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Merge pull request #3064 from rbberger/collected-small-changes

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Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
2021-12-23 16:13:35 -05:00
committed by GitHub
parent 09944f5d7a 1185591c76
commit 6af36075ba
23 changed files with 92 additions and 88 deletions
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3
cmake/CMakeLists.txt
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@ -339,7 +339,6 @@ pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
@ -609,7 +608,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

9
cmake/Modules/Packages/PHONON.cmake Normal file
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@ -0,0 +1,9 @@
# fix phonon may only be installed if also the FFT wrappers from KSPACE are installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

6
doc/src/Packages_details.rst
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@ -1880,6 +1880,12 @@ MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.

12
doc/src/dump.rst
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@ -137,7 +137,7 @@ Examples
dump myDump all atom/gz 100 dump.atom.gz
dump myDump all atom/zstd 100 dump.atom.zst
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
@ -219,6 +219,11 @@ you should thus consider the *atom* and *atom/mpiio* styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
The precision of values output to text-based dump files can be
controlled by the :doc:`dump_modify format <dump_modify>` command and
its options.
@ -452,6 +457,11 @@ use the :doc:`read_dump <read_dump>` command or perform other
post-processing, just as if the dump file was not written using
MPI-IO.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple

14
src/MC/fix_gcmc.cpp
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@ -504,8 +504,7 @@ void FixGCMC::init()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"Fix gcmc cannot exchange individual atoms belonging to a molecule");
error->all(FLERR, "Fix gcmc cannot exchange individual atoms belonging to a molecule");
}
// if molecules are exchanged or moved, check for unset mol IDs
@ -520,16 +519,13 @@ void FixGCMC::init()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"All mol IDs should be set for fix gcmc group atoms");
error->all(FLERR, "All mol IDs should be set for fix gcmc group atoms");
}
if (exchmode == EXCHMOL || movemode == MOVEMOL)
if (atom->molecule_flag == 0 || !atom->tag_enable
|| (atom->map_style == Atom::MAP_NONE))
error->all(FLERR,
"Fix gcmc molecule command requires that "
"atoms have molecule attributes");
error->all(FLERR, "Fix gcmc molecule command requires that atoms have molecule attributes");
// if rigidflag defined, check for rigid/small fix
// its molecule template must be same as this one
@ -541,9 +537,7 @@ void FixGCMC::init()
fixrigid = modify->fix[ifix];
int tmp;
if (&onemols[imol] != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix gcmc and fix rigid/small not using "
"same molecule template ID");
error->all(FLERR, "Fix gcmc and fix rigid/small not using same molecule template ID");
}
// if shakeflag defined, check for SHAKE fix

7
src/MC/fix_widom.cpp
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@ -310,16 +310,13 @@ void FixWidom::init()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"All mol IDs should be set for fix widom group atoms");
error->all(FLERR, "All mol IDs should be set for fix widom group atoms");
}
if (exchmode == EXCHMOL)
if (atom->molecule_flag == 0 || !atom->tag_enable
|| (atom->map_style == Atom::MAP_NONE))
error->all(FLERR,
"Fix widom molecule command requires that "
"atoms have molecule attributes");
error->all(FLERR, "Fix widom molecule command requires that atoms have molecule attributes");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix widom in a 2d simulation");

4
src/MOLECULE/fix_cmap.cpp
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@ -1072,10 +1072,10 @@ void FixCMAP::read_data_header(char *line)
store CMAP interactions as if newton_bond = OFF, even if actually ON
------------------------------------------------------------------------- */
void FixCMAP::read_data_section(char *keyword, int n, char *buf,
void FixCMAP::read_data_section(char * /*keyword*/, int /*n*/, char *buf,
tagint id_offset)
{
int m,tmp,itype;
int m,itype;
tagint atom1,atom2,atom3,atom4,atom5;
auto lines = utils::split_lines(buf);

