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Merge pull request #4146 from akohlmey/collected-small-changes

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Collected small changes
This commit is contained in:
Stan Moore
2024-05-13 11:00:18 -06:00
committed by GitHub
parent 628531dadb 74b3d15c3b
commit eb0640fbb5
11 changed files with 50 additions and 27 deletions
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4
.github/workflows/unittest-macos.yml vendored
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@ -15,7 +15,7 @@ jobs:
build:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
runs-on: macos-13
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
@ -43,6 +43,8 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m venv macosenv
source macosenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \

4
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

1
doc/utils/sphinx-config/false_positives.txt
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@ -4162,6 +4162,7 @@ zenodo
Zepeda
zflag
Zhang
Zhao
Zhen
zhi
Zhigilei

3
src/KOKKOS/pair_meam_kokkos.h
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@ -13,9 +13,6 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(meam/c/kk,PairMEAMKokkos<LMPDeviceType>);
PairStyle(meam/c/kk/device,PairMEAMKokkos<LMPDeviceType>);
PairStyle(meam/c/kk/host,PairMEAMKokkos<LMPHostType>);
PairStyle(meam/kk,PairMEAMKokkos<LMPDeviceType>);
PairStyle(meam/kk/device,PairMEAMKokkos<LMPDeviceType>);
PairStyle(meam/kk/host,PairMEAMKokkos<LMPHostType>);

1
src/MEAM/pair_meam.h
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@ -14,7 +14,6 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(meam,PairMEAM);
PairStyle(meam/c,PairMEAM);
// clang-format on
#else

3
src/QEQ/fix_qeq.cpp
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@ -74,6 +74,9 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
if ((nevery <= 0) || (cutoff <= 0.0) || (tolerance <= 0.0) || (maxiter <= 0))
error->all(FLERR,"Illegal fix qeq command");
// must have charges
if (!atom->q_flag) error->all(FLERR, "Fix {} requires atom attribute q", style);
alpha = 0.20;
swa = 0.0;
swb = cutoff;

21
src/fix.cpp
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@ -119,8 +119,8 @@ Fix::~Fix()
{
if (copymode) return;
delete [] id;
delete [] style;
delete[] id;
delete[] style;
memory->destroy(eatom);
memory->destroy(vatom);
memory->destroy(cvatom);
@ -133,36 +133,37 @@ Fix::~Fix()
void Fix::modify_params(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal fix_modify command");
if (narg == 0) utils::missing_cmd_args(FLERR, "fix_modify", error);
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dynamic/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify dynamic/dof", error);
dynamic = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify energy", error);
thermo_energy = utils::logical(FLERR,arg[iarg+1],false,lmp);
if (thermo_energy && !energy_global_flag && !energy_peratom_flag)
error->all(FLERR,"Fix {} {} does not support fix_modify energy command", id, style);
iarg += 2;
} else if (strcmp(arg[iarg],"virial") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify virial", error);
thermo_virial = utils::logical(FLERR,arg[iarg+1],false,lmp);
if (thermo_virial && !virial_global_flag && !virial_peratom_flag)
error->all(FLERR,"Fix {} {} does not support fix_modify virial command", id, style);
iarg += 2;
} else if (strcmp(arg[iarg],"respa") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix_modify respa", error);
if (!respa_level_support) error->all(FLERR,"Illegal fix_modify respa command");
int lvl = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (lvl < 0) error->all(FLERR,"Illegal fix_modify command");
if (lvl < 0) error->all(FLERR,"Illegal fix_modify respa command");
respa_level = lvl-1;
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal fix_modify command");
if (n == 0)
error->all(FLERR,"Fix {} {} does not support fix_modify {} command", id, style, arg[iarg]);
iarg += n;
}
}

3
src/pair_deprecated.cpp
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@ -56,6 +56,9 @@ void PairDeprecated::settings(int, char **)
utils::logmesg(lmp,
"\nPair style 'mesont/tpm' has been removed from LAMMPS. "
"Please use pair style 'mesocnt' instead\n\n");
} else if (utils::strmatch(my_style, "^meam/c")) {
if (lmp->comm->me == 0)
utils::logmesg(lmp, "\nPair style 'meam/c' has been renamed to 'meam'\n\n");
}
error->all(FLERR, "This pair style is no longer available");
}

1
src/pair_deprecated.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(DEPRECATED,PairDeprecated);
PairStyle(meam/c,PairDeprecated);
PairStyle(reax,PairDeprecated);
PairStyle(reax/c,PairDeprecated);
PairStyle(mesont/tpm,PairDeprecated);

1
src/version.h
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@ -1 +1,2 @@
#define LAMMPS_VERSION "17 Apr 2024"
#define LAMMPS_UPDATE "Development"

35
unittest/cplusplus/test_advanced_utils.cpp
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@ -110,16 +110,31 @@ TEST_F(Advanced_utils, expand_args)
{
atomic_system();
BEGIN_CAPTURE_OUTPUT();
command("compute temp all temp");
command("variable temp vector c_temp");
command("variable step equal step");
command("variable pe equal pe");
command("variable pe equal pe");
command("variable epair equal epair");
command("compute gofr all rdf 20 1 1 1 2");
command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair");
command("fix 2 all nve");
command("run 1 post no");
try {
command("compute temp all temp");
command("variable temp vector c_temp");
command("variable step equal step");
command("variable pe equal pe");
command("variable pe equal pe");
command("variable epair equal epair");
command("compute gofr all rdf 20 1 1 1 2");
command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair");
command("fix 2 all nve");
command("run 1 post no");
} catch (LAMMPSAbortException &ae) {
fprintf(stderr, "LAMMPS Error: %s\n", ae.what());
exit(2);
} catch (LAMMPSException &e) {
fprintf(stderr, "LAMMPS Error: %s\n", e.what());
exit(3);
} catch (fmt::format_error &fe) {
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
exit(4);
} catch (std::exception &e) {
fprintf(stderr, "General exception: %s\n", e.what());
exit(5);
}
auto output = END_CAPTURE_OUTPUT();
char **args, **earg;