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lammps/src/MANYBODY/fix_qeq_comb.cpp
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fix_qeq_comb.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 authors: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "pair_comb.h"
#include "pair_comb3.h"
#include "fix_qeq_comb.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "group.h"
#include "respa.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix qeq/comb command");
peratom_flag = 1;
size_peratom_cols = 0;
peratom_freq = 1;
nevery = force->inumeric(FLERR,arg[3]);
precision = force->numeric(FLERR,arg[4]);
if (nevery <= 0 || precision <= 0.0)
error->all(FLERR,"Illegal fix qeq/comb command");
MPI_Comm_rank(world,&me);
// optional args
fp = NULL;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/comb command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
iarg += 2;
} else error->all(FLERR,"Illegal fix qeq/comb command");
}
nmax = atom->nmax;
memory->create(qf,nmax,"qeq:qf");
memory->create(q1,nmax,"qeq:q1");
memory->create(q2,nmax,"qeq:q2");
vector_atom = qf;
// zero the vector since dump may access it on timestep 0
// zero the vector since a variable may access it before first run
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) qf[i] = 0.0;
comb = NULL;
comb3 = NULL;
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
FixQEQComb::~FixQEQComb()
{
if (me == 0 && fp) fclose(fp);
memory->destroy(qf);
memory->destroy(q1);
memory->destroy(q2);
}
/* ---------------------------------------------------------------------- */
int FixQEQComb::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/comb requires atom attribute q");
comb = (PairComb *) force->pair_match("comb",1);
comb3 = (PairComb3 *) force->pair_match("comb3",1);
if (comb == NULL && comb3 == NULL)
error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/comb group has no atoms");
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::setup(int vflag)
{
firstflag = 1;
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
firstflag = 0;
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::min_post_force(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::post_force(int vflag)
{
int i,ii,iloop,loopmax,inum,*ilist;
double heatpq,qmass,dtq,dtq2;
double enegchkall,enegmaxall;
if (update->ntimestep % nevery) return;
// reallocate work arrays if necessary
// qf = charge force
// q1 = charge displacement
// q2 = tmp storage of charge force for next iteration
if (atom->nmax > nmax) {
memory->destroy(qf);
memory->destroy(q1);
memory->destroy(q2);
nmax = atom->nmax;
memory->create(qf,nmax,"qeq:qf");
memory->create(q1,nmax,"qeq:q1");
memory->create(q2,nmax,"qeq:q2");
vector_atom = qf;
}
// more loops for first-time charge equilibrium
iloop = 0;
if (firstflag) loopmax = 200;
else loopmax = 100;
// charge-equilibration loop
if (me == 0 && fp)
fprintf(fp,"Charge equilibration on step " BIGINT_FORMAT "\n",
update->ntimestep);
heatpq = 0.05;
qmass = 0.016;
dtq = 0.01;
dtq2 = 0.5*dtq*dtq/qmass;
double enegchk = 0.0;
double enegtot = 0.0;
double enegmax = 0.0;
double *q = atom->q;
int *mask = atom->mask;
if (comb) {
inum = comb->list->inum;
ilist = comb->list->ilist;
}
if (comb3) {
inum = comb3->list->inum;
ilist = comb3->list->ilist;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
q1[i] = q2[i] = qf[i] = 0.0;
}
for (iloop = 0; iloop < loopmax; iloop ++ ) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
q[i] += q1[i];
}
}
comm->forward_comm_fix(this);
if(comb) enegtot = comb->yasu_char(qf,igroup);
if(comb3) enegtot = comb3->combqeq(qf,igroup);
enegtot /= ngroup;
enegchk = enegmax = 0.0;
for (ii = 0; ii < inum ; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
q2[i] = enegtot-qf[i];
enegmax = MAX(enegmax,fabs(q2[i]));
enegchk += fabs(q2[i]);
qf[i] = q2[i];
}
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
enegchk = enegchkall/ngroup;
MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world);
enegmax = enegmaxall;
if (enegchk <= precision && enegmax <= 100.0*precision) break;
if (me == 0 && fp)
fprintf(fp," iteration: %d, enegtot %.6g, "
"enegmax %.6g, fq deviation: %.6g\n",
iloop,enegtot,enegmax,enegchk);
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
}
}
if (me == 0 && fp) {
if (iloop == loopmax)
fprintf(fp,"Charges did not converge in %d iterations\n",iloop);
else
fprintf(fp,"Charges converged in %d iterations to %.10f tolerance\n",
iloop,enegchk);
}
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixQEQComb::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i ++) {
j = list[i];
buf[m++] = atom->q[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n ;
for (i = first; i < last; i++) atom->q[i] = buf[m++];
}
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