add doxygen style comments to document the new C library functions added
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Evangelos Voyiatzis
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src/library.cpp
230
src/library.cpp
@ -3159,7 +3159,81 @@ void lammps_gather_bonds(void *handle, void *data)
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END_CAPTURE
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END_CAPTURE
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}
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}
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// Gather function for angles
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/** Gather type and constituent atom info for all angles
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*
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\verbatim embed:rst
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This function copies the list of all angles into a buffer provided by
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the calling code. The buffer will be filled with angle type, angle atom 1,
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angle atom 2, angle atom 3 for each angle. Thus the buffer has to be allocated to the
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dimension of 4 times the **total** number of angles times the size of
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the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
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whether they are stored in 32-bit or 64-bit integers, respectively.
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This size depends on the compile time settings used when compiling
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the LAMMPS library and can be queried by calling
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:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
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When running in parallel, the data buffer must be allocated on **all**
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MPI ranks and will be filled with the information for **all** angles
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in the system.
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.. versionadded:: TBD
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Below is a brief C code demonstrating accessing this collected angle information.
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.. code-block:: c
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#include "library.h"
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#include <stdint.h>
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#include <stdio.h>
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#include <stdlib.h>
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int main(int argc, char **argv)
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{
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int tagintsize;
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int64_t i, nangles;
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void *handle, *angles;
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handle = lammps_open_no_mpi(0, NULL, NULL);
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lammps_file(handle, "in.some_input");
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tagintsize = lammps_extract_setting(handle, "tagint");
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if (tagintsize == 4)
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nangles = *(int32_t *)lammps_extract_global(handle, "nangles");
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else
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nangles = *(int64_t *)lammps_extract_global(handle, "nangles");
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angles = malloc(nangles * 4 * tagintsize);
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lammps_gather_angles(handle, angles);
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if (lammps_extract_setting(handle, "world_rank") == 0) {
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if (tagintsize == 4) {
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int32_t *angles_real = (int32_t *)angles;
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for (i = 0; i < nangles; ++i) {
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printf("angle % 4ld: type = %d, atoms: % 4d % 4d % 4d\n",i,
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angles_real[4*i], angles_real[4*i+1], angles_real[4*i+2], angles_real[4*i+3]);
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}
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} else {
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int64_t *angles_real = (int64_t *)angles;
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for (i = 0; i < nangles; ++i) {
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printf("angle % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld\n",i,
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angles_real[4*i], angles_real[4*i+1], angles_real[4*i+2], angles_real[4*i+3]);
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}
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}
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}
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lammps_close(handle);
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lammps_mpi_finalize();
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free(angles);
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return 0;
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}
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\endverbatim
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*
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* \param handle pointer to a previously created LAMMPS instance
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* \param data pointer to data to copy the result to */
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void lammps_gather_angles(void *handle, void *data)
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void lammps_gather_angles(void *handle, void *data)
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{
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{
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auto lmp = (LAMMPS *) handle;
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auto lmp = (LAMMPS *) handle;
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@ -3195,7 +3269,82 @@ void lammps_gather_angles(void *handle, void *data)
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END_CAPTURE
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END_CAPTURE
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}
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}
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// Gather function for dihedrals
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/** Gather type and constituent atom info for all dihedrals
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*
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\verbatim embed:rst
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This function copies the list of all dihedrals into a buffer provided by
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the calling code. The buffer will be filled with dihedral type, dihedral atom 1,
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dihedral atom 2, dihedral atom 3, dihedral atom 4 for each dihedral.
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Thus the buffer has to be allocated to the
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dimension of 5 times the **total** number of dihedrals times the size of
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the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
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whether they are stored in 32-bit or 64-bit integers, respectively.
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This size depends on the compile time settings used when compiling
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the LAMMPS library and can be queried by calling
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:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
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When running in parallel, the data buffer must be allocated on **all**
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MPI ranks and will be filled with the information for **all** dihedrals
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in the system.
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.. versionadded:: TBD
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Below is a brief C code demonstrating accessing this collected dihedral information.
