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Merge branch 'master' into progguide-axel

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This commit is contained in:
Axel Kohlmeyer
2020-10-06 17:11:47 -04:00
parent 9274912a81 887603d856
commit 1ee9e4eabd
31 changed files with 1252 additions and 67 deletions
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209
src/library.cpp
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@ -22,6 +22,7 @@
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "dump.h"
#include "error.h"
#include "fix.h"
#include "fix_external.h"
@ -31,10 +32,13 @@
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "region.h"
#include "output.h"
#include "thermo.h"
#include "timer.h"
#include "universe.h"
#include "update.h"
#include "variable.h"
@ -4013,18 +4017,17 @@ int lammps_style_count(void *handle, const char *category) {
/** Look up the name of a style by index in the list of style of a given category in the LAMMPS library.
*
\verbatim embed:rst
This function copies the name of the package with the index *idx* into the
provided C-style string buffer. The length of the buffer must be provided
as *buf_size* argument. If the name of the package exceeds the length of the
buffer, it will be truncated accordingly. If the index is out of range,
the function returns 0 and *buffer* is set to an empty string, otherwise 1.
Please see :cpp:func:`lammps_has_style` for a list of valid categories.
\endverbatim
*
* This function copies the name of the *category* style with the index
* *idx* into the provided C-style string buffer. The length of the buffer
* must be provided as *buf_size* argument. If the name of the style
* exceeds the length of the buffer, it will be truncated accordingly.
* If the index is out of range, the function returns 0 and *buffer* is
* set to an empty string, otherwise 1.
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \param category category of styles
* \param idx index of the package in the list of included packages (0 <= idx < style count)
* \param idx index of the style in the list of *category* styles (0 <= idx < style count)
* \param buffer string buffer to copy the name of the style to
* \param buf_size size of the provided string buffer
* \return 1 if successful, otherwise 0
@ -4046,6 +4049,167 @@ int lammps_style_name(void *handle, const char *category, int idx,
/* ---------------------------------------------------------------------- */
/** Check if a specific ID exists in the current LAMMPS instance
*
\verbatim embed:rst
This function checks if the current LAMMPS instance a *category* ID of
the given *name* exists. Valid categories are: *compute*\ , *dump*\ ,
*fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ .
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \param category category of the id
* \param name name of the id
* \return 1 if included, 0 if not.
*/
int lammps_has_id(void *handle, const char *category, const char *name) {
LAMMPS *lmp = (LAMMPS *) handle;
if (strcmp(category,"compute") == 0) {
int ncompute = lmp->modify->ncompute;
Compute **compute = lmp->modify->compute;
for (int i=0; i < ncompute; ++i) {
if (strcmp(name,compute[i]->id) == 0) return 1;
}
} else if (strcmp(category,"dump") == 0) {
int ndump = lmp->output->ndump;
Dump **dump = lmp->output->dump;
for (int i=0; i < ndump; ++i) {
if (strcmp(name,dump[i]->id) == 0) return 1;
}
} else if (strcmp(category,"fix") == 0) {
int nfix = lmp->modify->nfix;
Fix **fix = lmp->modify->fix;
for (int i=0; i < nfix; ++i) {
if (strcmp(name,fix[i]->id) == 0) return 1;
}
} else if (strcmp(category,"group") == 0) {
int ngroup = lmp->group->ngroup;
char **groups = lmp->group->names;
for (int i=0; i < ngroup; ++i) {
if (strcmp(groups[i],name) == 0) return 1;
}
} else if (strcmp(category,"molecule") == 0) {
int nmolecule = lmp->atom->nmolecule;
Molecule **molecule = lmp->atom->molecules;
for (int i=0; i < nmolecule; ++i) {
if (strcmp(name,molecule[i]->id) == 0) return 1;
}
} else if (strcmp(category,"region") == 0) {
int nregion = lmp->domain->nregion;
Region **region = lmp->domain->regions;
for (int i=0; i < nregion; ++i) {
if (strcmp(name,region[i]->id) == 0) return 1;
}
} else if (strcmp(category,"variable") == 0) {
int nvariable = lmp->input->variable->nvar;
char **varnames = lmp->input->variable->names;
for (int i=0; i < nvariable; ++i) {
if (strcmp(name,varnames[i]) == 0) return 1;
}
}
return 0;
}
/* ---------------------------------------------------------------------- */
/** Count the number of IDs of a category.
*
\verbatim embed:rst
This function counts how many IDs in the provided *category*
are defined in the current LAMMPS instance.
