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pair_tdpd.cpp
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pair_tdpd.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: Zhen Li (Brown University)
Email: zhen_li@brown.edu
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_tdpd.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 "citeme.h"
#include "memory.h"
#include "error.h"
#include <time.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
static const char cite_pair_tdpd[] =
"pair tdpd command:\n\n"
"@Article{ZLi2015_JCP,\n"
" author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G.E.},\n"
" title = {Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems},\n"
" journal = {The Journal of Chemical Physics},\n"
" year = {2015},\n"
" volume = {143},\n"
" pages = {014101}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairTDPD::PairTDPD(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_tdpd);
cc_species = atom->cc_species;
writedata = 1;
random = NULL;
}
/* ---------------------------------------------------------------------- */
PairTDPD::~PairTDPD()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(cutcc);
memory->destroy(a0);
memory->destroy(gamma);
memory->destroy(sigma);
memory->destroy(power);
memory->destroy(kappa);
memory->destroy(epsilon);
memory->destroy(powercc);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairTDPD::compute(int eflag, int vflag)
{
double 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;
double **cc = atom->cc;
double **cc_flux = atom->cc_flux;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
int inum = list->inum;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (int ii = 0; ii < inum; ii++) {
int i = ilist[ii];
double xtmp = x[i][0];
double ytmp = x[i][1];
double ztmp = x[i][2];
double vxtmp = v[i][0];
double vytmp = v[i][1];
double vztmp = v[i][2];
int itype = type[i];
int *jlist = firstneigh[i];
int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
double factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
double delx = xtmp - x[j][0];
double dely = ytmp - x[j][1];
double delz = ztmp - x[j][2];
double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
double r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
double rinv = 1.0/r;
double delvx = vxtmp - v[j][0];
double delvy = vytmp - v[j][1];
double delvz = vztmp - v[j][2];
double dot = delx*delvx + dely*delvy + delz*delvz;
double wc = 1.0 - r/cut[itype][jtype];
wc = MAX(0,MIN(1.0,wc));
double wr = pow(wc, 0.5*power[itype][jtype]);
double randnum = random->gaussian();
// conservative force = a0 * wc
// drag force = -gamma * wr^2 * (delx dot delv) / r
// random force = sigma * wr^(power/2) * rnd * dtinvsqrt;
double fpair = a0[itype][jtype]*wc;
fpair -= gamma[itype][jtype]*wr*wr*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;
// chemical concentration transport
if( r < cutcc[itype][jtype]) {
for(int k=0; k<cc_species; k++) {
double wcr = 1.0 - r/cutcc[itype][jtype];
wcr = MAX(0,wcr);
wcr = pow(wcr, 0.5*powercc[itype][jtype][k]);
double randnum = random->gaussian();
randnum = MAX(-5.0,MIN(randnum,5.0));
double dQc = -kappa[itype][jtype][k] * wcr*wcr *(cc[i][k]-cc[j][k]);
double dQr = epsilon[itype][jtype][k] *wcr* (cc[i][k]+cc[j][k]) *randnum*dtinvsqrt;
cc_flux[i][k] += (dQc + dQr);
if (newton_pair || j < nlocal)
cc_flux[j][k] -= ( dQc + dQr );
}
}
//-----------------------------------------------------------
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wc*wc;
evdwl *= factor_dpd;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairTDPD::allocate()
{
int i,j;
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (i = 1; i <= n; i++)
for (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(cutcc,n+1,n+1,"pair:cutcc");
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(gamma,n+1,n+1,"pair:gamma");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(power,n+1,n+1,"pair:power");
memory->create(kappa,n+1,n+1,cc_species,"pair:kappa");
memory->create(epsilon,n+1,n+1,cc_species,"pair:epsilon");
memory->create(powercc,n+1,n+1,cc_species,"pair:powercc");
for (i = 0; i <= atom->ntypes; i++)
for (j = 0; j <= atom->ntypes; j++)
sigma[i][j] = gamma[i][j] = 0.0;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairTDPD::settings(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
temperature = force->numeric(FLERR,arg[0]);
cut_global = force->numeric(FLERR,arg[1]);
seed = force->inumeric(FLERR,arg[2]);
// initialize Marsaglia RNG with processor-unique seed
if (seed <= 0 ) {
struct timespec time;
clock_gettime( CLOCK_REALTIME, &time );
seed = time.tv_nsec; // if seed is non-positive, get the current time as the seed
}
delete random;
random = new RanMars(lmp,(seed + comm->me) % 900000000);
// 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 PairTDPD::coeff(int narg, char **arg)
{
if (narg != 7 + 3*cc_species)
error->all(FLERR,"Incorrect args for pair tdpd 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 gamma_one = force->numeric(FLERR,arg[3]);
double power_one = force->numeric(FLERR,arg[4]);
double cut_one = force->numeric(FLERR,arg[5]);
double cutcc_one = force->numeric(FLERR,arg[6]);
double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species];
for(int k=0; k<cc_species; k++) {
kappa_one[k] = force->numeric(FLERR,arg[7+3*k]);
epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]);
powercc_one[k] = force->numeric(FLERR,arg[9+3*k]);
}
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;
power[i][j] = power_one;
cut[i][j] = cut_one;
cutcc[i][j] = cutcc_one;
for(int k=0; k<cc_species; k++)
{
kappa [i][j][k] = kappa_one[k];
epsilon[i][j][k]= epsilon_one[k];
powercc[i][j][k]= powercc_one[k];
}
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairTDPD::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair tdpd 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 tdpd needs newton pair on for momentum conservation");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairTDPD::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
cut[j][i] = cut[i][j];
cutcc[j][i] = cutcc[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
sigma[j][i] = sigma[i][j];
power[j][i] = power[i][j];
for(int k=0; k<cc_species; k++) {
kappa[j][i][k] = kappa[i][j][k];
epsilon[j][i][k] = epsilon[i][j][k];
powercc[j][i][k] = powercc[i][j][k];
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairTDPD::write_restart(FILE *fp)
{
write_restart_settings(fp);
for (int i = 1; i <= atom->ntypes; i++)
for (int 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(&power[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&cutcc[i][j],sizeof(double),1,fp);
for(int k=0; k<cc_species; k++) {
fwrite(&kappa[i][j][k],sizeof(double),1,fp);
fwrite(&epsilon[i][j][k],sizeof(double),1,fp);
fwrite(&powercc[i][j][k],sizeof(double),1,fp);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairTDPD::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int me = comm->me;
for (int i = 1; i <= atom->ntypes; i++)
for (int 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(&power[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
fread(&cutcc[i][j],sizeof(double),1,fp);
for(int k=0; k<cc_species; k++) {
fread(&kappa[i][j][k],sizeof(double),1,fp);
fread(&epsilon[i][j][k],sizeof(double),1,fp);
fread(&powercc[i][j][k],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(&power[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cutcc[i][j],1,MPI_DOUBLE,0,world);
for(int k=0; k<cc_species; k++) {
MPI_Bcast(&kappa[i][j][k],1,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[i][j][k],1,MPI_DOUBLE,0,world);
MPI_Bcast(&powercc[i][j][k],1,MPI_DOUBLE,0,world);
}
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairTDPD::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 PairTDPD::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);
}
/* ---------------------------------------------------------------------- */
double PairTDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
r = sqrt(rsq);
if (r < EPSILON) {
fforce = 0.0;
return 0.0;
}
rinv = 1.0/r;
wc = 1.0 - r/cut[itype][jtype];
fforce = a0[itype][jtype]*wc*factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*cut[itype][jtype]*wc*wc;
return factor_dpd*phi;
}

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