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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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192
src/input.cpp
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@ -157,7 +157,7 @@ void Input::file()
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) {
if (label_active) error->all("Label wasn't found in input script");
if (label_active) error->all(FLERR,"Label wasn't found in input script");
if (me == 0) {
if (infile != stdin) fclose(infile);
nfile--;
@ -175,7 +175,7 @@ void Input::file()
if (n == MAXLINE) {
char str[MAXLINE+32];
sprintf(str,"Input line too long: %s",line);
error->all(str);
error->all(FLERR,str);
}
// echo the command unless scanning for label
@ -200,7 +200,7 @@ void Input::file()
if (execute_command()) {
char str[MAXLINE];
sprintf(str,"Unknown command: %s",line);
error->all(str);
error->all(FLERR,str);
}
}
}
@ -217,13 +217,13 @@ void Input::file(const char *filename)
if (me == 0) {
if (nfile > 1)
error->one("Another input script is already being processed");
error->one(FLERR,"Another input script is already being processed");
if (infile != stdin) fclose(infile);
infile = fopen(filename,"r");
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",filename);
error->one(str);
error->one(FLERR,str);
}
infiles[0] = infile;
} else infile = NULL;
@ -262,7 +262,7 @@ char *Input::one(const char *single)
if (execute_command()) {
char str[MAXLINE];
sprintf(str,"Unknown command: %s",line);
error->all(str);
error->all(FLERR,str);
}
return command;
@ -339,7 +339,7 @@ void Input::parse()
narg++;
}
if (quote) error->all("Unbalanced quotes in input line");
if (quote) error->all(FLERR,"Unbalanced quotes in input line");
}
/* ----------------------------------------------------------------------
@ -367,7 +367,7 @@ void Input::substitute(char *str, int flag)
var = ptr+2;
int i = 0;
while (var[i] != '\0' && var[i] != '}') i++;
if (var[i] == '\0') error->one("Invalid variable name");
if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
var[i] = '\0';
beyond = ptr + strlen(var) + 3;
} else {
@ -377,15 +377,15 @@ void Input::substitute(char *str, int flag)
beyond = ptr + strlen(var) + 1;
}
value = variable->retrieve(var);
if (value == NULL) error->one("Substitution for illegal variable");
if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
*ptr = '\0';
strcpy(work,str);
if (strlen(work)+strlen(value) >= MAXLINE)
error->one("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("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);
@ -506,7 +506,7 @@ int Input::execute_command()
void Input::clear()
{
if (narg > 0) error->all("Illegal clear command");
if (narg > 0) error->all(FLERR,"Illegal clear command");
lmp->destroy();
lmp->create();
}
@ -515,7 +515,7 @@ void Input::clear()
void Input::echo()
{
if (narg != 1) error->all("Illegal echo command");
if (narg != 1) error->all(FLERR,"Illegal echo command");
if (strcmp(arg[0],"none") == 0) {
echo_screen = 0;
@ -529,14 +529,14 @@ void Input::echo()
} else if (strcmp(arg[0],"both") == 0) {
echo_screen = 1;
echo_log = 1;
} else error->all("Illegal echo command");
} else error->all(FLERR,"Illegal echo command");
}
/* ---------------------------------------------------------------------- */
void Input::ifthenelse()
{
if (narg < 3) error->all("Illegal if command");
if (narg < 3) error->all(FLERR,"Illegal if command");
// substitute for variables in Boolean expression for "if"
// in case expression was enclosed in quotes
@ -552,7 +552,7 @@ void Input::ifthenelse()
// bound "then" commands
if (strcmp(arg[1],"then") != 0) error->all("Illegal if command");
if (strcmp(arg[1],"then") != 0) error->all(FLERR,"Illegal if command");
int first = 2;
int iarg = first;
@ -567,13 +567,13 @@ void Input::ifthenelse()
if (btest != 0.0) {
int ncommands = last-first + 1;
if (ncommands <= 0) error->all("Illegal if command");
if (ncommands <= 0) error->all(FLERR,"Illegal if command");
char **commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
int n = strlen(arg[i]) + 1;
if (n == 1) error->all("Illegal if command");
if (n == 1) error->all(FLERR,"Illegal if command");
commands[ncommands] = new char[n];
strcpy(commands[ncommands],arg[i]);
ncommands++;
