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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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This commit is contained in:
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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150
src/input.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.
@ -93,8 +93,8 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
while (jarg < argc && argv[jarg][0] != '-') jarg++;
variable->set(argv[iarg+1],jarg-iarg-2,&argv[iarg+2]);
iarg = jarg;
} else if (strcmp(argv[iarg],"-echo") == 0 ||
strcmp(argv[iarg],"-e") == 0) {
} else if (strcmp(argv[iarg],"-echo") == 0 ||
strcmp(argv[iarg],"-e") == 0) {
narg = 1;
char **tmp = arg; // trick echo() into using argv instead of arg
arg = &argv[iarg+1];
@ -131,7 +131,7 @@ void Input::file()
int m,n;
while (1) {
// read a line from input script
// if line ends in continuation char '&', concatenate next line(s)
// n = length of line including str terminator, 0 if end of file
@ -140,12 +140,12 @@ void Input::file()
if (me == 0) {
m = 0;
while (1) {
if (fgets(&line[m],MAXLINE-m,infile) == NULL) n = 0;
else n = strlen(line) + 1;
if (n == 0) break;
m = n-2;
while (m >= 0 && isspace(line[m])) m--;
if (m < 0 || line[m] != '&') break;
if (fgets(&line[m],MAXLINE-m,infile) == NULL) n = 0;
else n = strlen(line) + 1;
if (n == 0) break;
m = n-2;
while (m >= 0 && isspace(line[m])) m--;
if (m < 0 || line[m] != '&') break;
}
}
@ -159,8 +159,8 @@ void Input::file()
if (n == 0) {
if (label_active) error->all(FLERR,"Label wasn't found in input script");
if (me == 0) {
if (infile != stdin) fclose(infile);
nfile--;
if (infile != stdin) fclose(infile);
nfile--;
}
MPI_Bcast(&nfile,1,MPI_INT,0,world);
if (nfile == 0) break;
@ -181,7 +181,7 @@ void Input::file()
// echo the command unless scanning for label
if (me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s",line);
if (echo_screen && screen) fprintf(screen,"%s",line);
if (echo_log && logfile) fprintf(logfile,"%s",line);
}
@ -241,9 +241,9 @@ char *Input::one(const char *single)
strcpy(line,single);
// echo the command unless scanning for label
if (me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s\n",line);
if (echo_screen && screen) fprintf(screen,"%s\n",line);
if (echo_log && logfile) fprintf(logfile,"%s\n",line);
}
@ -383,17 +383,17 @@ void Input::substitute(char *str, int flag)
while (*ptr) {
if (*ptr == '$' && !quote) {
if (*(ptr+1) == '{') {
var = ptr+2;
int i = 0;
while (var[i] != '\0' && var[i] != '}') i++;
if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
var[i] = '\0';
beyond = ptr + strlen(var) + 3;
var = ptr+2;
int i = 0;
while (var[i] != '\0' && var[i] != '}') i++;
if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
var[i] = '\0';
beyond = ptr + strlen(var) + 3;
} else {
var = ptr;
var[0] = var[1];
var[1] = '\0';
beyond = ptr + strlen(var) + 1;
var = ptr;
var[0] = var[1];
var[1] = '\0';
beyond = ptr + strlen(var) + 1;
}
value = variable->retrieve(var);
if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
@ -401,16 +401,16 @@ void Input::substitute(char *str, int flag)
*ptr = '\0';
strcpy(work,str);
if (strlen(work)+strlen(value) >= MAXLINE)
error->one(FLERR,"Input line too long after variable substitution");
error->one(FLERR,"Input line too long after variable substitution");
strcat(work,value);
if (strlen(work)+strlen(beyond) >= MAXLINE)
error->one(FLERR,"Input line too long after variable substitution");
error->one(FLERR,"Input line too long after variable substitution");
strcat(work,beyond);
strcpy(str,work);
ptr += strlen(value);
if (flag && me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s",str);
if (echo_log && logfile) fprintf(logfile,"%s",str);
if (echo_screen && screen) fprintf(screen,"%s",str);
if (echo_log && logfile) fprintf(logfile,"%s",str);
}
continue;
}
@ -507,7 +507,7 @@ int Input::execute_command()
#define COMMAND_CLASS
#define CommandStyle(key,Class) \
else if (strcmp(command,#key) == 0) { \
Class key(lmp); \
Class key(lmp); \
key.command(narg,arg); \
return 0; \
}
@ -578,8 +578,8 @@ void Input::ifthenelse()
int first = 2;
int iarg = first;
