Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F91098070
pair_mdpd_rhosum.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
Thu, Nov 7, 21:21
Size
7 KB
Mime Type
text/x-c
Expires
Sat, Nov 9, 21:21 (2 d)
Engine
blob
Format
Raw Data
Handle
22196164
Attached To
rLAMMPS lammps
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
Log In to Comment