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lammps/src/write_data.cpp
Steve Plimpton f1c2a22e2d more tweaks
2024-04-08 16:25:17 -06:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "write_data.h"
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "bond.h"
#include "comm.h"
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "improper.h"
#include "label_map.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "pair.h"
#include "thermo.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
enum{II,IJ};
enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in AtomVecHybrid
/* ---------------------------------------------------------------------- */
WriteData::WriteData(LAMMPS *lmp) : Command(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
}
/* ----------------------------------------------------------------------
called as write_data command in input script
------------------------------------------------------------------------- */
void WriteData::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Write_data command before simulation box is defined");
if (narg < 1) utils::missing_cmd_args(FLERR, "write_data", error);
// if filename contains a "*", replace with current timestep
std::string file = arg[0];
std::size_t found = file.find('*');
if (found != std::string::npos)
file.replace(found,1,fmt::format("{}",update->ntimestep));
// read optional args
// noinit is a hidden arg, only used by -r command-line switch
pairflag = II;
coeffflag = 1;
fixflag = 1;
triclinic_general = 0;
lmapflag = 1;
// store current (default) setting since we may change it
int domain_triclinic_general = domain->triclinic_general;
int types_style = atom->types_style;
int noinit = 0;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "write_data pair", error);
if (strcmp(arg[iarg+1],"ii") == 0) pairflag = II;
else if (strcmp(arg[iarg+1],"ij") == 0) pairflag = IJ;
else error->all(FLERR,"Unknown write_data pair option: {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"noinit") == 0) {
noinit = 1;
iarg++;
} else if (strcmp(arg[iarg],"nocoeff") == 0) {
coeffflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"nofix") == 0) {
fixflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"triclinic/general") == 0) {
triclinic_general = 1;
iarg++;
} else if (strcmp(arg[iarg],"nolabelmap") == 0) {
lmapflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"types") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "write_data types", error);
if (strcmp(arg[iarg+1],"numeric") == 0) atom->types_style = Atom::NUMERIC;
else if (strcmp(arg[iarg+1],"labels") == 0) atom->types_style = Atom::LABELS;
else error->all(FLERR,"Unknown write_data types option: {}", arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Unknown write_data keyword: {}", arg[iarg]);
}
// temporarily disable domain->triclinic_general if output not requested
if (triclinic_general && !domain->triclinic_general)
error->all(FLERR,"Write_data triclinic/general for system "
"that is not general triclinic");
if (!triclinic_general && domain->triclinic_general)
domain->triclinic_general = 0;
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
// exception is when called by -r command-line switch
// then write_data immediately follows reading of restart file
// assume that read_restart initialized necessary values
// if don't make exception:
// pair->init() can fail due to various unset values:
// e.g. pair hybrid coeffs, dpd ghost-atom velocity setting
if (noinit == 0) {
if (comm->me == 0) utils::logmesg(lmp,"System init for write_data ...\n");
lmp->init();
// move atoms to new processors before writing file
// do setup_pre_exchange to force update of per-atom info if needed
// enforce PBC in case atoms are outside box
// call borders() to rebuild atom map since exchange() destroys map
modify->setup_pre_exchange();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
}
write(file);
// restore saved settings
domain->triclinic_general = domain_triclinic_general;
atom->types_style = types_style;
}
/* ----------------------------------------------------------------------
called from command()
might later let it be directly called within run/minimize loop
------------------------------------------------------------------------- */
void WriteData::write(const std::string &file)
{
// special case where reneighboring is not done in integrator
// on timestep data file is written (due to build_once being set)
// if box is changing, must be reset, else data file will have
// wrong box size and atoms will be lost when data file is read
// other calls to pbc and domain and comm are not made,
// b/c they only make sense if reneighboring is actually performed
//if (neighbor->build_once) domain->reset_box();
// natoms = sum of nlocal = value to write into data file
// if unequal and thermo lostflag is "error", don't write data file
bigint nblocal = atom->nlocal;
bigint natoms;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && output->thermo->lostflag == Thermo::ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write data file");
// sum up bond,angle,dihedral,improper counts
// may be different than atom->nbonds,nangles, etc. if broken/turned-off
if (atom->molecular == Atom::MOLECULAR && (atom->nbonds || atom->nbondtypes)) {
nbonds_local = atom->avec->pack_bond(nullptr);
MPI_Allreduce(&nbonds_local,&nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->molecular == Atom::MOLECULAR && (atom->nangles || atom->nangletypes)) {
nangles_local = atom->avec->pack_angle(nullptr);
MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->molecular == Atom::MOLECULAR && (atom->ndihedrals || atom->ndihedraltypes)) {
ndihedrals_local = atom->avec->pack_dihedral(nullptr);
