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pair_dpd_omp.cpp
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Sun, Apr 6, 15:05

pair_dpd_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: Kurt Smith (U Pittsburgh)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_dpd_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "random_mars.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))
#define EPSILON 1.0e-20
/* ---------------------------------------------------------------------- */
PairDPDOMP::PairDPDOMP(LAMMPS *lmp) : PairOMP(lmp)
{
random = NULL;
}
/* ---------------------------------------------------------------------- */
PairDPDOMP::~PairDPDOMP()
{
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(a0);
memory->destroy_2d_double_array(gamma);
memory->destroy_2d_double_array(sigma);
allocated = 0;
}
if (random) {
for (int i=0; i < comm->nthreads; ++i)
delete random[i];
delete[] random;
random=NULL;
}
}
/* ---------------------------------------------------------------------- */
void PairDPDOMP::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 PairDPDOMP::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 vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,randnum,factor_dpd;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **v = atom->v;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int nthreads = comm->nthreads;
double *special_lj = force->special_lj;
double dtinvsqrt = 1.0/sqrt(update->dt);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
int iifrom, iito;
double **f = loop_setup_thr(atom->f,iifrom,iito,tid,inum,nall,nthreads);
RanMars *rng = random[tid];
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_dpd = 1.0;
else {
factor_dpd = 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]) && (rsq > EPSILON)) { // r can be 0.0 in DPD systems
r = sqrt(rsq);
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
randnum = rng->gaussian();
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
fpair = a0[itype][jtype]*wd;
fpair -= gamma[itype][jtype]*wd*wd*dot*rinv;
fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
fpair *= factor_dpd*rinv;
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) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
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 PairDPDOMP::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");
a0 = memory->create_2d_double_array(n+1,n+1,"pair:a0");
gamma = memory->create_2d_double_array(n+1,n+1,"pair:gamma");
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDOMP::settings(int narg, char **arg)
{
if (narg != 3) error->all("Illegal pair_style command");
temperature = force->numeric(arg[0]);
cut_global = force->numeric(arg[1]);
seed = force->inumeric(arg[2]);
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0) error->all("Illegal pair_style command");
// we need to set up individual RNGs for each thread.
int nthreads = comm->nthreads;
int tid;
if (random) {
for (tid=0; tid < nthreads; ++tid)
delete random[tid];
delete[] random;
}
random = new RanMars*[nthreads];
for (tid=0; tid < nthreads; ++tid)
random[tid] = new RanMars(lmp,seed + nthreads*comm->me + tid);
// 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 PairDPDOMP::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 a0_one = force->numeric(arg[2]);
double gamma_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++) {
a0[i][j] = a0_one;
gamma[i][j] = gamma_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDOMP::init_style()
{
if (comm->ghost_velocity == 0)
error->all("Pair dpd requires ghost atoms store velocity");
// if newton off, forces between atoms ij will be double computed
// using different random numbers
if (force->newton_pair == 0 && comm->me == 0) error->warning(
"Pair dpd needs newton pair on for momentum conservation");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairDPDOMP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
cut[j][i] = cut[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
sigma[j][i] = sigma[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDOMP::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(&a0[i][j],sizeof(double),1,fp);
fwrite(&gamma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDOMP::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(&a0[i][j],sizeof(double),1,fp);
fread(&gamma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDOMP::write_restart_settings(FILE *fp)
{
fwrite(&temperature,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&seed,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDOMP::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&temperature,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&seed,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&seed,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
// initialize Marsaglia RNG with processor-unique seed
// same seed that pair_style command initially specified
// we need to set up individual RNGs for each thread.
int nthreads = comm->nthreads;
int tid;
if (random) {
for (tid=0; tid < nthreads; ++tid)
delete random[tid];
delete[] random;
}
random = new RanMars*[nthreads];
for (tid=0; tid < nthreads; ++tid)
random[tid] = new RanMars(lmp,seed + nthreads*comm->me + tid);
}
/* ---------------------------------------------------------------------- */
double PairDPDOMP::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
if (rsq < EPSILON) {
fforce = 0.0;
return 0.0;
}
r = sqrt(rsq);
rinv = 1.0/r;
wd = 1.0 - r/cut[itype][jtype];
fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
phi = -a0[itype][jtype] * r * (1.0 - 0.5*r/cut[itype][jtype]);
return factor_dpd*phi;
}

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