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Merge pull request #3309 from akohlmey/collected-small-fixes

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More fixes and small changes for the stable release
This commit is contained in:
Axel Kohlmeyer
2022-06-22 15:16:01 -04:00
committed by GitHub
parent fe1feb58d8 1099199e93
commit ad35bbcb65
28 changed files with 198 additions and 441 deletions
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4
doc/src/Howto_structured_data.rst
View File

@ -184,7 +184,7 @@ frame.
.. code-block:: python
import re, yaml
import yaml
import pandas as pd
try:
@ -193,7 +193,7 @@ frame.
from yaml import SafeLoader as Loader
with open("ave.yaml") as f:
ave = yaml.load(docs, Loader=Loader)
ave = yaml.load(f, Loader=Loader)
keys = ave['keywords']
df = {}

3
doc/src/Speed_measure.rst
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@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
use the :doc:`timer sync <timer>` command to obtain synchronized timings.

102
doc/src/read_restart.rst
View File

@ -11,7 +11,6 @@ Syntax
read_restart file flag
* file = name of binary restart file to read in
* flag = remap (optional)
Examples
""""""""
@ -19,44 +18,40 @@ Examples
.. code-block:: LAMMPS
read_restart save.10000
read_restart save.10000 remap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
Description
"""""""""""
Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simulation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
information is stored (and not stored) in a restart file is given below.
Basically this operation will re-create the simulation box with all its
atoms and their attributes as well as some related global settings, at
the point in time it was written to the restart file by a previous
simulation. The simulation box will be partitioned into a regular 3d
grid of rectangular bricks, one per processor, based on the number of
processors in the current simulation and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
.. note::
Normally, restart files are written by the
:doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
so that all atoms in the restart file are inside the simulation box.
If this is not the case, the read_restart command will print an error
that atoms were "lost" when the file is read. This error should be
reported to the LAMMPS developers so the invalid writing of the
restart file can be fixed. If you still wish to use the restart file,
the optional *remap* flag can be appended to the read_restart command.
This should avoid the error, by explicitly remapping each atom back
into the simulation box, updating image flags for the atom
appropriately.
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
those produced by the original run had it continued on.
The binary restart file format was not designed with backward, forward,
or cross-platform compatibility in mind, so the files are only expected
to be read correctly by the same LAMMPS executable on the same platform.
Changes to the architecture, compilation settings, or LAMMPS version can
render a restart file unreadable or it may read the data incorrectly.
If you want a more portable format, you can use the data file format as
created by the :doc:`write_data <write_data>` command. Binary restart
files can also be converted into a data file from the command line by
the LAMMPS executable that wrote them using the :ref:`-restart2data
<restart2data>` command line flag.
Several things can prevent exact restarts due to round-off effects, in
which case the trajectories in the 2 runs will slowly diverge. These
include running on a different number of processors or changing
@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
these cases.
Certain fixes will not restart exactly, though they should provide
statistically similar results. These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
statistically similar results. These include :doc:`fix shake
<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
Certain pair styles will not restart exactly, though they should
provide statistically similar results. This is because the forces
@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
machines. In this case, you can use the :doc:`-restart command-line
switch <Run_options>` to convert a restart file to a data file.
Similar to how restart files are written (see the
:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
commands), the restart filename can contain two wild-card characters.
If a "\*" appears in the filename, the directory is searched for all
filenames that match the pattern where "\*" is replaced with a timestep
value. The file with the largest timestep value is read in. Thus,
this effectively means, read the latest restart file. It's useful if
you want your script to continue a run from where it left off. See
the :doc:`run <run>` command and its "upto" option for how to specify
the run command so it does not need to be changed either.
Similar to how restart files are written (see the :doc:`write_restart
<write_restart>` and :doc:`restart <restart>` commands), the restart
filename can contain two wild-card characters. If a "\*" appears in the
filename, the directory is searched for all filenames that match the
pattern where "\*" is replaced with a timestep value. The file with the
largest timestep value is read in. Thus, this effectively means, read
the latest restart file. It's useful if you want your script to
continue a run from where it left off. See the :doc:`run <run>` command
and its "upto" option for how to specify the run command so it does not
need to be changed either.
If a "%" character appears in the restart filename, LAMMPS expects a
set of multiple files to exist. The :doc:`restart <restart>` and
@ -222,17 +219,17 @@ its calculations in a consistent manner.
.. note::
There are a handful of commands which can be used before or
between runs which may require a system initialization. Examples
include the "balance", "displace_atoms", "delete_atoms", "set" (some
options), and "velocity" (some options) commands. This is because
they can migrate atoms to new processors. Thus they will also discard
unused "state" information from fixes. You will know the discard has
There are a handful of commands which can be used before or between
runs which may require a system initialization. Examples include the
"balance", "displace_atoms", "delete_atoms", "set" (some options),
and "velocity" (some options) commands. This is because they can
migrate atoms to new processors. Thus they will also discard unused
"state" information from fixes. You will know the discard has
occurred because a list of discarded fixes will be printed to the
screen and log file, as explained above. This means that if you wish
to retain that info in a restarted run, you must re-specify the
relevant fixes and computes (which create fixes) before those commands
are used.
relevant fixes and computes (which create fixes) before those
commands are used.
Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
use a fix to store "state" information that persists from timestep to
@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or
deleted in various ways, which can affect how their info is stored in
a restart file.
If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command,
their info will be written to a restart file as if they are turned on.
This means they will need to be turned off again in a new run after
the restart file is read.
If bonds (angles, etc) have been turned off by the :doc:`fix shake
<fix_shake>` or :doc:`delete_bonds <delete_bonds>` command, their info
will be written to a restart file as if they are turned on. This means
they will need to be turned off again in a new run after the restart
file is read.
Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
system. No information about these bonds is written to the restart
file.
Bonds that have been broken by the :doc:`fix bond/break
<fix_bond_break>` command have disappeared from the system. No
information about these bonds is written to the restart file.
----------

