Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/bond_hybrid.cpp
775e8f3cc8f5lammm-master-deprecated

Last Change
Raw File

bond_hybrid.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 <math.h>
#include <string.h>
#include <ctype.h>
#include "bond_hybrid.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EXTRA 1000
/* ---------------------------------------------------------------------- */
BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
{
writedata = 0;
nstyles = 0;
}
/* ---------------------------------------------------------------------- */
BondHybrid::~BondHybrid()
{
if (nstyles) {
for (int i = 0; i < nstyles; i++) delete styles[i];
delete [] styles;
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
delete [] keywords;
}
if (allocated) {
memory->destroy(setflag);
memory->destroy(map);
delete [] nbondlist;
delete [] maxbond;
for (int i = 0; i < nstyles; i++)
memory->destroy(bondlist[i]);
delete [] bondlist;
}
}
/* ---------------------------------------------------------------------- */
void BondHybrid::compute(int eflag, int vflag)
{
int i,j,m,n;
// save ptrs to original bondlist
int nbondlist_orig = neighbor->nbondlist;
int **bondlist_orig = neighbor->bondlist;
// if this is re-neighbor step, create sub-style bondlists
// nbondlist[] = length of each sub-style list
// realloc sub-style bondlist if necessary
// load sub-style bondlist with 3 values from original bondlist
if (neighbor->ago == 0) {
for (m = 0; m < nstyles; m++) nbondlist[m] = 0;
for (i = 0; i < nbondlist_orig; i++) {
m = map[bondlist_orig[i][2]];
if (m >= 0) nbondlist[m]++;
}
for (m = 0; m < nstyles; m++) {
if (nbondlist[m] > maxbond[m]) {
memory->destroy(bondlist[m]);
maxbond[m] = nbondlist[m] + EXTRA;
memory->create(bondlist[m],maxbond[m],3,"bond_hybrid:bondlist");
}
nbondlist[m] = 0;
}
for (i = 0; i < nbondlist_orig; i++) {
m = map[bondlist_orig[i][2]];
if (m < 0) continue;
n = nbondlist[m];
bondlist[m][n][0] = bondlist_orig[i][0];
bondlist[m][n][1] = bondlist_orig[i][1];
bondlist[m][n][2] = bondlist_orig[i][2];
nbondlist[m]++;
}
}
// call each sub-style's compute function
// set neighbor->bondlist to sub-style bondlist before call
// accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
for (m = 0; m < nstyles; m++) {
neighbor->nbondlist = nbondlist[m];
neighbor->bondlist = bondlist[m];
styles[m]->compute(eflag,vflag);
if (eflag_global) energy += styles[m]->energy;
if (vflag_global)
for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
if (eflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
double *eatom_substyle = styles[m]->eatom;
for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
}
if (vflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
for (j = 0; j < 6; j++)
vatom[i][j] += vatom_substyle[i][j];
}
}
// restore ptrs to original bondlist
neighbor->nbondlist = nbondlist_orig;
neighbor->bondlist = bondlist_orig;
}
/* ---------------------------------------------------------------------- */
void BondHybrid::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(map,n+1,"bond:map");
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
nbondlist = new int[nstyles];
maxbond = new int[nstyles];
bondlist = new int**[nstyles];
for (int m = 0; m < nstyles; m++) maxbond[m] = 0;
for (int m = 0; m < nstyles; m++) bondlist[m] = NULL;
}
/* ----------------------------------------------------------------------
create one bond style for each arg in list
------------------------------------------------------------------------- */
void BondHybrid::settings(int narg, char **arg)
{
int i,m,istyle;
if (narg < 1) error->all(FLERR,"Illegal bond_style command");
// delete old lists, since cannot just change settings
if (nstyles) {
for (int i = 0; i < nstyles; i++) delete styles[i];
delete [] styles;
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
delete [] keywords;
}
if (allocated) {
memory->destroy(setflag);
memory->destroy(map);
delete [] nbondlist;
delete [] maxbond;
for (int i = 0; i < nstyles; i++)
memory->destroy(bondlist[i]);
delete [] bondlist;
}
allocated = 0;
