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Sun, Jul 13, 23:48

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 "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 MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
Force::Force(LAMMPS *lmp) : Pointers(lmp)
{
newton = newton_pair = newton_bond = 1;
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);
}
/* ---------------------------------------------------------------------- */
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;
}
/* ---------------------------------------------------------------------- */
void Force::init()
{
qqrd2e = qqr2e/dielectric;
comm->maxforward_pair = comm->maxreverse_pair = 0;
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)
{
delete [] pair_style;
if (pair) delete pair;
pair = new_pair(style);
int n = strlen(style) + 1;
pair_style = new char[n];
strcpy(pair_style,style);
}
/* ----------------------------------------------------------------------
generate a pair class
------------------------------------------------------------------------- */
Pair *Force::new_pair(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
#define PAIR_CLASS
#define PairStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_pair.h"
#undef PAIR_CLASS
else error->all("Invalid pair style");
return NULL;
}
/* ----------------------------------------------------------------------
return ptr to current pair class or hybrid sub-class
if exact, then style name must be exact match to word
if not exact, style name must contain word
return NULL if no match
return NULL if not exact and multiple hybrid 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 (strcmp(pair_style,"hybrid") == 0) {
PairHybrid *hybrid = (PairHybrid *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++) {
if (exact && strcmp(hybrid->keywords[i],word) == 0)
return hybrid->styles[i];
if (!exact && strstr(hybrid->keywords[i],word)) {
iwhich = i;
count++;
}
}
if (!exact && count == 1) return hybrid->styles[iwhich];
} else if (strcmp(pair_style,"hybrid/overlay") == 0) {
PairHybridOverlay *hybrid = (PairHybridOverlay *) pair;
count = 0;
for (int i = 0; i < hybrid->nstyles; i++) {
if (exact && strcmp(hybrid->keywords[i],word) == 0)
return hybrid->styles[i];
else if (!exact && strstr(hybrid->keywords[i],word)) {
iwhich = i;
count++;
}
}
if (!exact && 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)
{
delete [] bond_style;
if (bond) delete bond;
bond = new_bond(style);
int n = strlen(style) + 1;
bond_style = new char[n];
strcpy(bond_style,style);
}
/* ----------------------------------------------------------------------
generate a bond class
------------------------------------------------------------------------- */
Bond *Force::new_bond(const char *style)
{
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("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)
{
delete [] angle_style;
if (angle) delete angle;
angle = new_angle(style);
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)
{
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("Invalid angle style");
return NULL;
}
/* ----------------------------------------------------------------------
create a dihedral style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_dihedral(const char *style)
{
delete [] dihedral_style;
if (dihedral) delete dihedral;
dihedral = new_dihedral(style);
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)
{
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 DIHEDRAL_CLASS
else error->all("Invalid dihedral style");
return NULL;
}
/* ----------------------------------------------------------------------
create an improper style, called from input script or restart file
------------------------------------------------------------------------- */
void Force::create_improper(const char *style)
{
delete [] improper_style;
if (improper) delete improper;
improper = new_improper(style);
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)
{
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("Invalid improper style");
return NULL;
}
/* ----------------------------------------------------------------------
new kspace style
------------------------------------------------------------------------- */
void Force::create_kspace(int narg, char **arg)
{
delete [] kspace_style;
if (kspace) delete kspace;
if (strcmp(arg[0],"none") == 0) kspace = NULL;
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) kspace = new Class(lmp,narg-1,&arg[1]);
#include "style_kspace.h"
#undef KSPACE_CLASS
else error->all("Invalid kspace style");
int n = strlen(arg[0]) + 1;
kspace_style = new char[n];
strcpy(kspace_style,arg[0]);
}
/* ----------------------------------------------------------------------
set special bond values
------------------------------------------------------------------------- */
void Force::set_special(int narg, char **arg)
{
if (narg == 0) error->all("Illegal special_bonds command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"amber") == 0) {
if (iarg+1 > narg) error->all("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("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("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("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("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("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("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("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("Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all("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("Illegal special_bonds command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all("Illegal special_bonds command");
special_extra = atoi(arg[iarg+1]);
iarg += 2;
} else error->all("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("Illegal special_bonds command");
if (special_extra < 0) error->all("Illegal special_bonds command");
}
/* ----------------------------------------------------------------------
compute bounds implied by numeric str with a possible wildcard asterik
nmax = upper bound
5 possibilities:
(1) i = i to i, (2) * = 1 to nmax,
(3) i* = i to nmax, (4) *j = 1 to j, (5) i*j = i to j
return nlo,nhi
------------------------------------------------------------------------- */
void Force::bounds(char *str, int nmax, int &nlo, int &nhi)
{
char *ptr = strchr(str,'*');
if (ptr == NULL) {
nlo = MAX(atoi(str),1);
nhi = MIN(atoi(str),nmax);
} else if (strlen(str) == 1) {
nlo = 1;
nhi = nmax;
} else if (ptr == str) {
nlo = 1;
nhi = MIN(atoi(ptr+1),nmax);
} else if (strlen(ptr+1) == 0) {
nlo = MAX(atoi(str),1);
nhi = nmax;
} else {
nlo = MAX(atoi(str),1);
nhi = MIN(atoi(ptr+1),nmax);
}
}
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
called by force fields to check validity of their arguments
------------------------------------------------------------------------- */
double Force::numeric(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("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 force fields to check validity of their arguments
------------------------------------------------------------------------- */
int Force::inumeric(char *str)
{
int n = strlen(str);
for (int i = 0; i < n; i++) {
if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
error->all("Expected integer parameter in input script or data file");
}
return atoi(str);
}
/* ----------------------------------------------------------------------
memory usage of force classes
------------------------------------------------------------------------- */
double Force::memory_usage()
{
double bytes = 0.0;
if (pair) bytes += pair->memory_usage();
if (bond) bytes += bond->memory_usage();
if (angle) bytes += angle->memory_usage();
if (dihedral) bytes += dihedral->memory_usage();
if (improper) bytes += improper->memory_usage();
if (kspace) bytes += kspace->memory_usage();
return bytes;
}

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