From 55fde76d597fbda9f105f165a8cbb637eb07ca77 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 16 Dec 2019 07:22:41 -0500
Subject: [PATCH 01/17] may only close files on MPI ranks that have a file
reader instance
---
src/read_dump.cpp | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index dd9395c092..c61c467a59 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -434,8 +434,9 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
// all filereader procs close all their files and return
if (ntimestep < 0) {
- for (int i = 0; i < nreader; i++)
- readers[i]->close_file();
+ if (filereader)
+ for (int i = 0; i < nreader; i++)
+ readers[i]->close_file();
return ntimestep;
}
From 92b2e4256b474f1e564a2918faad92c06a14beab Mon Sep 17 00:00:00 2001
From: Jianhua Pan <lucien.pan0927@gmail.com>
Date: Mon, 2 Dec 2019 23:07:58 -0500
Subject: [PATCH 02/17] Bug fix for lj/class2/coul/long/gpu
---
src/CLASS2/pair_lj_class2_coul_long.cpp | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index 1544232e49..0bb802579c 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -48,6 +48,7 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
respa_enable = 1;
writedata = 1;
ftable = NULL;
+ cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */
From 21f454c040d11fec1d8f27cbda10efc763a4db2d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 03:48:08 -0500
Subject: [PATCH 03/17] correct truncated AlCu.bop.table potential file from
Xiaoweng Zhou
---
potentials/AlCu.bop.table | 361 +++++++++++++++++++++++++++++++++++++-
1 file changed, 358 insertions(+), 3 deletions(-)
diff --git a/potentials/AlCu.bop.table b/potentials/AlCu.bop.table
index cc74dbb62a..8e19658c62 100644
--- a/potentials/AlCu.bop.table
+++ b/potentials/AlCu.bop.table
@@ -1,4 +1,4 @@
-# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, Phys. Chem. Chem. Phys., under consideration
+# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, J. Alloys Compd., 680, 752 (2016).
2
13 2.69800000e+01 Al
29 6.35500000e+01 Cu
@@ -4835,7 +4835,7 @@
0.00000000e+00
0.00000000e+00
0.00000000e+00
- 4.90000000e+00
+ 0.00000000e+00
0.00000000e+00
0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
@@ -5681,4 +5681,359 @@
0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
- 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
+ 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
From a72f53e367eaa42e25f11ff835eb72c863e1fc0e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 21 Dec 2019 16:18:26 -0500
Subject: [PATCH 04/17] add stan/steve as code owners for minimizer changes
---
.github/CODEOWNERS | 1 +
1 file changed, 1 insertion(+)
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 7d1f1a417b..a4fc5b7b4f 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -111,6 +111,7 @@ src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
+src/min* @sjplimp @stanmoore1
# tools
tools/msi2lmp/* @akohlmey
From e11374d433895faee5b34c56e106d36f487e7075 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:37:12 -0500
Subject: [PATCH 05/17] print intel package status message only once per run
---
src/USER-INTEL/fix_intel.cpp | 5 ++++-
src/USER-INTEL/fix_intel.h | 4 +++-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 83a22f0562..507ffa6d6f 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -63,6 +63,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
_three_body_neighbor = 0;
_pair_intel_count = 0;
_hybrid_nonpair = 0;
+ _print_pkg_info = 1;
_precision_mode = PREC_MODE_MIXED;
_offload_balance = -1.0;
@@ -290,6 +291,7 @@ int FixIntel::setmask()
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
#endif
+ mask |= POST_RUN;
return mask;
}
@@ -475,7 +477,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
set_offload_affinity();
#endif
- if (comm->me == 0) {
+ if (_print_pkg_info && comm->me == 0) {
if (screen) {
fprintf(screen,
"----------------------------------------------------------\n");
@@ -498,6 +500,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
"----------------------------------------------------------\n");
}
}
+ _print_pkg_info = 0;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index f23e305ca7..7c176fb069 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -54,6 +54,8 @@ class FixIntel : public Fix {
inline void min_pre_reverse(int eflag = 0, int vflag = 0)
{ pre_reverse(eflag, vflag); }
+ void post_run() { _print_pkg_info = 1; }
+
// Get all forces, calculation results from coprocesser
void sync_coprocessor();
@@ -101,7 +103,7 @@ class FixIntel : public Fix {
IntelBuffers<double,double> *_double_buffers;
int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor;
- int _pair_intel_count, _pair_hybrid_flag;
+ int _pair_intel_count, _pair_hybrid_flag, _print_pkg_info;
// These should be removed in subsequent update w/ simpler hybrid arch
int _pair_hybrid_zero, _hybrid_nonpair, _zero_master;
From 2f6018b099ddb58ca95d005e970fb360bc423e0a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:39:35 -0500
Subject: [PATCH 06/17] use regex pattern matching to make style lookup more
specific with less code
---
src/USER-INTEL/fix_intel.cpp | 21 +++++----------------
