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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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606
src/input.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,9 @@
#include "stdlib.h"
#include "string.h"
#include "input.h"
#include "system.h"
#include "universe.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "group.h"
#include "domain.h"
@ -40,18 +40,18 @@
#include "error.h"
#include "memory.h"
#define AtomInclude
#define CommandInclude
#include "style.h"
#undef AtomInclude
#undef CommandInclude
using namespace LAMMPS_NS;
#define MAXLINE 2048
#define DELTA 4
/* ---------------------------------------------------------------------- */
Input::Input(int argc, char **argv)
Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
@ -74,7 +74,7 @@ Input::Input(int argc, char **argv)
infiles[0] = infile;
} else infiles = NULL;
variable = new Variable;
variable = new Variable(lmp);
// process command-line args
// check for args "-var" and "-echo"
@ -119,7 +119,7 @@ Input::~Input()
void Input::file()
{
int n,flag;
int n;
while (1) {
@ -389,14 +389,25 @@ int Input::execute_command()
{
int flag = 1;
if (!strcmp(command,"angle_coeff")) angle_coeff();
if (!strcmp(command,"clear")) clear();
else if (!strcmp(command,"echo")) echo();
else if (!strcmp(command,"include")) include();
else if (!strcmp(command,"jump")) jump();
else if (!strcmp(command,"label")) label();
else if (!strcmp(command,"log")) log();
else if (!strcmp(command,"next")) next_command();
else if (!strcmp(command,"print")) print();
else if (!strcmp(command,"variable")) variable_command();
else if (!strcmp(command,"angle_coeff")) angle_coeff();
else if (!strcmp(command,"angle_style")) angle_style();
else if (!strcmp(command,"atom_modify")) atom_modify();
else if (!strcmp(command,"atom_style")) atom_style();
else if (!strcmp(command,"bond_coeff")) bond_coeff();
else if (!strcmp(command,"bond_style")) bond_style();
else if (!strcmp(command,"boundary")) boundary();
else if (!strcmp(command,"clear")) clear();
else if (!strcmp(command,"compute")) compute();
else if (!strcmp(command,"compute_modify")) compute_modify();
else if (!strcmp(command,"dielectric")) dielectric();
else if (!strcmp(command,"dihedral_coeff")) dihedral_coeff();
else if (!strcmp(command,"dihedral_style")) dihedral_style();
@ -404,39 +415,30 @@ int Input::execute_command()
else if (!strcmp(command,"dipole")) dipole();
else if (!strcmp(command,"dump")) dump();
else if (!strcmp(command,"dump_modify")) dump_modify();
else if (!strcmp(command,"echo")) echo();
else if (!strcmp(command,"fix")) fix();
else if (!strcmp(command,"fix_modify")) fix_modify();
else if (!strcmp(command,"group")) group_command();
else if (!strcmp(command,"improper_coeff")) improper_coeff();
else if (!strcmp(command,"improper_style")) improper_style();
else if (!strcmp(command,"include")) include();
else if (!strcmp(command,"jump")) jump();
else if (!strcmp(command,"kspace_modify")) kspace_modify();
else if (!strcmp(command,"kspace_style")) kspace_style();
else if (!strcmp(command,"label")) label();
else if (!strcmp(command,"lattice")) lattice();
else if (!strcmp(command,"log")) log();
else if (!strcmp(command,"mass")) mass();
else if (!strcmp(command,"min_modify")) min_modify();
else if (!strcmp(command,"min_style")) min_style();
else if (!strcmp(command,"neigh_modify")) neigh_modify();
else if (!strcmp(command,"neighbor")) neighbor_command();
else if (!strcmp(command,"newton")) newton();
else if (!strcmp(command,"next")) next_command();
else if (!strcmp(command,"pair_coeff")) pair_coeff();
else if (!strcmp(command,"pair_modify")) pair_modify();
else if (!strcmp(command,"pair_style")) pair_style();
else if (!strcmp(command,"pair_write")) pair_write();
else if (!strcmp(command,"print")) print();
else if (!strcmp(command,"processors")) processors();
else if (!strcmp(command,"region")) region();
else if (!strcmp(command,"reset_timestep")) reset_timestep();
else if (!strcmp(command,"restart")) restart();
else if (!strcmp(command,"run_style")) run_style();
else if (!strcmp(command,"special_bonds")) special_bonds();
else if (!strcmp(command,"temp_modify")) temp_modify();
else if (!strcmp(command,"temperature")) temperature();
else if (!strcmp(command,"thermo")) thermo();
else if (!strcmp(command,"thermo_modify")) thermo_modify();
else if (!strcmp(command,"thermo_style")) thermo_style();
@ -444,7 +446,7 @@ int Input::execute_command()
else if (!strcmp(command,"undump")) undump();
else if (!strcmp(command,"unfix")) unfix();
else if (!strcmp(command,"units")) units();
else if (!strcmp(command,"variable")) variable_command();
else flag = 0;
if (flag) return 0;
@ -454,7 +456,7 @@ int Input::execute_command()
#define CommandClass
#define CommandStyle(key,Class) \
else if (strcmp(command,#key) == 0) { \
Class key; \
Class key(lmp); \
key.command(narg,arg); \
return 0; \
}
