Homec4science
Diffusion lammps (master) Browse

lammps/src/REPLICA/fix_neb.cpp
e03cc994673emaster

Last Change
Raw File

fix_neb.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.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_neb.h"
#include "universe.h"
#include "update.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "memory.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};
/* ---------------------------------------------------------------------- */
FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
id_pe(NULL), pe(NULL), nlenall(NULL), xprev(NULL), xnext(NULL),
fnext(NULL), springF(NULL), tangent(NULL), xsend(NULL), xrecv(NULL),
fsend(NULL), frecv(NULL), tagsend(NULL), tagrecv(NULL),
xsendall(NULL), xrecvall(NULL), fsendall(NULL), frecvall(NULL),
tagsendall(NULL), tagrecvall(NULL), counts(NULL),
displacements(NULL)
{
NEBLongRange=false;
StandardNEB=true;
PerpSpring=FreeEndIni=FreeEndFinal=false;
FreeEndFinalWithRespToEIni=FinalAndInterWithRespToEIni=false;
kspringPerp=0.0;
kspring2=1.0;
if (narg < 4)
error->all(FLERR,"Illegal fix neb command, argument missing");
kspring = force->numeric(FLERR,arg[3]);
if (kspring <= 0.0)
error->all(FLERR,"Illegal fix neb command."
" The spring force was not provided properly");
int iarg =4;
while (iarg < narg) {
if (strcmp (arg[iarg],"nudg_style")==0) {
if (strcmp (arg[iarg+1],"idealpos")==0) {
NEBLongRange = true;
iarg+=2;}
else if (strcmp (arg[iarg+1],"neigh")==0) {
NEBLongRange = false;
StandardNEB = true;
iarg+=2;}
else error->all(FLERR,"Illegal fix neb command. Unknown keyword");}
else if (strcmp (arg[iarg],"perp")==0) {
PerpSpring=true;
kspringPerp = force->numeric(FLERR,arg[iarg+1]);
if (kspringPerp < 0.0)
error->all(FLERR,"Illegal fix neb command. "
"The perpendicular spring force was not provided properly");
iarg+=2;}
else if (strcmp (arg[iarg],"freeend")==0) {
if (strcmp (arg[iarg+1],"ini")==0)
FreeEndIni=true;
else if (strcmp (arg[iarg+1],"final")==0)
FreeEndFinal=true;
else if (strcmp (arg[iarg+1],"finaleini")==0)
FreeEndFinalWithRespToEIni=true;
else if (strcmp (arg[iarg+1],"final2eini")==0) {
FinalAndInterWithRespToEIni=true;
FreeEndFinalWithRespToEIni=true;}
else if (strcmp (arg[iarg+1],"none")!=0) error->all(FLERR,"Illegal fix neb command. Unknown keyword");
iarg+=2;}
else if (strcmp (arg[iarg],"freeend_kspring")==0) {
kspring2=force->numeric(FLERR,arg[iarg+1]);
iarg+=2; }
else error->all(FLERR,"Illegal fix neb command. Unknown keyword");
}
// nreplica = number of partitions
// ireplica = which world I am in universe
// nprocs_universe = # of procs in all replicase
// procprev,procnext = root proc in adjacent replicas
me = comm->me;
nprocs = comm->nprocs;
nprocs_universe = universe->nprocs;
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;
int *iroots = new int[nreplica];
MPI_Group uworldgroup,rootgroup;
if (NEBLongRange) {
for (int i=0; i<nreplica; i++)
iroots[i]=universe->root_proc[i];
MPI_Comm_group(uworld, &uworldgroup);
MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
MPI_Comm_create(uworld, rootgroup, &rootworld);
}
delete[] iroots;
// 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;
// initialize local storage
maxlocal = -1;
ntotal = -1;
}
/* ---------------------------------------------------------------------- */
FixNEB::~FixNEB()
{
modify->delete_compute(id_pe);
delete [] id_pe;
