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fix_reax_bonds.cpp
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Mon, Nov 4, 15:29

fix_reax_bonds.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 author: Aidan Thompson (Sandia)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_reax_bonds.h"
#include "pair_reax_fortran.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix reax/bonds command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery < 1) error->all("Illegal fix reax/bonds command");
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]);
error->one(str);
}
}
}
/* ---------------------------------------------------------------------- */
FixReaxBonds::~FixReaxBonds()
{
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixReaxBonds::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ----------------------------------------------------------------------
perform initial write
------------------------------------------------------------------------- */
void FixReaxBonds::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::init()
{
// insure ReaxFF is defined
if (force->pair_match("reax",1) == NULL)
error->all("Cannot use fix reax/bonds without pair_style reax");
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::end_of_step()
{
OutputReaxBonds(update->ntimestep,fp);
if (me == 0) fflush(fp);
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
{
int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
int nprocs,nlocal_tmp,itmp;
double cutof3;
double *buf;
MPI_Request irequest;
MPI_Status istatus;
MPI_Comm_size(world,&nprocs);
nparticles = atom->nlocal;
nparticles_tot = static_cast<int> (atom->natoms);
mbond = ReaxParams::mbond;
FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax);
FORTRAN(getcutof3,GETCUTOF3)(&cutof3);
MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
fprintf(fp,"# \n");
fprintf(fp,"# Number of particles %d \n",nparticles_tot);
fprintf(fp,"# \n");
fprintf(fp,"# Max number of bonds per atom %d with "
"coarse bond order cutoff %5.3f \n",
nsbmax_most,cutof3);
fprintf(fp,"# Particle connection table and bond orders \n");
fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
}
// allocate a temporary buffer for the snapshot info
// big enough for largest number of atoms on any one proc
// nbuf_local = size of local buffer for table of atom bonds
nbuf = 1+(2*nsbmax_most+7)*most;
memory->create(buf,nbuf,"reax/bonds:buf");
j = 2;
jn = ReaxParams::nat;
buf[0] = nparticles;
for (int iparticle=0;iparticle<nparticles;iparticle++) {
buf[j-1] = atom->tag[iparticle]; //atom tag
buf[j+0] = FORTRAN(cbkia,CBKIA).iag[iparticle]; //atom type
buf[j+1] = FORTRAN(cbkia,CBKIA).iag[iparticle+jn]; //no.bonds
int k;
numbonds = nint(buf[j+1]);
// connection table based on coarse bond order cutoff (> cutof3)
for (k=2;k<2+numbonds;k++) {
ii = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*k];
buf[j+k] = FORTRAN(cbkc,CBKC).itag[ii-1];
}
buf[j+k]=FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(mbond+2)]; //molec.id
j+=(3+numbonds);
// bond orders (> cutof3)
for (k=0;k<numbonds;k++) {
ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
buf[j+k] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
}
// sum of bond orders (abo), no. of lone pairs (vlp), charge (ch)
buf[j+k] = FORTRAN(cbkabo,CBKABO).abo[iparticle];
buf[j+k+1] = FORTRAN(cbklonpar,CBKLONPAR).vlp[iparticle];
// buf[j+k+2] = FORTRAN(cbkch,CBKCH).ch[iparticle];
buf[j+k+2] = atom->q[iparticle];
j+=(4+numbonds);
}
nbuf_local = j-1;
// node 0 pings each node, receives their buffer, writes to file
// all other nodes wait for ping, send buffer to node 0
if (me == 0) {
for (int inode = 0; inode<nprocs; inode++) {
if (inode == 0) {
nlocal_tmp = nparticles;
} else {
MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
MPI_Send(&itmp,0,MPI_INT,inode,0,world);
MPI_Wait(&irequest,&istatus);
nlocal_tmp = nint(buf[0]);
}
j = 2;
for (int iparticle=0;iparticle<nlocal_tmp;iparticle++) {
// print atom tag, atom type, no.bonds
fprintf(fp," %d %d %d",nint(buf[j-1]),nint(buf[j+0]),nint(buf[j+1]));
int k;
numbonds = nint(buf[j+1]);
if (numbonds > nsbmax_most) {
char str[128];
sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
error->one(str);
}
// print connection table
for (k=2;k<2+numbonds;k++)
fprintf(fp," %d",nint(buf[j+k]));
fprintf(fp," %d",nint(buf[j+k]));
j+=(3+numbonds);
// print bond orders
for (k=0;k<numbonds;k++)
fprintf(fp,"%14.3f",buf[j+k]);
// print sum of bond orders, no. of lone pairs, charge
fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j+k],buf[j+k+1],buf[j+k+2]);
j+=(4+numbonds);
}
}
} else {
MPI_Recv(&itmp,0,MPI_INT,0,0,world,&istatus);
MPI_Rsend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world);
}
if (me == 0) fprintf(fp,"# \n");
memory->destroy(buf);
}
/* ---------------------------------------------------------------------- */
int FixReaxBonds::nint(const double &r)
{
int i = 0;
if (r>0.0) i = static_cast<int>(r+0.5);
else if (r<0.0) i = static_cast<int>(r-0.5);
return i;
}

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