(fc5ef00c) · Commits · 郑智淋 / lammps

src/REAX/fix_reax_bonds.cpp

+16 −13

Original line number	Diff line number	Diff line
		@@ -57,7 +57,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS lmp, int narg, char *arg) :

		FixReaxBonds::~FixReaxBonds()
		{
		if (fp && me == 0) fclose(fp);
		if (me == 0) fclose(fp);
		}

		/* ---------------------------------------------------------------------- */
		@@ -93,7 +93,7 @@ void FixReaxBonds::init()
		void FixReaxBonds::end_of_step()
		{
		OutputReaxBonds(update->ntimestep,fp);
		fflush(fp);
		if (me == 0) fflush(fp);
		}

		/* ---------------------------------------------------------------------- */
		@@ -102,13 +102,12 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		{
		int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
		int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
		int node,nprocs,nlocal_tmp,itmp;
		int nprocs,nlocal_tmp,itmp;
		double cutof3;
		double *buf;
		MPI_Request irequest;
		MPI_Status istatus;

		node = me;
		MPI_Comm_size(world,&nprocs);

		nparticles = atom->nlocal;
		@@ -120,7 +119,7 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
		MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);

		if (node == 0) {
		if (me == 0) {
		fprintf(fp,"# Timestep %d \n",timestep);
		fprintf(fp,"# \n");
		fprintf(fp,"# Number of particles %d \n",nparticles_tot);
		@@ -174,8 +173,7 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		// node 0 pings each node, receives their buffer, writes to file
		// all other nodes wait for ping, send buffer to node 0

		if (node == 0) {

		if (me == 0) {
		for (int inode = 0; inode<nprocs; inode++) {
		if (inode == 0) {
		nlocal_tmp = nparticles;
		@@ -189,6 +187,7 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		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]);
		@@ -197,17 +196,21 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		sprintf(str,"numbonds > nsbmax_most");
		error->one(str);
		}

		// print connection table
		for (k=2;k<2+numbonds;k++) {

		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++) {

		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);
		}
		@@ -218,7 +221,7 @@ void FixReaxBonds::OutputReaxBonds(int timestep, FILE *fp)
		MPI_Rsend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world);
		}

		if (node == 0) fprintf(fp,"# \n");
		if (me == 0) fprintf(fp,"# \n");

		memory->sfree(buf);
		}

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