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Merge pull request #2850 from akohlmey/lammps-gather-bonds

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Implement lammps_gather_bonds() into the C-library interface and the Python module
This commit is contained in:
Axel Kohlmeyer
2021-07-27 11:30:19 -04:00
committed by GitHub
parent dab884fd1f a4ffffad33
commit 8838fbc1c3
14 changed files with 740 additions and 2 deletions
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127
src/library.cpp
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@ -367,7 +367,7 @@ must be explicitly shut down after any LAMMPS instance using it is
closed (to release associated resources).
After calling this function no Kokkos functionality may be used.
.. versionadded:: TBD
.. versionadded:: 2Jul2021
\endverbatim */
@ -2686,6 +2686,115 @@ void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count,
END_CAPTURE
}
/** Gather type and constituent atom info for all bonds
*
\verbatim embed:rst
This function copies the list of all bonds into a buffer provided by
the calling code. The buffer will be filled with bond type, bond atom 1,
bond atom 2 for each bond. Thus the buffer has to be allocated to the
dimension of 3 times the **total** number of bonds times the size of
the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
whether they are stored in 32-bit or 64-bit integers, respectively.
This size depends on the compile time settings used when compiling
the LAMMPS library and can be queried by calling
:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** bonds
in the system.
.. versionadded:: 28Jul2021
Below is a brief C code demonstrating accessing this collected bond information.
.. code-block:: c
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
#include "library.h"
int main(int argc, char **argv)
{
int tagintsize;
int64_t i, nbonds;
void *handle, *bonds;
handle = lammps_open_no_mpi(0, NULL, NULL);
lammps_file(handle, "in.some_input");
tagintsize = lammps_extract_setting(handle, "tagint");
if (tagintsize == 4)
nbonds = *(int32_t *)lammps_extract_global(handle, "nbonds");
else
nbonds = *(int64_t *)lammps_extract_global(handle, "nbonds");
bonds = malloc(nbonds * 3 * tagintsize);
lammps_gather_bonds(handle, bonds);
if (lammps_extract_setting(handle, "world_rank") == 0) {
if (tagintsize == 4) {
int32_t *bonds_real = (int32_t *)bonds;
for (i = 0; i < nbonds; ++i) {
printf("bond % 4ld: type = %d, atoms: % 4d % 4d\n",i,
bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]);
}
} else {
int64_t *bonds_real = (int64_t *)bonds;
for (i = 0; i < nbonds; ++i) {
printf("bond % 4ld: type = %ld, atoms: % 4ld % 4ld\n",i,
bonds_real[3*i], bonds_real[3*i+1], bonds_real[3*i+2]);
}
}
}
lammps_close(handle);
lammps_mpi_finalize();
free(bonds);
return 0;
}
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param data pointer to data to copy the result to */
void lammps_gather_bonds(void *handle, void *data)
{
LAMMPS *lmp = (LAMMPS *)handle;
BEGIN_CAPTURE {
void *val = lammps_extract_global(handle,"nbonds");
bigint nbonds = *(bigint *)val;
// no bonds
if (nbonds == 0) return;
// count per MPI rank bonds, determine offsets and allocate local buffers
int localbonds = lmp->atom->avec->pack_bond(nullptr);
int nprocs = lmp->comm->nprocs;
int *bufsizes = new int[nprocs];
int *bufoffsets = new int[nprocs];
MPI_Allgather(&localbonds, 1, MPI_INT, bufsizes, 1, MPI_INT, lmp->world);
bufoffsets[0] = 0;
bufsizes[0] *= 3; // 3 items per bond: type, atom1, atom2
for (int i = 1; i < nprocs; ++i) {
bufoffsets[i] = bufoffsets[i-1] + bufsizes[i-1];
bufsizes[i] *= 3; // 3 items per bond: type, atom1, atom2
}
tagint **bonds;
lmp->memory->create(bonds, localbonds, 3, "library:gather_bonds:localbonds");
lmp->atom->avec->pack_bond(bonds);
MPI_Allgatherv(&bonds[0][0], 3*localbonds, MPI_LMP_TAGINT, data, bufsizes,
bufoffsets, MPI_LMP_TAGINT, lmp->world);
lmp->memory->destroy(bonds);
delete[] bufsizes;
delete[] bufoffsets;
}
END_CAPTURE
}
/* ----------------------------------------------------------------------
Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France)
gather the named atom-based entity for all atoms
@ -4836,6 +4945,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionchanged:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4899,6 +5010,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4947,6 +5060,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -4996,6 +5111,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5045,6 +5162,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5097,6 +5216,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5142,6 +5263,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -5196,6 +5319,8 @@ Please see the documentation for :doc:`fix external <fix_external>` for
more information about how to use the fix and how to couple it with an
external code.
.. versionadded:: 28Jul2021
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.

2
src/library.h
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@ -152,6 +152,8 @@ void lammps_scatter_atoms(void *handle, char *name, int type, int count, void *d
void lammps_scatter_atoms_subset(void *handle, char *name, int type, int count, int ndata, int *ids,
void *data);
void lammps_gather_bonds(void *handle, void *data);
void lammps_gather(void *handle, char *name, int type, int count, void *data);
void lammps_gather_concat(void *handle, char *name, int type, int count, void *data);
void lammps_gather_subset(void *handle, char *name, int type, int count, int ndata, int *ids,