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -2369,6 +2369,7 @@ nopreliminary
Nord
norder
Nordlund
noremap
normals
normx
normy

182
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@ -23,6 +23,7 @@
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#define LAMMPS_LIB_MPI 1
#include <library.h>
#include <lammps.h>
#include <atom.h>
@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
if (size) return *size;
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
if (tmp) *ncols = *tmp;
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
if (size) return *size;
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
if (tmp) *ncols = *tmp;
return;
}
/* vim: set ts=3 sts=3 expandtab: */

4
examples/COUPLE/fortran2/LAMMPS-wrapper.h
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

4
examples/COUPLE/fortran2/LAMMPS.F90
View File

@ -1292,7 +1292,7 @@ contains !! Wrapper functions local to this module {{{1
Cname = string2Cstring (name)
Ccount = size(data) / natoms
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))
@ -1355,7 +1355,7 @@ contains !! Wrapper functions local to this module {{{1
Cname = string2Cstring (name)
Ccount = size(data) / ndata
if ( Ccount /= 1 .and. Ccount /= 3 ) &
call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
& count to be either 1 or 3')
Fdata = data
Cdata = C_loc (Fdata(1))

2
examples/COUPLE/fortran2/Makefile
View File

@ -14,7 +14,7 @@ CXXLIB = -lstdc++ # replace with your C++ runtime libs
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
FFLAGS = -O2 -fPIC
CXXFLAGS = -O2 -fPIC
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
all : liblammps_fortran.a liblammps_fortran.so

5
examples/COUPLE/fortran2/README
View File

@ -11,9 +11,8 @@ This interface was created by Karl Hammond who you can contact with
questions:
Karl D. Hammond
University of Tennessee, Knoxville
karlh at ugcs.caltech.edu
karlh at utk.edu
University of Missouri
hammondkd at missouri.edu
-------------------------------------

