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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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78
src/modify.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -56,7 +56,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
list_initial_integrate_respa = list_post_integrate_respa = NULL;
list_pre_force_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
list_min_pre_exchange = list_min_pre_force =
list_min_pre_exchange = list_min_pre_force =
list_min_post_force = list_min_energy = NULL;
end_of_step_every = NULL;
@ -139,15 +139,15 @@ void Modify::init()
list_init_thermo_energy(THERMO_ENERGY,n_thermo_energy,list_thermo_energy);
list_init(INITIAL_INTEGRATE_RESPA,
n_initial_integrate_respa,list_initial_integrate_respa);
n_initial_integrate_respa,list_initial_integrate_respa);
list_init(POST_INTEGRATE_RESPA,
n_post_integrate_respa,list_post_integrate_respa);
n_post_integrate_respa,list_post_integrate_respa);
list_init(POST_FORCE_RESPA,
n_post_force_respa,list_post_force_respa);
n_post_force_respa,list_post_force_respa);
list_init(PRE_FORCE_RESPA,
n_pre_force_respa,list_pre_force_respa);
n_pre_force_respa,list_pre_force_respa);
list_init(FINAL_INTEGRATE_RESPA,
n_final_integrate_respa,list_final_integrate_respa);
n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_PRE_FORCE,n_min_pre_force,list_min_pre_force);
@ -214,7 +214,7 @@ void Modify::init()
MPI_Allreduce(&check,&checkall,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0 && checkall)
error->warning(FLERR,
"One or more atoms are time integrated more than once");
"One or more atoms are time integrated more than once");
}
/* ----------------------------------------------------------------------
@ -669,13 +669,13 @@ void Modify::add_fix(int narg, char **arg, char *suffix)
for (int i = 0; i < nfix_restart_global; i++)
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
if (comm->me == 0) {
char *str = (char *) ("Resetting global state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
char *str = (char *) ("Resetting global state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
@ -684,14 +684,14 @@ void Modify::add_fix(int narg, char **arg, char *suffix)
for (int i = 0; i < nfix_restart_peratom; i++)
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
for (int j = 0; j < atom->nlocal; j++)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
if (comm->me == 0) {
char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
}
@ -710,7 +710,7 @@ void Modify::modify_fix(int narg, char **arg)
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix == nfix) error->all(FLERR,"Could not find fix_modify ID");
fix[ifix]->modify_params(narg-1,&arg[1]);
}
@ -822,7 +822,7 @@ void Modify::modify_compute(int narg, char **arg)
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0) break;
if (icompute == ncompute) error->all(FLERR,"Could not find compute_modify ID");
compute[icompute]->modify_params(narg-1,&arg[1]);
}
@ -906,7 +906,7 @@ void Modify::write_restart(FILE *fp)
int me = comm->me;
int count = 0;
for (int i = 0; i < nfix; i++)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
@ -915,18 +915,18 @@ void Modify::write_restart(FILE *fp)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
}
fix[i]->write_restart(fp);
}
count = 0;
for (int i = 0; i < nfix; i++)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
@ -934,14 +934,14 @@ void Modify::write_restart(FILE *fp)
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
n = fix[i]->maxsize_restart();
fwrite(&n,sizeof(int),1,fp);
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
n = fix[i]->maxsize_restart();
fwrite(&n,sizeof(int),1,fp);
}
}
}
@ -1149,9 +1149,9 @@ void Modify::list_init_compute()
bigint Modify::memory_usage()
{
bigint bytes = 0;
for (int i = 0; i < nfix; i++)
for (int i = 0; i < nfix; i++)
bytes += static_cast<bigint> (fix[i]->memory_usage());
for (int i = 0; i < ncompute; i++)
for (int i = 0; i < ncompute; i++)
bytes += static_cast<bigint> (compute[i]->memory_usage());
return bytes;
}