memory->destroy(xprev);
memory->destroy(xnext);
memory->destroy(tangent);
memory->destroy(fnext);
memory->destroy(springF);
memory->destroy(xsend);
memory->destroy(xrecv);
memory->destroy(fsend);
memory->destroy(frecv);
memory->destroy(tagsend);
memory->destroy(tagrecv);
memory->destroy(xsendall);
memory->destroy(xrecvall);
memory->destroy(fsendall);
memory->destroy(frecvall);
memory->destroy(tagsendall);
memory->destroy(tagrecvall);
memory->destroy(counts);
memory->destroy(displacements);
if (NEBLongRange) {
if (rootworld != MPI_COMM_NULL) MPI_Comm_free(&rootworld);
memory->destroy(nlenall);
}
}
/* ---------------------------------------------------------------------- */
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;
// nebatoms = # of atoms in fix group = atoms with inter-replica forces
bigint count = group->count(igroup);
if (count > MAXSMALLINT) error->all(FLERR,"Too many active NEB atoms");
nebatoms = count;
// comm mode for inter-replica exchange of coords
if (nreplica == nprocs_universe &&
nebatoms == atom->natoms && atom->sortfreq == 0)
cmode = SINGLE_PROC_DIRECT;
else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP;
else cmode = MULTI_PROC;
// ntotal = total # of atoms in system, NEB atoms or not
if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many atoms for NEB");
ntotal = atom->natoms;
if (atom->nmax > maxlocal) reallocate();
if (MULTI_PROC && counts == NULL) {
memory->create(xsendall,ntotal,3,"neb:xsendall");
memory->create(xrecvall,ntotal,3,"neb:xrecvall");
memory->create(fsendall,ntotal,3,"neb:fsendall");
memory->create(frecvall,ntotal,3,"neb:frecvall");
memory->create(tagsendall,ntotal,"neb:tagsendall");
memory->create(tagrecvall,ntotal,"neb:tagrecvall");
memory->create(counts,nprocs,"neb:counts");
memory->create(displacements,nprocs,"neb:displacements");
}
}
/* ---------------------------------------------------------------------- */
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;
double delxp,delyp,delzp,delxn,delyn,delzn;
double vIni=0.0;
vprev=vnext=veng=pe->compute_scalar();
if (ireplica < nreplica-1 && me ==0)
MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
if (ireplica > 0 && me ==0)
MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
if (ireplica > 0 && me == 0)
MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1 && me == 0)
MPI_Recv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,MPI_STATUS_IGNORE);
if (cmode == MULTI_PROC) {
MPI_Bcast(&vprev,1,MPI_DOUBLE,0,world);
MPI_Bcast(&vnext,1,MPI_DOUBLE,0,world);
}
if (FreeEndFinal && (update->ntimestep == 0)) EFinalIni = veng;
if (ireplica == 0) vIni=veng;
if (FreeEndFinalWithRespToEIni) {
if (me == 0) {
int procFirst;
procFirst=universe->root_proc[0];
MPI_Bcast(&vIni,1,MPI_DOUBLE,procFirst,uworld);
}
if (cmode == MULTI_PROC) {
MPI_Bcast(&vIni,1,MPI_DOUBLE,0,world);
}
}
if (FreeEndIni && ireplica == 0) {
if (me == 0 )
if (update->ntimestep == 0) {
EIniIni = veng;
if (cmode == MULTI_PROC)
MPI_Bcast(&EIniIni,1,MPI_DOUBLE,0,world);
}
}
// communicate atoms to/from adjacent replicas to fill xprev,xnext
inter_replica_comm();
// trigger potential energy computation on next timestep
pe->addstep(update->ntimestep+1);
double **x = atom->x;
int *mask = atom->mask;
double dot = 0.0;
double prefactor = 0.0;
double **f = atom->f;
int nlocal = atom->nlocal;
//calculating separation between images
