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lammps/src/DPD/pair_dpd.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.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "random_mars.h"
#include "memory.h"
#include "neighbor.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-10
/* ---------------------------------------------------------------------- */
PairDPD::PairDPD(LAMMPS *lmp) : Pair(lmp)
{
random = NULL;
}
/* ---------------------------------------------------------------------- */
PairDPD::~PairDPD()
{
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);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairDPD::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,randnum,fforce,factor_dpd,phi;
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;
double **v = atom->v;
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 dtinvsqrt = 1.0/sqrt(update->dt);
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
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];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
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]) {
r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
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 = random->gaussian();
// conservative force = a0 * wd
// drag force = -gamma * wd^2 * (delx dot delv) / r
// random force = sigma * wd * rnd * dtinvsqrt;
fforce = a0[itype][jtype]*wd;
fforce -= gamma[itype][jtype]*wd*wd*dot*rinv;
fforce += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
fforce *= factor_dpd*rinv;
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) {
phi = a0[itype][jtype] * r * (1.0 - 0.5*r/cut[itype][jtype]);
if (newton_pair || j < nlocal) eng_vdwl += factor_dpd*phi;
else eng_vdwl += 0.5*factor_dpd*phi;
}
if (vflag == 1) {
if (newton_pair || j < nlocal) {
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;
} else {
virial[0] += 0.5*delx*delx*fforce;
virial[1] += 0.5*dely*dely*fforce;
virial[2] += 0.5*delz*delz*fforce;
virial[3] += 0.5*delx*dely*fforce;
virial[4] += 0.5*delx*delz*fforce;
virial[5] += 0.5*dely*delz*fforce;
}
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDPD::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 PairDPD::settings(int narg, char **arg)
{
if (narg != 3) error->all("Illegal pair_style command");
temperature = atof(arg[0]);
cut_global = atof(arg[1]);
seed = atoi(arg[2]);
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0 || seed > 900000000)
error->all("Illegal fix pair_style command");
if (random) delete random;
random = new RanMars(lmp,seed + comm->me);
// 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 PairDPD::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 = atof(arg[2]);
double gamma_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++) {
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 for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairDPD::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*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];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPD::init_style()
{
// check that atom style is dpd
// else compute() will not have ghost atom velocities
if (atom->check_style("dpd") == 0)
error->all("Must use atom style dpd with pair style dpd");
// 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(
"DPD potential needs newton pair on for momentum conservation");
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPD::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 PairDPD::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 PairDPD::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 PairDPD::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
if (random) delete random;
random = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, int eflag,
One &one)
{
double r,rinv,wd,phi;
r = sqrt(rsq);
if (r < EPSILON) {
one.fforce = 0.0;
if (eflag) one.eng_vdwl = one.eng_coul = 0.0;
return;
}
rinv = 1.0/r;
wd = 1.0 - r/cut[itype][jtype];
one.fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
if (eflag) {
phi = a0[itype][jtype] * r * (1.0 - 0.5*r/cut[itype][jtype]);
one.eng_vdwl = factor_dpd*phi;
one.eng_coul = 0.0;
}
}
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