src/USER-INTEL/fix_intel.h | 5 ++---
2 files changed, 7 insertions(+), 19 deletions(-)
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 507ffa6d6f..be9d0c49b0 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -312,12 +312,7 @@ void FixIntel::init()
#endif
const int nstyles = _pair_intel_count;
- if (force->pair_match("hybrid", 1) != NULL) {
- _pair_hybrid_flag = 1;
- if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
- error->all(FLERR,
- "Intel package requires fdotr virial with newton on.");
- } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+ if (force->pair_match("^hybrid", 0) != NULL) {
_pair_hybrid_flag = 1;
if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
error->all(FLERR,
@@ -513,12 +508,9 @@ void FixIntel::bond_init_check()
"USER-INTEL package requires same setting for newton bond and non-bond.");
int intel_pair = 0;
- if (force->pair_match("/intel", 0) != NULL)
+ if (force->pair_match("/intel$", 0) != NULL)
intel_pair = 1;
- else if (force->pair_match("hybrid", 1) != NULL) {
- _hybrid_nonpair = 1;
- if (_pair_intel_count) intel_pair = 1;
- } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+ else if (force->pair_match("^hybrid", 1) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
}
@@ -533,12 +525,9 @@ void FixIntel::bond_init_check()
void FixIntel::kspace_init_check()
{
int intel_pair = 0;
- if (force->pair_match("/intel", 0) != NULL)
+ if (force->pair_match("/intel$", 0) != NULL)
intel_pair = 1;
- else if (force->pair_match("hybrid", 1) != NULL) {
- _hybrid_nonpair = 1;
- if (_pair_intel_count) intel_pair = 1;
- } else if (force->pair_match("hybrid/overlay", 1) != NULL) {
+ else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
}
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index 7c176fb069..a699a6d2b9 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -85,13 +85,12 @@ class FixIntel : public Fix {
}
inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; }
inline int lrt() {
- if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1)
+ if (force->kspace_match("^pppm/.*intel$", 0) && update->whichflag == 1)
return _lrt;
else return 0;
}
inline int pppm_table() {
- if (force->kspace_match("pppm/intel", 0) ||
- force->kspace_match("pppm/disp/intel",0))
+ if (force->kspace_match("^pppm/.*intel$", 0))
return INTEL_P3M_TABLE;
else return 0;
}
From a63792a07abe6a3482d1face4c315620315f7b21 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 3 Jan 2020 01:40:20 -0500
Subject: [PATCH 07/17] need to explicitly run pair_init_check() inside
kspace_init_check() for hybrid styles
---
src/USER-INTEL/fix_intel.cpp | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index be9d0c49b0..3d59a49acd 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -529,6 +529,7 @@ void FixIntel::kspace_init_check()
intel_pair = 1;
else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
+ pair_init_check(); // need to run this here explicitly, since pair->init() was not run yet.
if (_pair_intel_count) intel_pair = 1;
}
From 394e5459b63f99602f0fb94b54691e23bf6eafeb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 15:16:08 -0500
Subject: [PATCH 08/17] correct whitespace issues in pair_meamc.cpp
---
src/USER-MEAMC/pair_meamc.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 9733ee2dad..3d7d0b2a17 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -438,7 +438,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
found[i] = true;
// map lat string to an integer
-
+
if (!MEAM::str_to_lat(words[1], true, lat[i]))
error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
@@ -464,7 +464,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
if (!isone(t0[i]))
error->all(FLERR,"Unsupported parameter in MEAM potential file: t0!=1");
-
+
// z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
if (z[i] != MEAM::get_Zij(lat[i]))
error->all(FLERR,"Mismatched parameter in MEAM potential file: z!=lat");
From 5500198b4eb712c78665c17065a6cb2a6fa2163f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 15:21:18 -0500
Subject: [PATCH 09/17] correct whitespace issue in dynamical_matrix.cpp
---
src/USER-PHONON/dynamical_matrix.cpp | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index 6bb843c16e..d03a8d3ab0 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -408,7 +408,8 @@ void DynamicalMatrix::update_force()
timer->stamp(Timer::COMM);
}
- // force modifications,
+ // force modifications
+
if (n_post_force) modify->post_force(vflag);
timer->stamp(Timer::MODIFY);
From 8ac2da792c26b4e4fdf03895d84ad6e00226e622 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 16:18:23 -0500
Subject: [PATCH 10/17] fix typo in fix ave/atom docs
---
doc/src/fix_ave_atom.rst | 2 +-
doc/txt/fix_ave_atom.txt | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst
index 2886eb8f4e..3a066ab55b 100644
--- a/doc/src/fix_ave_atom.rst
+++ b/doc/src/fix_ave_atom.rst
@@ -88,7 +88,7 @@ command creates a per-atom array with 6 columns:
compute my_stress all stress/atom NULL
fix 1 all ave/atom 10 20 1000 c_my_stress[\*]
- fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
+ fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[2] &