@ -601,7 +601,7 @@ void Input::ifthenelse()
// bound and execute "elif" or "else" commands
while (1) {
if (iarg+2 > narg) error->all("Illegal if command");
if (iarg+2 > narg) error->all(FLERR,"Illegal if command");
if (strcmp(arg[iarg],"elif") == 0) {
strcpy(scopy,arg[iarg+1]);
substitute(scopy,0);
@ -621,13 +621,13 @@ void Input::ifthenelse()
if (btest == 0.0) continue;
int ncommands = last-first + 1;
if (ncommands <= 0) error->all("Illegal if command");
if (ncommands <= 0) error->all(FLERR,"Illegal if command");
char **commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
int n = strlen(arg[i]) + 1;
if (n == 1) error->all("Illegal if command");
if (n == 1) error->all(FLERR,"Illegal if command");
commands[ncommands] = new char[n];
strcpy(commands[ncommands],arg[i]);
ncommands++;
@ -651,7 +651,7 @@ void Input::ifthenelse()
void Input::include()
{
if (narg != 1) error->all("Illegal include command");
if (narg != 1) error->all(FLERR,"Illegal include command");
if (me == 0) {
if (nfile == maxfile) {
@ -663,7 +663,7 @@ void Input::include()
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",arg[0]);
error->one(str);
error->one(FLERR,str);
}
infiles[nfile++] = infile;
}
@ -673,7 +673,7 @@ void Input::include()
void Input::jump()
{
if (narg < 1 || narg > 2) error->all("Illegal jump command");
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal jump command");
if (jump_skip) {
jump_skip = 0;
@ -688,7 +688,7 @@ void Input::jump()
if (infile == NULL) {
char str[128];
sprintf(str,"Cannot open input script %s",arg[0]);
error->one(str);
error->one(FLERR,str);
}
infiles[nfile-1] = infile;
}
@ -707,7 +707,7 @@ void Input::jump()
void Input::label()
{
if (narg != 1) error->all("Illegal label command");
if (narg != 1) error->all(FLERR,"Illegal label command");
if (label_active && strcmp(labelstr,arg[0]) == 0) label_active = 0;
}
@ -715,7 +715,7 @@ void Input::label()
void Input::log()
{
if (narg != 1) error->all("Illegal log command");
if (narg != 1) error->all(FLERR,"Illegal log command");
if (me == 0) {
if (logfile) fclose(logfile);
@ -725,7 +725,7 @@ void Input::log()
if (logfile == NULL) {
char str[128];
sprintf(str,"Cannot open logfile %s",arg[0]);
error->one(str);
error->one(FLERR,str);
}
}
if (universe->nworlds == 1) universe->ulogfile = logfile;
@ -743,7 +743,7 @@ void Input::next_command()
void Input::print()
{
if (narg != 1) error->all("Illegal print command");
if (narg != 1) error->all(FLERR,"Illegal print command");
// substitute for $ variables (no printing) and print arg
@ -758,14 +758,14 @@ void Input::print()
void Input::shell()
{
if (narg < 1) error->all("Illegal shell command");
if (narg < 1) error->all(FLERR,"Illegal shell command");
if (strcmp(arg[0],"cd") == 0) {
if (narg != 2) error->all("Illegal shell command");
if (narg != 2) error->all(FLERR,"Illegal shell command");
chdir(arg[1]);
} else if (strcmp(arg[0],"mkdir") == 0) {
if (narg < 2) error->all("Illegal shell command");
if (narg < 2) error->all(FLERR,"Illegal shell command");
#if !defined(WINDOWS) && !defined(__MINGW32_VERSION)
if (me == 0)
for (int i = 1; i < narg; i++)
@ -773,16 +773,16 @@ void Input::shell()
#endif
} else if (strcmp(arg[0],"mv") == 0) {
if (narg != 3) error->all("Illegal shell command");
if (narg != 3) error->all(FLERR,"Illegal shell command");
if (me == 0) rename(arg[1],arg[2]);
} else if (strcmp(arg[0],"rm") == 0) {
if (narg < 2) error->all("Illegal shell command");
if (narg < 2) error->all(FLERR,"Illegal shell command");
if (me == 0)
for (int i = 1; i < narg; i++) unlink(arg[i]);
} else if (strcmp(arg[0],"rmdir") == 0) {
if (narg < 2) error->all("Illegal shell command");
if (narg < 2) error->all(FLERR,"Illegal shell command");
if (me == 0)
for (int i = 1; i < narg; i++) rmdir(arg[i]);
@ -819,11 +819,11 @@ void Input::variable_command()
void Input::angle_coeff()
{
if (domain->box_exist == 0)
error->all("Angle_coeff command before simulation box is defined");
error->all(FLERR,"Angle_coeff command before simulation box is defined");
if (force->angle == NULL)
error->all("Angle_coeff command before angle_style is defined");
error->all(FLERR,"Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0)
error->all("Angle_coeff command when no angles allowed");