7
src/MPIIO/dump_atom_mpiio.cpp
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@ -38,7 +38,12 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg) {}
DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg)
: DumpAtom(lmp, narg, arg)
{
if (me == 0)
error->warning(FLERR,"MPI-IO output is unmaintained and unreliable. Use with caution.");
}
/* ---------------------------------------------------------------------- */

6
src/MPIIO/dump_cfg_mpiio.cpp
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@ -51,7 +51,11 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DumpCFGMPIIO::DumpCFGMPIIO(LAMMPS *lmp, int narg, char **arg) :
DumpCFG(lmp, narg, arg) {}
DumpCFG(lmp, narg, arg)
{
if (me == 0)
error->warning(FLERR,"MPI-IO output is unmaintained and unreliable. Use with caution.");
}
/* ---------------------------------------------------------------------- */

7
src/MPIIO/dump_custom_mpiio.cpp
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@ -53,7 +53,12 @@ enum{ LT, LE, GT, GE, EQ, NEQ };
// clang-format on
/* ---------------------------------------------------------------------- */
DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg) {}
DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg)
: DumpCustom(lmp, narg, arg)
{
if (me == 0)
error->warning(FLERR,"MPI-IO output is unmaintained and unreliable. Use with caution.");
}
/* ---------------------------------------------------------------------- */

5
src/MPIIO/dump_xyz_mpiio.cpp
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@ -52,7 +52,10 @@ enum{LT,LE,GT,GE,EQ,NEQ};
/* ---------------------------------------------------------------------- */
DumpXYZMPIIO::DumpXYZMPIIO(LAMMPS *lmp, int narg, char **arg) :
DumpXYZ(lmp, narg, arg) {}
DumpXYZ(lmp, narg, arg) {
if (me == 0)
error->warning(FLERR,"MPI-IO output is unmaintained and unreliable. Use with caution.");
}
/* ---------------------------------------------------------------------- */

10
src/PHONON/Install.sh
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@ -26,16 +26,6 @@ action () {
fi
}
# PHONON uses the parallel FFT wrapper used in PPPM,
# so we must require the KSPACE package to be installed.
if (test $1 = 1) then
if (test ! -e ../fft3d_wrap.h) then
echo "Must install KSPACE package with PHONON"
exit 1
fi
fi
# list of files with optional dependcies
action fix_phonon.cpp fft3d_wrap.h

23
src/REAXFF/fix_reaxff_species.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -247,8 +246,8 @@ FixReaxFFSpecies::~FixReaxFFSpecies()
if (posflag && multipos_opened) fclose(pos);
}
modify->delete_compute("SPECATOM");
modify->delete_fix("SPECBOND");
modify->delete_compute(fmt::format("SPECATOM_{}",id));
modify->delete_fix(fmt::format("SPECBOND_{}",id));
}
/* ---------------------------------------------------------------------- */
@ -288,22 +287,16 @@ void FixReaxFFSpecies::init()
if (nvalid != update->ntimestep)
nvalid = update->ntimestep+nfreq;
// check if this fix has been called twice
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"reaxff/species") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one fix reaxff/species");
if (!setupflag) {
// create a compute to store properties
modify->add_compute("SPECATOM all SPEC/ATOM q x y z vx vy vz abo01 abo02 abo03 abo04 "
"abo05 abo06 abo07 abo08 abo09 abo10 abo11 abo12 abo13 abo14 "
"abo15 abo16 abo17 abo18 abo19 abo20 abo21 abo22 abo23 abo24");
modify->add_compute(fmt::format("SPECATOM_{} all SPEC/ATOM q x y z vx vy vz abo01 abo02 "
"abo03 abo04 abo05 abo06 abo07 abo08 abo09 abo10 abo11 "
"abo12 abo13 abo14 abo15 abo16 abo17 abo18 abo19 abo20 "
"abo21 abo22 abo23 abo24",id));
// create a fix to point to fix_ave_atom for averaging stored properties
auto fixcmd = fmt::format("SPECBOND all ave/atom {} {} {}",nevery,nrepeat,nfreq);
for (int i = 1; i < 32; ++i) fixcmd += " c_SPECATOM[" + std::to_string(i) + "]";
auto fixcmd = fmt::format("SPECBOND_{} all ave/atom {} {} {}",id,nevery,nrepeat,nfreq);
for (int i = 1; i < 32; ++i) fixcmd += fmt::format(" c_SPECATOM_{}[{}]",id,i);
f_SPECBOND = (FixAveAtom *) modify->add_fix(fixcmd);
setupflag = 1;
}

