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force.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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
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.
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "force.h"
#include "style_bond.h"
#include "style_angle.h"
#include "style_dihedral.h"
#include "style_improper.h"
#include "style_pair.h"
#include "style_kspace.h"
#include "atom.h"
#include "comm.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "pair_hybrid_overlay.h"
#include "bond.h"
#include "bond_hybrid.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
Force::Force(LAMMPS *lmp) : Pointers(lmp)
{
newton = newton_pair = newton_bond = 1;
special_lj[0] = special_coul[0] = 1.0;
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = 0;
special_extra = 0;
dielectric = 1.0;
qqr2e_lammps_real = 332.06371; // these constants are toggled
qqr2e_charmm_real = 332.0716; // by new CHARMM pair styles
pair = NULL;
bond = NULL;
angle = NULL;
dihedral = NULL;
improper = NULL;
kspace = NULL;
char *str = (char *) "none";
int n = strlen(str) + 1;
pair_style = new char[n];
strcpy(pair_style,str);
bond_style = new char[n];
strcpy(bond_style,str);
angle_style = new char[n];
strcpy(angle_style,str);
dihedral_style = new char[n];
strcpy(dihedral_style,str);
improper_style = new char[n];
strcpy(improper_style,str);
kspace_style = new char[n];
strcpy(kspace_style,str);
// fill pair map with pair styles listed in style_pair.h
pair_map = new PairCreatorMap();
#define PAIR_CLASS
#define PairStyle(key,Class) \
(*pair_map)[#key] = &pair_creator<Class>;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
bond_map = new BondCreatorMap();
#define BOND_CLASS
#define BondStyle(key,Class) \
(*bond_map)[#key] = &bond_creator<Class>;
#include "style_bond.h"
#undef BondStyle
#undef BOND_CLASS
angle_map = new AngleCreatorMap();
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
(*angle_map)[#key] = &angle_creator<Class>;
#include "style_angle.h"
#undef AngleStyle
#undef ANGLE_CLASS
dihedral_map = new DihedralCreatorMap();
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
(*dihedral_map)[#key] = &dihedral_creator<Class>;
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
improper_map = new ImproperCreatorMap();
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
(*improper_map)[#key] = &improper_creator<Class>;
#include "style_improper.h"
#undef ImproperStyle
#undef IMPROPER_CLASS
kspace_map = new KSpaceCreatorMap();
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
(*kspace_map)[#key] = &kspace_creator<Class>;
#include "style_kspace.h"
#undef KSpaceStyle
#undef KSPACE_CLASS
}
/* ---------------------------------------------------------------------- */
Force::~Force()
{
delete [] pair_style;
delete [] bond_style;
delete [] angle_style;
delete [] dihedral_style;
delete [] improper_style;
delete [] kspace_style;
if (pair) delete pair;
if (bond) delete bond;
if (angle) delete angle;
if (dihedral) delete dihedral;
if (improper) delete improper;
if (kspace) delete kspace;
pair = NULL;
bond = NULL;
angle = NULL;
dihedral = NULL;
improper = NULL;
kspace = NULL;
delete pair_map;
delete bond_map;
delete angle_map;
delete dihedral_map;
delete improper_map;
delete kspace_map;
}
/* ---------------------------------------------------------------------- */
void Force::init()
{
qqrd2e = qqr2e/dielectric;
if (kspace) kspace->init(); // kspace must come before pair
if (pair) pair->init(); // so g_ewald is defined
if (bond) bond->init();
if (angle) angle->init();
if (dihedral) dihedral->init();
if (improper) improper->init();
}
/* ---------------------------------------------------------------------- */
void Force::setup()
{
if (pair) pair->setup();
}
/* ----------------------------------------------------------------------
create a pair style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_pair(const char *style, int trysuffix)
{
delete [] pair_style;
if (pair) delete pair;
pair_style = NULL;
pair = NULL;
int sflag;
pair = new_pair(style,trysuffix,sflag);
store_style(pair_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a pair class
if trysuffix = 1, try first with suffix1/2 appended
return sflag = 0 for no suffix added, 1 or 2 for suffix1/2 added
------------------------------------------------------------------------- */
Pair *Force::new_pair(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (pair_map->find(estyle) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[estyle];
return pair_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (pair_map->find(style) != pair_map->end()) {
PairCreator pair_creator = (*pair_map)[style];
return pair_creator(lmp);
}
char str[128];
sprintf(str,"Unknown pair style %s",style);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per pair style in style_pair.h
------------------------------------------------------------------------- */