error->all(FLERR,"Angle_coeff command when no angles allowed");
force->angle->coeff(narg,arg);
}
@ -831,9 +831,9 @@ void Input::angle_coeff()
void Input::angle_style()
{
if (narg < 1) error->all("Illegal angle_style command");
if (narg < 1) error->all(FLERR,"Illegal angle_style command");
if (atom->avec->angles_allow == 0)
error->all("Angle_style command when no angles allowed");
error->all(FLERR,"Angle_style command when no angles allowed");
force->create_angle(arg[0]);
if (force->angle) force->angle->settings(narg-1,&arg[1]);
}
@ -849,9 +849,9 @@ void Input::atom_modify()
void Input::atom_style()
{
if (narg < 1) error->all("Illegal atom_style command");
if (narg < 1) error->all(FLERR,"Illegal atom_style command");
if (domain->box_exist)
error->all("Atom_style command after simulation box is defined");
error->all(FLERR,"Atom_style command after simulation box is defined");
atom->create_avec(arg[0],narg-1,&arg[1],lmp->suffix);
}
@ -860,11 +860,11 @@ void Input::atom_style()
void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all("Bond_coeff command before simulation box is defined");
error->all(FLERR,"Bond_coeff command before simulation box is defined");
if (force->bond == NULL)
error->all("Bond_coeff command before bond_style is defined");
error->all(FLERR,"Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0)
error->all("Bond_coeff command when no bonds allowed");
error->all(FLERR,"Bond_coeff command when no bonds allowed");
force->bond->coeff(narg,arg);
}
@ -872,9 +872,9 @@ void Input::bond_coeff()
void Input::bond_style()
{
if (narg < 1) error->all("Illegal bond_style command");
if (narg < 1) error->all(FLERR,"Illegal bond_style command");
if (atom->avec->bonds_allow == 0)
error->all("Bond_style command when no bonds allowed");
error->all(FLERR,"Bond_style command when no bonds allowed");
force->create_bond(arg[0]);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
}
@ -884,7 +884,7 @@ void Input::bond_style()
void Input::boundary()
{
if (domain->box_exist)
error->all("Boundary command after simulation box is defined");
error->all(FLERR,"Boundary command after simulation box is defined");
domain->set_boundary(narg,arg);
}
@ -913,7 +913,7 @@ void Input::compute_modify()
void Input::dielectric()
{
if (narg != 1) error->all("Illegal dielectric command");
if (narg != 1) error->all(FLERR,"Illegal dielectric command");
force->dielectric = atof(arg[0]);
}
@ -922,11 +922,11 @@ void Input::dielectric()
void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all("Dihedral_coeff command before simulation box is defined");
error->all(FLERR,"Dihedral_coeff command before simulation box is defined");
if (force->dihedral == NULL)
error->all("Dihedral_coeff command before dihedral_style is defined");
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0)
error->all("Dihedral_coeff command when no dihedrals allowed");
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
force->dihedral->coeff(narg,arg);
}
@ -934,9 +934,9 @@ void Input::dihedral_coeff()
void Input::dihedral_style()
{
if (narg < 1) error->all("Illegal dihedral_style command");
if (narg < 1) error->all(FLERR,"Illegal dihedral_style command");
if (atom->avec->dihedrals_allow == 0)
error->all("Dihedral_style command when no dihedrals allowed");
error->all(FLERR,"Dihedral_style command when no dihedrals allowed");
force->create_dihedral(arg[0]);
if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
}
@ -945,12 +945,12 @@ void Input::dihedral_style()
void Input::dimension()
{
if (narg != 1) error->all("Illegal dimension command");
if (narg != 1) error->all(FLERR,"Illegal dimension command");
if (domain->box_exist)
error->all("Dimension command after simulation box is defined");
error->all(FLERR,"Dimension command after simulation box is defined");
domain->dimension = atoi(arg[0]);
if (domain->dimension != 2 && domain->dimension != 3)
error->all("Illegal dimension command");
error->all(FLERR,"Illegal dimension command");
// must reset default extra_dof of all computes
// since some were created before dimension command is encountered
@ -999,11 +999,11 @@ void Input::group_command()
void Input::improper_coeff()
{
if (domain->box_exist == 0)
error->all("Improper_coeff command before simulation box is defined");
