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enable write_data for atom styles with bonus data

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This commit is contained in:
Steve Plimpton
2020-07-06 17:30:45 -06:00
parent 6bf329098e
commit 7918919d30
15 changed files with 447 additions and 128 deletions
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146
src/write_data.cpp
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@ -39,6 +39,7 @@
using namespace LAMMPS_NS;
enum{II,IJ};
enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in AtomVecHybrid
/* ---------------------------------------------------------------------- */
@ -173,17 +174,6 @@ void WriteData::write(const std::string &file)
MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// check for bonus data.
if (me == 0) {
if ((atom->nellipsoids > 0)
|| (atom->nlines > 0)
|| (atom->ntris > 0)
|| (atom->nbodies > 0))
error->warning(FLERR,"System has ellipsoids, lines, triangles, or bodies. "
"Those are not yet supported by write_data. The data file "
"will thus be incomplete.");
}
// open data file
if (me == 0) {
@ -201,19 +191,30 @@ void WriteData::write(const std::string &file)
if (coeffflag) force_fields();
}
// per atom info
// do not write molecular topology for atom_style template
// per atom info in Atoms and Velocities sections
if (natoms) atoms();
if (natoms) velocities();
// molecular topology info if defined
// do not write molecular topology for atom_style template
if (atom->molecular == 1) {
if (atom->nbonds && nbonds) bonds();
if (atom->nangles && nangles) angles();
if (atom->ndihedrals) dihedrals();
if (atom->nimpropers) impropers();
}
// bonus info if defined
if (natoms && atom->ellipsoid_flag) bonus(ELLIPSOID);
if (natoms && atom->line_flag) bonus(LINE);
if (natoms && atom->tri_flag) bonus(TRIANGLE);
if (natoms && atom->body_flag) bonus(BODY);
// extra sections managed by fixes
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_section)
@ -252,6 +253,15 @@ void WriteData::header()
nimpropers,atom->nimpropertypes);
}
// bonus info
if (atom->ellipsoid_flag) fmt::print(fp,"{} ellipsoids\n",atom->nellipsoids);
if (atom->line_flag) fmt::print(fp,"{} lines\n",atom->nlines);
if (atom->tri_flag) fmt::print(fp,"{} triangles\n",atom->ntris);
if (atom->body_flag) fmt::print(fp,"{} bodies\n",atom->nbodies);
// fix info
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_header)
@ -322,10 +332,9 @@ void WriteData::force_fields()
void WriteData::atoms()
{
// communication buffer for all my Atom info
// max_size = largest buffer needed by any proc
// maxrow X ncol = largest buffer needed by any proc
int ncol = atom->avec->size_data_atom + 3;
int sendrow = atom->nlocal;
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
@ -376,10 +385,9 @@ void WriteData::atoms()
void WriteData::velocities()
{
// communication buffer for all my Atom info
// max_size = largest buffer needed by any proc
// maxrow X ncol = largest buffer needed by any proc
int ncol = atom->avec->size_velocity + 1;
int sendrow = atom->nlocal;
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
@ -430,6 +438,7 @@ void WriteData::velocities()
void WriteData::bonds()
{
// communication buffer for all my Bond info
// maxrow X ncol = largest buffer needed by any proc
int ncol = 3;
int sendrow = static_cast<int> (nbonds_local);
@ -484,6 +493,7 @@ void WriteData::bonds()
void WriteData::angles()
{
// communication buffer for all my Angle info
// maxrow X ncol = largest buffer needed by any proc
int ncol = 4;
int sendrow = static_cast<int> (nangles_local);
@ -538,27 +548,10 @@ void WriteData::angles()
void WriteData::dihedrals()
{
// communication buffer for all my Dihedral info
// max_size = largest buffer needed by any proc
// maxrow X ncol = largest buffer needed by any proc
int ncol = 5;
tagint *tag = atom->tag;
int *num_dihedral = atom->num_dihedral;
tagint **dihedral_atom2 = atom->dihedral_atom2;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int i,j;
int sendrow = 0;
if (newton_bond) {
for (i = 0; i < nlocal; i++)
sendrow += num_dihedral[i];
} else {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++)
if (tag[i] == dihedral_atom2[i][j]) sendrow++;
}
int sendrow = static_cast<int> (ndihedrals_local);
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
@ -610,29 +603,11 @@ void WriteData::dihedrals()
void WriteData::impropers()
{
// communication buffer for all my Improper info
// max_size = largest buffer needed by any proc
// maxrow X ncol = largest buffer needed by any proc
int ncol = 5;
tagint *tag = atom->tag;
int *num_improper = atom->num_improper;
tagint **improper_atom2 = atom->improper_atom2;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int i,j;
int sendrow = 0;
if (newton_bond) {
for (i = 0; i < nlocal; i++)
sendrow += num_improper[i];
} else {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_improper[i]; j++)
if (tag[i] == improper_atom2[i][j]) sendrow++;
}
int sendrow = static_cast<int> (nimpropers_local);
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
tagint **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
@ -675,6 +650,64 @@ void WriteData::impropers()
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Bonus sections of data file
flag indicates which bonus section it is
------------------------------------------------------------------------- */
void WriteData::bonus(int flag)
{
// communication buffer for all my Bonus info
// maxrow X ncol = largest buffer needed by any proc
int ncol = atom->avec->size_data_bonus_query(flag);
int sendrow = atom->avec->pack_data_bonus(NULL,flag);
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
double **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my bonus data into buf
atom->avec->pack_data_bonus(buf,flag);
// write one chunk of info per proc to file
// proc 0 pings each proc, receives its chunk, writes to file
// all other procs wait for ping, send their chunk to proc 0
int tmp,recvrow;
if (me == 0) {
MPI_Status status;
MPI_Request request;
if (flag == ELLIPSOID) fprintf(fp,"\nEllipsoids\n\n");
if (flag == LINE) fprintf(fp,"\nLines\n\n");
if (flag == TRIANGLE) fprintf(fp,"\nTriangles\n\n");
if (flag == BODY) fprintf(fp,"\nBodies\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_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_bonus(fp,recvrow,buf,flag);
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Mth section of data file owned by Fix ifix
------------------------------------------------------------------------- */
@ -682,6 +715,7 @@ void WriteData::impropers()
void WriteData::fix(int ifix, int mth)
{
// communication buffer for Fix info
// maxrow X ncol = largest buffer needed by any proc
int sendrow,ncol;
modify->fix[ifix]->write_data_section_size(mth,sendrow,ncol);