template <typename T>
Pair *Force::pair_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to Pair class if matches word or matches hybrid sub-style
if exact, then style name must be exact match to word
if not exact, style name must contain word
if nsub > 0, match Nth hybrid sub-style
return NULL if no match or if nsub=0 and multiple sub-styles match
------------------------------------------------------------------------- */
Pair *Force::pair_match(const char *word, int exact, int nsub)
{
int iwhich,count;
if (exact && strcmp(pair_style,word) == 0) return pair;
else if (!exact && strstr(pair_style,word)) return pair;
else if (strstr(pair_style,"hybrid/overlay")) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
(!exact && strstr(hybrid->keywords[i],word))) {
iwhich = i;
count++;
if (nsub == count) return hybrid->styles[iwhich];
}
if (count == 1) return hybrid->styles[iwhich];
} else if (strstr(pair_style,"hybrid")) {
PairHybrid *hybrid = (PairHybrid *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++)
if ((exact && strcmp(hybrid->keywords[i],word) == 0) ||
(!exact && strstr(hybrid->keywords[i],word))) {
iwhich = i;
count++;
if (nsub == count) return hybrid->styles[iwhich];
}
if (count == 1) return hybrid->styles[iwhich];
}
return NULL;
}
/* ----------------------------------------------------------------------
return style name of Pair class that matches Pair ptr
called by Neighbor::print_neigh_info()
return NULL if no match
------------------------------------------------------------------------- */
char *Force::pair_match_ptr(Pair *ptr)
{
if (ptr == pair) return pair_style;
if (strstr(pair_style,"hybrid")) {
PairHybrid *hybrid = (PairHybrid *) pair;
for (int i = 0; i < hybrid->nstyles; i++)
if (ptr == hybrid->styles[i]) return hybrid->keywords[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
create a bond style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_bond(const char *style, int trysuffix)
{
delete [] bond_style;
if (bond) delete bond;
int sflag;
bond = new_bond(style,trysuffix,sflag);
store_style(bond_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a bond class, fist with suffix appended
------------------------------------------------------------------------- */
Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (bond_map->find(estyle) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[estyle];
return bond_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (bond_map->find(estyle) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[estyle];
return bond_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (bond_map->find(style) != bond_map->end()) {
BondCreator bond_creator = (*bond_map)[style];
return bond_creator(lmp);
}
char str[128];
sprintf(str,"Unknown bond style %s",style);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per bond style in style_bond.h
------------------------------------------------------------------------- */
template <typename T>
Bond *Force::bond_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to current bond class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Bond *Force::bond_match(const char *style)
{
if (strcmp(bond_style,style) == 0) return bond;
else if (strcmp(bond_style,"hybrid") == 0) {
BondHybrid *hybrid = (BondHybrid *) bond;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
create an angle style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_angle(const char *style, int trysuffix)
{
delete [] angle_style;
if (angle) delete angle;
int sflag;
angle = new_angle(style,trysuffix,sflag);
store_style(angle_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate an angle class
------------------------------------------------------------------------- */
Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (angle_map->find(estyle) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[estyle];
return angle_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (angle_map->find(estyle) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[estyle];
return angle_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (angle_map->find(style) != angle_map->end()) {
AngleCreator angle_creator = (*angle_map)[style];
return angle_creator(lmp);
}
char str[128];
sprintf(str,"Unknown angle style %s",style);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per angle style in style_angle.h
------------------------------------------------------------------------- */
template <typename T>
Angle *Force::angle_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to current angle class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Angle *Force::angle_match(const char *style)
{
if (strcmp(angle_style,style) == 0) return angle;
else if (strcmp(angle_style,"hybrid") == 0) {
AngleHybrid *hybrid = (AngleHybrid *) angle;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
create a dihedral style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_dihedral(const char *style, int trysuffix)