error->all(FLERR,"Improper_coeff command before simulation box is defined");
if (force->improper == NULL)
error->all("Improper_coeff command before improper_style is defined");
error->all(FLERR,"Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0)
error->all("Improper_coeff command when no impropers allowed");
error->all(FLERR,"Improper_coeff command when no impropers allowed");
force->improper->coeff(narg,arg);
}
@ -1011,9 +1011,9 @@ void Input::improper_coeff()
void Input::improper_style()
{
if (narg < 1) error->all("Illegal improper_style command");
if (narg < 1) error->all(FLERR,"Illegal improper_style command");
if (atom->avec->impropers_allow == 0)
error->all("Improper_style command when no impropers allowed");
error->all(FLERR,"Improper_style command when no impropers allowed");
force->create_improper(arg[0]);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
}
@ -1022,7 +1022,7 @@ void Input::improper_style()
void Input::kspace_modify()
{
if (force->kspace == NULL) error->all("KSpace style has not yet been set");
if (force->kspace == NULL) error->all(FLERR,"KSpace style has not yet been set");
force->kspace->modify_params(narg,arg);
}
@ -1044,9 +1044,9 @@ void Input::lattice()
void Input::mass()
{
if (narg != 2) error->all("Illegal mass command");
if (narg != 2) error->all(FLERR,"Illegal mass command");
if (domain->box_exist == 0)
error->all("Mass command before simulation box is defined");
error->all(FLERR,"Mass command before simulation box is defined");
atom->set_mass(narg,arg);
}
@ -1062,7 +1062,7 @@ void Input::min_modify()
void Input::min_style()
{
if (domain->box_exist == 0)
error->all("Min_style command before simulation box is defined");
error->all(FLERR,"Min_style command before simulation box is defined");
update->create_minimize(narg,arg);
}
@ -1089,25 +1089,25 @@ void Input::newton()
if (narg == 1) {
if (strcmp(arg[0],"off") == 0) newton_pair = newton_bond = 0;
else if (strcmp(arg[0],"on") == 0) newton_pair = newton_bond = 1;
else error->all("Illegal newton command");
else error->all(FLERR,"Illegal newton command");
} else if (narg == 2) {
if (strcmp(arg[0],"off") == 0) newton_pair = 0;
else if (strcmp(arg[0],"on") == 0) newton_pair= 1;
else error->all("Illegal newton command");
else error->all(FLERR,"Illegal newton command");
if (strcmp(arg[1],"off") == 0) newton_bond = 0;
else if (strcmp(arg[1],"on") == 0) newton_bond = 1;
else error->all("Illegal newton command");
} else error->all("Illegal newton command");
else error->all(FLERR,"Illegal newton command");
} else error->all(FLERR,"Illegal newton command");
force->newton_pair = newton_pair;
if (newton_bond == 0) {
if (domain->box_exist && force->newton_bond == 1)
error->all("Newton bond change after simulation box is defined");
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 0;
} else {
if (domain->box_exist && force->newton_bond == 0)
error->all("Newton bond change after simulation box is defined");
error->all(FLERR,"Newton bond change after simulation box is defined");
force->newton_bond = 1;
}
@ -1120,12 +1120,12 @@ void Input::newton()
void Input::package()
{
if (domain->box_exist)
error->all("Package command after simulation box is defined");
if (narg < 1) error->all("Illegal package command");
error->all(FLERR,"Package command after simulation box is defined");
if (narg < 1) error->all(FLERR,"Illegal package command");
if (strcmp(arg[0],"cuda") == 0) {
if (!lmp->cuda)
error->all("Package cuda command without USER-CUDA installed");
error->all(FLERR,"Package cuda command without USER-CUDA installed");
lmp->cuda->accelerator(narg-1,&arg[1]);
} else if (strcmp(arg[0],"gpu") == 0) {
@ -1142,9 +1142,9 @@ void Input::package()
} else if (strcmp(arg[0],"omp") == 0) {
#ifdef _OPENMP
if (narg != 2) error->all("Illegal package command");
if (narg != 2) error->all(FLERR,"Illegal package command");
comm->nthreads = atoi(arg[1]);
if (comm->nthreads < 1) error->all("Illegal package command");
if (comm->nthreads < 1) error->all(FLERR,"Illegal package command");
omp_set_num_threads(comm->nthreads);
if (me == 0) {
@ -1156,10 +1156,10 @@ void Input::package()
comm->nthreads);
}
#else
error->all("Cannot use package omp command with no OpenMP support");
