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pair_buck_coul_cut.cpp
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Thu, Nov 7, 00:50

pair_buck_coul_cut.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eduardo Bringa (LLNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_buck_coul_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairBuckCoulCut::PairBuckCoulCut(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairBuckCoulCut::~PairBuckCoulCut()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut_lj);
memory->destroy_2d_double_array(cut_ljsq);
memory->destroy_2d_double_array(cut_coul);
memory->destroy_2d_double_array(cut_coulsq);
memory->destroy_2d_double_array(a);
memory->destroy_2d_double_array(rho);
memory->destroy_2d_double_array(c);
memory->destroy_2d_double_array(rhoinv);
memory->destroy_2d_double_array(buck1);
memory->destroy_2d_double_array(buck2);
memory->destroy_2d_double_array(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCut::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcebuck,fforce,factor_coul,factor_lj;
double factor,phicoul,phibuck,r,rexp;
int *neighs;
double **f;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
if (eflag) {
if (newton_pair || j < nlocal) factor = 1.0;
else factor = 0.5;
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
eng_coul += factor*factor_coul*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
eng_vdwl += factor*factor_lj*phibuck;
}
}
if (vflag == 1) {
if (newton_pair || j < nlocal) {
virial[0] += delx*delx*fforce;
virial[1] += dely*dely*fforce;
virial[2] += delz*delz*fforce;
virial[3] += delx*dely*fforce;
virial[4] += delx*delz*fforce;
virial[5] += dely*delz*fforce;
} else {
virial[0] += 0.5*delx*delx*fforce;
virial[1] += 0.5*dely*dely*fforce;
virial[2] += 0.5*delz*delz*fforce;
virial[3] += 0.5*delx*dely*fforce;
virial[4] += 0.5*delx*delz*fforce;
virial[5] += 0.5*dely*delz*fforce;
}
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBuckCoulCut::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj");
cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq");
cut_coul = memory->create_2d_double_array(n+1,n+1,"pair:cut_coul");
cut_coulsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_coulsq");
a = memory->create_2d_double_array(n+1,n+1,"pair:a");
rho = memory->create_2d_double_array(n+1,n+1,"pair:rho");
c = memory->create_2d_double_array(n+1,n+1,"pair:c");
rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv");
buck1 = memory->create_2d_double_array(n+1,n+1,"pair:buck1");
buck2 = memory->create_2d_double_array(n+1,n+1,"pair:buck2");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBuckCoulCut::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all("Illegal pair_style command");
cut_lj_global = atof(arg[0]);
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = atof(arg[1]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBuckCoulCut::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 7) error->all("Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double a_one = atof(arg[2]);
double rho_one = atof(arg[3]);
double c_one = atof(arg[4]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
if (narg >= 6) cut_coul_one = cut_lj_one = atof(arg[5]);
if (narg == 7) cut_coul_one = atof(arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a[i][j] = a_one;
rho[i][j] = rho_one;
c[i][j] = c_one;
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBuckCoulCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
rhoinv[i][j] = 1.0/rho[i][j];
buck1[i][j] = a[i][j]/rho[i][j];
buck2[i][j] = 6.0*c[i][j];
if (offset_flag) {
double rexp = exp(-cut_lj[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0);
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
a[j][i] = a[i][j];
c[j][i] = c[i][j];
rhoinv[j][i] = rhoinv[i][j];
buck1[j][i] = buck1[i][j];
buck2[j][i] = buck2[i][j];
offset[j][i] = offset[i][j];
return cut;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBuckCoulCut::init_style()
{
// require an atom style with charge defined
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBuckCoulCut::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a[i][j],sizeof(double),1,fp);
fwrite(&rho[i][j],sizeof(double),1,fp);
fwrite(&c[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBuckCoulCut::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&a[i][j],sizeof(double),1,fp);
fread(&rho[i][j],sizeof(double),1,fp);
fread(&c[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBuckCoulCut::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBuckCoulCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCut::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
{
double r2inv,r6inv,r,rexp,forcecoul,forcebuck,phicoul,phibuck;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
one.fforce = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype]) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
one.eng_coul = factor_coul*phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
phibuck = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
one.eng_vdwl = factor_lj*phibuck;
} else one.eng_vdwl = 0.0;
}
}

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