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.. code-block:: c
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#include "library.h"
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#include <stdint.h>
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#include <stdio.h>
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#include <stdlib.h>
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int main(int argc, char **argv)
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{
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int tagintsize;
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int64_t i, ndihedrals;
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void *handle, *dihedrals;
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handle = lammps_open_no_mpi(0, NULL, NULL);
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lammps_file(handle, "in.some_input");
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tagintsize = lammps_extract_setting(handle, "tagint");
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if (tagintsize == 4)
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ndihedrals = *(int32_t *)lammps_extract_global(handle, "ndihedrals");
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else
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ndihedrals = *(int64_t *)lammps_extract_global(handle, "ndihedrals");
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dihedrals = malloc(ndihedrals * 5 * tagintsize);
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lammps_gather_dihedrals(handle, dihedrals);
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if (lammps_extract_setting(handle, "world_rank") == 0) {
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if (tagintsize == 4) {
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int32_t *dihedrals_real = (int32_t *)dihedrals;
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for (i = 0; i < ndihedrals; ++i) {
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printf("dihedral % 4ld: type = %d, atoms: % 4d % 4d % 4d % 4d\n",i,
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dihedrals_real[5*i], dihedrals_real[5*i+1], dihedrals_real[5*i+2], dihedrals_real[5*i+3], dihedrals_real[5*i+4]);
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}
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} else {
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int64_t *dihedrals_real = (int64_t *)dihedrals;
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for (i = 0; i < ndihedrals; ++i) {
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printf("dihedral % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld % 4ld\n",i,
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dihedrals_real[5*i], dihedrals_real[5*i+1], dihedrals_real[5*i+2], dihedrals_real[5*i+3], dihedrals_real[5*i+4]);
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}
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}
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}
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lammps_close(handle);
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lammps_mpi_finalize();
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free(dihedrals);
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return 0;
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}
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\endverbatim
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*
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* \param handle pointer to a previously created LAMMPS instance
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* \param data pointer to data to copy the result to */
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void lammps_gather_dihedrals(void *handle, void *data)
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void lammps_gather_dihedrals(void *handle, void *data)
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{
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{
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auto lmp = (LAMMPS *) handle;
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auto lmp = (LAMMPS *) handle;
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@ -3231,7 +3380,82 @@ void lammps_gather_dihedrals(void *handle, void *data)
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END_CAPTURE
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END_CAPTURE
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}
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}
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// Gather function for impropers
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/** Gather type and constituent atom info for all impropers
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*
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\verbatim embed:rst
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This function copies the list of all impropers into a buffer provided by
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the calling code. The buffer will be filled with improper type, improper atom 1,
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improper atom 2, improper atom 3, improper atom 4 for each improper.
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Thus the buffer has to be allocated to the
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dimension of 5 times the **total** number of impropers times the size of
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the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
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whether they are stored in 32-bit or 64-bit integers, respectively.
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This size depends on the compile time settings used when compiling
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the LAMMPS library and can be queried by calling
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:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
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When running in parallel, the data buffer must be allocated on **all**
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MPI ranks and will be filled with the information for **all** impropers
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in the system.
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.. versionadded:: TBD
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Below is a brief C code demonstrating accessing this collected improper information.
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.. code-block:: c
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#include "library.h"
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#include <stdint.h>
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#include <stdio.h>
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#include <stdlib.h>
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int main(int argc, char **argv)
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{
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int tagintsize;
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int64_t i, nimpropers;
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void *handle, *impropers;
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handle = lammps_open_no_mpi(0, NULL, NULL);
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lammps_file(handle, "in.some_input");
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tagintsize = lammps_extract_setting(handle, "tagint");
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if (tagintsize == 4)
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nimpropers = *(int32_t *)lammps_extract_global(handle, "nimpropers");
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else
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nimpropers = *(int64_t *)lammps_extract_global(handle, "nimpropers");
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impropers = malloc(nimpropers * 5 * tagintsize);
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lammps_gather_impropers(handle, impropers);
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if (lammps_extract_setting(handle, "world_rank") == 0) {
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if (tagintsize == 4) {
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int32_t *impropers_real = (int32_t *)impropers;
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for (i = 0; i < nimpropers; ++i) {
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printf("improper % 4ld: type = %d, atoms: % 4d % 4d % 4d % 4d\n",i,
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impropers_real[5*i], impropers_real[5*i+1], impropers_real[5*i+2], impropers_real[5*i+3], impropers_real[5*i+4]);
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}
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} else {
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int64_t *impropers_real = (int64_t *)impropers;
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for (i = 0; i < nimpropers; ++i) {
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printf("improper % 4ld: type = %ld, atoms: % 4ld % 4ld % 4ld % 4ld\n",i,
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impropers_real[5*i], impropers_real[5*i+1], impropers_real[5*i+2], impropers_real[5*i+3], impropers_real[5*i+4]);
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}
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}
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}
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lammps_close(handle);
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lammps_mpi_finalize();
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free(impropers);
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return 0;
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}
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\endverbatim
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*
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* \param handle pointer to a previously created LAMMPS instance
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* \param data pointer to data to copy the result to */
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void lammps_gather_impropers(void *handle, void *data)
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void lammps_gather_impropers(void *handle, void *data)
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{
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{
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auto lmp = (LAMMPS *) handle;
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auto lmp = (LAMMPS *) handle;
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