error->all(FLERR,"Cannot use package omp command with no OpenMP support");
#endif
} else error->all("Illegal package command");
} else error->all(FLERR,"Illegal package command");
}
/* ---------------------------------------------------------------------- */
@ -1167,9 +1167,9 @@ void Input::package()
void Input::pair_coeff()
{
if (domain->box_exist == 0)
error->all("Pair_coeff command before simulation box is defined");
error->all(FLERR,"Pair_coeff command before simulation box is defined");
if (force->pair == NULL)
error->all("Pair_coeff command before pair_style is defined");
error->all(FLERR,"Pair_coeff command before pair_style is defined");
force->pair->coeff(narg,arg);
}
@ -1178,7 +1178,7 @@ void Input::pair_coeff()
void Input::pair_modify()
{
if (force->pair == NULL)
error->all("Pair_modify command before pair_style is defined");
error->all(FLERR,"Pair_modify command before pair_style is defined");
force->pair->modify_params(narg,arg);
}
@ -1189,7 +1189,7 @@ void Input::pair_modify()
void Input::pair_style()
{
if (narg < 1) error->all("Illegal pair_style command");
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
if (force->pair && strcmp(arg[0],force->pair_style) == 0) {
force->pair->settings(narg-1,&arg[1]);
return;
@ -1203,7 +1203,7 @@ void Input::pair_style()
void Input::pair_write()
{
if (force->pair == NULL)
error->all("Pair_write command before pair_style is defined");
error->all(FLERR,"Pair_write command before pair_style is defined");
force->pair->write_file(narg,arg);
}
@ -1211,9 +1211,9 @@ void Input::pair_write()
void Input::processors()
{
if (narg != 3) error->all("Illegal processors command");
if (narg != 3) error->all(FLERR,"Illegal processors command");
if (domain->box_exist)
error->all("Processors command after simulation box is defined");
error->all(FLERR,"Processors command after simulation box is defined");
if (strcmp(arg[0],"*") == 0) comm->user_procgrid[0] = 0;
else comm->user_procgrid[0] = atoi(arg[0]);
@ -1223,7 +1223,7 @@ void Input::processors()
else comm->user_procgrid[2] = atoi(arg[2]);
if (comm->user_procgrid[0] < 0 || comm->user_procgrid[1] < 0 ||
comm->user_procgrid[2] < 0) error->all("Illegal processors command");
comm->user_procgrid[2] < 0) error->all(FLERR,"Illegal processors command");
}
/* ---------------------------------------------------------------------- */
@ -1252,7 +1252,7 @@ void Input::restart()
void Input::run_style()
{
if (domain->box_exist == 0)
error->all("Run_style command before simulation box is defined");
error->all(FLERR,"Run_style command before simulation box is defined");
update->create_integrate(narg,arg,lmp->suffix);
}
@ -1291,7 +1291,7 @@ void Input::special_bonds()
void Input::suffix()
{
if (narg != 1) error->all("Illegal suffix command");
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;
@ -1308,7 +1308,7 @@ void Input::suffix()
void Input::thermo()
{
if (narg != 1) error->all("Illegal thermo command");
if (narg != 1) error->all(FLERR,"Illegal thermo command");
output->thermo_every = atoi(arg[0]);
}
@ -1330,7 +1330,7 @@ void Input::thermo_style()
void Input::timestep()
{
if (narg != 1) error->all("Illegal timestep command");
if (narg != 1) error->all(FLERR,"Illegal timestep command");
update->dt = atof(arg[0]);
}
@ -1338,7 +1338,7 @@ void Input::timestep()
void Input::uncompute()
{
if (narg != 1) error->all("Illegal uncompute command");
if (narg != 1) error->all(FLERR,"Illegal uncompute command");
modify->delete_compute(arg[0]);
}
@ -1346,7 +1346,7 @@ void Input::uncompute()
void Input::undump()
{
if (narg != 1) error->all("Illegal undump command");
if (narg != 1) error->all(FLERR,"Illegal undump command");
output->delete_dump(arg[0]);
}
@ -1354,7 +1354,7 @@ void Input::undump()
void Input::unfix()
{
if (narg != 1) error->all("Illegal unfix command");
if (narg != 1) error->all(FLERR,"Illegal unfix command");
modify->delete_fix(arg[0]);
}
@ -1362,8 +1362,8 @@ void Input::unfix()
void Input::units()
{
if (narg != 1) error->all("Illegal units command");
if (narg != 1) error->all(FLERR,"Illegal units command");
if (domain->box_exist)
error->all("Units command after simulation box is defined");
error->all(FLERR,"Units command after simulation box is defined");
update->set_units(arg[0]);
}