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pair_lj_class2.cpp
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Thu, May 23, 17:13

pair_lj_class2.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 "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_class2.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.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))
/* ---------------------------------------------------------------------- */
PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJClass2::~PairLJClass2()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJClass2::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rinv,r2inv,r3inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
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;
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJClass2::settings(int narg, char **arg)
{
if (narg != 1) error->all("Illegal pair_style command");
cut_global = force->numeric(arg[0]);
// 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[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJClass2::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) 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 epsilon_one = force->numeric(arg[2]);
double sigma_one = force->numeric(arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = force->numeric(arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut[i][j] = cut_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 PairLJClass2::init_one(int i, int j)
{
// always mix epsilon,sigma via sixthpower rules
// mix distance via user-defined rule
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
lj1[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j],9.0);
lj2[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 2.0 * epsilon[i][j] * pow(sigma[i][j],9.0);
lj4[i][j] = 3.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = epsilon[i][j] * (2.0*pow(ratio,9.0) - 3.0*pow(ratio,6.0));
} else offset[i][j] = 0.0;
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double PI = 4.0*atan(1.0);
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
ptail_ij = 2.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2::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(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJClass2::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(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2::write_restart_settings(FILE *fp)
{
fwrite(&cut_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 PairLJClass2::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
return factor_lj*philj;
}

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