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fix_neb.cpp
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Fri, Nov 1, 23:59

fix_neb.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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_neb.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "compute.h"
#include "atom.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal fix neb command");
kspring = atof(arg[3]);
if (kspring <= 0.0) error->all(FLERR,"Illegal fix neb command");
// nreplica = number of partitions
// ireplica = which world I am in universe
// procprev,procnext = root proc in adjacent replicas
nreplica = universe->nworlds;
ireplica = universe->iworld;
if (ireplica > 0) procprev = universe->root_proc[ireplica-1];
else procprev = -1;
if (ireplica < nreplica-1) procnext = universe->root_proc[ireplica+1];
else procnext = -1;
uworld = universe->uworld;
// create a new compute pe style
// id = fix-ID + pe, compute group = all
int n = strlen(id) + 4;
id_pe = new char[n];
strcpy(id_pe,id);
strcat(id_pe,"_pe");
char **newarg = new char*[3];
newarg[0] = id_pe;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pe";
modify->add_compute(3,newarg);
delete [] newarg;
xprev = xnext = tangent = NULL;
}
/* ---------------------------------------------------------------------- */
FixNEB::~FixNEB()
{
modify->delete_compute(id_pe);
delete [] id_pe;
memory->destroy(xprev);
memory->destroy(xnext);
memory->destroy(tangent);
}
/* ---------------------------------------------------------------------- */
int FixNEB::setmask()
{
int mask = 0;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNEB::init()
{
int icompute = modify->find_compute(id_pe);
if (icompute < 0)
error->all(FLERR,"Potential energy ID for fix neb does not exist");
pe = modify->compute[icompute];
// turn off climbing mode, NEB command turns it on after init()
rclimber = -1;
// setup xprev and xnext arrays
memory->destroy(xprev);
memory->destroy(xnext);
memory->destroy(tangent);
nebatoms = atom->nlocal;
memory->create(xprev,nebatoms,3,"neb:xprev");
memory->create(xnext,nebatoms,3,"neb:xnext");
memory->create(tangent,nebatoms,3,"neb:tangent");
}
/* ---------------------------------------------------------------------- */
void FixNEB::min_setup(int vflag)
{
min_post_force(vflag);
// trigger potential energy computation on next timestep
pe->addstep(update->ntimestep+1);
}
/* ---------------------------------------------------------------------- */
void FixNEB::min_post_force(int vflag)
{
double vprev,vnext,vmax,vmin;
double delx,dely,delz;
double delta1[3],delta2[3];
MPI_Status status;
MPI_Request request;
// veng = PE of this replica
// vprev,vnext = PEs of adjacent replicas
veng = pe->compute_scalar();
if (ireplica < nreplica-1) MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
if (ireplica > 0) MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,&status);
if (ireplica > 0) MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1)
MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,&status);
// xprev,xnext = atom coords of adjacent replicas
// assume order of atoms in all replicas is the same
// check that number of atoms hasn't changed
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal != nebatoms) error->one(FLERR,"Atom count changed in fix neb");
if (ireplica > 0)
MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
if (ireplica < nreplica-1)
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
if (ireplica > 0) MPI_Wait(&request,&status);
if (ireplica < nreplica-1)
MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
if (ireplica > 0)
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1) MPI_Wait(&request,&status);
// trigger potential energy computation on next timestep