@ -468,168 +470,13 @@ int Input::execute_command()
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
one function for each input command executed here
------------------------------------------------------------------------- */
void Input::angle_coeff()
{
if (domain->box_exist == 0)
error->all("Angle_coeff command before simulation box is defined");
if (force->angle == NULL)
error->all("Angle_coeff command before angle_style is defined");
if (atom->angles_allow == 0)
error->all("Angle_coeff command when no angles allowed");
force->angle->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::angle_style()
{
if (narg < 1) error->all("Illegal angle_style command");
force->create_angle(arg[0]);
if (force->angle) force->angle->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::atom_modify()
{
if (domain->box_exist)
error->all("Atom_modify command after simulation box is defined");
if (!atom) error->all("Atom_modify command before atom_style command");
atom->modify_params(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::atom_style()
{
if (domain->box_exist)
error->all("Atom_style command after simulation box is defined");
if (narg < 1) error->all("Illegal atom_style command");
Atom *old = atom;
if (strcmp(arg[0],"none") == 0) error->all("Invalid atom style");
#define AtomClass
#define AtomStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) atom = new Class(narg,arg);
#include "style.h"
#undef AtomClass
else error->all("Invalid atom style");
if (old) {
atom->settings(old);
delete old;
}
}
/* ---------------------------------------------------------------------- */
void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all("Bond_coeff command before simulation box is defined");
if (force->bond == NULL)
error->all("Bond_coeff command before bond_style is defined");
if (atom->bonds_allow == 0)
error->all("Bond_coeff command when no bonds allowed");
force->bond->coeff(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::bond_style()
{
if (narg < 1) error->all("Illegal bond_style command");
force->create_bond(arg[0]);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::boundary()
{
if (domain->box_exist)
error->all("Boundary command after simulation box is defined");
domain->set_boundary(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::clear()
{
if (narg > 0) error->all("Illegal clear command");
sys->destroy();
sys->create();
}
/* ---------------------------------------------------------------------- */
void Input::dielectric()
{
if (narg != 1) error->all("Illegal dielectric command");
force->dielectric = atof(arg[0]);
}
/* ---------------------------------------------------------------------- */
void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all("Dihedral_coeff command before simulation box is defined");
if (force->dihedral == NULL)
error->all("Dihedral_coeff command before dihedral_style is defined");
if (atom->dihedrals_allow == 0)
error->all("Dihedral_coeff command when no dihedrals allowed");
force->dihedral->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dihedral_style()
{
if (narg < 1) error->all("Illegal dihedral_style command");
force->create_dihedral(arg[0]);
if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::dimension()
{
if (domain->box_exist)
error->all("Dimension command after simulation box is defined");
if (narg != 1) error->all("Illegal dimension command");
force->dimension = atoi(arg[0]);
}
/* ---------------------------------------------------------------------- */
void Input::dipole()
{
if (domain->box_exist == 0)
error->all("Dipole command before simulation box is defined");
if (narg != 2) error->all("Illegal dipole command");
atom->set_dipole(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dump()
{
output->add_dump(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dump_modify()
{
output->modify_dump(narg,arg);
lmp->destroy();
lmp->create();
}
/* ---------------------------------------------------------------------- */
@ -655,49 +502,6 @@ void Input::echo()
/* ---------------------------------------------------------------------- */
void Input::fix()
{
modify->add_fix(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::fix_modify()
{
modify->modify_fix(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::group_command()
{
group->assign(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::improper_coeff()
{
if (domain->box_exist == 0)
error->all("Improper_coeff command before simulation box is defined");
if (force->improper == NULL)
error->all("Improper_coeff command before improper_style is defined");
if (atom->impropers_allow == 0)
error->all("Improper_coeff command when no impropers allowed");
force->improper->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::improper_style()
{
if (narg < 1) error->all("Illegal improper_style command");
force->create_improper(arg[0]);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::include()
{
