest/formats/test_pair_unit_convert.cpp | 6 ++---- unittest/formats/test_potential_file_reader.cpp | 5 ++--- unittest/utils/test_fmtlib.cpp | 1 - unittest/utils/test_tokenizer.cpp | 1 + unittest/utils/test_utils.cpp | 2 +- 6 files changed, 7 insertions(+), 9 deletions(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index a409f3547c..80ee3926c8 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -28,6 +28,7 @@ #include #include #include +#include #include #if !defined(_FORTIFY_SOURCE) || (_FORTIFY_SOURCE == 0) diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index 6c4b38397d..8571c7b442 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -15,17 +15,15 @@ #include "force.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "output.h" #include "pair.h" #include "thermo.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include +#include #include -#include +#include // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index f5b298874f..aaa52b1142 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -13,7 +13,6 @@ #include "MANYBODY/pair_comb.h" #include "MANYBODY/pair_comb3.h" -#include "MANYBODY/pair_eim.h" #include "MANYBODY/pair_gw.h" #include "MANYBODY/pair_gw_zbl.h" #include "MANYBODY/pair_nb3b_harmonic.h" @@ -26,13 +25,13 @@ #include "USER-MISC/pair_tersoff_table.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "potential_file_reader.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include +#include +#include #include #if defined(OMPI_MAJOR_VERSION) diff --git a/unittest/utils/test_fmtlib.cpp b/unittest/utils/test_fmtlib.cpp index fd9a4a06a2..7233d0ab1a 100644 --- a/unittest/utils/test_fmtlib.cpp +++ b/unittest/utils/test_fmtlib.cpp @@ -16,7 +16,6 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" #include -#include using namespace LAMMPS_NS; using ::testing::Eq; diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 7cef3cead0..28656ef9c8 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "tokenizer.h" #include "gmock/gmock.h" #include "gtest/gtest.h" diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 1a3ca9fa0c..a78830c9d1 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include #include -#include #include #include