diff --git a/src/pair_dpd.h b/src/pair_dpd.h index 2237ae6fdd..0784eefb6c 100644 --- a/src/pair_dpd.h +++ b/src/pair_dpd.h @@ -27,19 +27,19 @@ namespace LAMMPS_NS { class PairDPD : public Pair { public: PairDPD(class LAMMPS *); - ~PairDPD(); - void compute(int, int); - void settings(int, char **); - void coeff(int, char **); + virtual ~PairDPD(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); void init_style(); double init_one(int, int); void write_restart(FILE *); void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); double single(int, int, int, int, double, double, double, double &); - private: + protected: double cut_global,temperature; int seed; double **cut; diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp new file mode 100644 index 0000000000..83f7488c6c --- /dev/null +++ b/src/pair_dpd_tstat.cpp @@ -0,0 +1,245 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "math.h" +#include "pair_dpd_tstat.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "neigh_list.h" +#include "comm.h" +#include "random_mars.h" +#include "error.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 + +/* ---------------------------------------------------------------------- */ + +PairDPDTstat::PairDPDTstat(LAMMPS *lmp) : PairDPD(lmp) +{ + single_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDTstat::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv,dot,wd,randnum,factor_dpd; + int *ilist,*jlist,*numneigh,**firstneigh; + + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + // adjust sigma if target T is changing + + if (t_start != t_stop) { + double delta = update->ntimestep - update->beginstep; + 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+1; j <= atom->ntypes; j++) + sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]); + } + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + 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]; + + if (j < nall) factor_dpd = 1.0; + else { + factor_dpd = special_lj[j/nall]; + j %= nall; + } + + 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; + wd = 1.0 - r/cut[itype][jtype]; + randnum = random->gaussian(); + + // drag force = -gamma * wd^2 * (delx dot delv) / r + // random force = sigma * wd * rnd * dtinvsqrt; + + fpair = gamma[itype][jtype]*wd*wd*dot*rinv; + fpair += sigma[itype][jtype]*wd*randnum*dtinvsqrt; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + 0.0,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_compute(); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDTstat::settings(int narg, char **arg) +{ + if (narg != 4) error->all("Illegal pair_style command"); + + t_start = force->numeric(arg[0]); + t_stop = force->numeric(arg[1]); + cut_global = force->numeric(arg[2]); + seed = force->inumeric(arg[3]); + + temperature = t_start; + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all("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+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDTstat::coeff(int narg, char **arg) +{ + if (narg < 3 || narg > 4) error->all("Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a0_one = 0.0; + double gamma_one = force->numeric(arg[2]); + + double cut_one = cut_global; + if (narg == 4) cut_one = force->numeric(arg[3]); + + 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; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all("Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDTstat::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 PairDPDTstat::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&t_start,sizeof(double),1,fp); + fread(&t_stop,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(&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); + + // 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); +} + diff --git a/src/pair_dpd_tstat.h b/src/pair_dpd_tstat.h new file mode 100644 index 0000000000..f50ddcaa67 --- /dev/null +++ b/src/pair_dpd_tstat.h @@ -0,0 +1,44 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpd/tstat,PairDPDTstat) + +#else + +#ifndef LMP_PAIR_DPD_TSTAT_H +#define LMP_PAIR_DPD_TSTAT_H + +#include "pair_dpd.h" + +namespace LAMMPS_NS { + +class PairDPDTstat : public PairDPD { + public: + PairDPDTstat(class LAMMPS *); + ~PairDPDTstat() {} + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + private: + double t_start,t_stop; +}; + +} + +#endif +#endif