241 lines
6.8 KiB
C++
241 lines
6.8 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Aidan Thompson (Sandia)
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "fix_reax_bonds.h"
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#include "lmptype.h"
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#include "pair_reax_fortran.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "modify.h"
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#include "compute.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 5) error->all("Illegal fix reax/bonds command");
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MPI_Comm_rank(world,&me);
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nevery = atoi(arg[3]);
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if (nevery < 1) error->all("Illegal fix reax/bonds command");
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if (me == 0) {
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fp = fopen(arg[4],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]);
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error->one(str);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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FixReaxBonds::~FixReaxBonds()
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{
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if (me == 0) fclose(fp);
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}
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/* ---------------------------------------------------------------------- */
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int FixReaxBonds::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ----------------------------------------------------------------------
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perform initial write
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------------------------------------------------------------------------- */
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void FixReaxBonds::setup(int vflag)
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{
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end_of_step();
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxBonds::init()
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{
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// insure ReaxFF is defined
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if (force->pair_match("reax",1) == NULL)
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error->all("Cannot use fix reax/bonds without pair_style reax");
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxBonds::end_of_step()
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{
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OutputReaxBonds(update->ntimestep,fp);
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if (me == 0) fflush(fp);
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}
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/* ---------------------------------------------------------------------- */
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void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
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{
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int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
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int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
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int nprocs,nlocal_tmp,itmp;
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double cutof3;
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double *buf;
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MPI_Request irequest;
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MPI_Status istatus;
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MPI_Comm_size(world,&nprocs);
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nparticles = atom->nlocal;
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nparticles_tot = static_cast<int> (atom->natoms);
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mbond = ReaxParams::mbond;
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FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax);
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FORTRAN(getcutof3,GETCUTOF3)(&cutof3);
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MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
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MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
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if (me == 0) {
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char fstr[32];
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sprintf(fstr,"# Timestep %d \n",BIGINT_FORMAT);
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fprintf(fp,fstr,ntimestep);
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fprintf(fp,"# \n");
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fprintf(fp,"# Number of particles %d \n",nparticles_tot);
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fprintf(fp,"# \n");
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fprintf(fp,"# Max.number of bonds per atom %d with "
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"coarse bond order cutoff %5.3f \n",
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nsbmax_most,cutof3);
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fprintf(fp,"# Particle connection table and bond orders \n");
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fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
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}
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// allocate a temporary buffer for the snapshot info
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// big enough for largest number of atoms on any one proc
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// nbuf_local = size of local buffer for table of atom bonds
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nbuf = 1+(2*nsbmax_most+7)*most;
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buf = (double *) memory->smalloc(nbuf*sizeof(double),"reax/bonds:buf");
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j = 2;
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jn = ReaxParams::nat;
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buf[0] = nparticles;
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for (int iparticle=0;iparticle<nparticles;iparticle++) {
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buf[j-1] = atom->tag[iparticle]; //atom tag
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buf[j+0] = FORTRAN(cbkia,CBKIA).iag[iparticle]; //atom type
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buf[j+1] = FORTRAN(cbkia,CBKIA).iag[iparticle+jn]; //no.bonds
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int k;
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numbonds = nint(buf[j+1]);
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// connection table based on coarse bond order cutoff (> cutof3)
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for (k=2;k<2+numbonds;k++) {
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ii = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*k];
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buf[j+k] = FORTRAN(cbkc,CBKC).itag[ii-1];
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}
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buf[j+k]=FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(mbond+2)]; //molec.id
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j+=(3+numbonds);
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// bond orders (> cutof3)
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for (k=0;k<numbonds;k++) {
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ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
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buf[j+k] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
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}
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// sum of bond orders (abo), no. of lone pairs (vlp), charge (ch)
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buf[j+k] = FORTRAN(cbkabo,CBKABO).abo[iparticle];
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buf[j+k+1] = FORTRAN(cbklonpar,CBKLONPAR).vlp[iparticle];
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// buf[j+k+2] = FORTRAN(cbkch,CBKCH).ch[iparticle];
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buf[j+k+2] = atom->q[iparticle];
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j+=(4+numbonds);
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}
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nbuf_local = j-1;
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// node 0 pings each node, receives their buffer, writes to file
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// all other nodes wait for ping, send buffer to node 0
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if (me == 0) {
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for (int inode = 0; inode<nprocs; inode++) {
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if (inode == 0) {
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nlocal_tmp = nparticles;
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} else {
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MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
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MPI_Send(&itmp,0,MPI_INT,inode,0,world);
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MPI_Wait(&irequest,&istatus);
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nlocal_tmp = nint(buf[0]);
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}
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j = 2;
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for (int iparticle=0;iparticle<nlocal_tmp;iparticle++) {
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// print atom tag, atom type, no.bonds
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fprintf(fp," %d %d %d",nint(buf[j-1]),nint(buf[j+0]),nint(buf[j+1]));
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int k;
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numbonds = nint(buf[j+1]);
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if (numbonds > nsbmax_most) {
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char str[128];
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sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
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error->one(str);
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}
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// print connection table
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for (k=2;k<2+numbonds;k++)
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fprintf(fp," %d",nint(buf[j+k]));
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fprintf(fp," %d",nint(buf[j+k]));
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j+=(3+numbonds);
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// print bond orders
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for (k=0;k<numbonds;k++)
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fprintf(fp,"%14.3f",buf[j+k]);
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// print sum of bond orders, no. of lone pairs, charge
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fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j+k],buf[j+k+1],buf[j+k+2]);
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j+=(4+numbonds);
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}
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}
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} else {
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MPI_Recv(&itmp,0,MPI_INT,0,0,world,&istatus);
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MPI_Rsend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world);
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}
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if (me == 0) fprintf(fp,"# \n");
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memory->sfree(buf);
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}
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/* ---------------------------------------------------------------------- */
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int FixReaxBonds::nint(const double &r)
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{
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int i = 0;
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if (r>0.0) i = static_cast<int>(r+0.5);
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else if (r<0.0) i = static_cast<int>(r-0.5);
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return i;
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}
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