New package DPD-BASIC with pair styles dpd, dpd/tstat, dpd/ext, dpd/ext/tstat
This commit is contained in:
Axel Kohlmeyer
309
src/DPD-BASIC/pair_dpd_tstat.cpp
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309
src/DPD-BASIC/pair_dpd_tstat.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "pair_dpd_tstat.h"
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#include <cmath>
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "neigh_list.h"
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#include "comm.h"
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#include "random_mars.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define EPSILON 1.0e-10
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/* ---------------------------------------------------------------------- */
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PairDPDTstat::PairDPDTstat(LAMMPS *lmp) : PairDPD(lmp)
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{
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single_enable = 0;
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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void PairDPDTstat::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,fpair;
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double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
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double rsq,r,rinv,dot,wd,randnum,factor_dpd;
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int *ilist,*jlist,*numneigh,**firstneigh;
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ev_init(eflag,vflag);
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// adjust sigma if target T is changing
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if (t_start != t_stop) {
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double delta = update->ntimestep - update->beginstep;
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if (delta != 0.0) delta /= update->endstep - update->beginstep;
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temperature = t_start + delta * (t_stop-t_start);
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double boltz = force->boltz;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++)
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sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
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}
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double dtinvsqrt = 1.0/sqrt(update->dt);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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vxtmp = v[i][0];
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vytmp = v[i][1];
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vztmp = v[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_dpd = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r = sqrt(rsq);
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if (r < EPSILON) continue; // r can be 0.0 in DPD systems
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rinv = 1.0/r;
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delvx = vxtmp - v[j][0];
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delvy = vytmp - v[j][1];
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delvz = vztmp - v[j][2];
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dot = delx*delvx + dely*delvy + delz*delvz;
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wd = 1.0 - r/cut[itype][jtype];
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randnum = random->gaussian();
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// drag force = -gamma * wd^2 * (delx dot delv) / r
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// random force = sigma * wd * rnd * dtinvsqrt;
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fpair = -gamma[itype][jtype]*wd*wd*dot*rinv;
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fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt;
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fpair *= factor_dpd*rinv;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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0.0,0.0,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairDPDTstat::settings(int narg, char **arg)
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{
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if (narg != 4) error->all(FLERR,"Illegal pair_style command");
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t_start = utils::numeric(FLERR,arg[0],false,lmp);
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t_stop = utils::numeric(FLERR,arg[1],false,lmp);
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cut_global = utils::numeric(FLERR,arg[2],false,lmp);
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seed = utils::inumeric(FLERR,arg[3],false,lmp);
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temperature = t_start;
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// initialize Marsaglia RNG with processor-unique seed
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if (seed <= 0) error->all(FLERR,"Illegal pair_style command");
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delete random;
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random = new RanMars(lmp,seed + comm->me);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairDPDTstat::coeff(int narg, char **arg)
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{
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if (narg < 3 || narg > 4)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
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utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
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double a0_one = 0.0;
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double gamma_one = utils::numeric(FLERR,arg[2],false,lmp);
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double cut_one = cut_global;
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if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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a0[i][j] = a0_one;
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gamma[i][j] = gamma_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairDPDTstat::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&gamma[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairDPDTstat::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
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}
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MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairDPDTstat::write_restart_settings(FILE *fp)
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{
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fwrite(&t_start,sizeof(double),1,fp);
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fwrite(&t_stop,sizeof(double),1,fp);
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&seed,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairDPDTstat::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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utils::sfread(FLERR,&t_start,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error);
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utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
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}
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MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&t_stop,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&seed,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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temperature = t_start;
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// initialize Marsaglia RNG with processor-unique seed
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// same seed that pair_style command initially specified
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if (random) delete random;
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random = new RanMars(lmp,seed + comm->me);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void PairDPDTstat::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp,"%d %g\n",i,gamma[i][i]);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes all pairs to data file
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------------------------------------------------------------------------- */
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void PairDPDTstat::write_data_all(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = i; j <= atom->ntypes; j++)
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fprintf(fp,"%d %d %g %g\n",i,j,gamma[i][j],cut[i][j]);
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}
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