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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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This commit is contained in:
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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52
src/write_data.cpp
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@ -117,6 +117,18 @@ void WriteData::write(char *file)
if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
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
if (me == 0) {
@ -166,14 +178,10 @@ void WriteData::header()
fprintf(fp,"%d atom types\n",atom->ntypes);
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,"%d bond types\n",atom->nbondtypes);
}
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,"%d angle types\n",atom->nangletypes);
}
@ -278,8 +286,9 @@ void WriteData::atoms()
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_data(fp,recvrow,buf);
}
@ -330,6 +339,7 @@ void WriteData::velocities()
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_vel(fp,recvrow,buf);
@ -362,7 +372,7 @@ void WriteData::bonds()
// 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
// proc 0 pings each proc, receives its chunk, writes to file
@ -377,19 +387,20 @@ void WriteData::bonds()
fprintf(fp,"\nBonds\n\n");
for (int iproc = 0; iproc < nprocs; 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_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_bond(fp,recvrow,buf,index);
index += recvrow;
}
} else {
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);
@ -429,10 +440,11 @@ void WriteData::angles()
fprintf(fp,"\nAngles\n\n");
for (int iproc = 0; iproc < nprocs; 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_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_angle(fp,recvrow,buf,index);
@ -441,7 +453,7 @@ void WriteData::angles()
} else {
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);
@ -499,10 +511,11 @@ void WriteData::dihedrals()
fprintf(fp,"\nDihedrals\n\n");
for (int iproc = 0; iproc < nprocs; 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_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_dihedral(fp,recvrow,buf,index);
@ -511,7 +524,7 @@ void WriteData::dihedrals()
} else {
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);
@ -569,10 +582,11 @@ void WriteData::impropers()
fprintf(fp,"\nImpropers\n\n");
for (int iproc = 0; iproc < nprocs; 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_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
MPI_Get_count(&status,MPI_INT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_improper(fp,recvrow,buf,index);
@ -581,7 +595,7 @@ void WriteData::impropers()
} else {
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);