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pair_lj_gromacs_coul_gromacs.cpp
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Wed, Jul 24, 01:15

pair_lj_gromacs_coul_gromacs.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: Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_gromacs_coul_gromacs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.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))
/* ---------------------------------------------------------------------- */
PairLJGromacsCoulGromacs::PairLJGromacsCoulGromacs(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(epsilon);
memory->destroy_2d_double_array(sigma);
memory->destroy_2d_double_array(lj1);
memory->destroy_2d_double_array(lj2);
memory->destroy_2d_double_array(lj3);
memory->destroy_2d_double_array(lj4);
memory->destroy_2d_double_array(ljsw1);
memory->destroy_2d_double_array(ljsw2);
memory->destroy_2d_double_array(ljsw3);
memory->destroy_2d_double_array(ljsw4);
memory->destroy_2d_double_array(ljsw5);
}
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double r,tlj,tc,fswitch,fswitchcoul,eswitch,ecoulswitch;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = 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;
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];
qtmp = q[i];
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];
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;
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
// skip if qi or qj = 0.0 since this potential may be used as
// coarse-grain model with many uncharged atoms
if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
r = sqrt(rsq);
tc = r - cut_coul_inner;
fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc);
forcecoul += fswitchcoul;
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
r = sqrt(rsq);
tlj = r - cut_lj_inner;
fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
ljsw2[itype][jtype]*tlj);
forcelj += fswitch;
}
} else forcelj = 0.0;
fpair = (factor_coul*forcecoul + 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) {
if (rsq < cut_coulsq) {
ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
if (rsq > cut_coul_innersq) {
ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc);
ecoul += qqrd2e*qtmp*q[j]*ecoulswitch;
}
ecoul *= factor_coul;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
eswitch = tlj*tlj*tlj *
(ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj) +
ljsw5[itype][jtype];
evdwl += eswitch;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::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");
epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1");
ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2");
ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3");
ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4");
ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::settings(int narg, char **arg)
{
if (narg != 2 && narg != 4)
error->all("Illegal pair_style command");
cut_lj_inner = force->numeric(arg[0]);
cut_lj = force->numeric(arg[1]);
if (narg == 2) {
cut_coul_inner = cut_lj_inner;
cut_coul = cut_lj;
} else {
cut_coul_inner = force->numeric(arg[2]);
cut_coul = force->numeric(arg[3]);
}
if (cut_lj_inner <= 0.0 || cut_coul_inner < 0.0)
error->all("Illegal pair_style command");
if (cut_lj_inner > cut_lj || cut_coul_inner > cut_coul)
error->all("Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::coeff(int narg, char **arg)
{
if (narg != 4) 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]);
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;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::init_style()
{
if (!atom->q_flag)
error->all("Pair style lj/gromacs/coul/gromacs requires atom attribute q");
int irequest = neighbor->request(this);
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
cut_ljsq = cut_lj * cut_lj;
cut_coul_innersq = cut_coul_inner * cut_coul_inner;
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJGromacsCoulGromacs::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
}
double cut = MAX(cut_lj,cut_coul);
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
double r6inv = 1.0/pow(cut_lj,6.0);
double r8inv = 1.0/pow(cut_lj,8.0);
double t = cut_lj - cut_lj_inner;
double t2inv = 1.0/(t*t);
double t3inv = t2inv/t;
double t3 = 1.0/t3inv;
double a6 = (7.0*cut_lj_inner - 10.0*cut_lj)*r8inv*t2inv;
double b6 = (9.0*cut_lj - 7.0*cut_lj_inner)*r8inv*t3inv;
double a12 = (13.0*cut_lj_inner - 16.0*cut_lj)*r6inv*r8inv*t2inv;
double b12 = (15.0*cut_lj - 13.0*cut_lj_inner)*r6inv*r8inv*t3inv;
double c6 = r6inv - t3*(6.0*a6/3.0 + 6.0*b6*t/4.0);
double c12 = r6inv*r6inv - t3*(12.0*a12/3.0 + 12.0*b12*t/4.0);
ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6;
ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6;
ljsw3[i][j] = -lj3[i][j]*12.0*a12/3.0 + lj4[i][j]*6.0*a6/3.0;
ljsw4[i][j] = -lj3[i][j]*12.0*b12/4.0 + lj4[i][j]*6.0*b6/4.0;
ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6;
double r3inv = 1.0/pow(cut_coul,3.0);
t = cut_coul - cut_coul_inner;
t2inv = 1.0/(t*t);
t3inv = t2inv/t;
double a1 = (2.0*cut_coul_inner - 5.0*cut_coul) * r3inv*t2inv;
double b1 = (4.0*cut_coul - 2.0*cut_coul_inner) * r3inv*t3inv;
coulsw1 = a1;
coulsw2 = b1;
coulsw3 = -a1/3.0;
coulsw4 = -b1/4.0;
coulsw5 = 1.0/cut_coul - t*t*t*(a1/3.0 + b1*t/4.0);
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
ljsw1[j][i] = ljsw1[i][j];
ljsw2[j][i] = ljsw2[i][j];
ljsw3[j][i] = ljsw3[i][j];
ljsw4[j][i] = ljsw4[i][j];
ljsw5[j][i] = ljsw5[i][j];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::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);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::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);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_inner,sizeof(double),1,fp);
fwrite(&cut_lj,sizeof(double),1,fp);
fwrite(&cut_coul_inner,sizeof(double),1,fp);
fwrite(&cut_coul,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 PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,sizeof(double),1,fp);
fread(&cut_coul_inner,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
if (rsq > cut_coul_innersq) {
r = sqrt(rsq);
tc = r - cut_coul_inner;
fswitchcoul = force->qqrd2e *
atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tc);
forcecoul += fswitchcoul;
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
r = sqrt(rsq);
tlj = r - cut_lj_inner;
fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*tlj);
forcelj += fswitch;
}
} else forcelj = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * (sqrt(r2inv)-coulsw5);
if (rsq > cut_coul_innersq) {
phiswitchcoul = force->qqrd2e * atom->q[i]*atom->q[j] *
tc*tc*tc * (coulsw3 + coulsw4*tc);
phicoul += phiswitchcoul;
}
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq) {
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
phiswitch = tlj*tlj*tlj *
(ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj) +
ljsw5[itype][jtype];
philj += phiswitch;
}
eng += factor_lj*philj;
}
return eng;
}

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