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Merge pull request #2614 from akohlmey/collected-small-changes

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Collected small changes and bugfixes
This commit is contained in:
Axel Kohlmeyer
2021-02-22 13:31:37 -05:00
committed by GitHub
parent 2378850085 f3ee948450
commit 1bf2e18bcd
10 changed files with 36 additions and 32 deletions
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4
cmake/CMakeLists.txt
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@ -777,9 +777,7 @@ if(PKG_GPU)
message(STATUS "<<< GPU package settings >>>
-- GPU API: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OpenCL tuning: ${OCL_TUNE}")
message(STATUS "GPU default architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "HIP")
message(STATUS "HIP platform: ${HIP_PLATFORM}")
message(STATUS "HIP architecture: ${HIP_ARCH}")

16
cmake/Modules/GTest.cmake
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@ -20,10 +20,10 @@ ExternalProject_Add(googletest
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
@ -39,10 +39,10 @@ file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
ExternalProject_Get_Property(googletest BINARY_DIR)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
# Prevent GoogleTest from overriding our compiler/linker options
# when building with Visual Studio

4
cmake/Modules/YAML.cmake
View File

@ -12,7 +12,7 @@ ExternalProject_Add(libyaml
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")
ExternalProject_Get_Property(libyaml INSTALL_DIR)
@ -23,7 +23,7 @@ set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
add_library(Yaml::Yaml UNKNOWN IMPORTED)
set_target_properties(Yaml::Yaml PROPERTIES

2
doc/src/compute_temp_chunk.rst
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@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
----------

2
src/atom.cpp
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@ -1752,7 +1752,7 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
if (lo < 1 || hi > ntypes) error->all(file,line,"Invalid type for mass set");
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = atof(arg[1]);
mass[itype] = utils::numeric(FLERR,arg[1],false,lmp);
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(file,line,"Invalid mass value");

2
src/citeme.cpp
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@ -118,7 +118,7 @@ void CiteMe::flush()
if (!citefile.empty())
logbuffer += fmt::format(cite_file,"file",citefile);
if (screen_flag == VERBOSE)
scrbuffer += fmt::format(cite_file,"screen","output");
logbuffer += fmt::format(cite_file,"screen","output");
logbuffer += cite_separator;
if (logfile) fputs(logbuffer.c_str(),logfile);
logbuffer.clear();

4
src/compute_reduce.cpp
View File

@ -148,8 +148,8 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
if (iarg+3 > narg) error->all(FLERR,"Illegal compute reduce command");
if (mode != MINN && mode != MAXX)
error->all(FLERR,"Compute reduce replace requires min or max mode");
int col1 = atoi(arg[iarg+1]) - 1;
int col2 = atoi(arg[iarg+2]) - 1;
int col1 = utils::inumeric(FLERR,arg[iarg+1],false,lmp) - 1;
int col2 = utils::inumeric(FLERR,arg[iarg+2],false,lmp) - 1;
if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues)
error->all(FLERR,"Illegal compute reduce command");
if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");

2
src/fix_addforce.cpp
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@ -83,7 +83,7 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix addforce command");
nevery = atoi(arg[iarg+1]);
nevery = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix addforce command");
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {

20
src/fix_property_atom.cpp
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@ -254,13 +254,19 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[j+1]);
else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]);
else if (style[j] == RMASS) atom->rmass[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
else if (style[j] == DOUBLE)
atom->dvector[index[j]][m] = atof(values[j+1]);
if (style[j] == MOLECULE) {
atom->molecule[m] = utils::tnumeric(FLERR,values[j+1],false,lmp);
} else if (style[j] == CHARGE) {
atom->q[m] = utils::numeric(FLERR,values[j+1],false,lmp);
} else if (style[j] == RMASS) {
atom->rmass[m] = utils::numeric(FLERR,values[j+1],false,lmp);
} else if (style[j] == INTEGER) {
atom->ivector[index[j]][m] = utils::inumeric(FLERR,values[j+1],
false,lmp);
} else if (style[j] == DOUBLE) {
atom->dvector[index[j]][m] = utils::numeric(FLERR,values[j+1],
true,lmp);
}
}
}

12
src/kspace.cpp
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@ -564,9 +564,9 @@ void KSpace::modify_params(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"kmax/ewald") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal kspace_modify command");
kx_ewald = atoi(arg[iarg+1]);
ky_ewald = atoi(arg[iarg+2]);
kz_ewald = atoi(arg[iarg+3]);
kx_ewald = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
ky_ewald = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
kz_ewald = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
if (kx_ewald < 0 || ky_ewald < 0 || kz_ewald < 0)
error->all(FLERR,"Bad kspace_modify kmax/ewald parameter");
if (kx_ewald > 0 && ky_ewald > 0 && kz_ewald > 0)
@ -583,15 +583,15 @@ void KSpace::modify_params(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"force/disp/real") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
accuracy_real_6 = atof(arg[iarg+1]);
accuracy_real_6 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"force/disp/kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
accuracy_kspace_6 = atof(arg[iarg+1]);
accuracy_kspace_6 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"eigtol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
splittol = atof(arg[iarg+1]);
splittol = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (splittol >= 1.0)
error->all(FLERR,"Kspace_modify eigtol must be smaller than one");
iarg += 2;