implement and document noaccel flag for read_restart (ce3e4b50) · Commits · 郑智淋 / lammps

doc/src/read_restart.rst

+27 −6

Original line number	Diff line number	Diff line
		@@ -9,10 +9,16 @@ Syntax

		.. parsed-literal::

		read_restart file flag
		read_restart file flags

		* file = name of binary restart file to read in
		* flag = remap (optional)
		* optional flags may be appended

		.. parsed-literal::

		flag = remap or noaccel
		remap = enforce remapping of atoms into the simulation box
		noaccel = remove known accelerator suffixes from styles

		Examples
		""""""""
		@@ -55,12 +61,27 @@ changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` comm
		into the simulation box, updating image flags for the atom
		appropriately.

		.. note::

		By default, read_restart will recreate atom, pair and other styles
		exactly as they were stored in the restart file. In a run using the
		:doc:`suffix command <suffix>` or
		:doc:`suffix command line flag <Run_options>`, that will include the
		appended (accelerator) suffix. When restarting with a LAMMPS executable
		that does not include those styles, the restart will fail. With the
		optional noaccel flag, this behavior is changed. With that flag
		any known suffix of an :doc:`accelerated style <Speed_packages>` will
		be removed. In case the suffix flag or command line option
		is used during reading the restart this suffix will be tried, regardless
		of whether the noaccel flag is used.

		Restart files are saved in binary format to enable exact restarts,
		meaning that the trajectories of a restarted run will precisely match
		meaning that the trajectories of a restarted run will closely match
		those produced by the original run had it continued on.

		Several things can prevent exact restarts due to round-off effects, in
		which case the trajectories in the 2 runs will slowly diverge. These
		Several things can prevent exact restarts due to propagation of round-off
		effects, in which case the trajectories in the 2 runs will at some point
		start diverging exponentially. These
		include running on a different number of processors or changing
		certain settings such as those set by the :doc:`newton <newton>` or
		:doc:`processors <processors>` commands. LAMMPS will issue a warning in
		@@ -83,7 +104,7 @@ produced the restart file, it could be a LAMMPS bug, so consider
		:doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.

		Because restart files are binary, they may not be portable to other
		machines. In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
		machines. In this case, you can use the :doc:`-r2data command-line switch <Run_options>` to convert a restart file to a data file.

		Similar to how restart files are written (see the
		:doc:`write_restart <write_restart>` and :doc:`restart <restart>`

src/read_restart.cpp

+20 −10

Original line number	Diff line number	Diff line
		@@ -69,7 +69,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,

		/* ---------------------------------------------------------------------- */

		ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {}
		ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {
		noaccelflag = 0;
		}

		/* ---------------------------------------------------------------------- */

		@@ -89,8 +91,9 @@ void ReadRestart::command(int narg, char **arg)
		// check for remap option

		int remapflag = 0;
		if (narg == 2) {
		if (strcmp(arg[1],"remap") == 0) remapflag = 1;
		for (int iarg=1; iarg < narg; ++iarg) {
		if (strcmp(arg[iarg],"remap") == 0) remapflag = 1;
		else if (strcmp(arg[iarg],"noaccel") == 0) noaccelflag = 1;
		else error->all(FLERR,"Illegal read_restart command");
		}

		@@ -856,7 +859,8 @@ void ReadRestart::header(int incompatible)
		// create new AtomVec class using any stored args

		} else if (flag == ATOM_STYLE) {
		char *style = utils::stripsuffix(read_string());
		char *style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		int nargcopy = read_int();
		char *argcopy = new char[nargcopy];
		for (int i = 0; i < nargcopy; i++)
		@@ -996,7 +1000,8 @@ void ReadRestart::force_fields()
		while (flag >= 0) {

		if (flag == PAIR) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		force->create_pair(style,1);
		delete [] style;
		if (comm->me ==0) {
		@@ -1008,7 +1013,8 @@ void ReadRestart::force_fields()
		force->pair->read_restart(fp);

		} else if (flag == NO_PAIR) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		if (comm->me ==0) {
		if (screen) fprintf(screen," pair style %s stores no "
		"restart info\n", style);
		@@ -1019,7 +1025,8 @@ void ReadRestart::force_fields()
		force->pair_restart = style;

		} else if (flag == BOND) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		force->create_bond(style,1);
		delete [] style;
		if (comm->me ==0) {
		@@ -1031,7 +1038,8 @@ void ReadRestart::force_fields()
		force->bond->read_restart(fp);

		} else if (flag == ANGLE) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		force->create_angle(style,1);
		delete [] style;
		if (comm->me ==0) {
		@@ -1043,7 +1051,8 @@ void ReadRestart::force_fields()
		force->angle->read_restart(fp);

		} else if (flag == DIHEDRAL) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		force->create_dihedral(style,1);
		delete [] style;
		if (comm->me ==0) {
		@@ -1055,7 +1064,8 @@ void ReadRestart::force_fields()
		force->dihedral->read_restart(fp);

		} else if (flag == IMPROPER) {
		style = utils::stripsuffix(read_string());
		style = read_string();
		if (noaccelflag) style = utils::stripsuffix(style);
		force->create_improper(style,1);
		delete [] style;
		if (comm->me ==0) {

src/read_restart.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -37,6 +37,8 @@ class ReadRestart : protected Pointers {
		// 1 = restart file is parallel (multiple files)
		int multiproc_file; // # of parallel files in restart
		int nprocs_file; // total # of procs that wrote restart file
		int noaccelflag; // 1 if stripping accelerator suffixes from styles
		// 0 if leaving style names unchanged

		// MPI-IO values

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