Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/src/force.cpp
cccc6475d994lammps-icms

Last Change
Raw File

force.cpp
View Options

/* ----------------------------------------------------------------------
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;
/* ---------------------------------------------------------------------- */
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;
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 std::map<std::string,PairCreator>();
#define PAIR_CLASS
#define PairStyle(key,Class) \
(*pair_map)[#key] = &pair_creator<Class>;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_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;
delete pair_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();
}
/* ----------------------------------------------------------------------
create a pair style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_pair(const char *style, const char *suffix)
{
delete [] pair_style;
if (pair) delete pair;
int sflag;
pair = new_pair(style,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
pair_style = new char[n];
strcpy(pair_style,estyle);
} else {
int n = strlen(style) + 1;
pair_style = new char[n];
strcpy(pair_style,style);
}
}
/* ----------------------------------------------------------------------
generate a pair class
try first with suffix appended
------------------------------------------------------------------------- */
Pair *Force::new_pair(const char *style, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
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);
}
error->all(FLERR,"Invalid pair style");
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
return NULL if no match or multiple sub-styles match
------------------------------------------------------------------------- */
Pair *Force::pair_match(const char *word, int exact)
{
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 (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 (count == 1) return hybrid->styles[iwhich];
}
return NULL;
}
/* ----------------------------------------------------------------------
create a bond style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_bond(const char *style, const char *suffix)
{
delete [] bond_style;
if (bond) delete bond;
int sflag;
bond = new_bond(style,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
bond_style = new char[n];
strcpy(bond_style,estyle);
} else {
int n = strlen(style) + 1;
bond_style = new char[n];
strcpy(bond_style,style);
}
}
/* ----------------------------------------------------------------------
generate a bond class, fist with suffix appended
------------------------------------------------------------------------- */
Bond *Force::new_bond(const char *style, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
if (0) return NULL;
#define BOND_CLASS
#define BondStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_bond.h"
#undef BondStyle
#undef BOND_CLASS
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define BOND_CLASS
#define BondStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_bond.h"
#undef BOND_CLASS
else error->all(FLERR,"Invalid bond style");
return NULL;
}
/* ----------------------------------------------------------------------
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, const char *suffix)
{
delete [] angle_style;
if (angle) delete angle;
int sflag;
angle = new_angle(style,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
angle_style = new char[n];
strcpy(angle_style,estyle);
} else {
int n = strlen(style) + 1;
angle_style = new char[n];
strcpy(angle_style,style);
}
}
/* ----------------------------------------------------------------------
generate an angle class
------------------------------------------------------------------------- */
Angle *Force::new_angle(const char *style, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
if (0) return NULL;
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_angle.h"
#undef AngleStyle
#undef ANGLE_CLASS
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_angle.h"
#undef ANGLE_CLASS
else error->all(FLERR,"Invalid angle style");
return NULL;
}
/* ----------------------------------------------------------------------
create a dihedral style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_dihedral(const char *style, const char *suffix)
{
delete [] dihedral_style;
if (dihedral) delete dihedral;
int sflag;
dihedral = new_dihedral(style,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
dihedral_style = new char[n];
strcpy(dihedral_style,estyle);
} else {
int n = strlen(style) + 1;
dihedral_style = new char[n];
strcpy(dihedral_style,style);
}
}
/* ----------------------------------------------------------------------
generate a dihedral class
------------------------------------------------------------------------- */
Dihedral *Force::new_dihedral(const char *style, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
if (0) return NULL;
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
else error->all(FLERR,"Invalid dihedral style");
return NULL;
}
/* ----------------------------------------------------------------------
create an improper style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_improper(const char *style, const char *suffix)
{
delete [] improper_style;
if (improper) delete improper;
int sflag;
improper = new_improper(style,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
improper_style = new char[n];
strcpy(improper_style,estyle);
} else {
int n = strlen(style) + 1;
improper_style = new char[n];
strcpy(improper_style,style);
}
}
/* ----------------------------------------------------------------------
generate a improper class
------------------------------------------------------------------------- */
Improper *Force::new_improper(const char *style, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
if (0) return NULL;
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_improper.h"
#undef ImproperStyle
#undef IMPROPER_CLASS
}
sflag = 0;
if (strcmp(style,"none") == 0) return NULL;
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_improper.h"
#undef IMPROPER_CLASS
else error->all(FLERR,"Invalid improper style");
return NULL;
}
/* ----------------------------------------------------------------------
new kspace style
------------------------------------------------------------------------- */
void Force::create_kspace(int narg, char **arg, const char *suffix)
{
delete [] kspace_style;
if (kspace) delete kspace;
int sflag;
kspace = new_kspace(narg,arg,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],suffix);
int n = strlen(estyle) + 1;
kspace_style = new char[n];
strcpy(kspace_style,estyle);
} else {
int n = strlen(arg[0]) + 1;
kspace_style = new char[n];
strcpy(kspace_style,arg[0]);
}
}
/* ----------------------------------------------------------------------
generate a kspace class
------------------------------------------------------------------------- */
KSpace *Force::new_kspace(int narg, char **arg, const char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",arg[0],suffix);
if (0) return NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSpaceStyle
#undef KSPACE_CLASS
}
sflag = 0;
if (strcmp(arg[0],"none") == 0) return NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) return new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSPACE_CLASS
else error->all(FLERR,"Invalid kspace style");
return NULL;
}
/* ----------------------------------------------------------------------
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;
}
/* ----------------------------------------------------------------------
set special bond values
------------------------------------------------------------------------- */
void Force::set_special(int narg, char **arg)
{
if (narg == 0) error->all(FLERR,"Illegal special_bonds command");
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] = atof(arg[iarg+1]);
special_lj[2] = special_coul[2] = atof(arg[iarg+2]);
special_lj[3] = special_coul[3] = atof(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] = atof(arg[iarg+1]);
special_lj[2] = atof(arg[iarg+2]);
special_lj[3] = atof(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] = atof(arg[iarg+1]);
special_coul[2] = atof(arg[iarg+2]);
special_coul[3] = atof(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 if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
special_extra = atoi(arg[iarg+1]);
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");
if (special_extra < 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(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)
error->all(FLERR,"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)
{
int n = strlen(str);
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)
{
int n = strlen(str);
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);
}
/* ----------------------------------------------------------------------
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;
}
c4science · Help