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fix_reaxc_bonds.cpp
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Sun, Nov 17, 19:13

fix_reaxc_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: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_bonds.h"
#include "atom.h"
#include "update.h"
#include "pair_reax_c.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "reaxc_list.h"
#include "reaxc_types.h"
#include "reaxc_defs.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal fix reax/c/bonds command");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
ntypes = atom->ntypes;
nmax = atom->nmax;
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0 )
error->all(FLERR,"Illegal fix reax/c/bonds command");
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]);
error->one(FLERR,str);
}
}
if (atom->tag_consecutive() == 0)
error->all(FLERR,"Atom IDs must be consecutive for fix reax/c bonds");
abo = NULL;
neighid = NULL;
numneigh = NULL;
allocate();
}
/* ---------------------------------------------------------------------- */
FixReaxCBonds::~FixReaxCBonds()
{
MPI_Comm_rank(world,&me);
destroy();
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixReaxCBonds::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::init()
{
Pair *pair_kk = force->pair_match("reax/c/kk",1);
if (pair_kk != NULL) error->all(FLERR,"Cannot (yet) use fix reax/c/bonds with "
"pair_style reax/c/kk");
reaxc = (PairReaxC *) force->pair_match("reax/c",1);
if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/bonds without "
"pair_style reax/c");
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::end_of_step()
{
Output_ReaxC_Bonds(update->ntimestep,fp);
if (me == 0) fflush(fp);
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
{
int i, j;
int nbuf, nbuf_local;
int nlocal_max, numbonds, numbonds_max;
double *buf;
int nlocal = atom->nlocal;
int nlocal_tot = static_cast<int> (atom->natoms);
if (atom->nmax > nmax) {
destroy();
nmax = atom->nmax;
allocate();
}
for (i = 0; i < nmax; i++) {
numneigh[i] = 0;
for (j = 0; j < MAXREAXBOND; j++) {
neighid[i][j] = 0;
abo[i][j] = 0.0;
}
}
numbonds = 0;
FindBond(lists, numbonds);
// allocate a temporary buffer for the snapshot info
MPI_Allreduce(&numbonds,&numbonds_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world);
nbuf = 1+(numbonds_max*2+10)*nlocal_max;
memory->create(buf,nbuf,"reax/c/bonds:buf");
for (i = 0; i < nbuf; i ++) buf[i] = 0.0;
// Pass information to buffer
PassBuffer(buf, nbuf_local);
// Receive information from buffer for output
RecvBuffer(buf, nbuf, nbuf_local, nlocal_tot, numbonds_max);
memory->destroy(buf);
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::FindBond(struct _reax_list *lists, int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj;
tagint jtag;
double bo_tmp,bo_cut;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
bond_data *bo_ij;
bo_cut = reaxc->control->bg_cut;
tagint *tag = atom->tag;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
nj = 0;
for( pj = Start_Index(i, reaxc->lists); pj < End_Index(i, reaxc->lists); ++pj ) {
bo_ij = &( reaxc->lists->select.bond_list[pj] );
j = bo_ij->nbr;
jtag = tag[j];
bo_tmp = bo_ij->bo_data.BO;
if (bo_tmp > bo_cut) {
neighid[i][nj] = jtag;
abo[i][nj] = bo_tmp;
nj ++;
}
}
numneigh[i] = nj;
if (nj > numbonds) numbonds = nj;
}
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local)
{
int i, j, k, numbonds;
int nlocal = atom->nlocal;
j = 2;
buf[0] = nlocal;
for (i = 0; i < nlocal; i++) {
buf[j-1] = atom->tag[i];
buf[j+0] = atom->type[i];
buf[j+1] = reaxc->workspace->total_bond_order[i];
buf[j+2] = reaxc->workspace->nlp[i];
buf[j+3] = atom->q[i];
buf[j+4] = numneigh[i];
numbonds = nint(buf[j+4]);
for (k = 5; k < 5+numbonds; k++) {
buf[j+k] = neighid[i][k-5];
}
j += (5+numbonds);
if (atom->molecule == NULL ) buf[j] = 0.0;
else buf[j] = atom->molecule[i];
j ++;
for (k = 0; k < numbonds; k++) {
buf[j+k] = abo[i][k];
}
j += (1+numbonds);
}
nbuf_local = j - 1;
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
int natoms, int maxnum)
{
int i, j, k, itype;
int inode, nlocal_tmp, numbonds;
tagint itag,jtag;
int nlocal = atom->nlocal;
bigint ntimestep = update->ntimestep;
double sbotmp, nlptmp, avqtmp, abotmp;
double cutof3 = reaxc->control->bg_cut;
MPI_Request irequest, irequest2;
if (me == 0 ){
fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
fprintf(fp,"# \n");
fprintf(fp,"# Number of particles %d \n",natoms);
fprintf(fp,"# \n");
fprintf(fp,"# Max number of bonds per atom %d with "
"coarse bond order cutoff %5.3f \n",maxnum,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");
}
j = 2;
if (me == 0) {
for (inode = 0; inode < nprocs; inode ++) {
if (inode == 0) {
nlocal_tmp = nlocal;
} else {
MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
MPI_Wait(&irequest,MPI_STATUS_IGNORE);
nlocal_tmp = nint(buf[0]);
}
j = 2;
for (i = 0; i < nlocal_tmp; i ++) {
itag = static_cast<tagint> (buf[j-1]);
itype = nint(buf[j+0]);
sbotmp = buf[j+1];
nlptmp = buf[j+2];
avqtmp = buf[j+3];
numbonds = nint(buf[j+4]);
fprintf(fp," " TAGINT_FORMAT " %d %d",itag,itype,numbonds);
for (k = 5; k < 5+numbonds; k++) {
jtag = static_cast<tagint> (buf[j+k]);
fprintf(fp," " TAGINT_FORMAT,jtag);
}
j += (5+numbonds);
fprintf(fp," " TAGINT_FORMAT,static_cast<tagint> (buf[j]));
j ++;
for (k = 0; k < numbonds; k++) {
abotmp = buf[j+k];
fprintf(fp,"%14.3f",abotmp);
}
j += (1+numbonds);
fprintf(fp,"%14.3f%14.3f%14.3f\n",sbotmp,nlptmp,avqtmp);
}
}
} else {
MPI_Isend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world,&irequest2);
MPI_Wait(&irequest2,MPI_STATUS_IGNORE);
}
if(me ==0) fprintf(fp,"# \n");
}
/* ---------------------------------------------------------------------- */
int FixReaxCBonds::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;
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::destroy()
{
memory->destroy(abo);
memory->destroy(neighid);
memory->destroy(numneigh);
}
/* ---------------------------------------------------------------------- */
void FixReaxCBonds::allocate()
{
memory->create(abo,nmax,MAXREAXBOND,"reax/c/bonds:abo");
memory->create(neighid,nmax,MAXREAXBOND,"reax/c/bonds:neighid");
memory->create(numneigh,nmax,"reax/c/bonds:numneigh");
}
/* ---------------------------------------------------------------------- */
double FixReaxCBonds::memory_usage()
{
double bytes;
bytes = 3.0*nmax*sizeof(double);
bytes += nmax*sizeof(int);
bytes += 1.0*nmax*MAXREAXBOND*sizeof(double);
bytes += 1.0*nmax*MAXREAXBOND*sizeof(int);
return bytes;
}

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