182
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@ -23,6 +23,7 @@
#include <mpi.h>
#include "LAMMPS-wrapper.h"
#define LAMMPS_LIB_MPI 1
#include <library.h>
#include <lammps.h>
#include <atom.h>
@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 ) return 0;
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->vector_flag )
return 0;
else
return compute->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !compute->local_flag )
return 0;
else
return compute->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
if (size) return *size;
return 0;
}
void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if ( icompute < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Compute *compute = lmp->modify->compute[icompute];
if ( style == 0 )
{
if ( !compute->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_array_rows;
*ncols = compute->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !compute->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = compute->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !compute->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = compute->size_local_rows;
*ncols = compute->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
if (tmp) *ncols = *tmp;
return;
}
int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 ) return 0;
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->vector_flag )
return 0;
else
return fix->size_vector;
}
else if ( style == 1 )
{
return lammps_get_natoms (ptr);
}
else if ( style == 2 )
{
if ( !fix->local_flag )
return 0;
else
return fix->size_local_rows;
}
else
return 0;
int *size;
size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
if (size) return *size;
return 0;
}
void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
int *nrows, int *ncols)
{
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if ( ifix < 0 )
{
*nrows = 0;
*ncols = 0;
}
class Fix *fix = lmp->modify->fix[ifix];
if ( style == 0 )
{
if ( !fix->array_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_array_rows;
*ncols = fix->size_array_cols;
}
}
else if ( style == 1 )
{
if ( !fix->peratom_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = lammps_get_natoms (ptr);
*ncols = fix->size_peratom_cols;
}
}
else if ( style == 2 )
{
if ( !fix->local_flag )
{
*nrows = 0;
*ncols = 0;
}
else
{
*nrows = fix->size_local_rows;
*ncols = fix->size_local_cols;
}
}
else
{
*nrows = 0;
*ncols = 0;
}
int *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
if (tmp) *nrows = *tmp;
tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
if (tmp) *ncols = *tmp;
return;
}
/* vim: set ts=3 sts=3 expandtab: */

4
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
View File

@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
University of Missouri (USA), 2012
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

3
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
View File

@ -12,8 +12,7 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
University of Tennessee, Knoxville (USA), 2012
Contributing author: Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ------------------------------------------------------------------------
Contributing author: Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
Contributing author: Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
------------------------------------------------------------------------- */
/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

4
examples/COUPLE/fortran_dftb/LAMMPS.F90
View File

@ -12,8 +12,8 @@
!--------------------------------------------------------------------------
!! ------------------------------------------------------------------------
! Contributing author: Karl D. Hammond <karlh@ugcs.caltech.edu>
! University of Tennessee, Knoxville (USA), 2012
! Contributing author: Karl D. Hammond <hammondkd@missouri.edu>
! University of Missouri (USA), 2012
!--------------------------------------------------------------------------
!! LAMMPS, a Fortran 2003 module containing an interface between Fortran

37
python/lammps/core.py
View File

@ -188,20 +188,17 @@ class lammps(object):
[c_void_p,POINTER(c_double),POINTER(c_double),c_double,c_double,c_double]
self.lib.lammps_reset_box.restype = None
self.lib.lammps_gather_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.restype = None
self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.restype = None
self.lib.lammps_scatter_atoms_subset.argtypes = \
@ -211,20 +208,17 @@ class lammps(object):
self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
self.lib.lammps_gather_bonds.restype = None
self.lib.lammps_gather.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather.restype = None
self.lib.lammps_gather_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_concat.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_concat.restype = None
self.lib.lammps_gather_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_subset.restype = None
self.lib.lammps_scatter.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter.argtypes = [c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter.restype = None
self.lib.lammps_scatter_subset.argtypes = \
@ -244,7 +238,8 @@ class lammps(object):
self.lib.lammps_neighlist_num_elements.argtypes = [c_void_p, c_int]
self.lib.lammps_neighlist_num_elements.restype = c_int
self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.argtypes = \
[c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
self.lib.lammps_neighlist_element_neighbors.restype = None
self.lib.lammps_is_running.argtypes = [c_void_p]
@ -368,11 +363,9 @@ class lammps(object):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, \
MPI_Comm, c_void_p]
self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, MPI_Comm, c_void_p]
else:
self.lib.lammps_open.argtypes = [c_int, c_char_p, \
MPI_Comm, c_void_p]
self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p]
self.opened = 1
comm_ptr = self.MPI._addressof(comm)
@ -390,8 +383,7 @@ class lammps(object):
if type(cmdargs[i]) is str:
cmdargs[i] = cmdargs[i].encode()
cargs = (c_char_p*narg)(*cmdargs)
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, \
c_void_p]
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, c_void_p]
self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))
else:
self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p]
@ -963,17 +955,14 @@ class lammps(object):
return ptr
elif ctype == LMP_SIZE_COLS:
if cstyle == LMP_STYLE_GLOBAL \
or cstyle == LMP_STYLE_ATOM \
or cstyle == LMP_STYLE_LOCAL:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
return ptr[0]
elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
if cstyle == LMP_STYLE_GLOBAL \
or cstyle == LMP_STYLE_LOCAL:
if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
with ExceptionCheck(self):
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)