{
delete [] dihedral_style;
if (dihedral) delete dihedral;
int sflag;
dihedral = new_dihedral(style,trysuffix,sflag);
store_style(dihedral_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a dihedral class
------------------------------------------------------------------------- */
Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (dihedral_map->find(estyle) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
return dihedral_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (dihedral_map->find(estyle) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
return dihedral_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (dihedral_map->find(style) != dihedral_map->end()) {
DihedralCreator dihedral_creator = (*dihedral_map)[style];
return dihedral_creator(lmp);
}
char str[128];
sprintf(str,"Unknown dihedral style %s",style);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per dihedral style in style_dihedral.h
------------------------------------------------------------------------- */
template <typename T>
Dihedral *Force::dihedral_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to current angle class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Dihedral *Force::dihedral_match(const char *style)
{
if (strcmp(dihedral_style,style) == 0) return dihedral;
else if (strcmp(dihedral_style,"hybrid") == 0) {
DihedralHybrid *hybrid = (DihedralHybrid *) dihedral;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
create an improper style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_improper(const char *style, int trysuffix)
{
delete [] improper_style;
if (improper) delete improper;
int sflag;
improper = new_improper(style,trysuffix,sflag);
store_style(improper_style,style,sflag);
}
/* ----------------------------------------------------------------------
generate a improper class
------------------------------------------------------------------------- */
Improper *Force::new_improper(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (improper_map->find(estyle) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[estyle];
return improper_creator(lmp);
}
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (improper_map->find(estyle) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[estyle];
return improper_creator(lmp);
}
}
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
if (improper_map->find(style) != improper_map->end()) {
ImproperCreator improper_creator = (*improper_map)[style];
return improper_creator(lmp);
}
char str[128];
sprintf(str,"Unknown improper style %s",style);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per improper style in style_improper.h
------------------------------------------------------------------------- */
template <typename T>
Improper *Force::improper_creator(LAMMPS *lmp)
{
return new T(lmp);
}
/* ----------------------------------------------------------------------
return ptr to current improper class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
Improper *Force::improper_match(const char *style)
{
if (strcmp(improper_style,style) == 0) return improper;
else if (strcmp(improper_style,"hybrid") == 0) {
ImproperHybrid *hybrid = (ImproperHybrid *) improper;
for (int i = 0; i < hybrid->nstyles; i++)
if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
new kspace style
------------------------------------------------------------------------- */
void Force::create_kspace(int narg, char **arg, int trysuffix)
{
delete [] kspace_style;
if (kspace) delete kspace;
int sflag;
kspace = new_kspace(narg,arg,trysuffix,sflag);
store_style(kspace_style,arg[0],sflag);
if (comm->style == 1 && !kspace_match("ewald",0))
error->all(FLERR,
"Cannot yet use KSpace solver with grid with comm style tiled");
}
/* ----------------------------------------------------------------------
generate a kspace class
------------------------------------------------------------------------- */
KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],lmp->suffix);
if (kspace_map->find(estyle) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[estyle];
return kspace_creator(lmp, narg-1, &arg[1]);
}
}
if (lmp->suffix2) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],lmp->suffix2);
if (kspace_map->find(estyle) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[estyle];
return kspace_creator(lmp, narg-1, &arg[1]);
}
}
}
sflag = 0;
if (strcmp(arg[0],"none") == 0) return NULL;
if (kspace_map->find(arg[0]) != kspace_map->end()) {
KSpaceCreator kspace_creator = (*kspace_map)[arg[0]];
return kspace_creator(lmp, narg-1, &arg[1]);
}
char str[128];
sprintf(str,"Unknown kspace style %s",arg[0]);
error->all(FLERR,str);
return NULL;
}
/* ----------------------------------------------------------------------
one instance per kspace style in style_kspace.h
------------------------------------------------------------------------- */