plen = 0.0;
nlen = 0.0;
double tlen = 0.0;
double gradnextlen = 0.0;
dotgrad = gradlen = dotpath = dottangrad = 0.0;
if (ireplica == nreplica-1) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delxp = x[i][0] - xprev[i][0];
delyp = x[i][1] - xprev[i][1];
delzp = x[i][2] - xprev[i][2];
domain->minimum_image(delxp,delyp,delzp);
plen += delxp*delxp + delyp*delyp + delzp*delzp;
dottangrad += delxp* f[i][0]+ delyp*f[i][1]+delzp*f[i][2];
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
if (FreeEndFinal||FreeEndFinalWithRespToEIni) {
tangent[i][0]=delxp;
tangent[i][1]=delyp;
tangent[i][2]=delzp;
tlen += tangent[i][0]*tangent[i][0]
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
dot += f[i][0]*tangent[i][0]
+ f[i][1]*tangent[i][1] + f[i][2]*tangent[i][2];
}
}
} else if (ireplica == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delxn = xnext[i][0] - x[i][0];
delyn = xnext[i][1] - x[i][1];
delzn = xnext[i][2] - x[i][2];
domain->minimum_image(delxn,delyn,delzn);
nlen += delxn*delxn + delyn*delyn + delzn*delzn;
gradnextlen += fnext[i][0]*fnext[i][0]
+ fnext[i][1]*fnext[i][1] +fnext[i][2] * fnext[i][2];
dotgrad += f[i][0]*fnext[i][0]
+ f[i][1]*fnext[i][1] + f[i][2]*fnext[i][2];
dottangrad += delxn*f[i][0]+ delyn*f[i][1] + delzn*f[i][2];
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
if (FreeEndIni) {
tangent[i][0]=delxn;
tangent[i][1]=delyn;
tangent[i][2]=delzn;
tlen += tangent[i][0]*tangent[i][0]
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
dot += f[i][0]*tangent[i][0]
+ f[i][1]*tangent[i][1] + f[i][2]*tangent[i][2];
}
}
} else {
// not the first or last replica
double vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
double vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delxp = x[i][0] - xprev[i][0];
delyp = x[i][1] - xprev[i][1];
delzp = x[i][2] - xprev[i][2];
domain->minimum_image(delxp,delyp,delzp);
plen += delxp*delxp + delyp*delyp + delzp*delzp;
delxn = xnext[i][0] - x[i][0];
delyn = xnext[i][1] - x[i][1];
delzn = xnext[i][2] - x[i][2];
domain->minimum_image(delxn,delyn,delzn);
if (vnext > veng && veng > vprev) {
tangent[i][0]=delxn;
tangent[i][1]=delyn;
tangent[i][2]=delzn;
} else if (vnext < veng && veng < vprev) {
tangent[i][0]=delxp;
tangent[i][1]=delyp;
tangent[i][2]=delzp;
} else {
if (vnext > vprev) {
tangent[i][0] = vmax*delxn + vmin*delxp;
tangent[i][1] = vmax*delyn + vmin*delyp;
tangent[i][2] = vmax*delzn + vmin*delzp;
} else {
tangent[i][0] = vmin*delxn + vmax*delxp;
tangent[i][1] = vmin*delyn + vmax*delyp;
tangent[i][2] = vmin*delzn + vmax*delzp;
}
}
nlen += delxn*delxn + delyn*delyn + delzn*delzn;
tlen += tangent[i][0]*tangent[i][0]
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
dotpath += delxp*delxn + delyp*delyn + delzp*delzn;
dottangrad += tangent[i][0]* f[i][0]
+ tangent[i][1]*f[i][1] + tangent[i][2]*f[i][2];
gradnextlen += fnext[i][0]*fnext[i][0]
+ fnext[i][1]*fnext[i][1] +fnext[i][2] * fnext[i][2];
dotgrad += f[i][0]*fnext[i][0]
+ f[i][1]*fnext[i][1] + f[i][2]*fnext[i][2];
springF[i][0]=kspringPerp*(delxn-delxp);
springF[i][1]=kspringPerp*(delyn-delyp);
springF[i][2]=kspringPerp*(delzn-delzp);
}
}
#define BUFSIZE 8
double bufin[BUFSIZE], bufout[BUFSIZE];
bufin[0] = nlen;
bufin[1] = plen;
bufin[2] = tlen;
bufin[3] = gradlen;
bufin[4] = gradnextlen;
bufin[5] = dotpath;
bufin[6] = dottangrad;
bufin[7] = dotgrad;
