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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11079 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-12-02 23:49:46 +00:00
parent 28981227c4
commit 00700346c6
2 changed files with 30 additions and 16 deletions
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3
src/lammps.cpp
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@ -442,6 +442,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
// if restartflag set, process 2 command and quit // if restartflag set, process 2 command and quit
// add args between wdfirst and wdlast to write_data // add args between wdfirst and wdlast to write_data
// also add "noinit" to prevent write_data from doing system init
if (restartflag) { if (restartflag) {
char cmd[128]; char cmd[128];
@ -450,7 +451,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
sprintf(cmd,"write_data %s",dfile); sprintf(cmd,"write_data %s",dfile);
for (iarg = wdfirst; iarg < wdlast; iarg++) for (iarg = wdfirst; iarg < wdlast; iarg++)
sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]); sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]);
strcat(cmd,"\n"); strcat(cmd," noinit\n");
input->one(cmd); input->one(cmd);
error->done(); error->done();
} }

43
src/write_data.cpp
View File

@ -71,8 +71,10 @@ void WriteData::command(int narg, char **arg)
} else strcpy(file,arg[0]); } else strcpy(file,arg[0]);
// read optional args // read optional args
// noinit is a hidden arg, only used by -r command-line switch
pairflag = II; pairflag = II;
int noinit = 0;
int iarg = 1; int iarg = 1;
while (iarg < narg) { while (iarg < narg) {
@ -82,29 +84,40 @@ void WriteData::command(int narg, char **arg)
else if (strcmp(arg[iarg+1],"ij") == 0) pairflag = IJ; else if (strcmp(arg[iarg+1],"ij") == 0) pairflag = IJ;
else error->all(FLERR,"Illegal write_data command"); else error->all(FLERR,"Illegal write_data command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"noinit") == 0) {
noinit = 1;
iarg++;
} else error->all(FLERR,"Illegal write_data command"); } else error->all(FLERR,"Illegal write_data command");
} }
// init entire system since comm->exchange is done // init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc // comm::init needs neighbor::init needs pair::init needs kspace::init, etc
// exception is when called by -r command-line switch
// then write_data immediately follows reading of restart file
// assume that read_restart initialized necessary values
// if don't make exception:
// pair->init() can fail due to various unset values:
// e.g. pair hybrid coeffs, dpd ghost-atom velocity setting
if (comm->me == 0 && screen) if (noinit == 0) {
fprintf(screen,"System init for write_data ...\n"); if (comm->me == 0 && screen)
lmp->init(); fprintf(screen,"System init for write_data ...\n");
lmp->init();
// move atoms to new processors before writing file // move atoms to new processors before writing file
// do setup_pre_exchange to force update of per-atom info if needed // do setup_pre_exchange to force update of per-atom info if needed
// enforce PBC in case atoms are outside box // enforce PBC in case atoms are outside box
// call borders() to rebuild atom map since exchange() destroys map // call borders() to rebuild atom map since exchange() destroys map
modify->setup_pre_exchange(); modify->setup_pre_exchange();
if (domain->triclinic) domain->x2lamda(atom->nlocal); if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc(); domain->pbc();
domain->reset_box(); domain->reset_box();
comm->setup(); comm->setup();
comm->exchange(); comm->exchange();
comm->borders(); comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
}
write(file); write(file);