add separator comment lines (1ad82d7c) · Commits · 郑智淋 / lammps

src/library.cpp

+74 −0

Original line number	Diff line number	Diff line
		@@ -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

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