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pair_edpd.cpp
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pair_edpd.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_edpd.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>
#include <string.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_edpd[] =
"pair edpd command:\n\n"
"@Article{ZLi2014_JCP,\n"
" author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G.E.},\n"
" title = {Energy-conserving dissipative particle dynamics with temperature-dependent properties},\n"
" journal = {Journal of Computational Physics},\n"
" year = {2014},\n"
" volume = {265},\n"
" pages = {113--127}\n"
"}\n\n"
"@Article{ZLi2015_CC,\n"
" author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G.E.},\n"
" title = {Mesoscale modeling of phase transition dynamics of thermoresponsive polymers},\n"
" journal = {Chemical Communications},\n"
" year = {2015},\n"
" volume = {51},\n"
" pages = {11038--11040}\n"
"}\n\n";
;
/* ---------------------------------------------------------------------- */
PairEDPD::PairEDPD(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_edpd);
writedata = 1;
random = NULL;
randomT = NULL;
}
/* ---------------------------------------------------------------------- */
PairEDPD::~PairEDPD()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(cutT);
memory->destroy(a0);
memory->destroy(gamma);
memory->destroy(power);
memory->destroy(kappa);
memory->destroy(powerT);
}
if (power_flag) memory->destroy(sc);
if (kappa_flag) memory->destroy(kc);
if (random) delete random;
if (randomT) delete randomT;
}
/* ---------------------------------------------------------------------- */
void PairEDPD::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 *T = atom->edpd_temp;
double *Q = atom->edpd_flux;
double *cv = atom->edpd_cv;
int *type = atom->type;
double *mass = atom->mass;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double dtinvsqrt = 1.0/sqrt(update->dt);
double kboltz = 1.0;
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;
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 vijeij = dot*rinv;
double randnum = random->gaussian();
double T_ij=0.5*(T[i]+T[j]);
double T_pow[4];
T_pow[0] = T_ij - 1.0;
T_pow[1] = T_pow[0]*T_pow[0];
T_pow[2] = T_pow[0]*T_pow[1];
T_pow[3] = T_pow[0]*T_pow[2];
double power_d = power[itype][jtype];
if(power_flag){
double factor = 1.0;
for(int k = 0; k < 4; k++)
factor += sc[itype][jtype][k]*T_pow[k];
power_d *= factor;
}
power_d = MAX(0.01,power_d);
double wc = 1.0 - r/cut[itype][jtype];
wc = MAX(0.0,MIN(1.0,wc));
double wr = pow(wc, 0.5*power_d);
double GammaIJ = gamma[itype][jtype];
double SigmaIJ = 4.0*GammaIJ*kboltz*T[i]*T[j]/(T[i]+T[j]);
SigmaIJ = sqrt(SigmaIJ);
double fpair = a0[itype][jtype]*T_ij*wc;
fpair -= GammaIJ *wr*wr *dot*rinv;
fpair += SigmaIJ * wr *randnum * dtinvsqrt;
fpair *= factor_dpd*rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
// heat transfer
double dQc,dQd,dQr;
if( r < cutT[itype][jtype]) {
double wrT = 1.0 - r/cutT[itype][jtype];
wrT = MAX(0.0,MIN(1.0,wrT));
wrT = pow(wrT, 0.5*powerT[itype][jtype]);
double randnumT = randomT->gaussian();
randnumT = MAX(-5.0,MIN(randnum,5.0));
double kappaT = kappa[itype][jtype];
if(kappa_flag) {
double factor = 1.0;
for(int k = 0; k < 4; k++)
factor += kc[itype][jtype][k]*T_pow[k];
kappaT *= factor;
}
double kij = cv[i]*cv[j]*kappaT * T_ij*T_ij;
double alphaij = sqrt(2.0*kboltz*kij);
dQc = kij * wrT*wrT * ( T[j] - T[i] )/(T[i]*T[j]);
dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass[itype] ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cv[i]+cv[j]);
dQr = alphaij * wrT * dtinvsqrt * randnumT;
Q[i] += (dQc + dQd + dQr );
}
//-----------------------------------------------------------
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
Q[j] -= ( dQc - dQd + dQr );
}
if (eflag) {
evdwl = 0.5*a0[itype][jtype]*T_ij*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 PairEDPD::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(cutT,n+1,n+1,"pair:cutT");
