Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F69871831
pair_dpd_tstat.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 3, 23:19
Size
8 KB
Mime Type
text/x-c
Expires
Fri, Jul 5, 23:19 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
18762919
Attached To
rLAMMPS lammps
pair_dpd_tstat.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.
------------------------------------------------------------------------- */
#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 EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairDPDTstat::PairDPDTstat(LAMMPS *lmp) : PairDPD(lmp)
{
single_enable = 0;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
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;
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]);
}
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;
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_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDTstat::settings(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Illegal pair_style command");
t_start = force->numeric(FLERR,arg[0]);
t_stop = force->numeric(FLERR,arg[1]);
cut_global = force->numeric(FLERR,arg[2]);
seed = force->inumeric(FLERR,arg[3]);
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+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(FLERR,"Incorrect args for pair 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 = 0.0;
double gamma_one = force->numeric(FLERR,arg[2]);
double cut_one = cut_global;
if (narg == 4) cut_one = force->numeric(FLERR,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(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDTstat::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(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDTstat::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) 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(&gamma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
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);
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 PairDPDTstat::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g\n",i,gamma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairDPDTstat::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\n",i,j,gamma[i][j],cut[i][j]);
}
Event Timeline
Log In to Comment