c_my_stress[3] c_my_stress[4] &
c_my_stress[5] c_my_stress[6]
diff --git a/doc/txt/fix_ave_atom.txt b/doc/txt/fix_ave_atom.txt
index 10deaf64cd..596f9ee46c 100644
--- a/doc/txt/fix_ave_atom.txt
+++ b/doc/txt/fix_ave_atom.txt
@@ -80,7 +80,7 @@ command creates a per-atom array with 6 columns:
compute my_stress all stress/atom NULL
fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
-fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
+fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[2\] &
c_my_stress\[3\] c_my_stress\[4\] &
c_my_stress\[5\] c_my_stress\[6\] :pre
From 66a473455e3c6fa206c0efacccb61a8f9785e279 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 6 Jan 2020 17:34:26 -0500
Subject: [PATCH 11/17] silence warnings from generic OpenCL header files (as
seen on Fedora 31)
---
lib/gpu/geryon/ocl_device.h | 8 ++++++++
lib/gpu/geryon/ocl_macros.h | 8 ++++++++
2 files changed, 16 insertions(+)
diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h
index 14455e38a5..e414e7b69c 100644
--- a/lib/gpu/geryon/ocl_device.h
+++ b/lib/gpu/geryon/ocl_device.h
@@ -28,6 +28,14 @@
#include <vector>
#include <iostream>
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
#ifdef __APPLE__
#include <OpenCL/cl.h>
#include <OpenCL/cl_platform.h>
diff --git a/lib/gpu/geryon/ocl_macros.h b/lib/gpu/geryon/ocl_macros.h
index 5fb7665817..aeff689859 100644
--- a/lib/gpu/geryon/ocl_macros.h
+++ b/lib/gpu/geryon/ocl_macros.h
@@ -4,6 +4,14 @@
#include <cstdio>
#include <cassert>
+/* We default to OpenCL 1.2 as target version for now as
+ * there are known issues with OpenCL 2.0 and later.
+ * This is also to silence warnings from generic OpenCL headers */
+
+#if !defined(CL_TARGET_OPENCL_VERSION)
+#define CL_TARGET_OPENCL_VERSION 120
+#endif
+
#ifdef __APPLE__
#include <OpenCL/cl.h>
#else
From 7470a120bb1ba629d288bf7825282f715cadbca4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 11:13:43 -0500
Subject: [PATCH 12/17] fix small memory leak in USER-INTEL binning style
---
src/USER-INTEL/nbin_intel.cpp | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index 8359587eb2..78c6246389 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -56,6 +56,8 @@ NBinIntel::~NBinIntel() {
nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
+ memory->destroy(_atombin);
+ memory->destroy(_binpacked);
}
/* ----------------------------------------------------------------------
From 4c974c6d5e93d3c55805f9a526781a7d5b93508a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 11:14:22 -0500
Subject: [PATCH 13/17] avoid uninitialized memory access when used with hybrid
styles
---
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
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 929ac2123f..243c7f577d 100644
--- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -525,8 +525,10 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
double cut;
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
cut = init_one(i, j);
- else
+ else { // need to set cutsq and cut_ljsq for hybrid pair_style
cut = 0.0;
+ cut_ljsq[i][j] = cut_ljsq[j][i] = 0.0;
+ }
cutsq[i][j] = cutsq[j][i] = cut*cut;
}
}
From f8ad7cc90f393782bebaa28c640bc443a31186a8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 15:09:50 -0500
Subject: [PATCH 14/17] refactor fix for detecting intel pair styles in hybrid
pair styles
---
src/USER-INTEL/fix_intel.cpp | 24 +++++++++++++++++++-----
src/USER-INTEL/fix_intel.h | 1 +
src/pair.h | 1 +
3 files changed, 21 insertions(+), 5 deletions(-)
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 3d59a49acd..5ecae79b30 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -16,6 +16,7 @@
Anupama Kurpad (Intel) - Host Affinitization
------------------------------------------------------------------------- */
+#include "fix_intel.h"
#include "comm.h"
#include "error.h"
#include "force.h"
@@ -27,7 +28,7 @@
#include "timer.h"
#include "universe.h"
#include "update.h"
-#include "fix_intel.h"
+#include "utils.h"
#include <cstring>
#include <cstdlib>
@@ -391,6 +392,20 @@ void FixIntel::setup_pre_reverse(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
+bool FixIntel::pair_hybrid_check()
+{
+ PairHybrid *ph = (PairHybrid *)force->pair;
+ bool has_intel = false;
+ int nstyles = ph->nstyles;
+
+ for (int i = 0; i < nstyles; ++i)
+ if (ph->styles[i]->suffix_flag & Suffix::INTEL) has_intel = true;
+
+ return has_intel;
+}
+
+/* ---------------------------------------------------------------------- */
+
void FixIntel::pair_init_check(const bool cdmessage)
{
#ifdef INTEL_VMASK
@@ -510,9 +525,9 @@ void FixIntel::bond_init_check()
int intel_pair = 0;
if (force->pair_match("/intel$", 0) != NULL)
intel_pair = 1;
- else if (force->pair_match("^hybrid", 1) != NULL) {
+ else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
- if (_pair_intel_count) intel_pair = 1;
+ if (pair_hybrid_check()) intel_pair = 1;
}
if (intel_pair == 0)
@@ -529,8 +544,7 @@ void FixIntel::kspace_init_check()
intel_pair = 1;
else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
- pair_init_check(); // need to run this here explicitly, since pair->init() was not run yet.
