Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/QEQ/fix_qeq_dynamic.cpp
e6ac7757a374efficient_neuronet

Last Change
Raw File

fix_qeq_dynamic.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_dynamic.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 "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) :
FixQEq(lmp, narg, arg)
{
qdamp = 0.10;
qstep = 0.02;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"qdamp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command");
qdamp = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"qstep") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/dynamic command");
qstep = atof(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix qeq/dynamic command");
}
}
/* ---------------------------------------------------------------------- */
void FixQEqDynamic::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/dynamic requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/dynamic 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 = 1;
neighbor->requests[irequest]->full = 0;
if (tolerance < 1e-4)
if (comm->me == 0)
error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small"
" for damped dynamics");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixQEqDynamic::pre_force(int vflag)
{
int i,ii,iloop,inum,*ilist;
double qmass,dtq2;
double enegchkall,enegmaxall;
double *q = atom->q;
int *mask = atom->mask;
double enegchk = 0.0;
double enegtot = 0.0;
double enegmax = 0.0;
if (update->ntimestep % nevery) return;
if( atom->nmax > nmax ) reallocate_storage();
inum = list->inum;
ilist = list->ilist;
qmass = 0.016;
dtq2 = 0.5*qstep*qstep/qmass;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
q1[i] = q2[i] = qf[i] = 0.0;
}
for (iloop = 0; iloop < maxiter; iloop ++ ) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
q1[i] += qf[i]*dtq2 - qdamp*q1[i];
q[i] += q1[i];
}
}
pack_flag = 1;
comm->forward_comm_fix(this);
enegtot = compute_eneg();
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 <= tolerance && enegmax <= 100.0*tolerance) break;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
q1[i] += qf[i]*dtq2 - qdamp*q1[i];
}
}
if (comm->me == 0) {
if (iloop == maxiter) {
char str[128];
sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
": %lg",update->ntimestep,enegchk);
error->warning(FLERR,str);
}
}
if (force->kspace) force->kspace->qsum_qsq();
}
/* ---------------------------------------------------------------------- */
double FixQEqDynamic::compute_eneg()
{
int i, j, ii, jj, inum, jnum, itype;
int *ilist, *jlist, *numneigh, **firstneigh;
double eneg, enegtot;
double r, rsq, delr[3], rinv;
int *type = atom->type;
int *mask = atom->mask;
double *q = atom->q;
double **x = atom->x;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
qf[i] = 0.0;
}
// communicating charge force to all nodes, first forward then reverse
pack_flag = 2;
comm->forward_comm_fix(this);
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
if (mask[i] & groupbit) {
qf[i] += chi[itype] + eta[itype] * q[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
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);
rinv = 1.0/r;
qf[i] += q[j] * rinv;
qf[j] += q[i] * rinv;
}
}
}
pack_flag = 2;
comm->reverse_comm_fix(this);
// sum charge force on each node and return it
eneg = enegtot = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
eneg += qf[i];
}
MPI_Allreduce(&eneg,&enegtot,1,MPI_DOUBLE,MPI_SUM,world);
return enegtot;
}
/* ---------------------------------------------------------------------- */
int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int m;
if( pack_flag == 1 )
for(m = 0; m < n; m++) buf[m] = atom->q[list[m]];
else if( pack_flag == 2 )
for(m = 0; m < n; m++) buf[m] = qf[list[m]];
return m;
}
/* ---------------------------------------------------------------------- */
void FixQEqDynamic::unpack_forward_comm(int n, int first, double *buf)
{
int i, m;
if( pack_flag == 1)
for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m];
else if( pack_flag == 2)
for(m = 0, i = first; m < n; m++, i++) qf[i] = buf[m];
}
/* ---------------------------------------------------------------------- */
int FixQEqDynamic::pack_reverse_comm(int n, int first, double *buf)
{
int i, m;
for(m = 0, i = first; m < n; m++, i++) buf[m] = qf[i];
return m;
}
/* ---------------------------------------------------------------------- */
void FixQEqDynamic::unpack_reverse_comm(int n, int *list, double *buf)
{
int m;
for(m = 0; m < n; m++) qf[list[m]] += buf[m];
}
/* ---------------------------------------------------------------------- */
c4science · Help