Page MenuHomec4science
Files F64883193

pair_mdpd_rhosum.cpp
No OneTemporary
Actions

File Metadata

Created
Thu, May 30, 04:33

pair_mdpd_rhosum.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.
------------------------------------------------------------------------- */
/*-----------------------------------------------------------------------
This is a Child Class PairMDPD for taking care of density summation
before the force calculation.
The code uses 3D Lucy kernel, it can be modified for other kernels.
Contributing author: Zhen Li (Brown University)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "pair_mdpd_rhosum.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include "update.h"
#include "domain.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMDPDRhoSum::PairMDPDRhoSum(LAMMPS *lmp) : Pair(lmp)
{
restartinfo = 0;
// set comm size needed by this Pair
comm_forward = 1;
first = 1;
}
/* ---------------------------------------------------------------------- */
PairMDPDRhoSum::~PairMDPDRhoSum() {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMDPDRhoSum::init_style() {
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ---------------------------------------------------------------------- */
void PairMDPDRhoSum::compute(int eflag, int vflag) {
int i, j, ii, jj, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz;
double r, rsq, h, ih, ihsq;
int *jlist;
double wf;
// neighbor list variables
int inum, *ilist, *numneigh, **firstneigh;
if (eflag || vflag)
ev_setup(eflag, vflag);
else
evflag = vflag_fdotr = 0;
double **x = atom->x;
double *rho = atom->rho;
int *type = atom->type;
double *mass = atom->mass;
// check consistency of pair coefficients
if (first) {
for (i = 1; i <= atom->ntypes; i++)
for (j = 1; i <= atom->ntypes; i++)
if (cutsq[i][j] > 0.0)
if (!setflag[i][i] || !setflag[j][j])
if (comm->me == 0)
printf("mDPD particle types %d and %d interact, but not all of their single particle properties are set.\n", i, j);
first = 0;
}
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// recompute density
// we use a full neighborlist here
// initialize density with zero self-contribution,
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
h = cut[itype][itype];
// Lucy kernel, 3d
wf = 2.0889086280811262819e0 / (h * h * h);
rho[i] = 0;
}
// add density at each atom via kernel function overlap
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq[itype][jtype]) {
h = cut[itype][jtype];
ih = 1.0 / h;
ihsq = ih * ih;
// Lucy kernel, 3d
r = sqrt(rsq);
wf = (h - r) * ihsq;
wf = 2.0889086280811262819e0 * (h + 3. * r) * wf * wf * wf * ih;
rho[i] += mass[jtype]*wf;
}
}
}
// communicate densities
comm->forward_comm_pair(this);
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairMDPDRhoSum::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int 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");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMDPDRhoSum::settings(int narg, char **arg) {
if (narg != 0)
error->all(FLERR,"Illegal number of setting arguments for pair_style mdpd/rhosum");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMDPDRhoSum::coeff(int narg, char **arg) {
if (narg != 3)
error->all(FLERR,"Incorrect number of args for mdpd/rhosum 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 cut_one = force->numeric(FLERR,arg[2]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0)
error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMDPDRhoSum::init_one(int i, int j) {
if (setflag[i][j] == 0) {
error->all(FLERR,"All pair mdpd/rhosum coeffs are not set");
}
cut[j][i] = cut[i][j];
return cut[i][j];
}
/* ---------------------------------------------------------------------- */
double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &fforce) {
fforce = 0.0;
return 0.0;
}
/* ---------------------------------------------------------------------- */
int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc) {
int i, j, m;
double *rho = atom->rho;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rho[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairMDPDRhoSum::unpack_forward_comm(int n, int first, double *buf) {
int i, m, last;
double *rho = atom->rho;
m = 0;
last = first + n;
for (i = first; i < last; i++)
rho[i] = buf[m++];
}

Event Timeline

c4science · Help