9
python/lammps/numpy_wrapper.py
View File

@ -165,7 +165,7 @@ class numpy_wrapper:
"""
value = self.lmp.extract_compute(cid, cstyle, ctype)
if cstyle in (LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL):
if cstyle == LMP_STYLE_GLOBAL:
if ctype == LMP_TYPE_VECTOR:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_VECTOR)
return self.darray(value, nrows)
@ -173,6 +173,13 @@ class numpy_wrapper:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
return self.darray(value, nrows, ncols)
elif cstyle == LMP_STYLE_LOCAL:
nrows = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_ROWS)
ncols = self.lmp.extract_compute(cid, cstyle, LMP_SIZE_COLS)
if ncols == 0:
return self.darray(value, nrows)
else:
return self.darray(value, nrows, ncols)
elif cstyle == LMP_STYLE_ATOM:
if ctype == LMP_TYPE_VECTOR:
nlocal = self.lmp.extract_global("nlocal")

5
src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
View File

@ -266,7 +266,7 @@ void ComputeStressCartesian::compute_array()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
double xi1, xi2, xj1, xj2;
double xi1, xi2;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -305,9 +305,6 @@ void ComputeStressCartesian::compute_array()
}
}
}
xj1 = x[j][dir1];
xj2 = x[j][dir2];
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;

6
src/EXTRA-DUMP/dump_yaml.cpp
View File

@ -124,6 +124,12 @@ void DumpYAML::write_data(int n, double *mybuf)
}
fputs("]\n", fp);
}
}
/* ---------------------------------------------------------------------- */
void DumpYAML::write_footer()
{
fputs("...\n", fp);
}

1
src/EXTRA-DUMP/dump_yaml.h
View File

@ -35,6 +35,7 @@ class DumpYAML : public DumpCustom {
void write() override;
void write_header(bigint) override;
void write_data(int, double *) override;
void write_footer() override;
int modify_param(int, char **) override;
};

2
src/dump.cpp
View File

@ -517,6 +517,8 @@ void Dump::write()
if (refreshflag) modify->compute[irefresh]->refresh();
if (filewriter && fp != nullptr) write_footer();
// if file per timestep, close file if I am filewriter
if (multifile) {

2
src/dump.h
View File

@ -153,6 +153,8 @@ class Dump : protected Pointers {
virtual void pack(tagint *) = 0;
virtual int convert_string(int, double *) { return 0; }
virtual void write_data(int, double *) = 0;
virtual void write_footer() {}
void pbc_allocate();
double compute_time();

9
src/library.cpp
View File

@ -1659,14 +1659,18 @@ lists the available options.
- LMP_TYPE_ARRAY
- ``double **``
- Local data array
* - LMP_STYLE_LOCAL
- LMP_SIZE_VECTOR
- ``int *``
- Alias for using LMP_SIZE_ROWS
* - LMP_STYLE_LOCAL
- LMP_SIZE_ROWS
- ``int *``
- Number of local data rows
- Number of local array rows or length of vector
* - LMP_STYLE_LOCAL
- LMP_SIZE_COLS
- ``int *``
- Number of local data columns
- Number of local array columns, 0 if vector
.. warning::
@ -1749,6 +1753,7 @@ void *lammps_extract_compute(void *handle, const char *id, int style, int type)
if (type == LMP_TYPE_SCALAR) return (void *) &compute->size_local_rows; /* for backward compatibility */
if (type == LMP_TYPE_VECTOR) return (void *) compute->vector_local;
if (type == LMP_TYPE_ARRAY) return (void *) compute->array_local;
if (type == LMP_SIZE_VECTOR) return (void *) &compute->size_local_rows; /* alias for LMP_SIZE_ROWS */
if (type == LMP_SIZE_ROWS) return (void *) &compute->size_local_rows;
if (type == LMP_SIZE_COLS) return (void *) &compute->size_local_cols;
}

