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Merge pull request #2993 from akohlmey/collected_small_changes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2021-10-14 15:32:42 -04:00
committed by GitHub
parent 5a90bca49e 64268de24b
commit ef04f6ca69
15 changed files with 77 additions and 50 deletions
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15
cmake/CMakeLists.txt
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@ -617,15 +617,12 @@ foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
endforeach()
if(PKG_PLUGIN)
if(BUILD_SHARED_LIBS)
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
else()
message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
endif()
# link with -ldl or equivalent for plugin loading; except on Windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
endif()
######################################################################

6
doc/src/plugin.rst
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@ -65,10 +65,8 @@ only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for
more info. Plugins are not available on Windows.
For the loading of plugins to work the LAMMPS library must be
:ref:`compiled as a shared library <library>`. If plugins
access functions or classes from a package, LAMMPS must have
been compiled with that package included.
If plugins access functions or classes from a package, LAMMPS must
have been compiled with that package included.
Plugins are dependent on the LAMMPS binary interface (ABI)
and particularly the MPI library used. So they are not guaranteed

12
lib/gpu/lal_device.cpp
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@ -1039,10 +1039,18 @@ Device<PRECISION,ACC_PRECISION> global_device;
using namespace LAMMPS_AL;
bool lmp_has_gpu_device()
// check if a suitable GPU is present.
// for mixed and double precision GPU library compilation
// also the GPU needs to support double precision.
bool lmp_has_compatible_gpu_device()
{
UCL_Device gpu;
return (gpu.num_platforms() > 0);
bool compatible_gpu = gpu.num_platforms() > 0;
#if defined(_SINGLE_DOUBLE) || defined(_DOUBLE_DOUBLE)
if (!gpu.double_precision(0))
compatible_gpu = false;
#endif
return compatible_gpu;
}
std::string lmp_gpu_device_info()

2
src/.gitignore vendored
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@ -1395,6 +1395,8 @@
/fix_drude_transform.h
/fix_langevin_drude.cpp
/fix_langevin_drude.h
/fix_mol_swap.cpp
/fix_mol_swap.h
/fix_pimd.cpp
/fix_pimd.h
/fix_qbmsst.cpp

2
src/BROWNIAN/fix_brownian.cpp
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@ -45,7 +45,7 @@ void FixBrownian::init()
{
FixBrownianBase::init();
g1 /= gamma_t;
g2 *= sqrt(gamma_t);
g2 /= sqrt(gamma_t);
}
/* ---------------------------------------------------------------------- */

3
src/MAKE/MACHINES/Makefile.cygwin
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@ -65,6 +65,9 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, but should be empty on Windows)
override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section

5
src/MAKE/Makefile.mpi
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@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section

7
src/MAKE/Makefile.serial
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@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

5
src/Makefile
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@ -2,6 +2,7 @@
SHELL = /bin/bash
PYTHON = python
DYN_LIB = -ldl
#.IGNORE:
@ -400,14 +401,14 @@ ifeq ($(mode),static)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \
"LMPLIB = $(ARLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \
"LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE)
"LMPLINK = $(LMPLINK)" "DYN_LIB = $(DYN_LIB)" "EXE = ../$(EXE)" ../$(EXE)
@ln -s $(ARLIB) $(ARLINK)
endif
ifeq ($(mode),shared)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \
"LMPLIB = $(SHLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \
"LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE)
"LMPLINK = $(LMPLINK)" "DYN_LIB = $(DYN_LIB)" "EXE = ../$(EXE)" ../$(EXE)
@ln -s $(SHLIB) $(SHLINK)
endif
# backward compatibility

13
src/REAXFF/fix_acks2_reaxff.cpp
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@ -866,15 +866,14 @@ void FixACKS2ReaxFF::more_reverse_comm(double *vec)
double FixACKS2ReaxFF::memory_usage()
{
double bytes;
int size = 2*nmax + 2;
const double size = 2.0*nmax + 2.0;
bytes = size*nprev * sizeof(double); // s_hist
bytes += nmax*4 * sizeof(double); // storage
bytes += size*11 * sizeof(double); // storage
bytes += n_cap*4 * sizeof(int); // matrix...
bytes += m_cap*2 * sizeof(int);
bytes += m_cap*2 * sizeof(double);
bytes += nmax*4.0 * sizeof(double); // storage
bytes += size*11.0 * sizeof(double); // storage
bytes += n_cap*4.0 * sizeof(int); // matrix...
bytes += m_cap*2.0 * sizeof(int);
bytes += m_cap*2.0 * sizeof(double);
return bytes;
}

