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pair_lj_cut.cpp
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pair_lj_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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "update.h"
#include "integrate.h"
#include "respa.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))
/* ---------------------------------------------------------------------- */
PairLJCut::PairLJCut(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
}
/* ---------------------------------------------------------------------- */
PairLJCut::~PairLJCut()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut);
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(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
int *neighs;
double **f;
eng_vdwl = 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;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; 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_lj = 1.0;
else {
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;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*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) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
if (newton_pair || j < nlocal) eng_vdwl += factor_lj*philj;
else eng_vdwl += 0.5*factor_lj*philj;
}
if (vflag == 1) {
if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
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;
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_inner()
{
int i,j,k,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
double rsw;
int *neighs;
double **f;
f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_inner[i];
numneigh = neighbor->numneigh_inner[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_lj = 1.0;
else {
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_out_off_sq) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
}
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;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_middle()
{
int i,j,k,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
double rsw;
int *neighs;
double **f;
f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_middle[i];
numneigh = neighbor->numneigh_middle[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_lj = 1.0;
else {
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_out_off_sq && rsq > cut_in_off_sq) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fforce *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
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;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCut::compute_outer(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
double rsw;
int *neighs;
double **f;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; 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_lj = 1.0;
else {
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]) {
if (rsq > cut_in_off_sq) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fforce *= rsw*rsw*(3.0 - 2.0*rsw);
}
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) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
if (newton_pair || j < nlocal) eng_vdwl += factor_lj*philj;
else eng_vdwl += 0.5*factor_lj*philj;
}
if (vflag) {
if (rsq <= cut_in_off_sq) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
} else if (rsq < cut_in_on_sq)
fforce = factor_lj*forcelj*r2inv;
if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
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;
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCut::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 = memory->create_2d_double_array(n+1,n+1,"pair:cut");
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");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCut::settings(int narg, char **arg)
{
if (narg != 1) error->all("Illegal pair_style command");
cut_global = atof(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 PairLJCut::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 = atof(arg[2]);
double sigma_one = atof(arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = atof(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 PairLJCut::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]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
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);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - 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];
// set & error check interior rRESPA cutoff
if (strcmp(update->integrate_style,"respa") == 0) {
if (((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
if (cut[i][j] < cut_respa[3])
error->all("Pair cutoff < Respa interior cutoff");
}
} else cut_respa = NULL;
// 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 sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCut::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 PairLJCut::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 PairLJCut::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 PairLJCut::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);
}
/* ---------------------------------------------------------------------- */
void PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, int eflag,
One &one)
{
double r2inv,r6inv,forcelj,philj;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
one.fforce = factor_lj*forcelj*r2inv;
if (eflag) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
one.eng_coul = 0.0;
}
}

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