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source code for gaussian bond_style
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Evangelos Voyiatzis
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src/USER-MISC/bond_gaussian.cpp
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287
src/USER-MISC/bond_gaussian.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "bond_gaussian.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "force.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define SMALL 1.0e-10
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/* ---------------------------------------------------------------------- */
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BondGaussian::BondGaussian(LAMMPS *lmp) : Bond(lmp)
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{
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reinitflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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BondGaussian::~BondGaussian()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(nterms);
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memory->destroy(bond_temperature);
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for (int i = 1; i <= atom->nbondtypes; i++) {
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if (alpha[i]) delete [] alpha[i];
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if (width[i]) delete [] width[i];
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if (r0[i]) delete [] r0[i];
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}
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delete [] alpha;
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delete [] width;
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delete [] r0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondGaussian::compute(int eflag, int vflag)
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{
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int i1,i2,n,type;
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double delx,dely,delz,ebond,fbond;
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double rsq,r,dr;
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double prefactor, exponent, g_i, sum_g_i, sum_numerator;
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ebond = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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int **bondlist = neighbor->bondlist;
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int nbondlist = neighbor->nbondlist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nbondlist; n++) {
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i1 = bondlist[n][0];
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i2 = bondlist[n][1];
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type = bondlist[n][2];
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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rsq = delx*delx + dely*dely + delz*delz;
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r = sqrt(rsq);
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sum_g_i = 0.0;
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sum_numerator = 0.0;
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for (int i = 0; i < nterms[type]; i++) {
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dr = r - this->r0[type][i];
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prefactor = (this->alpha[type][i]/(this->width[type][i]*sqrt(MY_PI2)));
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exponent = -2*dr*dr/(this->width[type][i]*this->width[type][i]);
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g_i = prefactor*exp(exponent);
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sum_g_i += g_i;
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sum_numerator += g_i*dr/(this->width[type][i]*this->width[type][i]);
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}
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// force & energy
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if (sum_g_i < SMALL) sum_g_i = SMALL;
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if (r > 0.0) fbond = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
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else fbond = 0.0;
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if (eflag) ebond = -(force->boltz*bond_temperature[type])*log(sum_g_i);
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// apply force to each of 2 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx*fbond;
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f[i1][1] += dely*fbond;
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f[i1][2] += delz*fbond;
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= delx*fbond;
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f[i2][1] -= dely*fbond;
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f[i2][2] -= delz*fbond;
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}
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if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondGaussian::allocate()
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{
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allocated = 1;
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int n = atom->nbondtypes;
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memory->create(nterms,n+1,"bond:nterms");
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memory->create(bond_temperature,n+1,"bond:bond_temperature");
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alpha = new double *[n+1];
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width = new double *[n+1];
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r0 = new double *[n+1];
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for (int i = 1; i <= n; i++) {
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alpha[i] = 0;
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width[i] = 0;
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r0[i] = 0;
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}
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memory->create(setflag,n+1,"bond:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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void BondGaussian::coeff(int narg, char **arg)
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{
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if (narg < 6) error->all(FLERR,"Incorrect args for bond coefficients");
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int ilo,ihi;
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utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
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double bond_temp_one = utils::numeric(FLERR,arg[1],false,lmp);
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int n = utils::inumeric(FLERR,arg[2],false,lmp);
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if (narg != 3*n + 3)
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error->all(FLERR,"Incorrect args for bond coefficients");
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if (!allocated) allocate();
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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bond_temperature[i] = bond_temp_one;
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nterms[i] = n;
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alpha[i] = new double [n];
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width[i] = new double [n];
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r0[i] = new double [n];
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for (int j = 0; j < n; j++ ) {
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alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
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width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
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r0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp);
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setflag[i] = 1;
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}
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
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}
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/* ----------------------------------------------------------------------
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return an equilbrium bond length
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------------------------------------------------------------------------- */
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double BondGaussian::equilibrium_distance(int i)
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{
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return r0[i][0];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void BondGaussian::write_restart(FILE *fp)
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{
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fwrite(&bond_temperature[1],sizeof(double),atom->nbondtypes,fp);
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fwrite(&nterms[1],sizeof(int),atom->nbondtypes,fp);
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for(int i = 1; i <= atom->nbondtypes; i++) {
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fwrite(alpha[i],sizeof(double),nterms[i],fp);
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fwrite(width[i],sizeof(double),nterms[i],fp);
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fwrite(r0[i],sizeof(double),nterms[i],fp);
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void BondGaussian::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0) {
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utils::sfread(FLERR,&bond_temperature[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
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utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nbondtypes,fp,nullptr,error);
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}
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MPI_Bcast(&bond_temperature[1],atom->nbondtypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&nterms[1],atom->nbondtypes,MPI_INT,0,world);
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// allocate
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for(int i = 1; i <= atom->nbondtypes; i++) {
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alpha[i] = new double [nterms[i]];
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width[i] = new double [nterms[i]];
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r0[i] = new double [nterms[i]];
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}
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if (comm->me == 0) {
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for(int i = 1; i <= atom->nbondtypes; i++) {
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utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
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utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
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utils::sfread(FLERR,r0[i],sizeof(double),nterms[i],fp,nullptr,error);
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}
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}
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for(int i = 1; i <= atom->nbondtypes; i++) {
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MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
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MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
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MPI_Bcast(r0[i],nterms[i],MPI_DOUBLE,0,world);
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}
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for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void BondGaussian::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nbondtypes; i++) {
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fprintf(fp,"%d %g %d",i,bond_temperature[i],nterms[i]);
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for (int j = 0; j < nterms[i]; j++) {
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fprintf(fp," %g %g %g",alpha[i][j],width[i][j],r0[i][j]);
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}
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fprintf(fp, "\n");
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}
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}
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/* ---------------------------------------------------------------------- */
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double BondGaussian::single(int type, double rsq, int /*i*/, int /*j*/,
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double &fforce)
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{
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double r = sqrt(rsq);
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fforce = 0;
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double sum_g_i = 0.0;
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double sum_numerator = 0.0;
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for (int i = 0; i < nterms[type]; i++) {
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double dr = r - this->r0[type][i];
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double prefactor = (this->alpha[type][i]/(this->width[type][i]*sqrt(MY_PI2)));
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double exponent = -2*dr*dr/(this->width[type][i]*this->width[type][i]);
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double g_i = prefactor*exp(exponent);
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sum_g_i += g_i;
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sum_numerator += g_i*dr/(this->width[type][i]*this->width[type][i]);
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}
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if (r > 0.0) fforce = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
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return -(force->boltz*bond_temperature[type])*log(sum_g_i);
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}
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58
src/USER-MISC/bond_gaussian.h
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58
src/USER-MISC/bond_gaussian.h
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@ -0,0 +1,58 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef BOND_CLASS
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BondStyle(gaussian,BondGaussian)
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#else
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#ifndef LMP_BOND_GAUSSIAN_H
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#define LMP_BOND_GAUSSIAN_H
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#include "bond.h"
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namespace LAMMPS_NS {
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class BondGaussian : public Bond {
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public:
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BondGaussian(class LAMMPS *);
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virtual ~BondGaussian();
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virtual void compute(int, int);
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virtual void coeff(int, char **);
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double equilibrium_distance(int);
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void write_restart(FILE *);
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virtual void read_restart(FILE *);
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void write_data(FILE *);
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double single(int, double, int, int, double &);
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protected:
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int *nterms;
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double *bond_temperature;
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double **alpha,**width,**r0;
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virtual void allocate();
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Incorrect args for bond coefficients
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Self-explanatory. Check the input script or data file.
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*/
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