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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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184
src/lammps.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.
@ -78,87 +78,87 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"-partition") == 0 ||
strcmp(arg[iarg],"-p") == 0) {
if (strcmp(arg[iarg],"-partition") == 0 ||
strcmp(arg[iarg],"-p") == 0) {
universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg++;
while (iarg < narg && arg[iarg][0] != '-') {
universe->add_world(arg[iarg]);
iarg++;
universe->add_world(arg[iarg]);
iarg++;
}
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-screen") == 0 ||
strcmp(arg[iarg],"-sc") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-screen") == 0 ||
strcmp(arg[iarg],"-sc") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
screenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-log") == 0 ||
strcmp(arg[iarg],"-l") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-log") == 0 ||
strcmp(arg[iarg],"-l") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
logflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-var") == 0 ||
strcmp(arg[iarg],"-v") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-var") == 0 ||
strcmp(arg[iarg],"-v") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 3;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
} else if (strcmp(arg[iarg],"-echo") == 0 ||
strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-echo") == 0 ||
strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-pscreen") == 0 ||
strcmp(arg[iarg],"-ps") == 0) {
if (iarg+2 > narg)
} else if (strcmp(arg[iarg],"-pscreen") == 0 ||
strcmp(arg[iarg],"-ps") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partscreenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-plog") == 0 ||
strcmp(arg[iarg],"-pl") == 0) {
if (iarg+2 > narg)
} else if (strcmp(arg[iarg],"-plog") == 0 ||
strcmp(arg[iarg],"-pl") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partlogflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-cuda") == 0 ||
strcmp(arg[iarg],"-c") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-cuda") == 0 ||
strcmp(arg[iarg],"-c") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (strcmp(arg[iarg+1],"on") == 0) cudaflag = 1;
else if (strcmp(arg[iarg+1],"off") == 0) cudaflag = 0;
else error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-suffix") == 0 ||
strcmp(arg[iarg],"-sf") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-suffix") == 0 ||
strcmp(arg[iarg],"-sf") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
delete [] suffix;
int n = strlen(arg[iarg+1]) + 1;
suffix = new char[n];
strcpy(suffix,arg[iarg+1]);
suffix_enable = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (universe->existflag)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"-help") == 0 ||
strcmp(arg[iarg],"-h") == 0) {
if (iarg+1 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
} else if (strcmp(arg[iarg],"-help") == 0 ||
strcmp(arg[iarg],"-h") == 0) {
if (iarg+1 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
helpflag = 1;
iarg += 1;
} else error->universe_all(FLERR,"Invalid command-line argument");
@ -197,19 +197,19 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
universe->uscreen = NULL;
else {
universe->uscreen = fopen(arg[screenflag],"w");
if (universe->uscreen == NULL)
error->universe_one(FLERR,"Cannot open universe screen file");
if (universe->uscreen == NULL)
error->universe_one(FLERR,"Cannot open universe screen file");
}
if (logflag == 0) {
universe->ulogfile = fopen("log.lammps","w");
if (universe->ulogfile == NULL)
error->universe_one(FLERR,"Cannot open log.lammps");
if (universe->ulogfile == NULL)
error->universe_one(FLERR,"Cannot open log.lammps");
} else if (strcmp(arg[logflag],"none") == 0)
universe->ulogfile = NULL;
else {
universe->ulogfile = fopen(arg[logflag],"w");
if (universe->ulogfile == NULL)
error->universe_one(FLERR,"Cannot open universe log file");
if (universe->ulogfile == NULL)
error->universe_one(FLERR,"Cannot open universe log file");
}
}
@ -234,9 +234,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (inflag == 0) infile = stdin;
else infile = fopen(arg[inflag],"r");
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
char str[128];
sprintf(str,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
}
}
@ -271,14 +271,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
}
else if (strcmp(arg[partscreenflag],"none") == 0)
screen = NULL;
screen = NULL;
else {
char str[128];
sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld);
screen = fopen(str,"w");
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
char str[128];
sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld);
screen = fopen(str,"w");
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
} else screen = NULL;
if (me == 0)
if (partlogflag == 0)
if (logflag == 0) {
@ -295,46 +295,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
}
else if (strcmp(arg[partlogflag],"none") == 0)
logfile = NULL;
logfile = NULL;
else {
char str[128];
sprintf(str,"%s.%d",arg[partlogflag],universe->iworld);
logfile = fopen(str,"w");
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
char str[128];
sprintf(str,"%s.%d",arg[partlogflag],universe->iworld);
logfile = fopen(str,"w");
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
} else logfile = NULL;
if (me == 0) {
infile = fopen(arg[inflag],"r");
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
char str[128];
sprintf(str,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
}
} else infile = NULL;
// screen and logfile messages for universe and world
if (universe->me == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
fprintf(universe->uscreen,"Running on %d partitions of processors\n",
universe->nworlds);
fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
fprintf(universe->uscreen,"Running on %d partitions of processors\n",
universe->nworlds);
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,"LAMMPS (%s)\n",universe->version);
fprintf(universe->ulogfile,"Running on %d partitions of processors\n",
universe->nworlds);
fprintf(universe->ulogfile,"LAMMPS (%s)\n",universe->version);
fprintf(universe->ulogfile,"Running on %d partitions of processors\n",
universe->nworlds);
}
}
if (me == 0) {
if (screen) {
fprintf(screen,"LAMMPS (%s)\n",universe->version);
fprintf(screen,"Processor partition = %d\n",universe->iworld);
fprintf(screen,"LAMMPS (%s)\n",universe->version);
fprintf(screen,"Processor partition = %d\n",universe->iworld);
}
if (logfile) {
fprintf(logfile,"LAMMPS (%s)\n",universe->version);
fprintf(logfile,"Processor partition = %d\n",universe->iworld);
fprintf(logfile,"LAMMPS (%s)\n",universe->version);
fprintf(logfile,"Processor partition = %d\n",universe->iworld);
}
}
}
@ -352,11 +352,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
MPI_Type_size(MPI_LMP_TAGINT,&mpisize);
if (mpisize != sizeof(tagint))
error->all(FLERR,
"MPI_LMP_TAGINT and tagint in lmptype.h are not compatible");
"MPI_LMP_TAGINT and tagint in lmptype.h are not compatible");
MPI_Type_size(MPI_LMP_BIGINT,&mpisize);
if (mpisize != sizeof(bigint))
error->all(FLERR,
"MPI_LMP_BIGINT and bigint in lmptype.h are not compatible");
"MPI_LMP_BIGINT and bigint in lmptype.h are not compatible");
#ifdef LAMMPS_SMALLBIG
if (sizeof(smallint) != 4 || sizeof(tagint) != 4 || sizeof(bigint) != 8)
@ -371,7 +371,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->all(FLERR,"Small, tag, big integers are not sized correctly");
#endif
if (sizeof(tagint) == 8)
if (sizeof(tagint) == 8)
error->all(FLERR,"64-bit atom IDs are not yet supported");
// create CUDA class if USER-CUDA installed, unless explicitly switched off
@ -390,7 +390,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
cuda = NULL;
}
}
int me;
MPI_Comm_rank(world,&me);
if (cuda && me == 0) error->message(FLERR,"USER-CUDA mode is enabled");
@ -496,7 +496,7 @@ void LAMMPS::post_create()
void LAMMPS::init()
{
if (cuda) cuda->accelerator(0,NULL);
update->init();
force->init(); // pair must come after update due to minimizer
domain->init();