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fix_qeq_point.cpp
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Tue, Nov 5, 06:21

fix_qeq_point.cpp
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/* ----------------------------------------------------------------------
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 author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_point.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixQEqPoint::FixQEqPoint(LAMMPS *lmp, int narg, char **arg) :
FixQEq(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixQEqPoint::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/point requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/point group has no atoms");
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
int ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixQEqPoint::pre_force(int vflag)
{
if (update->ntimestep % nevery) return;
nlocal = atom->nlocal;
if( atom->nmax > nmax ) reallocate_storage();
if( nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE )
reallocate_matrix();
init_matvec();
matvecs = CG(b_s, s); // CG on s - parallel
matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->qsum_qsq();
}
/* ---------------------------------------------------------------------- */
void FixQEqPoint::init_matvec()
{
compute_H();
int inum, ii, i;
int *ilist;
inum = list->inum;
ilist = list->ilist;
for( ii = 0; ii < inum; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -( chi[atom->type[i]] + chizj[i] );
b_t[i] = -1.0;
t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1] );
s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
}
}
pack_flag = 2;
comm->forward_comm_fix(this); //Dist_vector( s );
pack_flag = 3;
comm->forward_comm_fix(this); //Dist_vector( t );
}
/* ---------------------------------------------------------------------- */
void FixQEqPoint::compute_H()
{
int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh;
int i, j, ii, jj;
double **x;
double dx, dy, dz, r_sqr, r;
x = atom->x;
int *mask = atom->mask;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// fill in the H matrix
m_fill = 0;
for( ii = 0; ii < inum; ii++ ) {
i = ilist[ii];
if (mask[i] & groupbit) {
jlist = firstneigh[i];
jnum = numneigh[i];
H.firstnbr[i] = m_fill;
for( jj = 0; jj < jnum; jj++ ) {
j = jlist[jj];
j &= NEIGHMASK;
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = dx*dx + dy*dy + dz*dz;
if (r_sqr <= cutoff_sq) {
H.jlist[m_fill] = j;
r = sqrt(r_sqr);
H.val[m_fill] = 0.5/r;
m_fill++;
}
}
H.numnbrs[i] = m_fill - H.firstnbr[i];
}
}
if (m_fill >= H.m) {
char str[128];
sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
m_fill, H.m );
error->warning(FLERR,str);
error->all(FLERR,"Fix qeq/point has insufficient QEq matrix size");
}
}
/* ---------------------------------------------------------------------- */

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