8
src/read_restart.cpp
View File

@ -61,9 +61,10 @@ void ReadRestart::command(int narg, char **arg)
// check for remap option
int remapflag = 0;
int remapflag = 1;
if (narg == 2) {
if (strcmp(arg[1],"remap") == 0) remapflag = 1;
if (strcmp(arg[1],"noremap") == 0) remapflag = 0;
else if (strcmp(arg[1],"remap") == 0) remapflag = 1; // for backward compatibility
else error->all(FLERR,"Illegal read_restart command");
}
@ -643,8 +644,7 @@ void ReadRestart::header()
int dimension = read_int();
domain->dimension = dimension;
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,
"Cannot run 2d simulation with non-periodic Z dimension");
error->all(FLERR, "Cannot run 2d simulation with non-periodic Z dimension");
// read nprocs from restart file, warn if different

4
tools/msi2lmp/src/msi2lmp.c
View File

@ -66,9 +66,9 @@
* The program is started by supplying information at the command prompt
* according to the usage described below.
*
* USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle}
* USAGE: msi2lmp ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle}
*
* -- msi2lmp3 is the name of the executable
* -- msi2lmp is the name of the executable
* -- ROOTNAME is the base name of the .car and .mdf files
* -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)
*

2
unittest/force-styles/tests/manybody-pair-pace_product.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:48 2022
epsilon: 1e-12
epsilon: 5e-12
skip_tests:
prerequisites: ! |
pair pace

2
unittest/force-styles/tests/manybody-pair-pace_recursive.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Wed Apr 7 19:30:07 2021
epsilon: 1e-12
epsilon: 5e-12
prerequisites: ! |
pair pace
pre_commands: ! |

12
unittest/python/python-commands.py
View File

@ -1,6 +1,8 @@
import sys,os,unittest,ctypes
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL
from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
has_manybody=False
try:
@ -311,6 +313,14 @@ create_atoms 1 single &
self.assertEqual(minval,1.0)
self.assertEqual(maxval,2.1)
ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR)
ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS)
ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS)
self.assertEqual(ndist1,21)
self.assertEqual(ndist2,21)
self.assertEqual(ndist3,0)
self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1)

38
unittest/python/python-numpy.py
View File

@ -93,17 +93,39 @@ class PythonNumpy(unittest.TestCase):
# TODO
pass
def testExtractComputeLocalScalar(self):
# TODO
pass
def testExtractComputeLocalVector(self):
# TODO
pass
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
self.lmp.command("mass 1 1.0")
self.lmp.command("pair_style lj/cut 1.9")
self.lmp.command("pair_coeff 1 1 1.0 1.0")
self.lmp.command("compute r0 all pair/local dist")
self.lmp.command("run 0 post no")
values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR)
self.assertEqual(values.ndim, 1)
self.assertEqual(values.size, 2)
self.assertEqual(values[0], 0.5)
self.assertEqual(values[1], 1.5)
def testExtractComputeLocalArray(self):
# TODO
pass
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.0")
self.lmp.command("create_atoms 1 single 1.0 1.0 1.5")
self.lmp.command("mass 1 1.0")
self.lmp.command("pair_style lj/cut 1.9")
self.lmp.command("pair_coeff 1 1 1.0 1.0")
self.lmp.command("compute r0 all pair/local dist dx dy dz")
self.lmp.command("run 0 post no")
values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY)
self.assertEqual(values.ndim, 2)
self.assertEqual(values.size, 8)
self.assertEqual(values[0,0], 0.5)
self.assertEqual(values[0,3], -0.5)
self.assertEqual(values[1,0], 1.5)
self.assertEqual(values[1,3], 1.5)
def testExtractAtomDeprecated(self):
self.lmp.command("units lj")