template <typename T>
KSpace *Force::kspace_creator(LAMMPS *lmp, int narg, char ** arg)
{
return new T(lmp, narg, arg);
}
/* ----------------------------------------------------------------------
return ptr to Kspace class if matches word
if exact, then style name must be exact match to word
if not exact, style name must contain word
return NULL if no match
------------------------------------------------------------------------- */
KSpace *Force::kspace_match(const char *word, int exact)
{
if (exact && strcmp(kspace_style,word) == 0) return kspace;
else if (!exact && strstr(kspace_style,word)) return kspace;
return NULL;
}
/* ----------------------------------------------------------------------
store style name in str allocated here
if sflag = 0, no suffix
if sflag = 1/2, append suffix or suffix2 to style
------------------------------------------------------------------------- */
void Force::store_style(char *&str, const char *style, int sflag)
{
if (sflag) {
char estyle[256];
if (sflag == 1) sprintf(estyle,"%s/%s",style,lmp->suffix);
else sprintf(estyle,"%s/%s",style,lmp->suffix2);
int n = strlen(estyle) + 1;
str = new char[n];
strcpy(str,estyle);
} else {
int n = strlen(style) + 1;
str = new char[n];
strcpy(str,style);
}
}
/* ----------------------------------------------------------------------
set special bond values
------------------------------------------------------------------------- */
void Force::set_special(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal special_bonds command");
// defaults, but do not reset special_extra
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"amber") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.5;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 5.0/6.0;
iarg += 1;
} else if (strcmp(arg[iarg],"charmm") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 0.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 0.0;
iarg += 1;
} else if (strcmp(arg[iarg],"dreiding") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 0.0;
special_lj[3] = 1.0;
special_coul[1] = 0.0;
special_coul[2] = 0.0;
special_coul[3] = 1.0;
iarg += 1;
} else if (strcmp(arg[iarg],"fene") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = 0.0;
special_lj[2] = 1.0;
special_lj[3] = 1.0;
special_coul[1] = 0.0;
special_coul[2] = 1.0;
special_coul[3] = 1.0;
iarg += 1;
} else if (strcmp(arg[iarg],"lj/coul") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = special_coul[1] = numeric(FLERR,arg[iarg+1]);
special_lj[2] = special_coul[2] = numeric(FLERR,arg[iarg+2]);
special_lj[3] = special_coul[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"lj") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_lj[1] = numeric(FLERR,arg[iarg+1]);
special_lj[2] = numeric(FLERR,arg[iarg+2]);
special_lj[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"coul") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal special_bonds command");
special_coul[1] = numeric(FLERR,arg[iarg+1]);
special_coul[2] = numeric(FLERR,arg[iarg+2]);
special_coul[3] = numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
if (strcmp(arg[iarg+1],"no") == 0) special_angle = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) special_angle = 1;
else error->all(FLERR,"Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
if (strcmp(arg[iarg+1],"no") == 0) special_dihedral = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) special_dihedral = 1;
else error->all(FLERR,"Illegal special_bonds command");
iarg += 2;
} else error->all(FLERR,"Illegal special_bonds command");
}
for (int i = 1; i <= 3; i++)
if (special_lj[i] < 0.0 || special_lj[i] > 1.0 ||
special_coul[i] < 0.0 || special_coul[i] > 1.0)
error->all(FLERR,"Illegal special_bonds command");
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterik
1 = lower bound, nmax = upper bound
5 possibilities:
(1) i = i to i, (2) * = nmin to nmax,
(3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
return nlo,nhi
------------------------------------------------------------------------- */
void Force::bounds(const char *file, int line, char *str,
int nmax, int &nlo, int &nhi, int nmin)
{
char *ptr = strchr(str,'*');
if (ptr == NULL) {
nlo = nhi = atoi(str);
} else if (strlen(str) == 1) {
nlo = nmin;
nhi = nmax;
} else if (ptr == str) {
nlo = nmin;
nhi = atoi(ptr+1);
} else if (strlen(ptr+1) == 0) {
nlo = atoi(str);
nhi = nmax;
} else {
nlo = atoi(str);
nhi = atoi(ptr+1);
}
if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(file,line,"Numeric index is out of bounds");
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterik
1 = lower bound, nmax = upper bound
5 possibilities:
(1) i = i to i, (2) * = nmin to nmax,
(3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
return nlo,nhi
------------------------------------------------------------------------- */
void Force::boundsbig(const char *file, int line, char *str,
bigint nmax, bigint &nlo, bigint &nhi, bigint nmin)