- if (_pair_intel_count) intel_pair = 1;
+ if (pair_hybrid_check()) intel_pair = 1;
}
if (intel_pair == 0)
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index a699a6d2b9..4c50164d31 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -46,6 +46,7 @@ class FixIntel : public Fix {
inline void min_setup(int in) { setup(in); }
void setup_pre_reverse(int eflag = 0, int vflag = 0);
+ bool pair_hybrid_check();
void pair_init_check(const bool cdmessage=false);
void bond_init_check();
void kspace_init_check();
diff --git a/src/pair.h b/src/pair.h
index 0aa48761ee..d578908b20 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -26,6 +26,7 @@ class Pair : protected Pointers {
friend class DihedralCharmm;
friend class DihedralCharmmOMP;
friend class FixGPU;
+ friend class FixIntel;
friend class FixOMP;
friend class ThrOMP;
friend class Info;
From 23b73a0ebcba58a6c640daa471133daf401834c7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Jan 2020 15:32:44 -0500
Subject: [PATCH 15/17] plug small memory leak
---
src/USER-INTEL/pair_lj_cut_intel.cpp | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp
index f6f83b752a..b484cb68d9 100644
--- a/src/USER-INTEL/pair_lj_cut_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_intel.cpp
@@ -459,11 +459,8 @@ void PairLJCutIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
const int cop) {
if (ntypes != _ntypes) {
if (_ntypes > 0) {
- fc_packed1 *oljc12o = ljc12o[0];
- fc_packed2 *olj34 = lj34[0];
-
- _memory->destroy(oljc12o);
- _memory->destroy(olj34);
+ _memory->destroy(ljc12o);
+ _memory->destroy(lj34);
}
if (ntypes > 0) {
_cop = cop;
From 9e3364ed39aec3078e3e3e10a75dd76c3c80bd8e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 15:13:34 -0500
Subject: [PATCH 16/17] no need to flag ibody as private
---
src/USER-OMP/fix_rigid_omp.cpp | 2 +-
src/USER-OMP/fix_rigid_small_omp.cpp | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 1cdf1018b2..770361d557 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -261,7 +261,7 @@ void FixRigidOMP::compute_forces_and_torques()
if (id_gravity) {
#if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
#endif
for (int ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] += gvec[0]*masstotal[ibody];
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index bdd10b0ca7..fc6b6fa57a 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -201,7 +201,7 @@ void FixRigidSmallOMP::compute_forces_and_torques()
if (id_gravity) {
#if defined(_OPENMP)
-#pragma omp parallel for default(none) private(ibody) schedule(static)
+#pragma omp parallel for default(none) schedule(static)
#endif
for (int ibody = 0; ibody < nbody; ibody++) {
double * _noalias const fcm = body[ibody].fcm;
From 2d71d9d47bf51d0975ca9681d2ddb9a9d407abd2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 8 Jan 2020 16:15:18 -0500
Subject: [PATCH 17/17] add citation for GPU accelerated TIP4P style
---
src/GPU/fix_gpu.cpp | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index d4397503dc..cb2930a3ea 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -88,6 +88,12 @@ static const char cite_gpu_package[] =
" year = 2017,\n"
" volume = 212,\n"
" pages = {113--122}\n"
+ "}\n\n"
+ "@Article{Nikolskiy19,\n"
+ " author = {V. Nikolskiy, V. Stegailov},\n"
+ " title = {GPU acceleration of four-site water models in LAMMPS},\n"
+ " journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},\n"
+ " year = 2019\n"
"}\n\n";
/* ---------------------------------------------------------------------- */