MPI_Allreduce(bufin,bufout,BUFSIZE,MPI_DOUBLE,MPI_SUM,world);
nlen = sqrt(bufout[0]);
plen = sqrt(bufout[1]);
tlen = sqrt(bufout[2]);
gradlen = sqrt(bufout[3]);
gradnextlen = sqrt(bufout[4]);
dotpath = bufout[5];
dottangrad = bufout[6];
dotgrad = bufout[7];
// 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;
}
}
// first or last replica has no change to forces, just return
if(ireplica>0 && ireplica<nreplica-1)
dottangrad = dottangrad/(tlen*gradlen);
if (ireplica == 0)
dottangrad = dottangrad/(nlen*gradlen);
if (ireplica == nreplica-1)
dottangrad = dottangrad/(plen*gradlen);
if (ireplica < nreplica-1)
dotgrad = dotgrad /(gradlen*gradnextlen);
if (FreeEndIni && ireplica == 0) {
if (tlen > 0.0) {
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-EIniIni);
else prefactor = -dot + kspring2*(veng-EIniIni);
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];
}
}
}
if (FreeEndFinal && ireplica == nreplica -1) {
if (tlen > 0.0) {
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-EFinalIni);
else prefactor = -dot + kspring2*(veng-EFinalIni);
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];
}
}
}
if (FreeEndFinalWithRespToEIni&&ireplica == nreplica -1) {
if (tlen > 0.0) {
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall/tlen;
if (dot<0) prefactor = -dot - kspring2*(veng-vIni);
else prefactor = -dot + kspring2*(veng-vIni);
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];
}
}
}
double lentot = 0;
double meanDist,idealPos,lenuntilIm,lenuntilClimber;
lenuntilClimber=0;
if (NEBLongRange) {
if (cmode == SINGLE_PROC_DIRECT || cmode == SINGLE_PROC_MAP) {
MPI_Allgather(&nlen,1,MPI_DOUBLE,&nlenall[0],1,MPI_DOUBLE,uworld);
} else {
if (me == 0)
MPI_Allgather(&nlen,1,MPI_DOUBLE,&nlenall[0],1,MPI_DOUBLE,rootworld);
MPI_Bcast(nlenall,nreplica,MPI_DOUBLE,0,world);
}
lenuntilIm = 0;
for (int i = 0; i < ireplica; i++)
lenuntilIm += nlenall[i];
for (int i = 0; i < nreplica; i++)
lentot += nlenall[i];
meanDist = lentot/(nreplica -1);
if (rclimber>0) {
for (int i = 0; i < rclimber; i++)
lenuntilClimber += nlenall[i];
double meanDistBeforeClimber = lenuntilClimber/rclimber;
double meanDistAfterClimber =
(lentot-lenuntilClimber)/(nreplica-rclimber-1);
if (ireplica<rclimber)
idealPos = ireplica * meanDistBeforeClimber;
else
idealPos = lenuntilClimber+ (ireplica-rclimber)*meanDistAfterClimber;
} else idealPos = ireplica * meanDist;
}
if (ireplica == 0 || ireplica == nreplica-1) return ;
double AngularContr;
dotpath = dotpath/(plen*nlen);
AngularContr = 0.5 *(1+cos(MY_PI * dotpath));
double dotSpringTangent;
dotSpringTangent=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];
dotSpringTangent += springF[i][0]*tangent[i][0]
+springF[i][1]*tangent[i][1]+springF[i][2]*tangent[i][2];}
}
double dotSpringTangentall;
MPI_Allreduce(&dotSpringTangent,&dotSpringTangentall,1,MPI_DOUBLE,MPI_SUM,world);
dotSpringTangent=dotSpringTangentall;
double dotall;
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
dot=dotall;
if (ireplica == rclimber) prefactor = -2.0*dot;
else {
if (NEBLongRange) {
prefactor = -dot - kspring*(lenuntilIm-idealPos)/(2*meanDist);
} else if (StandardNEB) {
prefactor = -dot + kspring*(nlen-plen);
}
if (FinalAndInterWithRespToEIni&& veng<vIni) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] = 0;
f[i][1] = 0;
f[i][2] = 0;
}
prefactor = kspring*(nlen-plen);
AngularContr=0;
}