while (iarg < narg &&
(strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
while (iarg < narg &&
(strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
iarg++;
int last = iarg-1;
@ -600,9 +600,9 @@ void Input::ifthenelse()
strcpy(commands[ncommands],arg[i]);
ncommands++;
}
for (int i = 0; i < ncommands; i++) one(commands[i]);
for (int i = 0; i < ncommands; i++) delete [] commands[i];
delete [] commands;
delete [] scopy;
@ -635,8 +635,8 @@ void Input::ifthenelse()
}
iarg = first;
while (iarg < narg &&
(strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
while (iarg < narg &&
(strcmp(arg[iarg],"elif") != 0 && strcmp(arg[iarg],"else") != 0))
iarg++;
last = iarg-1;
@ -654,11 +654,11 @@ void Input::ifthenelse()
strcpy(commands[ncommands],arg[i]);
ncommands++;
}
// execute the list of commands
for (int i = 0; i < ncommands; i++) one(commands[i]);
// clean up
for (int i = 0; i < ncommands; i++) delete [] commands[i];
@ -678,7 +678,7 @@ void Input::include()
if (me == 0) {
if (nfile == maxfile) {
maxfile++;
infiles = (FILE **)
infiles = (FILE **)
memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles");
}
infile = fopen(arg[0],"r");
@ -708,9 +708,9 @@ void Input::jump()
if (infile != stdin) fclose(infile);
infile = fopen(arg[0],"r");
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",arg[0]);
error->one(FLERR,str);
char str[128];
sprintf(str,"Cannot open input script %s",arg[0]);
error->one(FLERR,str);
}
infiles[nfile-1] = infile;
}
@ -745,9 +745,9 @@ void Input::log()
else {
logfile = fopen(arg[0],"w");
if (logfile == NULL) {
char str[128];
sprintf(str,"Cannot open logfile %s",arg[0]);
error->one(FLERR,str);
char str[128];
sprintf(str,"Cannot open logfile %s",arg[0]);
error->one(FLERR,str);
}
}
if (universe->nworlds == 1) universe->ulogfile = logfile;
@ -830,10 +830,10 @@ void Input::shell()
} else if (strcmp(arg[0],"mkdir") == 0) {
if (narg < 2) error->all(FLERR,"Illegal shell command");
#if !defined(WINDOWS) && !defined(__MINGW32_VERSION)
#if !defined(WINDOWS) && !defined(__MINGW32_VERSION)
if (me == 0)
for (int i = 1; i < narg; i++)
mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
#endif
} else if (strcmp(arg[0],"mv") == 0) {
@ -884,9 +884,9 @@ void Input::angle_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Angle_coeff command before simulation box is defined");
if (force->angle == NULL)
if (force->angle == NULL)
error->all(FLERR,"Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_coeff command when no angles allowed");
force->angle->coeff(narg,arg);
}
@ -896,7 +896,7 @@ void Input::angle_coeff()
void Input::angle_style()
{
if (narg < 1) error->all(FLERR,"Illegal angle_style command");
if (atom->avec->angles_allow == 0)
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_style command when no angles allowed");
force->create_angle(arg[0],lmp->suffix);
if (force->angle) force->angle->settings(narg-1,&arg[1]);
@ -914,7 +914,7 @@ void Input::atom_modify()
void Input::atom_style()
{
if (narg < 1) error->all(FLERR,"Illegal atom_style command");
if (domain->box_exist)
if (domain->box_exist)
error->all(FLERR,"Atom_style command after simulation box is defined");
atom->create_avec(arg[0],narg-1,&arg[1],lmp->suffix);
}
@ -925,9 +925,9 @@ void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Bond_coeff command before simulation box is defined");
if (force->bond == NULL)
if (force->bond == NULL)
error->all(FLERR,"Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0)
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_coeff command when no bonds allowed");
force->bond->coeff(narg,arg);
}
@ -937,7 +937,7 @@ void Input::bond_coeff()
void Input::bond_style()
{
if (narg < 1) error->all(FLERR,"Illegal bond_style command");
if (atom->avec->bonds_allow == 0)
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_style command when no bonds allowed");
force->create_bond(arg[0],lmp->suffix);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
@ -987,9 +987,9 @@ void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
if (force->dihedral == NULL)
if (force->dihedral == NULL)
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
force->dihedral->coeff(narg,arg);