MPI_Allreduce(&ndihedrals_local,&ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->molecular == Atom::MOLECULAR && (atom->nimpropers || atom->nimpropertypes)) {
nimpropers_local = atom->avec->pack_improper(nullptr);
MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// open data file
if (me == 0) {
fp = fopen(file.c_str(),"w");
if (fp == nullptr)
error->one(FLERR,"Cannot open data file {}: {}", file, utils::getsyserror());
}
// proc 0 writes header, ntype-length arrays, force fields
// label map must come before coeffs
if (me == 0) {
header();
if (lmapflag && atom->labelmapflag) atom->lmap->write_data(fp);
type_arrays();
if (coeffflag) force_fields();
}
// if general triclinic output:
// reset internal per-atom data that needs rotation
if (domain->triclinic_general) atom->avec->write_data_restricted_to_general();
// per atom info in Atoms and Velocities sections
// must not write velocities without tags since we cannot read them back
if (natoms) atoms();
if (atom->tag_enable) {
if (natoms) velocities();
} else {
if (me == 0)
error->warning(FLERR, "Not writing Velocities section of data file without atom IDs");
}
// molecular topology info if defined
// do not write molecular topology for atom_style template
if (atom->molecular == Atom::MOLECULAR) {
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 (auto &ifix : modify->get_fix_list())
if (ifix->wd_section)
for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m);
// if general triclinic output:
// restore internal per-atom data that was rotated
if (domain->triclinic_general) atom->avec->write_data_restore_restricted();
// close data file
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out data file header
------------------------------------------------------------------------- */
void WriteData::header()
{
fmt::print(fp,"LAMMPS data file via write_data, version {}, timestep = {}, units = {}\n\n",
lmp->version, update->ntimestep, update->unit_style);
fmt::print(fp,"{} atoms\n{} atom types\n",atom->natoms,atom->ntypes);
// only write out number of types for atom style template
if (atom->molecular == Atom::MOLECULAR) {
if (atom->nbonds || atom->nbondtypes)
fmt::print(fp,"{} bonds\n{} bond types\n",
nbonds,atom->nbondtypes);
if (atom->nangles || atom->nangletypes)
fmt::print(fp,"{} angles\n{} angle types\n",
nangles,atom->nangletypes);
if (atom->ndihedrals || atom->ndihedraltypes)
fmt::print(fp,"{} dihedrals\n{} dihedral types\n",
ndihedrals,atom->ndihedraltypes);
if (atom->nimpropers || atom->nimpropertypes)
fmt::print(fp,"{} impropers\n{} improper types\n",
nimpropers,atom->nimpropertypes);
}
if (atom->molecular == Atom::TEMPLATE) {
if (atom->nbondtypes) fmt::print(fp,"{} bond types\n",atom->nbondtypes);
if (atom->nangletypes) fmt::print(fp,"{} angle types\n",atom->nangletypes);
if (atom->ndihedraltypes) fmt::print(fp,"{} dihedral types\n",atom->ndihedraltypes);
if (atom->nimpropertypes) fmt::print(fp,"{} improper types\n",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 (auto &ifix : modify->get_fix_list())
if (ifix->wd_header)
for (int m = 0; m < ifix->wd_header; m++)
ifix->write_data_header(fp,m);
// box info: orthogonal, restricted triclinic, or general triclinic (if requested)
if (!domain->triclinic_general) {
fmt::print(fp,"\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n",
domain->boxlo[0],domain->boxhi[0],
domain->boxlo[1],domain->boxhi[1],
domain->boxlo[2],domain->boxhi[2]);
if (domain->triclinic)
fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
} else if (domain->triclinic_general) {
fmt::print(fp,"\n{} {} {} avec\n{} {} {} bvec\n{} {} {} cvec\n",
domain->avec[0],domain->avec[1],domain->avec[2],
domain->bvec[0],domain->bvec[1],domain->bvec[2],
domain->cvec[0],domain->cvec[1],domain->cvec[2]);
fmt::print(fp,"{} {} {} abc origin\n",
domain->boxlo[0],domain->boxlo[1],domain->boxlo[2]);
}
}
/* ----------------------------------------------------------------------
proc 0 writes out any type-based arrays that are defined
------------------------------------------------------------------------- */
void WriteData::type_arrays()
{
if (atom->mass) {
double *mass = atom->mass;
fputs("\nMasses\n\n",fp);
for (int i = 1; i <= atom->ntypes; i++)
fmt::print(fp,"{} {:.16g}\n",i,mass[i]);
}
}
/* ----------------------------------------------------------------------
proc 0 writes out force field info
------------------------------------------------------------------------- */
void WriteData::force_fields()
{
if (force->pair && force->pair->writedata) {
if (pairflag == II) {
if ((comm->me == 0) && (force->pair->mixed_flag == 0))
error->warning(FLERR,"Not all mixed pair coeffs generated from mixing. "
"Use write_data with 'pair ij' option to store all pair coeffs.");
fmt::print(fp,"\nPair Coeffs # {}\n\n", force->pair_style);
force->pair->write_data(fp);
} else if (pairflag == IJ) {
fmt::print(fp,"\nPairIJ Coeffs # {}\n\n", force->pair_style);
force->pair->write_data_all(fp);
}
}
if (force->bond && force->bond->writedata && atom->nbondtypes) {
fmt::print(fp,"\nBond Coeffs # {}\n\n", force->bond_style);
force->bond->write_data(fp);
}
if (force->angle && force->angle->writedata && atom->nangletypes) {
fmt::print(fp,"\nAngle Coeffs # {}\n\n", force->angle_style);
force->angle->write_data(fp);
}
if (force->dihedral && force->dihedral->writedata && atom->ndihedraltypes) {
fmt::print(fp,"\nDihedral Coeffs # {}\n\n", force->dihedral_style);
force->dihedral->write_data(fp);
}
if (force->improper && force->improper->writedata && atom->nimpropertypes) {
fmt::print(fp,"\nImproper Coeffs # {}\n\n", force->improper_style);
force->improper->write_data(fp);
}
}
/* ----------------------------------------------------------------------
write out Atoms section of data file
------------------------------------------------------------------------- */
