From fd24820603e12875ea167cf66ccde71a94b4bd76 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 29 Jun 2021 15:45:50 -0400 Subject: [PATCH] rename USER-PACE to ML-PACE --- .github/CODEOWNERS | 2 +- cmake/CMakeLists.txt | 4 +-- .../{USER-PACE.cmake => ML-PACE.cmake} | 4 +-- cmake/presets/all_off.cmake | 2 +- cmake/presets/all_on.cmake | 2 +- cmake/presets/download.cmake | 2 +- cmake/presets/nolib.cmake | 2 +- doc/src/Build_extras.rst | 12 ++++---- doc/src/Build_package.rst | 2 +- doc/src/Packages_details.rst | 13 +++++---- doc/src/Packages_user.rst | 2 +- doc/src/pair_pace.rst | 2 +- lib/pace/Makefile | 6 ++-- lib/pace/Makefile.lammps | 2 +- lib/pace/README | 28 ++++++++----------- src/{USER-PACE => ML-PACE}/Install.sh | 0 src/{USER-PACE => ML-PACE}/README | 4 +-- src/{USER-PACE => ML-PACE}/pair_pace.cpp | 0 src/{USER-PACE => ML-PACE}/pair_pace.h | 0 src/Makefile | 6 ++-- 20 files changed, 46 insertions(+), 49 deletions(-) rename cmake/Modules/Packages/{USER-PACE.cmake => ML-PACE.cmake} (95%) rename src/{USER-PACE => ML-PACE}/Install.sh (100%) rename src/{USER-PACE => ML-PACE}/README (89%) rename src/{USER-PACE => ML-PACE}/pair_pace.cpp (100%) rename src/{USER-PACE => ML-PACE}/pair_pace.h (100%) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 656a56e85e..3e6f9eddcb 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -37,7 +37,7 @@ src/USER-MESONT/* @iafoss src/USER-MOFFF/* @hheenen src/USER-MOLFILE/* @akohlmey src/USER-NETCDF/* @pastewka -src/USER-PACE/* @yury-lysogorskiy +src/ML-PACE/* @yury-lysogorskiy src/USER-PLUMED/* @gtribello src/USER-PHONON/* @lingtikong src/USER-PTM/* @pmla diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a74b13839b..e48dad549d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -146,7 +146,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-H5MD ML-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN) + USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) @@ -351,7 +351,7 @@ else() endif() foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI USER-COLVARS ML-HDNNP USER-MDI USER-MOLFILE USER-NETCDF - USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) + USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake similarity index 95% rename from cmake/Modules/Packages/USER-PACE.cmake rename to cmake/Modules/Packages/ML-PACE.cmake index ccc7423355..7cfaf78aa0 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/ML-PACE.cmake @@ -14,8 +14,8 @@ execute_process( WORKING_DIRECTORY ${CMAKE_BINARY_DIR} ) -file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE) -file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp) +file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/ML-PACE) +file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/ML-PACE/*.cpp) list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 2c9487b948..50ae9fbca1 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -9,7 +9,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN + ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index acbace570a..807e48a26b 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -11,7 +11,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD ML-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN + ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) diff --git a/cmake/presets/download.cmake b/cmake/presets/download.cmake index ebab6ab658..0cfbb55348 100644 --- a/cmake/presets/download.cmake +++ b/cmake/presets/download.cmake @@ -1,7 +1,7 @@ # Preset that turns on packages with automatic downloads of sources or potentials. # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time. -set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE) +set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI ML-PACE) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index a5e367e641..667f22bfae 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -4,7 +4,7 @@ set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG PYTHON VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD ML-HDNNP USER-LB USER-MOLFILE - USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP + USER-MESONT USER-MDI USER-NETCDF ML-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index e90bf6409c..f56dd724ce 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -54,7 +54,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` - * :ref:`USER-PACE ` + * :ref:`ML-PACE ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -1261,9 +1261,9 @@ be built for the most part with all major versions of the C++ language. ---------- -.. _user-pace: +.. _ml-pace: -USER-PACE package +ML-PACE package ----------------------------- This package requires a library that can be downloaded and built @@ -1276,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`ML-HDNNP ` | :ref:`USER-INTEL ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | +| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`ML-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ | :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 0cfba0bd5f..9c5f9961cd 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -94,7 +94,7 @@ page gives those details. * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` * :ref:`USER-OMP ` - * :ref:`USER-PACE ` + * :ref:`ML-PACE ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` * :ref:`USER-PTM ` @@ -2075,16 +2075,16 @@ This package has :ref:`specific installation instructions ` on the :do ---------- -.. _PKG-USER-PACE: +.. _PKG-ML-PACE: -USER-PACE package +ML-PACE package ------------------- **Contents:** A pair style for the Atomic Cluster Expansion potential (ACE). ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. The USER-PACE +fit to a large archive of quantum mechanical (DFT) data. The ML-PACE package provides an efficient implementation for running simulations with ACE potentials. @@ -2105,11 +2105,12 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. **Install:** -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. **Supporting info:** -* src/USER-PACE: filenames -> commands +* src/ML-PACE: filenames -> commands * :doc:`pair_style pace ` * examples/PACKAGES/pace diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 0ec78ef63c..4de8439ff3 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -89,7 +89,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | +| :ref:`ML-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 56ae0f32dc..e737072e7b 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -91,7 +91,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +This pair style is part of the ML-PACE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/lib/pace/Makefile b/lib/pace/Makefile index c2e1892ddd..ac9f3a3151 100644 --- a/lib/pace/Makefile +++ b/lib/pace/Makefile @@ -2,8 +2,8 @@ SHELL = /bin/sh # ------ FILES ------ -SRC_FILES = $(wildcard src/USER-PACE/*.cpp) -SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES)) +SRC_FILES = $(wildcard src/ML-PACE/*.cpp) +SRC = $(filter-out src/ML-PACE/pair_pace.cpp, $(SRC_FILES)) # ------ DEFINITIONS ------ @@ -12,7 +12,7 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE +CXXFLAGS = -O3 -fPIC -Isrc/ML-PACE ARCHIVE = ar ARCHFLAG = -rc diff --git a/lib/pace/Makefile.lammps b/lib/pace/Makefile.lammps index 17820716df..89761c1b4b 100644 --- a/lib/pace/Makefile.lammps +++ b/lib/pace/Makefile.lammps @@ -1,3 +1,3 @@ -pace_SYSINC =-I../../lib/pace/src/USER-PACE +pace_SYSINC =-I../../lib/pace/src/ML-PACE pace_SYSLIB = -L../../lib/pace/ -lpace pace_SYSPATH = diff --git a/lib/pace/README b/lib/pace/README index ddc6f7f7a7..1cbc9fad68 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -1,18 +1,14 @@ -This directory contains files required to use the USER-PACE package, -which provides the pace pair style, an efficient implementation of -the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. -This package was written by Yury Lysogorskiy and others -at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, -Ruhr University Bochum, Germany, http://www.icams.de +This directory contains files required to use the ML-PACE package, which +provides the pace pair style, an efficient implementation of the Atomic +Cluster Expansion potential (ACE). ACE is a methodology for deriving a +highly accurate classical potential fit to a large archive of quantum +mechanical (DFT) data. This package was written by Yury Lysogorskiy and +others at ICAMS, the Interdisciplinary Centre for Advanced Materials +Simulation, Ruhr University Bochum, Germany, http://www.icams.de -You can type "make lib-pace" from the src directory to see help on -how to download and build this library via make commands, or you can -do the same thing by typing "python Install.py" from within this -directory. +You can type "make lib-pace" from the src directory to see help on how +to download and build this library via make commands, or you can do the +same thing by typing "python Install.py" from within this directory. -More information about the USER-PACE implementation of ACE -is available here: - -https://github.com/ICAMS/lammps-user-pace +More information about the ML-PACE implementation of ACE is available +here: https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/Install.sh b/src/ML-PACE/Install.sh similarity index 100% rename from src/USER-PACE/Install.sh rename to src/ML-PACE/Install.sh diff --git a/src/USER-PACE/README b/src/ML-PACE/README similarity index 89% rename from src/USER-PACE/README rename to src/ML-PACE/README index c701a615f7..7909b68dd3 100644 --- a/src/USER-PACE/README +++ b/src/ML-PACE/README @@ -1,4 +1,4 @@ -The USER-PACE package provides the pace pair style, +The ML-PACE package provides the pace pair style, an efficient implementation of the Atomic Cluster Expansion potential (ACE). @@ -17,7 +17,7 @@ provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. -More information about the USER-PACE implementation of ACE +More information about the ML-PACE implementation of ACE is available here: https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/pair_pace.cpp b/src/ML-PACE/pair_pace.cpp similarity index 100% rename from src/USER-PACE/pair_pace.cpp rename to src/ML-PACE/pair_pace.cpp diff --git a/src/USER-PACE/pair_pace.h b/src/ML-PACE/pair_pace.h similarity index 100% rename from src/USER-PACE/pair_pace.h rename to src/ML-PACE/pair_pace.h diff --git a/src/Makefile b/src/Makefile index 43d2f17423..ecb0e0c797 100644 --- a/src/Makefile +++ b/src/Makefile @@ -56,13 +56,13 @@ PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \ user-eff user-fep user-h5md ml-hdnnp user-intel user-lb user-manifold \ user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \ user-mofff user-molfile user-netcdf user-omp user-phonon \ - user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \ + ml-pace user-plumed user-ptm user-qmmm user-qtb user-quip \ user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ user-adios user-atc user-awpmd user-colvars user-h5md ml-hdnnp user-lb user-mdi \ - user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \ + user-mesont user-molfile user-netcdf ml-pace user-plumed user-qmmm user-quip \ user-scafacos user-smd user-vtk PACKSYS = compress mpiio python user-lb @@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont user-mdi PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md ml-hdnnp user-molfile user-netcdf user-pace user-plumed \ + user-adios user-h5md ml-hdnnp user-molfile user-netcdf ml-pace user-plumed \ user-qmmm user-quip user-scafacos user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER)