Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F120108454
pair_tdpd.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Jul 2, 00:21
Size
14 KB
Mime Type
text/x-c
Expires
Fri, Jul 4, 00:21 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
27140718
Attached To
rLAMMPS lammps
pair_tdpd.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: 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;
}
Event Timeline
Log In to Comment