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lammps/src/DPD-BASIC/pair_dpd_ext_tstat.cpp

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ 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 authors: Martin Svoboda (ICPF, UJEP), Martin Lísal (ICPF, UJEP)
------------------------------------------------------------------------- */
#include "pair_dpd_ext_tstat.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neigh_list.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairDPDExtTstat::PairDPDExtTstat(LAMMPS *lmp) : PairDPDExt(lmp)
{
single_enable = 0;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
void PairDPDExtTstat::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpairx,fpairy,fpairz,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,wdPar,wdPerp,randnum,randnumx,randnumy,randnumz,factor_dpd;
double P[3][3];
int *ilist,*jlist,*numneigh,**firstneigh;
ev_init(eflag,vflag);
// adjust sigma if target T is changing
if (t_start != t_stop) {
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
temperature = t_start + delta * (t_stop-t_start);
double boltz = force->boltz;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
sigmaT[i][j] = sigmaT[j][i] = sqrt(2.0*boltz*temperature*gammaT[i][j]);
}
}
}
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
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);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (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;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
dot = delx*delvx + dely*delvy + delz*delvz;
P[0][0] = 1.0 - delx*delx*rinv*rinv;
P[0][1] = - delx*dely*rinv*rinv;
P[0][2] = - delx*delz*rinv*rinv;
P[1][0] = P[0][1];
P[1][1] = 1.0 - dely*dely*rinv*rinv;
P[1][2] = - dely*delz*rinv*rinv;
P[2][0] = P[0][2];
P[2][1] = P[1][2];
P[2][2] = 1.0 - delz*delz*rinv*rinv;
wd = 1.0 - r/cut[itype][jtype];
wdPar = pow(wd,ws[itype][jtype]);
wdPerp = pow(wd,wsT[itype][jtype]);
randnum = random->gaussian();
randnumx = random->gaussian();
randnumy = random->gaussian();
randnumz = random->gaussian();
// drag force - parallel
fpair = -gamma[itype][jtype]*wdPar*wdPar*dot*rinv;
// random force - parallel
fpair += sigma[itype][jtype]*wdPar*randnum*dtinvsqrt;
fpairx = fpair*rinv*delx;
fpairy = fpair*rinv*dely;
fpairz = fpair*rinv*delz;
// drag force - perpendicular
fpairx -= gammaT[itype][jtype]*wdPerp*wdPerp*
(P[0][0]*delvx + P[0][1]*delvy + P[0][2]*delvz);
fpairy -= gammaT[itype][jtype]*wdPerp*wdPerp*
(P[1][0]*delvx + P[1][1]*delvy + P[1][2]*delvz);
fpairz -= gammaT[itype][jtype]*wdPerp*wdPerp*
(P[2][0]*delvx + P[2][1]*delvy + P[2][2]*delvz);
// random force - perpendicular
fpairx += sigmaT[itype][jtype]*wdPerp*
(P[0][0]*randnumx + P[0][1]*randnumy + P[0][2]*randnumz)*dtinvsqrt;
fpairy += sigmaT[itype][jtype]*wdPerp*
(P[1][0]*randnumx + P[1][1]*randnumy + P[1][2]*randnumz)*dtinvsqrt;
fpairz += sigmaT[itype][jtype]*wdPerp*
(P[2][0]*randnumx + P[2][1]*randnumy + P[2][2]*randnumz)*dtinvsqrt;
fpairx *= factor_dpd;
fpairy *= factor_dpd;
fpairz *= factor_dpd;
f[i][0] += fpairx;
f[i][1] += fpairy;
f[i][2] += fpairz;
if (newton_pair || j < nlocal) {
f[j][0] -= fpairx;
f[j][1] -= fpairy;
f[j][2] -= fpairz;
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,
fpairx, fpairy, fpairz,
delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDExtTstat::settings(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Illegal pair_style command");
t_start = utils::numeric(FLERR,arg[0],false,lmp);
t_stop = utils::numeric(FLERR,arg[1],false,lmp);
cut_global = utils::numeric(FLERR,arg[2],false,lmp);
seed = utils::inumeric(FLERR,arg[3],false,lmp);
temperature = t_start;
// 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; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairDPDExtTstat::coeff(int narg, char **arg)
{
if (narg < 6 || narg > 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
double a0_one = 0.0;
double gamma_one = utils::numeric(FLERR,arg[2],false,lmp);
double gammaT_one = utils::numeric(FLERR,arg[3],false,lmp);
double ws_one = utils::numeric(FLERR,arg[4],false,lmp);
double wsT_one = utils::numeric(FLERR,arg[5],false,lmp);
double cut_one = cut_global;
if (narg == 7) cut_one = utils::numeric(FLERR,arg[6],false,lmp);
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;
gammaT[i][j] = gammaT_one;
ws[i][j] = ws_one;
wsT[i][j] = wsT_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDExtTstat::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(&gamma[i][j],sizeof(double),1,fp);
fwrite(&gammaT[i][j],sizeof(double),1,fp);
fwrite(&ws[i][j],sizeof(double),1,fp);
fwrite(&wsT[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDExtTstat::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&gammaT[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&ws[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&wsT[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&gammaT[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&ws[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&wsT[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDExtTstat::write_restart_settings(FILE *fp)
{
fwrite(&t_start,sizeof(double),1,fp);
fwrite(&t_stop,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 PairDPDExtTstat::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world);
MPI_Bcast(&t_stop,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);
temperature = t_start;
// 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);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairDPDExtTstat::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairDPDExtTstat::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,
gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]);
}
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