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] += prefactor*tangent[i][0]
+AngularContr*(springF[i][0] -dotSpringTangent*tangent[i][0]);
f[i][1] += prefactor*tangent[i][1]
+ AngularContr*(springF[i][1] - dotSpringTangent*tangent[i][1]);
f[i][2] += prefactor*tangent[i][2]
+ AngularContr*(springF[i][2] - dotSpringTangent*tangent[i][2]);
}
}
/* ----------------------------------------------------------------------
send/recv NEB atoms to/from adjacent replicas
received atoms matching my local atoms are stored in xprev,xnext
replicas 0 and N-1 send but do not receive any atoms
------------------------------------------------------------------------- */
void FixNEB::inter_replica_comm()
{
int i,m;
MPI_Request request;
MPI_Request requests[2];
MPI_Status statuses[2];
// reallocate memory if necessary
if (atom->nmax > maxlocal) reallocate();
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// -----------------------------------------------------
// 3 cases: two for single proc per replica
// one for multiple procs per replica
// -----------------------------------------------------
// single proc per replica
// all atoms are NEB atoms and no atom sorting
// direct comm of x -> xprev and x -> xnext
if (cmode == SINGLE_PROC_DIRECT) {
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,MPI_STATUS_IGNORE);
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,MPI_STATUS_IGNORE);
if (ireplica < nreplica-1)
MPI_Irecv(fnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
if (ireplica > 0)
MPI_Send(f[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
return;
}
// single proc per replica
// but only some atoms are NEB atoms or atom sorting is enabled
// send atom IDs and coords of only NEB atoms to prev/next proc
// recv procs use atom->map() to match received coords to owned atoms
if (cmode == SINGLE_PROC_MAP) {
m = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tagsend[m] = tag[i];
xsend[m][0] = x[i][0];
xsend[m][1] = x[i][1];
xsend[m][2] = x[i][2];
fsend[m][0] = f[i][0];
fsend[m][1] = f[i][1];
fsend[m][2] = f[i][2];
m++;
}
if (ireplica > 0) {
MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,&requests[1]);
}
if (ireplica < nreplica-1) {
MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
}
if (ireplica > 0) {
MPI_Waitall(2,requests,statuses);
for (i = 0; i < nebatoms; i++) {
m = atom->map(tagrecv[i]);
xprev[m][0] = xrecv[i][0];
xprev[m][1] = xrecv[i][1];
xprev[m][2] = xrecv[i][2];
}
}
if (ireplica < nreplica-1) {
MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
MPI_Irecv(frecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,&requests[1]);
}
if (ireplica > 0) {
MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
MPI_Send(fsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
}
if (ireplica < nreplica-1) {
MPI_Waitall(2,requests,statuses);
for (i = 0; i < nebatoms; i++) {
m = atom->map(tagrecv[i]);
xnext[m][0] = xrecv[i][0];
xnext[m][1] = xrecv[i][1];
xnext[m][2] = xrecv[i][2];
fnext[m][0] = frecv[i][0];
fnext[m][1] = frecv[i][1];
fnext[m][2] = frecv[i][2];
}
}
return;
}
// multiple procs per replica
// MPI_Gather all coords and atom IDs to root proc of each replica
// send to root of adjacent replicas
// bcast within each replica
// each proc extracts info for atoms it owns via atom->map()
m = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
tagsend[m] = tag[i];