void WriteData::atoms()
{
// communication buffer for all my Atom info
// 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);
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 atom data into buf
atom->avec->pack_data(buf);
// write one chunk of atoms 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;
fmt::print(fp,"\nAtoms # {}\n\n",atom->atom_style);
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(fp,recvrow,buf);
}
} 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 Velocities section of data file
------------------------------------------------------------------------- */
void WriteData::velocities()
{
// communication buffer for all my Atom info
// 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);
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 velocity data into buf
atom->avec->pack_vel(buf);
// write one chunk of velocities 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;
fputs("\nVelocities\n\n",fp);
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_vel(fp,recvrow,buf);
}
} 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 Bonds section of data file
------------------------------------------------------------------------- */
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);
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");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my bond data into buf
atom->avec->pack_bond(buf);
// 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;
int index = 1;
if (me == 0) {
MPI_Status status;
MPI_Request request;
fputs("\nBonds\n\n",fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&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,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Angles section of data file
------------------------------------------------------------------------- */
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);
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");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my angle data into buf
atom->avec->pack_angle(buf);
// 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;
int index = 1;
if (me == 0) {
MPI_Status status;
MPI_Request request;
fputs("\nAngles\n\n",fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_angle(fp,recvrow,buf,index);
index += recvrow;
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Dihedrals section of data file
------------------------------------------------------------------------- */
void WriteData::dihedrals()
{
// communication buffer for all my Dihedral info
// maxrow X ncol = largest buffer needed by any proc
int ncol = 5;
int sendrow = static_cast<int> (ndihedrals_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");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my dihedral data into buf
atom->avec->pack_dihedral(buf);
// 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;
int index = 1;
if (me == 0) {
MPI_Status status;
MPI_Request request;
fputs("\nDihedrals\n\n",fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_dihedral(fp,recvrow,buf,index);
index += recvrow;
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Impropers section of data file
------------------------------------------------------------------------- */
void WriteData::impropers()
{
// communication buffer for all my Improper info
// maxrow X ncol = largest buffer needed by any proc
int ncol = 5;
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");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
// pack my improper data into buf
atom->avec->pack_improper(buf);
// 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;
int index = 1;
if (me == 0) {
MPI_Status status;
MPI_Request request;
fputs("\nImpropers\n\n",fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
atom->avec->write_improper(fp,recvrow,buf,index);
index += recvrow;
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
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
// maxvalues = largest buffer needed by any proc
int nvalues = atom->avec->pack_data_bonus(nullptr,flag);
int maxvalues;
MPI_Allreduce(&nvalues,&maxvalues,1,MPI_INT,MPI_MAX,world);
double *buf = nullptr;
if (me == 0) memory->create(buf,MAX(1,maxvalues),"write_data:buf");
else memory->create(buf,MAX(1,nvalues),"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;
if (me == 0) {
MPI_Status status;
MPI_Request request;
if (flag == ELLIPSOID) fputs("\nEllipsoids\n\n",fp);
if (flag == LINE) fputs("\nLines\n\n",fp);
if (flag == TRIANGLE) fputs("\nTriangles\n\n",fp);
if (flag == BODY) fputs("\nBodies\n\n",fp);
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxvalues,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,&nvalues);
}
atom->avec->write_data_bonus(fp,nvalues,buf,flag);
}
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(buf,nvalues,MPI_DOUBLE,0,0,world);
}
memory->destroy(buf);
}
/* ----------------------------------------------------------------------
write out Mth section of data file owned by Fix ifix
------------------------------------------------------------------------- */
void WriteData::fix(Fix *ifix, int mth)
{
// communication buffer for Fix info
// maxrow X ncol = largest buffer needed by any proc
int sendrow,ncol;
ifix->write_data_section_size(mth,sendrow,ncol);
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 fix data into buf
ifix->write_data_section_pack(mth,buf);
// 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;
int index = 1;
if (me == 0) {
MPI_Status status;
MPI_Request request;
ifix->write_data_section_keyword(mth,fp);
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;
ifix->write_data_section(mth,fp,recvrow,buf,index);
index += recvrow;
}
} 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);
}
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