if (narg != 1) error->all("Illegal include command");
@ -751,6 +555,277 @@ void Input::jump()
/* ---------------------------------------------------------------------- */
void Input::label()
{
if (narg != 1) error->all("Illegal label command");
if (label_active && strcmp(labelstr,arg[0]) == 0) label_active = 0;
}
/* ---------------------------------------------------------------------- */
void Input::log()
{
if (narg != 1) error->all("Illegal log command");
if (me == 0) {
if (logfile) fclose(logfile);
if (strcmp(arg[0],"none") == 0) logfile = NULL;
else {
logfile = fopen(arg[0],"w");
if (logfile == NULL) {
char str[128];
sprintf(str,"Cannot open logfile %s",arg[0]);
error->one(str);
}
}
if (universe->nworlds == 1) universe->ulogfile = logfile;
}
}
/* ---------------------------------------------------------------------- */
void Input::next_command()
{
if (variable->next(narg,arg)) jump_skip = 1;
}
/* ---------------------------------------------------------------------- */
void Input::print()
{
if (narg < 1) error->all("Illegal print command");
char *str = new char[MAXLINE];
str[0] = '\0';
for (int iarg = 0; iarg < narg; iarg++) {
strcat(str,arg[iarg]);
strcat(str," ");
}
if (me == 0) {
if (screen) fprintf(screen,"%s\n",str);
if (logfile) fprintf(logfile,"%s\n",str);
}
delete [] str;
}
/* ---------------------------------------------------------------------- */
void Input::variable_command()
{
variable->set(narg,arg);
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
one function for each LAMMPS-specific input script command
------------------------------------------------------------------------- */
void Input::angle_coeff()
{
if (domain->box_exist == 0)
error->all("Angle_coeff command before simulation box is defined");
if (force->angle == NULL)
error->all("Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0)
error->all("Angle_coeff command when no angles allowed");
force->angle->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::angle_style()
{
if (narg < 1) error->all("Illegal angle_style command");
if (atom->avec->angles_allow == 0)
error->all("Angle_style command when no angles allowed");
force->create_angle(arg[0]);
if (force->angle) force->angle->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::atom_modify()
{
if (domain->box_exist)
error->all("Atom_modify command after simulation box is defined");
atom->modify_params(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::atom_style()
{
if (narg < 1) error->all("Illegal atom_style command");
if (domain->box_exist)
error->all("Atom_style command after simulation box is defined");
atom->create_avec(arg[0],narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::bond_coeff()
{
if (domain->box_exist == 0)
error->all("Bond_coeff command before simulation box is defined");
if (force->bond == NULL)
error->all("Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0)
error->all("Bond_coeff command when no bonds allowed");
force->bond->coeff(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::bond_style()
{
if (narg < 1) error->all("Illegal bond_style command");
if (atom->avec->bonds_allow == 0)
error->all("Bond_style command when no bonds allowed");
force->create_bond(arg[0]);
if (force->bond) force->bond->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::boundary()
{
if (domain->box_exist)
error->all("Boundary command after simulation box is defined");
domain->set_boundary(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::compute()
{
modify->add_compute(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::compute_modify()
{
modify->modify_compute(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dielectric()
{
if (narg != 1) error->all("Illegal dielectric command");
force->dielectric = atof(arg[0]);
}
/* ---------------------------------------------------------------------- */
void Input::dihedral_coeff()
{
if (domain->box_exist == 0)
error->all("Dihedral_coeff command before simulation box is defined");
if (force->dihedral == NULL)
error->all("Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0)
error->all("Dihedral_coeff command when no dihedrals allowed");
force->dihedral->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dihedral_style()
{
if (narg < 1) error->all("Illegal dihedral_style command");
if (atom->avec->dihedrals_allow == 0)
error->all("Dihedral_style command when no dihedrals allowed");
force->create_dihedral(arg[0]);
if (force->dihedral) force->dihedral->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::dimension()
{
if (narg != 1) error->all("Illegal dimension command");
if (domain->box_exist)
error->all("Dimension command after simulation box is defined");
force->dimension = atoi(arg[0]);
}
/* ---------------------------------------------------------------------- */
void Input::dipole()
{
if (narg != 2) error->all("Illegal dipole command");
if (domain->box_exist == 0)
error->all("Dipole command before simulation box is defined");
