ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add separator comment lines

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-08-26 19:07:08 -04:00
parent f965786e74
commit 1ad82d7cdb
1 changed files with 74 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

74
src/library.cpp
View File

@ -155,6 +155,8 @@ void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr)
return (void *) lmp;
}
/* ---------------------------------------------------------------------- */
/** Variant of ``lammps_open()`` that implicitly uses ``MPI_COMM_WORLD``.
*
\verbatim embed:rst
@ -182,6 +184,8 @@ void *lammps_open_no_mpi(int argc, char **argv, void **ptr)
return lammps_open(argc,argv,MPI_COMM_WORLD,ptr);
}
/* ---------------------------------------------------------------------- */
/** Variant of ``lammps_open()`` using a Fortran MPI communicator.
*
\verbatim embed:rst
@ -209,6 +213,8 @@ void *lammps_open_fortran(int argc, char **argv, int f_comm, void **ptr)
return lammps_open(argc, argv, c_comm, ptr);
}
/* ---------------------------------------------------------------------- */
/** Delete a LAMMPS instance created by lammps_open() or its variants.
*
\verbatim embed:rst
@ -229,6 +235,8 @@ void lammps_close(void *handle)
delete lmp;
}
/* ---------------------------------------------------------------------- */
/** Ensure the MPI environment is initialized.
*
\verbatim embed:rst
@ -254,6 +262,8 @@ void lammps_mpi_init()
}
}
/* ---------------------------------------------------------------------- */
/** Shut down the MPI infrastructure.
*
\verbatim embed:rst
@ -274,6 +284,8 @@ void lammps_mpi_finalize()
MPI_Finalize();
}
/* ---------------------------------------------------------------------- */
/** Free memory buffer allocated by LAMMPS.
*
\verbatim embed:rst
@ -329,6 +341,8 @@ void lammps_file(void *handle, const char *filename)
END_CAPTURE
}
/* ---------------------------------------------------------------------- */
/** Process a single LAMMPS input command from a string.
*
\verbatim embed:rst
@ -367,6 +381,8 @@ char *lammps_command(void *handle, const char *cmd)
return result;
}
/* ---------------------------------------------------------------------- */
/** Process multiple LAMMPS input commands from list of strings.
*
\verbatim embed:rst
@ -407,6 +423,8 @@ void lammps_commands_list(void *handle, int ncmd, const char **cmds)
lmp->memory->sfree(str);
}
/* ---------------------------------------------------------------------- */
/** \brief Process a block of LAMMPS input commands from a single string.
*
\verbatim embed:rst
@ -493,6 +511,8 @@ int lammps_version(void *handle)
return atoi(lmp->universe->num_ver);
}
/* ---------------------------------------------------------------------- */
/** Return the total number of atoms in the system.
*
\verbatim embed:rst
@ -524,6 +544,8 @@ double lammps_get_natoms(void *handle)
return natoms;
}
/* ---------------------------------------------------------------------- */
/** Get current value of a thermo keyword.
*
\verbatim embed:rst
@ -553,6 +575,8 @@ double lammps_get_thermo(void *handle, char *keyword)
return dval;
}
/* ---------------------------------------------------------------------- */
/** Extract simulation box parameters.
*
\verbatim embed:rst
@ -618,6 +642,8 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
END_CAPTURE
}
/* ---------------------------------------------------------------------- */
/** Reset simulation box parameters.
*
\verbatim embed:rst
@ -667,6 +693,8 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
END_CAPTURE
}
/* ---------------------------------------------------------------------- */
/** Query LAMMPS about global settings.
*
\verbatim embed:rst
@ -751,6 +779,8 @@ int lammps_extract_setting(void * handle, char *name)
return -1;
}
/* ---------------------------------------------------------------------- */
/** Get pointer to internal global LAMMPS variables or arrays.
*
\verbatim embed:rst
@ -1052,6 +1082,8 @@ void *lammps_extract_global(void *handle, char *name)
return NULL;
}
/* ---------------------------------------------------------------------- */
/** Get pointer to a LAMMPS per-atom property.
*
\verbatim embed:rst
@ -1084,6 +1116,8 @@ void *lammps_extract_atom(void *handle, char *name)
return lmp->atom->extract(name);
}
/* ---------------------------------------------------------------------- */
/** Create N atoms from list of coordinates
*
\verbatim embed:rst
@ -1397,6 +1431,8 @@ void *lammps_extract_compute(void *handle, char *id, int style, int type)
return NULL;
}
/* ---------------------------------------------------------------------- */
/** Get pointer to data from a LAMMPS fix.
*
\verbatim embed:rst
@ -1579,6 +1615,8 @@ void *lammps_extract_fix(void *handle, char *id, int style, int type,
return NULL;
}
/* ---------------------------------------------------------------------- */
/** Get pointer to data from a LAMMPS variable.
*
\verbatim embed:rst