pe->addstep(update->ntimestep+1);
// Compute norm of GradV for log output
double **f = atom->f;
double fsq = 0.0;
for (int i = 0; i < nlocal; i++) {
fsq += f[i][0]*f[i][0]+f[i][1]*f[i][1]+f[i][2]*f[i][2];
}
MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_MAX,world);
gradvnorm = sqrt(gradvnorm);
// if this is first or last replica, no change to forces, just return
if (ireplica == 0 || ireplica == nreplica-1) {
plen = nlen = 0.0;
return;
}
// tangent = unit tangent vector in 3N space
// based on delta vectors between atoms and their images in adjacent replicas
// use one or two delta vecs to compute tangent,
// depending on relative PEs of 3 replicas
// see Henkelman & Jonsson 2000 paper, eqs 8-11
if (vnext > veng && veng > vprev) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tangent[i][0] = xnext[i][0] - x[i][0];
tangent[i][1] = xnext[i][1] - x[i][1];
tangent[i][2] = xnext[i][2] - x[i][2];
domain->minimum_image(tangent[i]);
}
} else if (vnext < veng && veng < vprev) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tangent[i][0] = x[i][0] - xprev[i][0];
tangent[i][1] = x[i][1] - xprev[i][1];
tangent[i][2] = x[i][2] - xprev[i][2];
domain->minimum_image(tangent[i]);
}
} else {
vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delta1[0] = xnext[i][0] - x[i][0];
delta1[1] = xnext[i][1] - x[i][1];
delta1[2] = xnext[i][2] - x[i][2];
domain->minimum_image(delta1);
delta2[0] = x[i][0] - xprev[i][0];
delta2[1] = x[i][1] - xprev[i][1];
delta2[2] = x[i][2] - xprev[i][2];
domain->minimum_image(delta2);
if (vnext > vprev) {
tangent[i][0] = vmax*delta1[0] + vmin*delta2[0];
tangent[i][1] = vmax*delta1[1] + vmin*delta2[1];
tangent[i][2] = vmax*delta1[2] + vmin*delta2[2];
} else {
tangent[i][0] = vmin*delta1[0] + vmax*delta2[0];
tangent[i][1] = vmin*delta1[1] + vmax*delta2[1];
tangent[i][2] = vmin*delta1[2] + vmax*delta2[2];
}
}
}
// tlen,plen,nlen = lengths of tangent, prev, next vectors
double tlen = 0.0;
plen = 0.0;
nlen = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tlen += tangent[i][0]*tangent[i][0] + tangent[i][1]*tangent[i][1] +
tangent[i][2]*tangent[i][2];
delx = x[i][0] - xprev[i][0];
dely = x[i][1] - xprev[i][1];
delz = x[i][2] - xprev[i][2];
domain->minimum_image(delx,dely,delz);
plen += delx*delx + dely*dely + delz*delz;
delx = xnext[i][0] - x[i][0];
dely = xnext[i][1] - x[i][1];
delz = xnext[i][2] - x[i][2];
domain->minimum_image(delx,dely,delz);
nlen += delx*delx + dely*dely + delz*delz;
}
tlen = sqrt(tlen);
plen = sqrt(plen);
nlen = sqrt(nlen);
// normalize tangent vector
if (tlen > 0.0) {
double tleninv = 1.0/tlen;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tangent[i][0] *= tleninv;
tangent[i][1] *= tleninv;
tangent[i][2] *= tleninv;
}
}
// reset force on each atom in this replica
// regular NEB for all replicas except rclimber does hill-climbing NEB
// currently have F = -Grad(V) = -Grad(V)_perp - Grad(V)_parallel
// want F = -Grad(V)_perp + Fspring for regular NEB
// thus Fdelta = Grad(V)_parallel + Fspring for regular NEB
// want F = -Grad(V) + 2 Grad(V)_parallel for hill-climbing NEB
// thus Fdelta = 2 Grad(V)_parallel for hill-climbing NEB
// Grad(V)_parallel = (Grad(V) . utan) * utangent = -(F . utan) * utangent
// Fspring = k (nlen - plen) * utangent
// see Henkelman & Jonsson 2000 paper, eqs 3,4,12
// see Henkelman & Jonsson 2000a paper, eq 5
double dot = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
f[i][2]*tangent[i][2];
}
double prefactor;
if (ireplica == rclimber) prefactor = -2.0*dot;
else prefactor = -dot + kspring*(nlen-plen);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] += prefactor*tangent[i][0];
f[i][1] += prefactor*tangent[i][1];
f[i][2] += prefactor*tangent[i][2];
}
}

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