atom->set_dipole(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dump()
{
output->add_dump(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::dump_modify()
{
output->modify_dump(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::fix()
{
modify->add_fix(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::fix_modify()
{
modify->modify_fix(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::group_command()
{
group->assign(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::improper_coeff()
{
if (domain->box_exist == 0)
error->all("Improper_coeff command before simulation box is defined");
if (force->improper == NULL)
error->all("Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0)
error->all("Improper_coeff command when no impropers allowed");
force->improper->coeff(0,narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::improper_style()
{
if (narg < 1) error->all("Illegal improper_style command");
if (atom->avec->impropers_allow == 0)
error->all("Improper_style command when no impropers allowed");
force->create_improper(arg[0]);
if (force->improper) force->improper->settings(narg-1,&arg[1]);
}
/* ---------------------------------------------------------------------- */
void Input::kspace_modify()
{
if (force->kspace == NULL) error->all("KSpace style has not yet been set");
@ -766,14 +841,6 @@ void Input::kspace_style()
/* ---------------------------------------------------------------------- */
void Input::label()
{
if (narg != 1) error->all("Illegal label command");
if (label_active && strcmp(labelstr,arg[0]) == 0) label_active = 0;
}
/* ---------------------------------------------------------------------- */
void Input::lattice()
{
domain->set_lattice(narg,arg);
@ -781,35 +848,11 @@ void Input::lattice()
/* ---------------------------------------------------------------------- */
void Input::log()
{
if (narg != 1) error->all("Illegal log command");
if (me == 0) {
if (logfile) fclose(logfile);
if (strcmp(arg[0],"none") == 0) logfile = NULL;
else {
// char fname[128];
// if (universe->nworlds == 1) strcpy(fname,arg[0]);
// else sprintf(fname,"%s.%d",arg[0],universe->iworld);
logfile = fopen(arg[0],"w");
if (logfile == NULL) {
char str[128];
sprintf(str,"Cannot open logfile %s",arg[0]);
error->one(str);
}
}
if (universe->nworlds == 1) universe->ulogfile = logfile;
}
}
/* ---------------------------------------------------------------------- */
void Input::mass()
{
if (narg != 2) error->all("Illegal mass command");
if (domain->box_exist == 0)
error->all("Mass command before simulation box is defined");
if (narg != 2) error->all("Illegal mass command");
atom->set_mass(narg,arg);
}
@ -885,13 +928,6 @@ void Input::newton()
/* ---------------------------------------------------------------------- */
void Input::next_command()
{
if (variable->next(narg,arg)) jump_skip = 1;
}
/* ---------------------------------------------------------------------- */
void Input::pair_coeff()
{
if (domain->box_exist == 0)
@ -937,32 +973,11 @@ void Input::pair_write()
/* ---------------------------------------------------------------------- */
void Input::print()
{
if (narg < 1) error->all("Illegal print command");
char *str = new char[MAXLINE];
str[0] = '\0';
for (int iarg = 0; iarg < narg; iarg++) {
strcat(str,arg[iarg]);
strcat(str," ");
}
if (me == 0) {
if (screen) fprintf(screen,"%s\n",str);
if (logfile) fprintf(logfile,"%s\n",str);
}
delete [] str;
}
/* ---------------------------------------------------------------------- */
void Input::processors()
{
if (narg != 3) error->all("Illegal processors command");
if (domain->box_exist)
error->all("Processors command after simulation box is defined");
if (narg != 3) error->all("Illegal processors command");
comm->user_procgrid[0] = atoi(arg[0]);
comm->user_procgrid[1] = atoi(arg[1]);
comm->user_procgrid[2] = atoi(arg[2]);
@ -1018,7 +1033,7 @@ 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]) {
Special special;
Special special(lmp);
special.build();
}
}
@ -1026,20 +1041,6 @@ void Input::special_bonds()
/* ---------------------------------------------------------------------- */
void Input::temp_modify()
{
force->modify_temp(narg,arg);
}
/* ---------------------------------------------------------------------- */
void Input::temperature()
{
force->add_temp(narg,arg,0);
}
/* ---------------------------------------------------------------------- */
void Input::thermo()
{
if (narg != 1) error->all("Illegal thermo command");
@ -1088,15 +1089,8 @@ void Input::unfix()
void Input::units()
{
if (narg != 1) error->all("Illegal units command");
if (domain->box_exist)
error->all("Units command after simulation box is defined");
if (narg != 1) error->all("Illegal units command");
update->set_units(arg[0]);
}
/* ---------------------------------------------------------------------- */
void Input::variable_command()
{
variable->set(narg,arg);
}