289 lines
8.4 KiB
C++
289 lines
8.4 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 "bond_gaussian.h"
|
|
|
|
#include <cmath>
|
|
#include <cstring>
|
|
#include "atom.h"
|
|
#include "neighbor.h"
|
|
#include "comm.h"
|
|
#include "force.h"
|
|
#include "math_const.h"
|
|
#include "memory.h"
|
|
#include "error.h"
|
|
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace MathConst;
|
|
|
|
#define SMALL 1.0e-10
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
BondGaussian::BondGaussian(LAMMPS *lmp) : Bond(lmp)
|
|
{
|
|
reinitflag = 1;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
BondGaussian::~BondGaussian()
|
|
{
|
|
if (allocated && !copymode) {
|
|
memory->destroy(setflag);
|
|
memory->destroy(nterms);
|
|
memory->destroy(bond_temperature);
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
if (alpha[i]) delete [] alpha[i];
|
|
if (width[i]) delete [] width[i];
|
|
if (r0[i]) delete [] r0[i];
|
|
}
|
|
delete [] alpha;
|
|
delete [] width;
|
|
delete [] r0;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::compute(int eflag, int vflag)
|
|
{
|
|
int i1,i2,n,type;
|
|
double delx,dely,delz,ebond,fbond;
|
|
double rsq,r,dr;
|
|
double prefactor, exponent, g_i, sum_g_i, sum_numerator;
|
|
|
|
ebond = 0.0;
|
|
ev_init(eflag,vflag);
|
|
|
|
double **x = atom->x;
|
|
double **f = atom->f;
|
|
int **bondlist = neighbor->bondlist;
|
|
int nbondlist = neighbor->nbondlist;
|
|
int nlocal = atom->nlocal;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
for (n = 0; n < nbondlist; n++) {
|
|
i1 = bondlist[n][0];
|
|
i2 = bondlist[n][1];
|
|
type = bondlist[n][2];
|
|
|
|
delx = x[i1][0] - x[i2][0];
|
|
dely = x[i1][1] - x[i2][1];
|
|
delz = x[i1][2] - x[i2][2];
|
|
|
|
rsq = delx*delx + dely*dely + delz*delz;
|
|
r = sqrt(rsq);
|
|
|
|
sum_g_i = 0.0;
|
|
sum_numerator = 0.0;
|
|
for (int i = 0; i < nterms[type]; i++) {
|
|
dr = r - r0[type][i];
|
|
prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
|
|
exponent = -2*dr*dr/(width[type][i]*width[type][i]);
|
|
g_i = prefactor*exp(exponent);
|
|
sum_g_i += g_i;
|
|
sum_numerator += g_i*dr/(width[type][i]*width[type][i]);
|
|
}
|
|
|
|
// force & energy
|
|
if (sum_g_i < SMALL) sum_g_i = SMALL;
|
|
|
|
if (r > 0.0) fbond = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
|
|
else fbond = 0.0;
|
|
|
|
if (eflag) ebond = -(force->boltz*bond_temperature[type])*log(sum_g_i);
|
|
|
|
// apply force to each of 2 atoms
|
|
|
|
if (newton_bond || i1 < nlocal) {
|
|
f[i1][0] += delx*fbond;
|
|
f[i1][1] += dely*fbond;
|
|
f[i1][2] += delz*fbond;
|
|
}
|
|
|
|
if (newton_bond || i2 < nlocal) {
|
|
f[i2][0] -= delx*fbond;
|
|
f[i2][1] -= dely*fbond;
|
|
f[i2][2] -= delz*fbond;
|
|
}
|
|
|
|
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::allocate()
|
|
{
|
|
allocated = 1;
|
|
int n = atom->nbondtypes;
|
|
|
|
memory->create(nterms,n+1,"bond:nterms");
|
|
memory->create(bond_temperature,n+1,"bond:bond_temperature");
|
|
|
|
alpha = new double *[n+1];
|
|
width = new double *[n+1];
|
|
r0 = new double *[n+1];
|
|
for (int i = 1; i <= n; i++) {
|
|
alpha[i] = 0;
|
|
width[i] = 0;
|
|
r0[i] = 0;
|
|
}
|
|
|
|
memory->create(setflag,n+1,"bond:setflag");
|
|
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more types
|
|
------------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::coeff(int narg, char **arg)
|
|
{
|
|
if (narg < 6) error->all(FLERR,"Incorrect args for bond coefficients");
|
|
|
|
int ilo,ihi;
|
|
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
|
|
|
double bond_temp_one = utils::numeric(FLERR,arg[1],false,lmp);
|
|
int n = utils::inumeric(FLERR,arg[2],false,lmp);
|
|
