ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
ee546e2fa3d583d4387347ebdc8ece76dc4ae7c1
lammps/src/USER-MISC/pair_dpd_ext.cpp
Axel Kohlmeyer bffee8dd6a silence compiler warning
2021-05-09 17:44:12 -04:00

495 lines
15 KiB
C++
Raw Blame History

/* ----------------------------------------------------------------------
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 authors: Martin Svoboda (ICPF, UJEP), Martin Lísal (ICPF, UJEP)
based on pair style dpd by: Kurt Smith (U Pittsburgh)
------------------------------------------------------------------------- */
#include "pair_dpd_ext.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
#define EPSILON 1.0e-10
/* ---------------------------------------------------------------------- */
PairDPDExt::PairDPDExt(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
random = nullptr;
}
/* ---------------------------------------------------------------------- */
PairDPDExt::~PairDPDExt()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(a0);
memory->destroy(gamma);
memory->destroy(gammaT);
memory->destroy(sigma);
memory->destroy(sigmaT);
memory->destroy(ws);
memory->destroy(wsT);
}
if (random) delete random;
}
/* ---------------------------------------------------------------------- */
void PairDPDExt::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,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;
evdwl = 0.0;
ev_init(eflag,vflag);
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();
// conservative force
fpair = a0[itype][jtype]*wd;
// 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 (eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
// eng shifted to 0.0 at cutoff
evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
evdwl *= factor_dpd;
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,
fpairx, fpairy, fpairz,
delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDPDExt::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(a0,n+1,n+1,"pair:a0");
memory->create(gamma,n+1,n+1,"pair:gamma");
memory->create(gammaT,n+1,n+1,"pair:gammaT");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(sigmaT,n+1,n+1,"pair:sigmaT");
memory->create(ws,n+1,n+1,"pair:ws");
memory->create(wsT,n+1,n+1,"pair:wsT");
for (i = 0; i <= atom->ntypes; i++)
{
for (j = 0; j <= atom->ntypes; j++)
{
sigma[i][j] = gamma[i][j] =sigmaT[i][j] = gammaT[i][j] = 0.0;
ws[i][j] = wsT[i][j] = 1.0;
}
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDExt::settings(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
temperature = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
seed = utils::inumeric(FLERR,arg[2],false,lmp);
// 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;
cutsq[i][j] = cut_global*cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairDPDExt::coeff(int narg, char **arg)
{
if (narg < 7 || narg > 8)
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 = utils::numeric(FLERR,arg[2],false,lmp);
double gamma_one = utils::numeric(FLERR,arg[3],false,lmp);
double gammaT_one = utils::numeric(FLERR,arg[4],false,lmp);
double ws_one = utils::numeric(FLERR,arg[5],false,lmp);
double wsT_one = utils::numeric(FLERR,arg[6],false,lmp);
double cut_one = cut_global;
if (narg == 8) cut_one = utils::numeric(FLERR,arg[7],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;
cutsq[i][j] = cut_one*cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDPDExt::init_style()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair dpd 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 dpd needs newton pair on for momentum conservation");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairDPDExt::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
sigmaT[i][j] = sqrt(2.0*force->boltz*temperature*gammaT[i][j]);
cut[j][i] = cut[i][j];
cutsq[j][i] = cutsq[i][j];
a0[j][i] = a0[i][j];
gamma[j][i] = gamma[i][j];
gammaT[j][i] = gammaT[i][j];
sigma[j][i] = sigma[i][j];
sigmaT[j][i] = sigmaT[i][j];
ws[j][i] = ws[i][j];
wsT[j][i] = wsT[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDPDExt::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(&a0[i][j],sizeof(double),1,fp);
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 PairDPDExt::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,&a0[i][j],sizeof(double),1,fp,nullptr,error);
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(&a0[i][j],1,MPI_DOUBLE,0,world);
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 PairDPDExt::write_restart_settings(FILE *fp)
{
fwrite(&temperature,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 PairDPDExt::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&temperature,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(&temperature,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);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairDPDExt::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,
a0[i][i],gamma[i][i],gammaT[i][i],ws[i][i],wsT[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairDPDExt::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 %g\n",i,j,
a0[i][j],gamma[i][j],gammaT[i][j],ws[i][j],wsT[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairDPDExt::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
r = sqrt(rsq);
if (r < EPSILON) {
fforce = 0.0;
return 0.0;
}
rinv = 1.0/r;
wd = 1.0 - r/cut[itype][jtype];
fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd*wd;
return factor_dpd*phi;
}
Reference in New Issue View Git Blame Copy Permalink