// count sub-styles by skipping numeric args
// one exception is 1st arg of style "table", which is non-numeric word
// need a better way to skip these exceptions
nstyles = 0;
i = 0;
while (i < narg) {
if (strcmp(arg[i],"table") == 0) i++;
i++;
while (i < narg && !isalpha(arg[i][0])) i++;
nstyles++;
}
// allocate list of sub-styles
styles = new Bond*[nstyles];
keywords = new char*[nstyles];
// allocate each sub-style and call its settings() with subset of args
// allocate uses suffix, but don't store suffix version in keywords,
// else syntax in coeff() will not match
// define subset of args for a sub-style by skipping numeric args
// one exception is 1st arg of style "table", which is non-numeric
// need a better way to skip these exceptions
int dummy;
nstyles = 0;
i = 0;
while (i < narg) {
for (m = 0; m < nstyles; m++)
if (strcmp(arg[i],keywords[m]) == 0)
error->all(FLERR,"Bond style hybrid cannot use same bond style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument");
if (strcmp(arg[i],"none") == 0)
error->all(FLERR,"Bond style hybrid cannot have none as an argument");
styles[nstyles] = force->new_bond(arg[i],1,dummy);
force->store_style(keywords[nstyles],arg[i],0);
istyle = i;
if (strcmp(arg[i],"table") == 0) i++;
i++;
while (i < narg && !isalpha(arg[i][0])) i++;
styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
nstyles++;
}
}
/* ----------------------------------------------------------------------
set coeffs for one type
---------------------------------------------------------------------- */
void BondHybrid::coeff(int narg, char **arg)
{
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
// 2nd arg = bond sub-style name
// allow for "none" as valid sub-style name
int m;
for (m = 0; m < nstyles; m++)
if (strcmp(arg[1],keywords[m]) == 0) break;
int none = 0;
if (m == nstyles) {
if (strcmp(arg[1],"none") == 0) none = 1;
else error->all(FLERR,"Bond coeff for hybrid has invalid style");
}
// move 1st arg to 2nd arg
// just copy ptrs, since arg[] points into original input line
arg[1] = arg[0];
// invoke sub-style coeff() starting with 1st arg
if (!none) styles[m]->coeff(narg-1,&arg[1]);
// set setflag and which type maps to which sub-style
// if sub-style is none: set hybrid setflag, wipe out map
for (int i = ilo; i <= ihi; i++) {
setflag[i] = 1;
if (none) map[i] = -1;
else map[i] = m;
}
}
/* ---------------------------------------------------------------------- */
void BondHybrid::init_style()
{
for (int m = 0; m < nstyles; m++)
if (styles[m]) styles[m]->init_style();
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHybrid::equilibrium_distance(int i)
{
if (map[i] < 0)
error->one(FLERR,"Invoked bond equil distance on bond style none");
return styles[map[i]]->equilibrium_distance(i);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondHybrid::write_restart(FILE *fp)
{
fwrite(&nstyles,sizeof(int),1,fp);
int n;
for (int m = 0; m < nstyles; m++) {
n = strlen(keywords[m]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(keywords[m],sizeof(char),n,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondHybrid::read_restart(FILE *fp)
{
int me = comm->me;
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
styles = new Bond*[nstyles];
keywords = new char*[nstyles];
allocate();
int n,dummy;
for (int m = 0; m < nstyles; m++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
keywords[m] = new char[n];
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
styles[m] = force->new_bond(keywords[m],0,dummy);
}
}
/* ---------------------------------------------------------------------- */
double BondHybrid::single(int type, double rsq, int i, int j,
double &fforce)
{
if (map[type] < 0) error->one(FLERR,"Invoked bond single on bond style none");
return styles[map[type]]->single(type,rsq,i,j,fforce);
}
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
double BondHybrid::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += maxbond[m]*3 * sizeof(int);
for (int m = 0; m < nstyles; m++)
if (styles[m]) bytes += styles[m]->memory_usage();
return bytes;
}
c4science · Help