forked from lijiext/lammps
added -restart2dump command-line option
This commit is contained in:
Steve Plimpton
parent
4015b36a1a
commit
d9dd80b368
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@ -24,8 +24,9 @@ letter abbreviation can be used:
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"-p or -partition"_#partition
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"-pl or -plog"_#plog
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"-ps or -pscreen"_#pscreen
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"-r or -restart"_#restart
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"-ro or -reorder"_#reorder
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"-r2data or -restart2data"_#restart2data
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"-r2dump or -restart2dump"_#restart2dump
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"-sc or -screen"_#screen
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"-sf or -suffix"_#suffix
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"-v or -var"_#var :ul
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@ -280,34 +281,6 @@ specified by the -screen command-line option.
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:line
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[-restart restartfile {remap} datafile keyword value ...] :link(restart)
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Convert the restart file into a data file and immediately exit. This
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is the same operation as if the following 2-line input script were
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run:
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read_restart restartfile {remap}
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write_data datafile keyword value ... :pre
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Note that the specified restartfile and datafile can have wild-card
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characters ("*",%") as described by the
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"read_restart"_read_restart.html and "write_data"_write_data.html
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commands. But a filename such as file.* will need to be enclosed in
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quotes to avoid shell expansion of the "*" character.
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Note that following restartfile, the optional flag {remap} can be
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used. This has the same effect as adding it to the
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"read_restart"_read_restart.html command, as explained on its doc
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page. This is only useful if the reading of the restart file triggers
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an error that atoms have been lost. In that case, use of the remap
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flag should allow the data file to still be produced.
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Also note that following datafile, the same optional keyword/value
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pairs can be listed as used by the "write_data"_write_data.html
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command.
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:line
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[-reorder] :link(reorder)
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This option has 2 forms:
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@ -381,6 +354,77 @@ the LAMMPS simulation domain.
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:line
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[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
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Convert the restart file into a data file and immediately exit. This
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is the same operation as if the following 2-line input script were
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run:
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read_restart restartfile (remap)
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write_data datafile keyword value ... :pre
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Note that the specified restartfile and/or datafile can have the
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wild-card character "*". The restartfile can also have the wild-card
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character "%". The meaning of these characters is explained on the
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"read_restart"_read_restart.html and "write_data"_write_data.html doc
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pages. The use of "%" means that a parallel restart file can be read.
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Note that a filename such as file.* will need to be enclosed in quotes
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to avoid shell expansion of the "*" character.
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Note that following restartfile, the optional word "remap" can be
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used. This has the effect of adding it to the
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"read_restart"_read_restart.html command, as explained on its doc
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page. This is useful if reading the restart file triggers an error
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that atoms have been lost. In that case, use of the remap flag should
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allow the data file to still be produced.
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The syntax following restartfile (or remap), namely
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datafile keyword value ... :pre
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is identical to the arguments of the "write_data"_write_data.html
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command. See its doc page for details. This includes its
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optional keyword/value settings.
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:line
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[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
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Convert the restart file into a dump file and immediately exit. This
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is the same operation as if the following 2-line input script were
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run:
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read_restart restartfile (remap)
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write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
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Note that the specified restartfile and dumpfile can have wild-card
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characters ("*","%") as explained on the
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"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
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pages. The use of "%" means that a parallel restart file and/or
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parallel dump file can be read and/or written. Note that a filename
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such as file.* will need to be enclosed in quotes to avoid shell
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expansion of the "*" character.
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Note that following restartfile, the optional word "remap" can be
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used. This has the effect as adding it to the
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"read_restart"_read_restart.html command, as explained on its doc
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page. This is useful if reading the restart file triggers an error
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that atoms have been lost. In that case, use of the remap flag should
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allow the dump file to still be produced.
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The syntax following restartfile (or remap), namely
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group-ID dumpstyle dumpfile arg1 arg2 ... :pre
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is identical to the arguments of the "write_dump"_write_dump.html
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command. See its doc page for details. This includes what per-atom
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fields are written to the dump file and optional dump_modify settings,
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including ones that affect how parallel dump files are written, e.g.
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the {nfile} and {fileper} keywords. See the
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"dump_modify"_dump_modify.html doc page for details.
