Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/USER-DPD/pair_dpd_fdt_energy.cpp
5cae3eca8c43lammm-devel

Last Change
Raw File

pair_dpd_fdt_energy.cpp
View Options

/* ----------------------------------------------------------------------
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: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "update.h"
#include "fix.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "modify.h"
#include "pair_dpd_fdt_energy.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairDPDfdtEnergy::PairDPDfdtEnergy(LAMMPS *lmp) : Pair(lmp)
{
random = NULL;
duCond = NULL;
duMech = NULL;
splitFDT_flag = false;
comm_reverse = 2;
}
/* ---------------------------------------------------------------------- */
PairDPDfdtEnergy::~PairDPDfdtEnergy()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(a0);
memory->destroy(sigma);
memory->destroy(kappa);
memory->destroy(duCond);
memory->destroy(duMech);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairDPDfdtEnergy::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,wd,wr,factor_dpd,uTmp;
double dot,randnum;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
double *rmass = atom->rmass;
double *mass = atom->mass;
double *dpdTheta = atom->dpdTheta;
double kappa_ij, alpha_ij, theta_ij, gamma_ij;
double mass_i, mass_j;
double massinv_i, massinv_j;
double randPair, mu_ij;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
if (splitFDT_flag) {
for (ii = 0; ii < inum; 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];
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
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;
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
// conservative force = a0 * wr
fpair = a0[itype][jtype]*wr;
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;
evdwl *= factor_dpd;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
} else {
// Allocate memory for duCond and duMech
if (allocated) {
memory->destroy(duCond);
memory->destroy(duMech);
}
memory->create(duCond,nlocal+nghost,"pair:duCond");
memory->create(duMech,nlocal+nghost,"pair:duMech");
for (int ii = 0; ii < nlocal+nghost; ii++) {
duCond[ii] = 0.0;
duMech[ii] = 0.0;
}
// loop over neighbors of my atoms
for (int ii = 0; ii < inum; 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];
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
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;
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
randnum = random->gaussian();
// Compute the current temperature
theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
theta_ij = 1.0/theta_ij;
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
/ (2.0*force->boltz*theta_ij);
// conservative force = a0 * wr
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr * rnd * dtinvsqrt;
fpair = a0[itype][jtype]*wr;
fpair -= gamma_ij*wd*dot*rinv;
fpair += sigma[itype][jtype]*wr*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 (rmass) {
mass_i = rmass[i];
mass_j = rmass[j];
} else {
mass_i = mass[itype];
mass_j = mass[jtype];
}
massinv_i = 1.0 / mass_i;
massinv_j = 1.0 / mass_j;
// Compute the mechanical and conductive energy, uMech and uCond
mu_ij = massinv_i + massinv_j;
mu_ij *= force->ftm2v;
uTmp = gamma_ij*wd*rinv*rinv*dot*dot
- 0.5*sigma[itype][jtype]*sigma[itype][jtype]*mu_ij*wd;
uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
uTmp *= 0.5;
duMech[i] += uTmp;
if (newton_pair || j < nlocal) {
duMech[j] += uTmp;
}
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
randPair = alpha_ij*wr*randnum*dtinvsqrt;
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
uTmp += randPair;
duCond[i] += uTmp;
if (newton_pair || j < nlocal) {
duCond[j] -= uTmp;
}
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;
evdwl *= factor_dpd;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
// Communicate the ghost delta energies to the locally owned atoms
comm->reverse_comm_pair(this);
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::allocate()
{
allocated = 1;
int n = atom->ntypes;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(kappa,n+1,n+1,"pair:kappa");
if (!splitFDT_flag) {
memory->create(duCond,nlocal+nghost+1,"pair:duCond");
memory->create(duMech,nlocal+nghost+1,"pair:duMech");
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::settings(int narg, char **arg)
{
// process keywords
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
seed = force->inumeric(FLERR,arg[1]);
if (atom->dpd_flag != 1)
error->all(FLERR,"pair_style dpd/fdt/energy requires atom_style with internal temperature and energies (e.g. dpd)");
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0) error->all(FLERR,"Illegal pair_style command");
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 PairDPDfdtEnergy::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double a0_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_one = cut_global;
double kappa_one;
kappa_one = force->numeric(FLERR,arg[4]);
if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a0[i][j] = a0_one;
sigma[i][j] = sigma_one;
kappa[i][j] = kappa_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd/fdt/energy 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(FLERR,
"Pair dpd/fdt/energy requires newton pair on");
splitFDT_flag = false;
int irequest = neighbor->request(this,instance_me);
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shardlow") == 0){
splitFDT_flag = true;
}
bool eos_flag = false;
for (int i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"eos",3) == 0) eos_flag = true;
if(!eos_flag) error->all(FLERR,"pair_style dpd/fdt/energy requires an EOS to be specified");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairDPDfdtEnergy::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cut[j][i] = cut[i][j];
a0[j][i] = a0[i][j];
sigma[j][i] = sigma[i][j];
kappa[j][i] = kappa[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::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(&sigma[i][j],sizeof(double),1,fp);
fwrite(&kappa[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::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(&sigma[i][j],sizeof(double),1,fp);
fread(&kappa[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(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDfdtEnergy::write_restart_settings(FILE *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 PairDPDfdtEnergy::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&seed,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
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);
}
/* ---------------------------------------------------------------------- */
double PairDPDfdtEnergy::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wr,wd,phi;
r = sqrt(rsq);
if (r < EPSILON) {
fforce = 0.0;
return 0.0;
}
rinv = 1.0/r;
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
fforce = a0[itype][jtype]*wr * factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd;
return factor_dpd*phi;
}
/* ---------------------------------------------------------------------- */
int PairDPDfdtEnergy::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = duCond[i];
buf[m++] = duMech[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairDPDfdtEnergy::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
duCond[j] += buf[m++];
duMech[j] += buf[m++];
}
}
c4science · Help