Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/QEQ/fix_qeq_fire.cpp
49804d97059fefficient_neuronet

Last Change
Raw File

fix_qeq_fire.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_fire.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 "pair_comb.h"
#include "pair_comb3.h"
#include "kspace.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define DELAYSTEP 0
#define DT_GROW 1.1
#define DT_SHRINK 0.5
#define ALPHA0 0.8
#define ALPHA_SHRINK 0.10
#define TMAX 10.0
/* ---------------------------------------------------------------------- */
FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
FixQEq(lmp, narg, arg)
{
qdamp = 0.20;
qstep = 0.20;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"qdamp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qeq/fire 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/fire command");
qstep = atof(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix qeq/fire command");
}
comb = NULL;
comb3 = NULL;
}
/* ---------------------------------------------------------------------- */
void FixQEqFire::init()
{
if (!atom->q_flag)
error->all(FLERR,"Fix qeq/fire requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/fire 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/fire tolerance may be too small"
" for damped fires");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
comb = (PairComb *) force->pair_match("comb",1);
comb3 = (PairComb3 *) force->pair_match("comb3",1);
}
/* ---------------------------------------------------------------------- */
void FixQEqFire::pre_force(int vflag)
{
int inum, *ilist;
int i,ii,iloop;
double *q = atom->q;
double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
double scale1,scale2;
double dtvone,dtv;
double enegtot,enegchk;
double alpha = qdamp;
double dt, dtmax;
double enegchkall;
bigint ntimestep = update->ntimestep;
bigint last_negative = 0;
if (ntimestep % nevery) return;
if( atom->nmax > nmax ) reallocate_storage();
inum = list->inum;
ilist = list->ilist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qv[i] = 0.0;
}
dt = qstep;
dtmax = TMAX * dt;
for (iloop = 0; iloop < maxiter; iloop ++ ) {
pack_flag = 1;
comm->forward_comm_fix(this);
if (comb) {
comb->yasu_char(qf,igroup);
enegtot = comb->enegtot / ngroup;
} else if (comb3) {
comb3->combqeq(qf,igroup);
enegtot = comb3->enegtot / ngroup;
} else {
enegtot = compute_eneg();
enegtot /= ngroup;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qf[i] -= enegtot; // Enforce adiabatic
}
// FIRE minimization algorithm
// vdotfall = v dot f = qv dot qf
vdotf = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
vdotf += (qv[i]*qf[i]);
}
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
if (vdotfall > 0.0) {
vdotv = fdotf = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
vdotv += qv[i]*qv[i];
fdotf += qf[i]*qf[i];
}
MPI_Allreduce(&vdotv,&vdotvall,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
scale1 = 1.0 - alpha;
if (fdotfall == 0.0) scale2 = 0.0;
else scale2 = alpha * sqrt(vdotvall/fdotfall);
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qv[i] = scale1*qv[i] + scale2*qf[i];
}
if (ntimestep - last_negative > DELAYSTEP) {
dt = MIN(dt*DT_GROW,dtmax);
alpha *= ALPHA_SHRINK;
}
} else {
last_negative = ntimestep;
dt *= DT_SHRINK;
alpha = ALPHA0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qv[i] = 0.0;
}
}
// limit timestep so no charges change more than dmax
dtvone = dt;
double dmax = 0.1;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
vmax = MAX(fabs(qv[i]),0);
if (dtvone*vmax > dmax) dtvone = dmax/vmax;
}
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
//dtv = dt;
// Euler integration step
enegchk = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
q[i] -= dtv * qv[i];
qv[i] += dtv * qf[i];
enegchk += fabs(qf[i]);
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
enegchk = enegchkall / ngroup;
if (enegchk < tolerance) break;
}
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 FixQEqFire::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 FixQEqFire::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int m = 0;
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 FixQEqFire::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 FixQEqFire::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 FixQEqFire::unpack_reverse_comm(int n, int *list, double *buf)
{
int m;
for(m = 0; m < n; m++) qf[list[m]] += buf[m];
}
/* ---------------------------------------------------------------------- */
c4science · Help