1
src/REAXFF/reaxff_ffield.cpp
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@ -583,6 +583,7 @@ namespace ReaxFF {
} catch (std::exception &e) {
error->one(FLERR,e.what());
}
fclose(fp);
}
// broadcast global parameters and allocate list on ranks != 0

3
src/dump.cpp
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@ -128,8 +128,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
char *ptr;
if ((ptr = strchr(filename,'%'))) {
if (strstr(style,"mpiio"))
error->all(FLERR,
"Dump file MPI-IO output not allowed with % in filename");
error->all(FLERR,"Dump file MPI-IO output not allowed with % in filename");
multiproc = 1;
nclusterprocs = 1;
filewriter = 1;

4
src/fix_nve_sphere.cpp
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@ -294,7 +294,6 @@ void FixNVESphere::final_integrate()
// update v,omega for all particles
// d_omega/dt = torque / inertia
double rke = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
@ -306,8 +305,5 @@ void FixNVESphere::final_integrate()
omega[i][0] += dtirotate * torque[i][0];
omega[i][1] += dtirotate * torque[i][1];
omega[i][2] += dtirotate * torque[i][2];
rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2])*radius[i]*radius[i]*rmass[i];
}
}

5
src/info.cpp
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@ -1059,8 +1059,9 @@ static void print_columns(FILE *fp, std::map<std::string, ValueType> *styles)
for (typename std::map<std::string, ValueType>::iterator it = styles->begin(); it != styles->end(); ++it) {
const std::string &style_name = it->first;
// skip "secret" styles
if (isupper(style_name[0])) continue;
// skip "internal" styles
if (isupper(style_name[0]) || utils::strmatch(style_name,"/kk/host$")
|| utils::strmatch(style_name,"/kk/device$")) continue;
int len = style_name.length();
if (pos + len > 80) {

6
src/lammps.cpp
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@ -1305,12 +1305,14 @@ void _noopt LAMMPS::help()
/* ----------------------------------------------------------------------
print style names in columns
skip any style that starts with upper-case letter, since internal
skip any internal style that starts with an upper-case letter
also skip "redundant" KOKKOS styles ending in kk/host or kk/device
------------------------------------------------------------------------- */
void print_style(FILE *fp, const char *str, int &pos)
{
if (isupper(str[0])) return;
if (isupper(str[0]) || utils::strmatch(str,"/kk/host$")
|| utils::strmatch(str,"/kk/device$")) return;
int len = strlen(str);
if (pos+len > 80) {

8
src/min_linesearch.cpp
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@ -328,7 +328,7 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
int i,m,n;
double fdothall,fdothme,hme,hmax,hmaxall;
double de_ideal,de;
double delfh,engprev,relerr,alphaprev,fhprev,ff,fh,alpha0;
double delfh,engprev,relerr,alphaprev,fhprev,fh,alpha0;
double dot[2],dotall[2];
double *xatom,*x0atom,*fatom,*hatom;
double alphamax;
@ -439,12 +439,8 @@ int MinLineSearch::linemin_quadratic(double eoriginal, double &alpha)
dotall[1] += fextra[i]*hextra[i];
}
}
ff = dotall[0];
fh = dotall[1];
if (output->thermo->normflag) {
ff /= atom->natoms;
fh /= atom->natoms;
}
if (output->thermo->normflag) fh /= atom->natoms;
delfh = fh - fhprev;