25
src/atom.cpp
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@ -260,6 +260,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
map_hash = nullptr;
unique_tags = nullptr;
reset_image_flag[0] = reset_image_flag[1] = reset_image_flag[2] = false;
atom_style = nullptr;
avec = nullptr;
@ -1134,7 +1135,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
// remap atom into simulation box
// if atom is in my sub-domain, unpack its values
int flagx = 0, flagy = 0, flagz = 0;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
@ -1154,9 +1154,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
if ((domain->dimension == 2) && (imz != 0))
error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
if ((!domain->xperiodic) && (imx != 0)) { flagx = 1; imx = 0; }
if ((!domain->yperiodic) && (imy != 0)) { flagy = 1; imy = 0; }
if ((!domain->zperiodic) && (imz != 0)) { flagz = 1; imz = 0; }
if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; }
if ((!domain->zperiodic) && (imz != 0)) { reset_image_flag[2] = true; imz = 0; }
}
imagedata = ((imageint) (imx + IMGMAX) & IMGMASK) |
(((imageint) (imy + IMGMAX) & IMGMASK) << IMGBITS) |
@ -1192,23 +1192,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
buf = next + 1;
}
// warn if reading data with non-zero image flags for non-periodic boundaries.
// we may want to turn this into an error at some point, since this essentially
// creates invalid position information that works by accident most of the time.
if (comm->me == 0) {
if (flagx)
error->warning(FLERR,"Non-zero imageflag(s) in x direction for "
"non-periodic boundary reset to zero");
if (flagy)
error->warning(FLERR,"Non-zero imageflag(s) in y direction for "
"non-periodic boundary reset to zero");
if (flagz)
error->warning(FLERR,"Non-zero imageflag(s) in z direction for "
"non-periodic boundary reset to zero");
}
delete [] values;
}

4
src/atom.h
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@ -270,6 +270,10 @@ class Atom : protected Pointers {
int *sametag; // sametag[I] = next atom with same ID, -1 if no more
// true if image flags were reset to 0 during data_atoms()
bool reset_image_flag[3];
// AtomVec factory types and map
typedef AtomVec *(*AtomVecCreator)(LAMMPS *);

6
src/info.cpp
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@ -1146,12 +1146,14 @@ bool Info::has_package(const std::string &package_name) {
#if defined(LMP_GPU)
extern bool lmp_gpu_config(const std::string &, const std::string &);
extern bool lmp_has_gpu_device();
extern bool lmp_has_compatible_gpu_device();
extern std::string lmp_gpu_device_info();
// we will only report compatible GPUs, i.e. when a GPU device is
// available *and* supports the required floating point precision
bool Info::has_gpu_device()
{
return lmp_has_gpu_device();
return lmp_has_compatible_gpu_device();
}
std::string Info::get_gpu_device_info()

2
src/lammps.cpp
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@ -1340,7 +1340,7 @@ void LAMMPS::print_config(FILE *fp)
fmt::print(fp,"Accelerator configuration:\n\n{}\n",
Info::get_accelerator_info());
#if defined(LMP_GPU)
fmt::print(fp,"GPU present: {}\n\n",Info::has_gpu_device() ? "yes" : "no");
fmt::print(fp,"Compatible GPU present: {}\n\n",Info::has_gpu_device() ? "yes" : "no");
#endif
fputs("Active compile time flags:\n\n",fp);

20
src/read_data.cpp
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@ -312,6 +312,10 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,fmt::format("Cannot open file {}: {}",
arg[0], utils::getsyserror()));
// reset so we can warn about reset image flags exactly once per data file
atom->reset_image_flag[0] = atom->reset_image_flag[1] = atom->reset_image_flag[2] = false;
// first time system initialization
if (addflag == NONE) {
@ -1238,6 +1242,22 @@ void ReadData::atoms()
nread += nchunk;
}
// warn if we have read data with non-zero image flags for non-periodic boundaries.
// we may want to turn this into an error at some point, since this essentially
// creates invalid position information that works by accident most of the time.
if (comm->me == 0) {
if (atom->reset_image_flag[0])
error->warning(FLERR,"Non-zero imageflag(s) in x direction for "
"non-periodic boundary reset to zero");
if (atom->reset_image_flag[1])
error->warning(FLERR,"Non-zero imageflag(s) in y direction for "
"non-periodic boundary reset to zero");
if (atom->reset_image_flag[2])
error->warning(FLERR,"Non-zero imageflag(s) in z direction for "
"non-periodic boundary reset to zero");
}
// check that all atoms were assigned correctly
bigint n = atom->nlocal;