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fix_qeq_slater.cpp
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rLAMMPS lammps
fix_qeq_slater.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_slater.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 "pair.h"
#include "kspace.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) :
FixQEq(lmp, narg, arg)
{
alpha = 0.20;
// optional arg
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"alpha") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/slater command");
alpha = atof(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix qeq/slater command");
}
if (streitz_flag) extract_streitz();
}
/* ---------------------------------------------------------------------- */
void FixQEqSlater::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/slater requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/slater 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;
for (int i = 1; i <= ntypes; i++) {
if (zeta[i] == 0.0)
error->all(FLERR,"Invalid param file for fix qeq/slater");
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixQEqSlater::extract_streitz()
{
Pair *pair = force->pair_match("coul/streitz",1);
if (pair == NULL) error->all(FLERR,"No pair coul/streitz for fix qeq/slater");
int tmp;
chi = (double *) pair->extract("chi",tmp);
eta = (double *) pair->extract("eta",tmp);
gamma = (double *) pair->extract("gamma",tmp);
zeta = (double *) pair->extract("zeta",tmp);
zcore = (double *) pair->extract("zcore",tmp);
if (chi == NULL || eta == NULL || gamma == NULL
|| zeta == NULL || zcore == NULL)
error->all(FLERR,
"Fix qeq/slater could not extract params from pair coul/streitz");
}
/* ---------------------------------------------------------------------- */
void FixQEqSlater::pre_force(int vflag)
{
if (update->ntimestep % nevery) return;
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
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 FixQEqSlater::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 FixQEqSlater::compute_H()
{
int i, j, ii, jj, inum, jnum, itype, jtype;
int *ilist, *jlist, *numneigh, **firstneigh;
double r, rsq, delr[3];
double zei, zej, zj, zjtmp;
int *type = atom->type;
double **x = atom->x;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
m_fill = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
zei = zeta[itype];
jlist = firstneigh[i];
jnum = numneigh[i];
H.firstnbr[i] = m_fill;
zjtmp = 0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
zej = zeta[jtype];
zj = zcore[jtype];
delr[0] = x[i][0] - x[j][0];
delr[1] = x[i][1] - x[j][1];
delr[2] = x[i][2] - x[j][2];
rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2];
if (rsq > cutoff_sq) continue;
r = sqrt(rsq);
H.jlist[m_fill] = j;
H.val[m_fill] = calculate_H(zei, zej, zj, r, zjtmp);
m_fill++;
}
H.numnbrs[i] = m_fill - H.firstnbr[i];
chizj[i] = zjtmp;
}
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/slater has insufficient QEq matrix size");
}
}
/* ---------------------------------------------------------------------- */
double FixQEqSlater::calculate_H(double zei, double zej, double zj,
double r, double &zjtmp)
{
double rinv = 1.0/r;
double exp2zir = exp(-2.0*zei*r);
double zei2 = zei*zei;
double zei4 = zei2*zei2;
double zei6 = zei2*zei4;
double exp2zjr = exp(-2.0*zej*r);
double zej2 = zej*zej;
double zej4 = zej2*zej2;
double zej6 = zej2*zej4;
double sm1 = 11.0/8.0;