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(gamma,n+1,n+1,"pair:gamma");
memory->create(power,n+1,n+1,"pair:power");
memory->create(kappa,n+1,n+1,"pair:kappa");
memory->create(powerT,n+1,n+1,"pair:powerT");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairEDPD::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
seed = force->inumeric(FLERR,arg[1]);
// 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);
randomT = new RanMars(lmp,(2*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 PairEDPD::coeff(int narg, char **arg)
{
if (narg < 9)
error->all(FLERR,"Incorrect args for pair edpd 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 kappa_one = force->numeric(FLERR,arg[6]);
double powerT_one= force->numeric(FLERR,arg[7]);
double cutT_one = force->numeric(FLERR,arg[8]);
int iarg = 9;
power_flag = kappa_flag = 0;
double sc_one[4], kc_one[4];
int n = atom->ntypes;
while (iarg < narg) {
if (strcmp(arg[iarg],"power") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients");
for (int i = 0; i < 4; i++)
sc_one[i] = force->numeric(FLERR,arg[iarg+i+1]);
iarg += 5;
power_flag = 1;
memory->create(sc,n+1,n+1,4,"pair:sc");
} else if (strcmp(arg[iarg],"kappa") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal pair edpd coefficients");
for (int i = 0; i < 4; i++)
kc_one[i] = force->numeric(FLERR,arg[iarg+i+1]);
iarg += 5;
kappa_flag = 1;
memory->create(kc,n+1,n+1,4,"pair:kc");
} else error->all(FLERR,"Illegal pair edpd coefficients");
}
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;
kappa[i][j] = kappa_one;
powerT[i][j]= powerT_one;
cutT[i][j] = cutT_one;
if(power_flag)
for (int k = 0; k < 4; k++)
sc[i][j][k] = sc_one[k];
if(kappa_flag)
for (int k = 0; k < 4; k++)
kc[i][j][k] = kc_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 PairEDPD::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair edpd 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 PairEDPD::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];
cutT[j][i] = cutT[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
power[j][i] = power[i][j];
kappa[j][i] = kappa[i][j];
powerT[j][i]= powerT[i][j];
if(power_flag)
for (int k = 0; k < 4; k++)
sc[j][i][k] = sc[i][j][k];
if(kappa_flag)
for (int k = 0; k < 4; k++)
kc[j][i][k] = kc[i][j][k];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairEDPD::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(&kappa[i][j],sizeof(double),1,fp);
fwrite(&powerT[i][j],sizeof(double),1,fp);
fwrite(&cutT[i][j],sizeof(double),1,fp);
if(power_flag)
for (int k = 0; k < 4; k++)
fwrite(&sc[i][j][k],sizeof(double),1,fp);
if(kappa_flag)
for (int k = 0; k < 4; k++)
fwrite(&kc[i][j][k],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairEDPD::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(&kappa[i][j],sizeof(double),1,fp);
fread(&powerT[i][j],sizeof(double),1,fp);
fread(&cutT[i][j],sizeof(double),1,fp);
if(power_flag)
for (int k = 0; k < 4; k++)
fread(&sc[i][j][k],sizeof(double),1,fp);
if(kappa_flag)
for (int k = 0; k < 4; k++)
fread(&kc[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(&kappa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&powerT[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cutT[i][j],1,MPI_DOUBLE,0,world);
if(power_flag)
for (int k = 0; k < 4; k++)
MPI_Bcast(&sc[i][j][k],1,MPI_DOUBLE,0,world);
if(kappa_flag)
for (int k = 0; k < 4; k++)
MPI_Bcast(&kc[i][j][k],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairEDPD::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 PairEDPD::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);
if (randomT) delete randomT;
randomT = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
double PairEDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
double *T = atom->edpd_temp;
r = sqrt(rsq);
if (r < EPSILON) {
fforce = 0.0;
return 0.0;
}
double T_ij = 0.5*(T[i]+T[j]);
rinv = 1.0/r;
wc = 1.0 - r/cut[itype][jtype];
fforce = a0[itype][jtype]*T_ij*wc*factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*T_ij*cut[itype][jtype]*wc*wc;
return factor_dpd*phi;
}

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