xsend[m][0] = x[i][0];
xsend[m][1] = x[i][1];
xsend[m][2] = x[i][2];
fsend[m][0] = f[i][0];
fsend[m][1] = f[i][1];
fsend[m][2] = f[i][2];
m++;
}
MPI_Gather(&m,1,MPI_INT,counts,1,MPI_INT,0,world);
displacements[0] = 0;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(tagsend,m,MPI_LMP_TAGINT,
tagsendall,counts,displacements,MPI_LMP_TAGINT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
if (xsend) {
MPI_Gatherv(xsend[0],3*m,MPI_DOUBLE,
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
MPI_Gatherv(fsend[0],3*m,MPI_DOUBLE,
fsendall[0],counts,displacements,MPI_DOUBLE,0,world);
} else {
MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
fsendall[0],counts,displacements,MPI_DOUBLE,0,world);
}
if (ireplica > 0 && me == 0) {
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld,
&requests[1]);
}
if (ireplica < nreplica-1 && me == 0) {
MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld);
MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld);
}
if (ireplica > 0) {
if (me == 0) MPI_Waitall(2,requests,statuses);
MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
for (i = 0; i < nebatoms; i++) {
m = atom->map(tagrecvall[i]);
if (m < 0 || m >= nlocal) continue;
xprev[m][0] = xrecvall[i][0];
xprev[m][1] = xrecvall[i][1];
xprev[m][2] = xrecvall[i][2];
}
}
if (ireplica < nreplica-1 && me == 0) {
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
MPI_Irecv(frecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,
&requests[1]);
}
if (ireplica > 0 && me == 0) {
MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
MPI_Send(fsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
}
if (ireplica < nreplica-1) {
if (me == 0) MPI_Waitall(2,requests,statuses);
MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
MPI_Bcast(frecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
for (i = 0; i < nebatoms; i++) {
m = atom->map(tagrecvall[i]);
if (m < 0 || m >= nlocal) continue;
xnext[m][0] = xrecvall[i][0];
xnext[m][1] = xrecvall[i][1];
xnext[m][2] = xrecvall[i][2];
fnext[m][0] = frecvall[i][0];
fnext[m][1] = frecvall[i][1];
fnext[m][2] = frecvall[i][2];
}
}
}
/* ----------------------------------------------------------------------
reallocate xprev,xnext,tangent arrays if necessary
reallocate communication arrays if necessary
------------------------------------------------------------------------- */
void FixNEB::reallocate()
{
maxlocal = atom->nmax;
memory->destroy(xprev);
memory->destroy(xnext);
memory->destroy(tangent);
memory->destroy(fnext);
memory->destroy(springF);
memory->create(xprev,maxlocal,3,"neb:xprev");
memory->create(xnext,maxlocal,3,"neb:xnext");
memory->create(tangent,maxlocal,3,"neb:tangent");
memory->create(fnext,maxlocal,3,"neb:fnext");
memory->create(springF,maxlocal,3,"neb:springF");
if (cmode != SINGLE_PROC_DIRECT) {
memory->destroy(xsend);
memory->destroy(fsend);
memory->destroy(xrecv);
memory->destroy(frecv);
memory->destroy(tagsend);
memory->destroy(tagrecv);
memory->create(xsend,maxlocal,3,"neb:xsend");
memory->create(fsend,maxlocal,3,"neb:fsend");
memory->create(xrecv,maxlocal,3,"neb:xrecv");
memory->create(frecv,maxlocal,3,"neb:frecv");
memory->create(tagsend,maxlocal,"neb:tagsend");
memory->create(tagrecv,maxlocal,"neb:tagrecv");
}
if (NEBLongRange) {
memory->destroy(nlenall);
memory->create(nlenall,nreplica,"neb:nlenall");
}
}
c4science · Help