{
char *ptr = strchr(str,'*');
if (ptr == NULL) {
nlo = nhi = ATOBIGINT(str);
} else if (strlen(str) == 1) {
nlo = nmin;
nhi = nmax;
} else if (ptr == str) {
nlo = nmin;
nhi = ATOBIGINT(ptr+1);
} else if (strlen(ptr+1) == 0) {
nlo = ATOBIGINT(str);
nhi = nmax;
} else {
nlo = ATOBIGINT(str);
nhi = ATOBIGINT(ptr+1);
}
if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(file,line,"Numeric index is out of bounds");
}
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
double Force::numeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i])) continue;
if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue;
if (str[i] == 'e' || str[i] == 'E') continue;
error->all(file,line,"Expected floating point parameter "
"in input script or data file");
}
return atof(str);
}
/* ----------------------------------------------------------------------
read an integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
int Force::inumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return atoi(str);
}
/* ----------------------------------------------------------------------
read a big integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
bigint Force::bnumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return ATOBIGINT(str);
}
/* ----------------------------------------------------------------------
read a tag integer value from a string
generate an error if not a legitimate integer value
called by various commands to check validity of their arguments
------------------------------------------------------------------------- */
tagint Force::tnumeric(const char *file, int line, char *str)
{
if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all(file,line,
"Expected integer parameter in input script or data file");
}
return ATOTAGINT(str);
}
/* ----------------------------------------------------------------------
open a potential file as specified by name
if fails, search in dir specified by env variable LAMMPS_POTENTIALS
------------------------------------------------------------------------- */
FILE *Force::open_potential(const char *name)
{
FILE *fp;
if (name == NULL) return NULL;
// attempt to open file directly
// if successful, return ptr
fp = fopen(name,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
return fp;
}
// try the environment variable directory
const char *path = getenv("LAMMPS_POTENTIALS");
if (path == NULL) return NULL;
const char *pot = potential_name(name);
if (pot == NULL) return NULL;
size_t len1 = strlen(path);
size_t len2 = strlen(pot);
char *newpath = new char[len1+len2+2];
strcpy(newpath,path);
#if defined(_WIN32)
newpath[len1] = '\\';
newpath[len1+1] = 0;
#else
newpath[len1] = '/';
newpath[len1+1] = 0;
#endif
strcat(newpath,pot);
fp = fopen(newpath,"r");
if (fp) {
if (comm->me == 0) potential_date(fp,name);
rewind(fp);
}
delete [] newpath;
return fp;
}
/* ----------------------------------------------------------------------
strip off leading part of path, return just the filename
------------------------------------------------------------------------- */
const char *Force::potential_name(const char *path)
{
const char *pot;
if (path == NULL) return NULL;
#if defined(_WIN32)
// skip over the disk drive part of windows pathnames
if (isalpha(path[0]) && path[1] == ':')
path += 2;
#endif
for (pot = path; *path != '\0'; ++path) {
#if defined(_WIN32)
if ((*path == '\\') || (*path == '/')) pot = path + 1;
#else
if (*path == '/') pot = path + 1;
#endif
}
return pot;
}
/* ----------------------------------------------------------------------
read first line of potential file
if has DATE field, print following word
------------------------------------------------------------------------- */
void Force::potential_date(FILE *fp, const char *name)
{
char line[MAXLINE];
char *ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) return;
char *word;
word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"DATE:") == 0) {
word = strtok(NULL," \t\n\r\f");
if (word == NULL) return;
if (screen)
fprintf(screen,"Reading potential file %s with DATE: %s\n",name,word);
if (logfile)
fprintf(logfile,"Reading potential file %s with DATE: %s\n",name,word);
return;
}
word = strtok(NULL," \t\n\r\f");
}
}
/* ----------------------------------------------------------------------
memory usage of force classes
------------------------------------------------------------------------- */
bigint Force::memory_usage()
{
bigint bytes = 0;
if (pair) bytes += static_cast<bigint> (pair->memory_usage());
if (bond) bytes += static_cast<bigint> (bond->memory_usage());
if (angle) bytes += static_cast<bigint> (angle->memory_usage());
if (dihedral) bytes += static_cast<bigint> (dihedral->memory_usage());
if (improper) bytes += static_cast<bigint> (improper->memory_usage());
if (kspace) bytes += static_cast<bigint> (kspace->memory_usage());
return bytes;
}
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