}
@ -999,7 +999,7 @@ void Input::dihedral_coeff()
void Input::dihedral_style()
{
if (narg < 1) error->all(FLERR,"Illegal dihedral_style command");
if (atom->avec->dihedrals_allow == 0)
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_style command when no dihedrals allowed");
force->create_dihedral(arg[0],lmp->suffix);
if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
@ -1010,7 +1010,7 @@ void Input::dihedral_style()
void Input::dimension()
{
if (narg != 1) error->all(FLERR,"Illegal dimension command");
if (domain->box_exist)
if (domain->box_exist)
error->all(FLERR,"Dimension command after simulation box is defined");
domain->dimension = atoi(arg[0]);
if (domain->dimension != 2 && domain->dimension != 3)
@ -1064,9 +1064,9 @@ void Input::improper_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Improper_coeff command before simulation box is defined");
if (force->improper == NULL)
if (force->improper == NULL)
error->all(FLERR,"Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0)
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_coeff command when no impropers allowed");
force->improper->coeff(narg,arg);
}
@ -1076,7 +1076,7 @@ void Input::improper_coeff()
void Input::improper_style()
{
if (narg < 1) error->all(FLERR,"Illegal improper_style command");
if (atom->avec->impropers_allow == 0)
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_style command when no impropers allowed");
force->create_improper(arg[0],lmp->suffix);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
@ -1086,7 +1086,7 @@ void Input::improper_style()
void Input::kspace_modify()
{
if (force->kspace == NULL)
if (force->kspace == NULL)
error->all(FLERR,"KSpace style has not yet been set");
force->kspace->modify_params(narg,arg);
}
@ -1167,11 +1167,11 @@ void Input::newton()
force->newton_pair = newton_pair;
if (newton_bond == 0) {
if (domain->box_exist && force->newton_bond == 1)
if (domain->box_exist && force->newton_bond == 1)
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 0;
} else {
if (domain->box_exist && force->newton_bond == 0)
if (domain->box_exist && force->newton_bond == 0)
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 1;
}
@ -1184,7 +1184,7 @@ void Input::newton()
void Input::package()
{
if (domain->box_exist)
if (domain->box_exist)
error->all(FLERR,"Package command after simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal package command");
@ -1220,7 +1220,7 @@ void Input::pair_coeff()
{
if (domain->box_exist == 0)
error->all(FLERR,"Pair_coeff command before simulation box is defined");
if (force->pair == NULL)
if (force->pair == NULL)
error->all(FLERR,"Pair_coeff command before pair_style is defined");
force->pair->coeff(narg,arg);
}
@ -1229,7 +1229,7 @@ void Input::pair_coeff()
void Input::pair_modify()
{
if (force->pair == NULL)
if (force->pair == NULL)
error->all(FLERR,"Pair_modify command before pair_style is defined");
force->pair->modify_params(narg,arg);
}
@ -1254,7 +1254,7 @@ void Input::pair_style()
void Input::pair_write()
{
if (force->pair == NULL)
if (force->pair == NULL)
error->all(FLERR,"Pair_write command before pair_style is defined");
force->pair->write_file(narg,arg);
}
@ -1319,10 +1319,10 @@ void Input::special_bonds()
if (domain->box_exist && atom->molecular) {
if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
angle != force->special_angle ||
dihedral != force->special_dihedral ||
extra != force->special_extra) {
coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
angle != force->special_angle ||
dihedral != force->special_dihedral ||
extra != force->special_extra) {
Special special(lmp);
special.build();
}
@ -1334,7 +1334,7 @@ void Input::special_bonds()
void Input::suffix()
{
if (narg != 1) error->all(FLERR,"Illegal suffix command");
if (strcmp(arg[0],"off") == 0) lmp->suffix_enable = 0;
else if (strcmp(arg[0],"on") == 0) lmp->suffix_enable = 1;
else {
@ -1407,7 +1407,7 @@ void Input::unfix()
void Input::units()
{
if (narg != 1) error->all(FLERR,"Illegal units command");
if (domain->box_exist)
if (domain->box_exist)
error->all(FLERR,"Units command after simulation box is defined");
update->set_units(arg[0]);
}