if (narg != 3*n + 3)
|
|
error->all(FLERR,"Incorrect args for bond coefficients");
|
|
|
|
if (!allocated) allocate();
|
|
|
|
int count = 0;
|
|
for (int i = ilo; i <= ihi; i++) {
|
|
bond_temperature[i] = bond_temp_one;
|
|
nterms[i] = n;
|
|
alpha[i] = new double [n];
|
|
width[i] = new double [n];
|
|
r0[i] = new double [n];
|
|
for (int j = 0; j < n; j++) {
|
|
alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
|
|
width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
|
|
r0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp);
|
|
setflag[i] = 1;
|
|
}
|
|
count++;
|
|
}
|
|
|
|
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return an equilbrium bond length
|
|
------------------------------------------------------------------------- */
|
|
|
|
double BondGaussian::equilibrium_distance(int i)
|
|
{
|
|
return r0[i][0];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes out coeffs to restart file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::write_restart(FILE *fp)
|
|
{
|
|
fwrite(&bond_temperature[1],sizeof(double),atom->nbondtypes,fp);
|
|
fwrite(&nterms[1],sizeof(int),atom->nbondtypes,fp);
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
fwrite(alpha[i],sizeof(double),nterms[i],fp);
|
|
fwrite(width[i],sizeof(double),nterms[i],fp);
|
|
fwrite(r0[i],sizeof(double),nterms[i],fp);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 reads coeffs from restart file, bcasts them
|
|
------------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::read_restart(FILE *fp)
|
|
{
|
|
allocate();
|
|
|
|
if (comm->me == 0) {
|
|
utils::sfread(FLERR,&bond_temperature[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
|
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nbondtypes,fp,nullptr,error);
|
|
}
|
|
MPI_Bcast(&bond_temperature[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&nterms[1],atom->nbondtypes,MPI_INT,0,world);
|
|
|
|
// allocate
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
alpha[i] = new double [nterms[i]];
|
|
width[i] = new double [nterms[i]];
|
|
r0[i] = new double [nterms[i]];
|
|
}
|
|
|
|
if (comm->me == 0) {
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
|
|
utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
|
|
utils::sfread(FLERR,r0[i],sizeof(double),nterms[i],fp,nullptr,error);
|
|
}
|
|
}
|
|
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
|
|
MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
|
|
MPI_Bcast(r0[i],nterms[i],MPI_DOUBLE,0,world);
|
|
}
|
|
|
|
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void BondGaussian::write_data(FILE *fp)
|
|
{
|
|
for (int i = 1; i <= atom->nbondtypes; i++) {
|
|
fprintf(fp,"%d %g %d",i,bond_temperature[i],nterms[i]);
|
|
for (int j = 0; j < nterms[i]; j++) {
|
|
fprintf(fp," %g %g %g",alpha[i][j],width[i][j],r0[i][j]);
|
|
}
|
|
fprintf(fp, "\n");
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double BondGaussian::single(int type, double rsq, int /*i*/, int /*j*/,
|
|
double &fforce)
|
|
{
|
|
double r = sqrt(rsq);
|
|
fforce = 0;
|
|
|
|
double sum_g_i = 0.0;
|
|
double sum_numerator = 0.0;
|
|
for (int i = 0; i < nterms[type]; i++) {
|
|
double dr = r - r0[type][i];
|
|
double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
|
|
double exponent = -2*dr*dr/(width[type][i]*width[type][i]);
|
|
double g_i = prefactor*exp(exponent);
|
|
sum_g_i += g_i;
|
|
sum_numerator += g_i*dr/(width[type][i]*width[type][i]);
|
|
}
|
|
|
|
if (sum_g_i < SMALL) sum_g_i = SMALL;
|
|
if (r > 0.0) fforce = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
|
|
|
|
return -(force->boltz*bond_temperature[type])*log(sum_g_i);
|
|
}
|
|
|