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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9772 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-04-12 22:24:18 +00:00
parent a741fcf859
commit d8509b5842
2 changed files with 54 additions and 48 deletions
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12
src/dump_cfg.cpp
View File

@ -143,7 +143,6 @@ void DumpCFG::write_header(bigint n)
} else if (unwrapflag == 1) scale = UNWRAPEXPAND; } else if (unwrapflag == 1) scale = UNWRAPEXPAND;
else scale = 1.0; else scale = 1.0;
if (me == 0 || multiproc) {
char str[64]; char str[64];
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
fprintf(fp,str,n); fprintf(fp,str,n);
@ -161,19 +160,12 @@ void DumpCFG::write_header(bigint n)
fprintf(fp,"entry_count = %d\n",nfield-2); fprintf(fp,"entry_count = %d\n",nfield-2);
for (int i = 0; i < nfield-5; i++) for (int i = 0; i < nfield-5; i++)
fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]); fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
}
// calculate total # of data lines to be written on a writing proc // allocate memory needed for data rearrangement
if (multiproc) nchosen = nme; nchosen = static_cast<int> (n);
else MPI_Reduce(&nme,&nchosen,1,MPI_INT,MPI_SUM,0,world);
// allocate memory needed for data rearrangement on writing proc(s)
if (multiproc || me == 0) {
if (rbuf) memory->destroy(rbuf); if (rbuf) memory->destroy(rbuf);
memory->create(rbuf,nchosen,size_one,"dump:rbuf"); memory->create(rbuf,nchosen,size_one,"dump:rbuf");
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

48
src/write_data.cpp
View File

@ -117,6 +117,18 @@ void WriteData::write(char *file)
if (natoms != atom->natoms && output->thermo->lostflag == ERROR) if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write data file"); error->all(FLERR,"Atom count is inconsistent, cannot write data file");
// sum up bond,angle counts
// may be different than atom->nbonds,nangles if broken/turned-off
if (atom->nbonds || atom->nbondtypes) {
nbonds_local = atom->avec->pack_bond(NULL);
MPI_Allreduce(&nbonds_local,&nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->nangles || atom->nangletypes) {
nangles_local = atom->avec->pack_angle(NULL);
MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// open data file // open data file
if (me == 0) { if (me == 0) {
@ -166,14 +178,10 @@ void WriteData::header()
fprintf(fp,"%d atom types\n",atom->ntypes); fprintf(fp,"%d atom types\n",atom->ntypes);
if (atom->nbonds || atom->nbondtypes) { if (atom->nbonds || atom->nbondtypes) {
nbonds_local = atom->avec->pack_bond(NULL);
MPI_Allreduce(&nbonds_local,&nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds); fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
fprintf(fp,"%d bond types\n",atom->nbondtypes); fprintf(fp,"%d bond types\n",atom->nbondtypes);
} }
if (atom->nangles || atom->nangletypes) { if (atom->nangles || atom->nangletypes) {
nangles_local = atom->avec->pack_angle(NULL);
MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
fprintf(fp,BIGINT_FORMAT " angles\n",nangles); fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
fprintf(fp,"%d angle types\n",atom->nangletypes); fprintf(fp,"%d angle types\n",atom->nangletypes);
} }
@ -278,6 +286,7 @@ void WriteData::atoms()
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_data(fp,recvrow,buf); atom->avec->write_data(fp,recvrow,buf);
@ -330,6 +339,7 @@ void WriteData::velocities()
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_vel(fp,recvrow,buf); atom->avec->write_vel(fp,recvrow,buf);
@ -362,7 +372,7 @@ void WriteData::bonds()
// pack my bond data into buf // pack my bond data into buf
atom->avec->pack_bond(buf); int foo = atom->avec->pack_bond(buf);
// write one chunk of atoms per proc to file // write one chunk of atoms per proc to file
// proc 0 pings each proc, receives its chunk, writes to file // proc 0 pings each proc, receives its chunk, writes to file
@ -377,10 +387,11 @@ void WriteData::bonds()
fprintf(fp,"\nBonds\n\n"); fprintf(fp,"\nBonds\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) { for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) { if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request); MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_bond(fp,recvrow,buf,index); atom->avec->write_bond(fp,recvrow,buf,index);
@ -389,7 +400,7 @@ void WriteData::bonds()
} else { } else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status); MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world); MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
} }
memory->destroy(buf); memory->destroy(buf);
@ -429,10 +440,11 @@ void WriteData::angles()
fprintf(fp,"\nAngles\n\n"); fprintf(fp,"\nAngles\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) { for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) { if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request); MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_angle(fp,recvrow,buf,index); atom->avec->write_angle(fp,recvrow,buf,index);
@ -441,7 +453,7 @@ void WriteData::angles()
} else { } else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status); MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world); MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
} }
memory->destroy(buf); memory->destroy(buf);
@ -499,10 +511,11 @@ void WriteData::dihedrals()
fprintf(fp,"\nDihedrals\n\n"); fprintf(fp,"\nDihedrals\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) { for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) { if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request); MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_dihedral(fp,recvrow,buf,index); atom->avec->write_dihedral(fp,recvrow,buf,index);
@ -511,7 +524,7 @@ void WriteData::dihedrals()
} else { } else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status); MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world); MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
} }
memory->destroy(buf); memory->destroy(buf);
@ -569,10 +582,11 @@ void WriteData::impropers()
fprintf(fp,"\nImpropers\n\n"); fprintf(fp,"\nImpropers\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) { for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) { if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request); MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world); MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status); MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow); MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow; } else recvrow = sendrow;
atom->avec->write_improper(fp,recvrow,buf,index); atom->avec->write_improper(fp,recvrow,buf,index);
@ -581,7 +595,7 @@ void WriteData::impropers()
} else { } else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status); MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world); MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
} }
memory->destroy(buf); memory->destroy(buf);