Please see :cpp:func:`lammps_has_id` for a list of valid
categories.
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \param category category of IDs
* \return number of IDs in category
*/
int lammps_id_count(void *handle, const char *category) {
LAMMPS *lmp = (LAMMPS *) handle;
if (strcmp(category,"compute") == 0) {
return lmp->modify->ncompute;
} else if (strcmp(category,"dump") == 0) {
return lmp->output->ndump;
} else if (strcmp(category,"fix") == 0) {
return lmp->modify->nfix;
} else if (strcmp(category,"group") == 0) {
return lmp->group->ngroup;
} else if (strcmp(category,"molecule") == 0) {
return lmp->atom->nmolecule;
} else if (strcmp(category,"region") == 0) {
return lmp->domain->nregion;
} else if (strcmp(category,"variable") == 0) {
return lmp->input->variable->nvar;
}
return 0;
}
/* ---------------------------------------------------------------------- */
/** Look up the name of an ID by index in the list of IDs of a given category.
*
* This function copies the name of the *category* ID with the index
* *idx* into the provided C-style string buffer. The length of the buffer
* must be provided as *buf_size* argument. If the name of the style
* exceeds the length of the buffer, it will be truncated accordingly.
* If the index is out of range, the function returns 0 and *buffer* is
* set to an empty string, otherwise 1.
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \param category category of IDs
* \param idx index of the ID in the list of *category* styles (0 <= idx < count)
* \param buffer string buffer to copy the name of the style to
* \param buf_size size of the provided string buffer
* \return 1 if successful, otherwise 0
*/
int lammps_id_name(void *handle, const char *category, int idx,
char *buffer, int buf_size) {
LAMMPS *lmp = (LAMMPS *) handle;
if (strcmp(category,"compute") == 0) {
if ((idx >=0) && (idx < lmp->modify->ncompute)) {
strncpy(buffer, lmp->modify->compute[idx]->id, buf_size);
return 1;
}
} else if (strcmp(category,"dump") == 0) {
if ((idx >=0) && (idx < lmp->output->ndump)) {
strncpy(buffer, lmp->output->dump[idx]->id, buf_size);
return 1;
}
} else if (strcmp(category,"fix") == 0) {
if ((idx >=0) && (idx < lmp->modify->nfix)) {
strncpy(buffer, lmp->modify->fix[idx]->id, buf_size);
return 1;
}
} else if (strcmp(category,"group") == 0) {
if ((idx >=0) && (idx < lmp->group->ngroup)) {
strncpy(buffer, lmp->group->names[idx], buf_size);
return 1;
}
} else if (strcmp(category,"molecule") == 0) {
if ((idx >=0) && (idx < lmp->atom->nmolecule)) {
strncpy(buffer, lmp->atom->molecules[idx]->id, buf_size);
return 1;
}
} else if (strcmp(category,"region") == 0) {
if ((idx >=0) && (idx < lmp->domain->nregion)) {
strncpy(buffer, lmp->domain->regions[idx]->id, buf_size);
return 1;
}
} else if (strcmp(category,"variable") == 0) {
if ((idx >=0) && (idx < lmp->input->variable->nvar)) {
strncpy(buffer, lmp->input->variable->names[idx], buf_size);
return 1;
}
}
buffer[0] = '\0';
return 0;
}
/* ---------------------------------------------------------------------- */
/** This function is used to query whether LAMMPS was compiled with
* a real MPI library or in serial.
*
@ -4395,6 +4559,33 @@ void lammps_decode_image_flags(imageint image, int *flags)
flags[2] = (image >> IMG2BITS) - IMGMAX;
}
/** Check if LAMMPS is currently inside a run or minimization
*
* This function can be used from signal handlers or multi-threaded
* applications to determine if the LAMMPS instance is currently active.
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
* \return 0 if idle or >0 if active */
int lammps_is_running(void *handle)
{
LAMMPS * lmp = (LAMMPS *) handle;
return lmp->update->whichflag;
}
/** Force a timeout to cleanly stop an ongoing run
*
* This function can be used from signal handlers or multi-threaded
* applications to cleanly terminate an ongoing run.
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *`` */
void lammps_force_timeout(void *handle)
{
LAMMPS * lmp = (LAMMPS *) handle;
return lmp->timer->force_timeout();
}
// ----------------------------------------------------------------------
// Library functions for error handling with exceptions enabled
// ----------------------------------------------------------------------