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Merge pull request #1817 from akohlmey/collected-small-fixes 

Collected small bugfixes and updates
This commit is contained in:
Axel Kohlmeyer 2020-01-08 17:16:34 -05:00 committed by GitHub
parent d3eed9dba4 2d71d9d47b
commit 18a0cd3ead
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
19 changed files with 434 additions and 42 deletions
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1
.github/CODEOWNERS vendored
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@ -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

2
doc/src/fix_ave_atom.rst
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@ -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]

2
doc/txt/fix_ave_atom.txt
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@ -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

8
lib/gpu/geryon/ocl_device.h
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@ -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>

8
lib/gpu/geryon/ocl_macros.h
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@ -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

361
potentials/AlCu.bop.table
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@ -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 @@
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@ -5681,4 +5681,359 @@
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0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00

1
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -48,6 +48,7 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
respa_enable = 1;
writedata = 1;
ftable = NULL;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

6
src/GPU/fix_gpu.cpp
View File

@ -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";
/* ---------------------------------------------------------------------- */

47
src/USER-INTEL/fix_intel.cpp
View File

@ -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>
@ -63,6 +64,7 @@ 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 +292,7 @@ int FixIntel::setmask()
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
#endif
mask |= POST_RUN;
return mask;
}
@ -310,12 +313,7 @@ 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,
@ -394,6 +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
@ -475,7 +487,7 @@ 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 +510,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
"----------------------------------------------------------\n");
}
}
_print_pkg_info = 0;
}
/* ---------------------------------------------------------------------- */
@ -510,14 +523,11 @@ 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$", 0) != NULL)
intel_pair = 1;
else if (force->pair_match("hybrid", 1) != NULL) {
else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
if (pair_hybrid_check()) intel_pair = 1;
}
if (intel_pair == 0)
@ -530,14 +540,11 @@ void FixIntel::bond_init_check()
void FixIntel::kspace_init_check()
{
int intel_pair = 0;
if (force->pair_match("/intel", 0) != NULL)
if (force->pair_match("/intel$", 0) != NULL)
intel_pair = 1;
else if (force->pair_match("hybrid", 1) != NULL) {
else if (force->pair_match("^hybrid", 0) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
} else if (force->pair_match("hybrid/overlay", 1) != NULL) {
_hybrid_nonpair = 1;
if (_pair_intel_count) intel_pair = 1;
if (pair_hybrid_check()) intel_pair = 1;
}
if (intel_pair == 0)

10
src/USER-INTEL/fix_intel.h
View File

@ -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();
@ -54,6 +55,8 @@ 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();
@ -83,13 +86,12 @@ 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;
}
@ -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;

2
src/USER-INTEL/nbin_intel.cpp
View File

@ -56,6 +56,8 @@ NBinIntel::~NBinIntel() {
nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
memory->destroy(_atombin);
memory->destroy(_binpacked);
}
/* ----------------------------------------------------------------------

4
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
View File

@ -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;
}
}

7
src/USER-INTEL/pair_lj_cut_intel.cpp
View File

@ -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;

4
src/USER-MEAMC/pair_meamc.cpp
View File

@ -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");

2
src/USER-OMP/fix_rigid_omp.cpp
View File

@ -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];

2
src/USER-OMP/fix_rigid_small_omp.cpp
View File

@ -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;

3
src/USER-PHONON/dynamical_matrix.cpp
View File

@ -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);

1
src/pair.h
View File

@ -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;

5
src/read_dump.cpp
View File

@ -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;
}