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:line
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[-screen file] :link(screen)
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Specify a file for LAMMPS to write its screen information to. In
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@ -121,8 +121,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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int partscreenflag = 0;
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int partlogflag = 0;
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int kokkosflag = 0;
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int restartflag = 0;
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int restartremapflag = 0;
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int restart2data = 0;
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int restart2dump = 0;
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int restartremap = 0;
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int citeflag = 1;
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int helpflag = 0;
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@ -132,9 +133,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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else exename = NULL;
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packargs = NULL;
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num_package = 0;
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char *rfile = NULL;
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char *dfile = NULL;
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int wdfirst,wdlast;
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char *restartfile = NULL;
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int wfirst,wlast;
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int kkfirst,kklast;
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int npack = 0;
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@ -248,26 +248,49 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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universe->reorder(arg[iarg+1],arg[iarg+2]);
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iarg += 3;
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} else if (strcmp(arg[iarg],"-restart") == 0 ||
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strcmp(arg[iarg],"-r") == 0) {
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} else if (strcmp(arg[iarg],"-restart2data") == 0 ||
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strcmp(arg[iarg],"-r2data") == 0) {
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if (iarg+3 > narg)
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error->universe_all(FLERR,"Invalid command-line argument");
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restartflag = 1;
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rfile = arg[iarg+1];
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dfile = arg[iarg+2];
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if (restart2dump)
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error->universe_all(FLERR,
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"Cannot use both -restart2data and -restart2dump");
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restart2data = 1;
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restartfile = arg[iarg+1];
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// check for restart remap flag
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if (strcmp(dfile,"remap") == 0) {
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if (strcmp(arg[iarg+2],"remap") == 0) {
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if (iarg+4 > narg)
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error->universe_all(FLERR,"Invalid command-line argument");
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restartremapflag = 1;
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dfile = arg[iarg+3];
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restartremap = 1;
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iarg++;
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}
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iarg += 3;
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// delimit any extra args for the write_data command
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wdfirst = iarg;
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iarg += 2;
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// delimit args for the write_data command
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wfirst = iarg;
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while (iarg < narg && arg[iarg][0] != '-') iarg++;
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wdlast = iarg;
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wlast = iarg;
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} else if (strcmp(arg[iarg],"-restart2dump") == 0 ||
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strcmp(arg[iarg],"-r2dump") == 0) {
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if (iarg+3 > narg)
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error->universe_all(FLERR,"Invalid command-line argument");
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if (restart2data)
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error->universe_all(FLERR,
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"Cannot use both -restart2data and -restart2dump");
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restart2dump = 1;
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restartfile = arg[iarg+1];
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// check for restart remap flag
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if (strcmp(arg[iarg+2],"remap") == 0) {
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if (iarg+4 > narg)
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error->universe_all(FLERR,"Invalid command-line argument");
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restartremap = 1;
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iarg++;
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}
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iarg += 2;
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// delimit args for the write_dump command
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wfirst = iarg;
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while (iarg < narg && arg[iarg][0] != '-') iarg++;
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wlast = iarg;
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} else if (strcmp(arg[iarg],"-screen") == 0 ||
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strcmp(arg[iarg],"-sc") == 0) {
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@ -547,6 +570,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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input = new Input(this,narg,arg);
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// copy package cmdline arguments
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if (npack > 0) {
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num_package = npack;
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packargs = new char**[npack];
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@ -573,19 +597,21 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
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error->done(0);
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}
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// if restartflag set, invoke 2 commands and quit
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// add args between wdfirst and wdlast to write_data command
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// also add "noinit" to prevent write_data from doing system init
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// if either restart conversion option was used, invoke 2 commands and quit
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// add args between wfirst and wlast to write_data or write_data command
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// add "noinit" to write_data to prevent a system init
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// write_dump will just give a warning message about no init
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if (restartflag) {
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char cmd[128];
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snprintf(cmd,128,"read_restart %s\n",rfile);
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if (restartremapflag) strcat(cmd," remap\n");
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if (restart2data || restart2dump) {
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char cmd[256];
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snprintf(cmd,256,"read_restart %s\n",restartfile);
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if (restartremap) strcat(cmd," remap\n");
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input->one(cmd);
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snprintf(cmd,128,"write_data %s",dfile);
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for (iarg = wdfirst; iarg < wdlast; iarg++)
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if (restart2data) snprintf(cmd,256,"write_data");
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else snprintf(cmd,256,"write_dump");
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for (iarg = wfirst; iarg < wlast; iarg++)
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sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]);
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strcat(cmd," noinit\n");
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if (restart2data) strcat(cmd," noinit\n");
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input->one(cmd);
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error->done(0);
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}
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