tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'develop' into kk_update_4.4.0

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-09-11 13:35:32 -04:00
parent 64db592a84 fcbc37d5a4
commit 9525dae7b9
10 changed files with 46 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
doc/src/group2ndx.rst
View File

@ -51,7 +51,7 @@ index file. When specifying group IDs, only those groups will be
written to the index file. In order to follow the Gromacs conventions,
the group *all* will be renamed to *System* in the index file.
The *ndx2group* command will create of update group definitions from
The *ndx2group* command will create or update group definitions from
those stored in an index file. Without specifying any group IDs, all
groups except *System* will be read from the index file and the
corresponding groups recreated. If a group of the same name already

2
lib/gpu/lal_neighbor.cpp
View File

@ -599,7 +599,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
_shared->k_transpose.set_size(g2x,g2y_m,b2x,b2y);
// number of chunks needed for the whole transpose
const int num_chunks = ceil(static_cast<double>(g2y) / g2y_m);
for (int i = 0; i < num_chunks; i++) {
for (int i = 0; i < num_chunks; i++) {
_shared->k_transpose.run(&dev_special,&dev_special_t,&_maxspecial,&nt,&shift);
shift += g2y_m*b2y;
}

10
python/lammps/numpy_wrapper.py
View File

@ -18,12 +18,10 @@
from ctypes import POINTER, c_void_p, c_char_p, c_double, c_int, c_int32, c_int64, cast
from .constants import LAMMPS_AUTODETECT, LAMMPS_INT, LAMMPS_INT_2D, \
LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, \
LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, \
LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, \
LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS, \
LMP_VAR_EQUAL, LMP_VAR_ATOM, LMP_VAR_VECTOR, LMP_VAR_STRING
from .constants import LAMMPS_AUTODETECT, LAMMPS_INT, LAMMPS_INT_2D, LAMMPS_DOUBLE, \
LAMMPS_DOUBLE_2D, LAMMPS_INT64, LAMMPS_INT64_2D, LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, \
LMP_STYLE_LOCAL, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, \
LMP_SIZE_COLS, LMP_VAR_EQUAL, LMP_VAR_ATOM
from .data import NeighList

10
src/.gitignore vendored
View File

@ -192,6 +192,8 @@
/colvarproxy_lammps_version.h
/fix_colvars.cpp
/fix_colvars.h
/inthash.cpp
/inthash.h
/fix_plumed.cpp
/fix_plumed.h
/dump_molfile.cpp
@ -1078,12 +1080,12 @@
/geturl.cpp
/geturl.h
/gpu_extra.h
/group_ndx.cpp
/group_ndx.h
/group2ndx.cpp
/group2ndx.h
/gz_file_writer.cpp
/gz_file_writer.h
/ndx_group.cpp
/ndx_group.h
/ndx2group.cpp
/ndx2group.h
/hyper.cpp
/hyper.h
/improper_class2.cpp

6
src/EXTRA-COMMAND/group_ndx.cpp → src/EXTRA-COMMAND/group2ndx.cpp
View File

@ -1,6 +1,4 @@
// -*- c++ -*-
/* ----------------------------------------------------------------------
/* -*- c++ -*--------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
@ -16,7 +14,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "group_ndx.h"
#include "group2ndx.h"
#include "atom.h"
#include "comm.h"

10
src/EXTRA-COMMAND/group_ndx.h → src/EXTRA-COMMAND/group2ndx.h
View File

@ -1,6 +1,4 @@
// -*- c++ -*-
/* ----------------------------------------------------------
/* -*- c++ -*-----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
@ -19,8 +17,8 @@ CommandStyle(group2ndx,Group2Ndx);
// clang-format on
#else
#ifndef LMP_GROUP_NDX_H
#define LMP_GROUP_NDX_H
#ifndef LMP_GROUP2NDX_H
#define LMP_GROUP2NDX_H
#include "command.h"
@ -28,7 +26,7 @@ namespace LAMMPS_NS {
class Group2Ndx : public Command {
public:
Group2Ndx(class LAMMPS *lmp) : Command(lmp){};
Group2Ndx(class LAMMPS *lmp) : Command(lmp) {};
void command(int, char **) override;
private:

9
src/EXTRA-COMMAND/ndx_group.cpp → src/EXTRA-COMMAND/ndx2group.cpp
View File

@ -1,6 +1,4 @@
// -*- c++ -*-
/* ----------------------------------------------------------------------
/* -*- c++ -*---------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
@ -16,7 +14,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "ndx_group.h"
#include "ndx2group.h"
#include "atom.h"
#include "comm.h"
@ -33,8 +31,7 @@ static std::string find_section(FILE *fp, const std::string &name)
{
char linebuf[BUFLEN];
if (!fgets(linebuf, BUFLEN, fp))
throw TokenizerException("Read error", utils::getsyserror());
if (!fgets(linebuf, BUFLEN, fp)) throw TokenizerException("Read error", utils::getsyserror());
while (!feof(fp)) {
if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
auto words = Tokenizer(linebuf).as_vector();

10
src/EXTRA-COMMAND/ndx_group.h → src/EXTRA-COMMAND/ndx2group.h
View File

@ -1,6 +1,4 @@
// -*- c++ -*-
/* ----------------------------------------------------------
/* -*- c++ -*-------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
@ -19,8 +17,8 @@ CommandStyle(ndx2group,Ndx2Group);
// clang-format on
#else
#ifndef LMP_NDX_GROUP_H
#define LMP_NDX_GROUP_H
#ifndef LMP_NDX2GROUP_H
#define LMP_NDX2GROUP_H
#include "command.h"
#include <vector>
@ -29,7 +27,7 @@ namespace LAMMPS_NS {
class Ndx2Group : public Command {
public:
Ndx2Group(class LAMMPS *lmp) : Command(lmp){};
Ndx2Group(class LAMMPS *lmp) : Command(lmp) {};
void command(int, char **) override;
private:

5
src/Purge.list
View File

@ -53,6 +53,11 @@ lmpinstalledpkgs.h
lmpgitversion.h
mliap_model_python_couple.cpp
mliap_model_python_couple.h
# renamed in September 2024
group_ndx.cpp
group_ndx.h
ndx_group.cpp
ndx_group.h
# removed in August 2023
dump_atom_mpiio.cpp
dump_atom_mpiio.h

16
tools/regression-tests/run_tests.py
View File

@ -1236,6 +1236,22 @@ if __name__ == "__main__":
os.remove(f"input-list-{idx}.txt")
except:
pass
filename = f"run-{idx}.log"
with open(filename, "w") as f:
f.write('\n')
f.close()
filename = f"progress-{idx}.yaml"
with open(filename, "w") as f:
f.write('\n')
f.close()
filename = f"output-{idx}.xml"
with open(filename, "w") as f:
f.write('\n')
f.close()
filename = f"failure-{idx}.yaml"
with open(filename, "w") as f:
f.write('\n')
f.close()
quit()
# if the example folders are not specified from the command-line argument --example-folders