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pair_lj_smooth_omp.cpp
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Sat, Nov 9, 23:40

pair_lj_smooth_omp.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: Craig Maloney (UCSB)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_smooth_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairLJSmoothOMP::PairLJSmoothOMP(LAMMPS *lmp) : PairOMP(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJSmoothOMP::~PairLJSmoothOMP()
{
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(cut_inner);
memory->destroy_2d_double_array(cut_inner_sq);
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(ljsw0);
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(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJSmoothOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
ev_setup_thr(eflag,vflag);
} else evflag = vflag_fdotr = 0;
if (evflag) {
if (eflag) {
if (force->newton_pair) return eval<1,1,1>();
else return eval<1,1,0>();
} else {
if (force->newton_pair) return eval<1,0,1>();
else return eval<1,0,0>();
}
} else {
if (force->newton_pair) return eval<0,0,1>();
else return eval<0,0,0>();
}
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJSmoothOMP::eval()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int i,j,ii,jj,inum,jnum,itype,jtype,tid;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t,tsq,fskin;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int nthreads = comm->nthreads;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
int iifrom, iito;
f = loop_setup_thr(f, iifrom, iito, tid, inum, nall, nthreads);
for (ii = iifrom; ii < iito; ++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];
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;
if (rsq < cut_inner_sq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else{
r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
tsq = t*t;
fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
forcelj = fskin*r;
}
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) {
if (rsq < cut_inner_sq[itype][jtype])
evdwl = r6inv * (lj3[itype][jtype]*r6inv -
lj4[itype][jtype]) - offset[itype][jtype];
else
evdwl = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
evdwl *= factor_lj;
}
if (EVFLAG) ev_tally_thr(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,tid);
}
}
}
// reduce per thread forces into global force array.
force_reduce_thr(atom->f, nall, nthreads, tid);
}
ev_reduce_thr();
if (vflag_fdotr) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJSmoothOMP::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");
cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner");
cut_inner_sq = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner_sq");
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");
ljsw0 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw0");
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");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJSmoothOMP::settings(int narg, char **arg)
{
if (narg != 2) error->all("Illegal pair_style command");
cut_inner_global = force->numeric(arg[0]);
cut_global = force->numeric(arg[1]);
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
error->all("Illegal pair_style command");
// 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_inner[i][j] = cut_inner_global;
cut[i][j] = cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJSmoothOMP::coeff(int narg, char **arg)
{
if (narg != 4 && narg != 6)
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_inner_one = cut_inner_global;
double cut_one = cut_global;
if (narg == 6) {
cut_inner_one = force->numeric(arg[4]);
cut_one = force->numeric(arg[5]);
}
if (cut_inner_one <= 0.0 || cut_inner_one > cut_one)
error->all("Incorrect args for pair coefficients");
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_inner[i][j] = cut_inner_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 PairLJSmoothOMP::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_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][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 (cut_inner[i][j] != cut[i][j]) {
double r6inv = 1.0/pow(cut_inner[i][j],6.0);
double t = cut[i][j] - cut_inner[i][j];
double tsq = t*t;
double ratio = sigma[i][j] / cut_inner[i][j];
ljsw0[i][j] = 4.0*epsilon[i][j]*(pow(ratio,12.0) - pow(ratio,6.0));
ljsw1[i][j] = r6inv*(lj1[i][j]*r6inv-lj2[i][j]) / cut_inner[i][j];
ljsw2[i][j] = -r6inv * (13.0*lj1[i][j]*r6inv - 7.0*lj2[i][j]) /
cut_inner_sq[i][j];
ljsw3[i][j] = -(3.0/tsq) * (ljsw1[i][j] + 2.0/3.0*ljsw2[i][j]*t);
ljsw4[i][j] = -1.0/(3.0*tsq) * (ljsw2[i][j] + 2.0*ljsw3[i][j]*t);
if (offset_flag)
offset[i][j] = ljsw0[i][j] - ljsw1[i][j]*t - ljsw2[i][j]*tsq/2.0 -
ljsw3[i][j]*tsq*t/3.0 - ljsw4[i][j]*tsq*tsq/4.0;
else offset[i][j] = 0.0;
} else {
ljsw0[i][j] = 0.0;
ljsw1[i][j] = 0.0;
ljsw2[i][j] = 0.0;
ljsw3[i][j] = 0.0;
ljsw4[i][j] = 0.0;
double ratio = sigma[i][j] / cut_inner[i][j];
if (offset_flag)
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
else offset[i][j] = 0.0;
}
cut_inner[j][i] = cut_inner[i][j];
cut_inner_sq[j][i] = cut_inner_sq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
ljsw0[j][i] = ljsw0[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];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSmoothOMP::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_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJSmoothOMP::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_inner[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_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSmoothOMP::write_restart_settings(FILE *fp)
{
fwrite(&cut_inner_global,sizeof(double),1,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 PairLJSmoothOMP::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
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 PairLJSmoothOMP::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t,tsq,fskin;
r2inv = 1.0/rsq;
if (rsq < cut_inner_sq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
} else {
r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
tsq = t*t;
fskin = ljsw1[itype][jtype] + ljsw2[itype][jtype]*t +
ljsw3[itype][jtype]*tsq + ljsw4[itype][jtype]*tsq*t;
forcelj = fskin*r;
}
fforce = factor_lj*forcelj*r2inv;
if (rsq < cut_inner_sq[itype][jtype])
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]) -
offset[itype][jtype];
else
philj = ljsw0[itype][jtype] - ljsw1[itype][jtype]*t -
ljsw2[itype][jtype]*tsq/2.0 - ljsw3[itype][jtype]*tsq*t/3.0 -
ljsw4[itype][jtype]*tsq*tsq/4.0 - offset[itype][jtype];
return factor_lj*philj;
}
/* ---------------------------------------------------------------------- */
double PairLJSmoothOMP::memory_usage()
{
const int n=atom->ntypes;
double bytes = PairOMP::memory_usage();
bytes += 9*((n+1)*(n+1) * sizeof(double) + (n+1)*sizeof(double *));
bytes += 1*((n+1)*(n+1) * sizeof(int) + (n+1)*sizeof(int *));
return bytes;
}

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