@ -1661,6 +1699,8 @@ void *lammps_extract_variable(void *handle, char *name, char *group)
return NULL;
}
/* ---------------------------------------------------------------------- */
/** Set the value of a string-style variable.
*
* This function assigns a new value from the string str to the
@ -2505,6 +2545,8 @@ int lammps_config_has_package(char * name) {
return Info::has_package(name) ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
/** \brief Count the number of installed packages in the LAMMPS library.
*
\verbatim embed:rst
@ -2522,6 +2564,8 @@ int lammps_config_package_count() {
return i;
}
/* ---------------------------------------------------------------------- */
/** \brief Get the name of a package in the list of installed packages in the LAMMPS library.
*
\verbatim embed:rst
@ -2548,6 +2592,8 @@ int lammps_config_package_name(int idx, char * buffer, int buf_size) {
return 1;
}
/* ---------------------------------------------------------------------- */
/** \brief Check if a specific style has been included in LAMMPS
*
\verbatim embed:rst
@ -2569,6 +2615,8 @@ int lammps_has_style(void * handle, char * category, char * name) {
return info.has_style(category, name) ? 0 : 1;
}
/* ---------------------------------------------------------------------- */
/** \brief Count the number of styles of category in the LAMMPS library.
*
\verbatim embed:rst
@ -2588,6 +2636,8 @@ int lammps_style_count(void * handle, char * category) {
return info.get_available_styles(category).size();
}
/* ---------------------------------------------------------------------- */
/** \brief 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
@ -2620,6 +2670,8 @@ int lammps_style_name(void* handle, char * category, int idx, char * buffer, int
return 0;
}
/* ---------------------------------------------------------------------- */
/** This function is used to query whether LAMMPS was compiled with
* a real MPI library or in serial.
*
@ -2634,6 +2686,8 @@ int lammps_config_has_mpi_support()
#endif
}
/* ---------------------------------------------------------------------- */
/** \brief Check if the LAMMPS library supports compressed files via a pipe to gzip
\verbatim embed:rst
@ -2651,6 +2705,8 @@ int lammps_config_has_gzip_support() {
return Info::has_gzip_support() ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
/** \brief Check if the LAMMPS library supports writing PNG format images
\verbatim embed:rst
@ -2668,6 +2724,8 @@ int lammps_config_has_png_support() {
return Info::has_png_support() ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
/** \brief Check if the LAMMPS library supports writing JPEG format images
\verbatim embed:rst
@ -2684,6 +2742,8 @@ int lammps_config_has_jpeg_support() {
return Info::has_jpeg_support() ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
/** \brief Check if the LAMMPS library supports creating movie files via a pipe to ffmpeg
\verbatim embed:rst
@ -2700,6 +2760,8 @@ int lammps_config_has_ffmpeg_support() {
return Info::has_ffmpeg_support() ? 1 : 0;
}
/* ---------------------------------------------------------------------- */
/** \brief Check whether LAMMPS errors will throw a C++ exception
*
\verbatim embed:rst
@ -2756,6 +2818,8 @@ int lammps_find_pair_neighlist(void* handle, char * style, int exact, int nsub,
return -1;
}
/* ---------------------------------------------------------------------- */
/** \brief Find neighbor list index of fix neighbor list
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -2791,6 +2855,8 @@ int lammps_find_fix_neighlist(void* handle, char * id, int request) {
return -1;
}
/* ---------------------------------------------------------------------- */
/** \brief Find neighbor list index of compute neighbor list
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -2826,6 +2892,8 @@ int lammps_find_compute_neighlist(void* handle, char * id, int request) {
return -1;
}
/* ---------------------------------------------------------------------- */
/** \brief Return the number of entries in the neighbor list with given index
*
* \param handle pointer to a previously created LAMMPS instance cast to ``void *``.
@ -2845,6 +2913,8 @@ int lammps_neighlist_num_elements(void * handle, int idx) {
return list->inum;
}
/* ---------------------------------------------------------------------- */
/** \brief Return atom local index, number of neighbors, and array of neighbor local
* atom indices of neighbor list entry
*
@ -2920,6 +2990,8 @@ imageint lammps_encode_image_flags(int ix, int iy, int iz)
return image;
}
/* ---------------------------------------------------------------------- */
/** Decode a single image flag integer into three regular integers
*
\verbatim embed:rst
@ -2978,6 +3050,8 @@ int lammps_has_error(void *handle) {
return (error->get_last_error().empty()) ? 0 : 1;
}
/* ---------------------------------------------------------------------- */
/** \brief Copy the last error message into the provided buffer
\verbatim embed:rst