double sm2 = 3.00/4.0;
double sm3 = 1.00/6.0;
double erfcr = erfc(alpha*r);
double qqrd2e = force->qqrd2e;
double etmp1, etmp2;
double e1, e2, e3, e4;
double ci_jfi, ci_fifj;
e1 = e2 = e3 = e4 = 0.0;
etmp1 = etmp2 = 0.0;
ci_jfi = -zei*exp2zir - rinv*exp2zir;
if (zei == zej) {
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r));
} else {
e1 = zei*zej4/((zei+zej)*(zei+zej)*(zei-zej)*(zei-zej));
e2 = zej*zei4/((zei+zej)*(zei+zej)*(zej-zei)*(zej-zei));
e3 = (3.0*zei2*zej4-zej6) /
((zei+zej)*(zei+zej)*(zei+zej)*(zei-zej)*(zei-zej)*(zei-zej));
e4 = (3.0*zej2*zei4-zei6) /
((zei+zej)*(zei+zej)*(zei+zej)*(zej-zei)*(zej-zei)*(zej-zei));
ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r);
}
etmp1 = 1.00 * (ci_jfi - ci_fifj);
etmp2 = 0.50 * (ci_fifj + erfcr*rinv);
zjtmp += qqrd2e * zj * etmp1;
return qqrd2e * etmp2;
}
/* ---------------------------------------------------------------------- */
double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
double r, double &zjtmp)
{
double rinv = 1.0/r;
double exp2zir = exp(-2.0*zei*r);
double zei2 = zei*zei;
double zei4 = zei2*zei2;
double zei6 = zei2*zei4;
double exp2zjr = exp(-2.0*zej*r);
double zej2 = zej*zej;
double zej4 = zej2*zej2;
double zej6 = zej2*zej4;
double sm1 = 11.0/8.0;
double sm2 = 3.00/4.0;
double sm3 = 1.00/6.0;
double e1, e2, e3, e4;
double rc = cutoff;
double rcinv = 1.0/rc;
double rcinv2 = rcinv*rcinv;
double exp2zirsh = exp(-2.0*zei*rc);
double exp2zjrsh = exp(-2.0*zej*rc);
double eshift, fshift, ci_jfi, ci_fifj;
double etmp1, etmp2, etmp3;
double a = alpha;
double erfcr = erfc(a*r);
double erfcrc = erfc(a*rc);
double qqrd2e = force->qqrd2e;
etmp1 = etmp2 = etmp3 = 0.0;
e1 = e2 = e3 = e4 = 0.0;
eshift = -zei*exp2zirsh - rcinv*exp2zirsh;
fshift = 2.0*zei2*exp2zirsh + rcinv2*exp2zirsh + 2.0*zei*rcinv*exp2zirsh;
ci_jfi = -zei*exp2zir - rinv*exp2zir - eshift - (r-rc)*fshift;
if (zei == zej) {
eshift = -exp2zirsh*(rcinv + zei*(sm1 + sm2*zei*rc + sm3*zei2*rc*rc));
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r))
- eshift - (r-rc)*fshift;
} else {
e1 = zei*zej4/((zei+zej)*(zei+zej)*(zei-zej)*(zei-zej));
e2 = zej*zei4/((zei+zej)*(zei+zej)*(zej-zei)*(zej-zei));
e3 = (3.0*zei2*zej4-zej6) /
((zei+zej)*(zei+zej)*(zei+zej)*(zei-zej)*(zei-zej)*(zei-zej));
e4 = (3.0*zej2*zei4-zei6) /
((zei+zej)*(zei+zej)*(zei+zej)*(zej-zei)*(zej-zei)*(zej-zei));
eshift = -exp2zirsh*(e1+e3/rc) - exp2zjrsh*(e2+e4/rc);
ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
- eshift - (r-rc)*fshift;
}
etmp1 = erfcr/r - erfcrc/rc;
etmp2 = 1.00 * (ci_jfi - ci_fifj);
etmp3 = 0.50 * (etmp1 + ci_fifj);
zjtmp += qqrd2e * zj * etmp2;
return qqrd2e * etmp3;
}
/* ---------------------------------------------------------------------- */
void FixQEqSlater::sparse_matvec( sparse_matrix *A, double *x, double *b )
{
int i, j, itr_j;
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
double r = cutoff;
double woself = 0.50*erfc(alpha*r)/r + alpha/MY_PIS;
for( i = 0; i < nlocal; ++i ) {
if (atom->mask[i] & groupbit)
b[i] = (eta[atom->type[i]] - 2.0*force->qqr2e*woself) * x[i];
}
for( i = nlocal; i < nall; ++i ) {
if (atom->mask[i] & groupbit)
b[i] = 0;
}
for( i = 0; i < nlocal; ++i ) {
if (atom->mask[i] & groupbit) {
for( itr_j=A->firstnbr[i]; itr_j<A->firstnbr[i]+A->numnbrs[i]; itr_j++) {
j = A->jlist[itr_j];
b[i] += A->val[itr_j] * x[j];
b[j] += A->val[itr_j] * x[i];
}
}
}
}
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