6
src/output.cpp
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@ -782,12 +782,12 @@ void Output::create_restart(int narg, char **arg)
}
int mpiioflag;
if (strstr(arg[1],".mpi")) mpiioflag = 1;
if (utils::strmatch(arg[1],"\\.mpiio$")) mpiioflag = 1;
else mpiioflag = 0;
if (nfile == 2) {
if (mpiioflag && !strstr(arg[2],".mpi"))
if (mpiioflag && !utils::strmatch(arg[2],"\\.mpiio$"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
if (!mpiioflag && strstr(arg[2],".mpi"))
if (!mpiioflag && utils::strmatch(arg[2],"\\.mpiio$"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
}

27
src/reader_native.cpp
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@ -63,10 +63,10 @@ int ReaderNative::read_time(bigint &ntimestep)
magic_string = "";
unit_style = "";
fread(&ntimestep, sizeof(bigint), 1, fp);
auto ret = fread(&ntimestep, sizeof(bigint), 1, fp);
// detect end-of-file
if (feof(fp)) return 1;
if (ret != 1 || feof(fp)) return 1;
// detect newer format
if (ntimestep < 0) {
@ -485,12 +485,8 @@ void ReaderNative::read_atoms(int n, int nfield, double **fields)
}
}
} else {
int i,m;
char *eof;
for (i = 0; i < n; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
for (int i = 0; i < n; i++) {
utils::sfgets(FLERR, line, MAXLINE, fp, nullptr, error);
// tokenize the line
std::vector<std::string> words = Tokenizer(line).as_vector();
@ -499,7 +495,7 @@ void ReaderNative::read_atoms(int n, int nfield, double **fields)
// convert selected fields to floats
for (m = 0; m < nfield; m++)
for (int m = 0; m < nfield; m++)
fields[i][m] = atof(words[fieldindex[m]].c_str());
}
}
@ -527,18 +523,14 @@ int ReaderNative::find_label(const std::string &label, const std::map<std::strin
void ReaderNative::read_lines(int n)
{
char *eof = nullptr;
if (n <= 0) return;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of dump file");
for (int i = 0; i < n; i++) {
utils::sfgets(FLERR, line, MAXLINE, fp, nullptr, error);
}
}
void ReaderNative::read_buf(void * ptr, size_t size, size_t count)
{
fread(ptr, size, count, fp);
// detect end-of-file
if (feof(fp)) error->one(FLERR,"Unexpected end of dump file");
utils::sfread(FLERR, ptr, size, count, fp, nullptr, error);
}
std::string ReaderNative::read_binary_str(size_t size)
@ -550,7 +542,6 @@ std::string ReaderNative::read_binary_str(size_t size)
void ReaderNative::read_double_chunk(size_t count)
{
if (count < 0) return;
// extend buffer to fit chunk size
if (count > maxbuf) {
memory->grow(databuf,count,"reader:databuf");

2
src/reader_native.h
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@ -52,7 +52,7 @@ class ReaderNative : public Reader {
int nwords; // # of per-atom columns in dump file
int size_one; // number of double for one atom
int maxbuf; // maximum buffer size
size_t maxbuf; // maximum buffer size
int nchunk; // number of chunks in the binary file
int ichunk; // index of current reading chunk
int natom_chunk; // number of atoms in the current chunks

5
src/write_restart.cpp
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@ -73,9 +73,12 @@ void WriteRestart::command(int narg, char **arg)
if (strchr(arg[0],'%')) multiproc = nprocs;
else multiproc = 0;
if (strstr(arg[0],".mpiio")) mpiioflag = 1;
if (utils::strmatch(arg[0],"\\.mpiio$")) mpiioflag = 1;
else mpiioflag = 0;
if ((comm->me == 0) && mpiioflag)
error->warning(FLERR,"MPI-IO output is unmaintained and unreliable. Use with caution.");
// setup output style and process optional args
// also called by Output class for periodic restart files