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write_data.cpp
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Thu, Nov 14, 21:18

write_data.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 <mpi.h>
#include <string.h>
#include "write_data.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "universe.h"
#include "comm.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
enum{II,IJ};
/* ---------------------------------------------------------------------- */
WriteData::WriteData(LAMMPS *lmp) : Pointers(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) error->all(FLERR,"Illegal write_data command");
// if filename contains a "*", replace with current timestep
char *ptr;
int n = strlen(arg[0]) + 16;
char *file = new char[n];
if ((ptr = strchr(arg[0],'*'))) {
*ptr = '\0';
sprintf(file,"%s" BIGINT_FORMAT "%s",arg[0],update->ntimestep,ptr+1);
} else strcpy(file,arg[0]);
// read optional args
// noinit is a hidden arg, only used by -r command-line switch
pairflag = II;
coeffflag = 1;
int noinit = 0;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal write_data command");
if (strcmp(arg[iarg+1],"ii") == 0) pairflag = II;
else if (strcmp(arg[iarg+1],"ij") == 0) pairflag = IJ;
else error->all(FLERR,"Illegal write_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"noinit") == 0) {
noinit = 1;
iarg++;
} else if (strcmp(arg[iarg],"nocoeff") == 0) {
coeffflag = 0;
iarg++;
} else error->all(FLERR,"Illegal write_data command");
}
// 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 && screen)
fprintf(screen,"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);
delete [] file;
}
/* ----------------------------------------------------------------------
called from command()
might later let it be directly called within run/minimize loop
------------------------------------------------------------------------- */
void WriteData::write(char *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 == 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->molecular == 1 && (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->molecular == 1 && (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) {
fp = fopen(file,"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open data file %s",file);
error->one(FLERR,str);
}
}
// proc 0 writes header, ntype-length arrays, force fields
if (me == 0) {
header();
type_arrays();
if (coeffflag) force_fields();
}
// per atom info
// do not write molecular topology for atom_style template
if (natoms) atoms();
if (natoms) velocities();
if (atom->molecular == 1) {
if (atom->nbonds && nbonds) bonds();
if (atom->nangles && nangles) angles();
if (atom->ndihedrals) dihedrals();
if (atom->nimpropers) impropers();
}
// extra sections managed by fixes
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_section)
for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
// close data file
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out data file header
------------------------------------------------------------------------- */
void WriteData::header()
{
fprintf(fp,"LAMMPS data file via write_data, version %s, "
"timestep = " BIGINT_FORMAT "\n",
universe->version,update->ntimestep);
fprintf(fp,"\n");
fprintf(fp,BIGINT_FORMAT " atoms\n",atom->natoms);
fprintf(fp,"%d atom types\n",atom->ntypes);
// do not write molecular topology info for atom_style template
if (atom->molecular == 1) {
if (atom->nbonds || atom->nbondtypes) {
fprintf(fp,BIGINT_FORMAT " bonds\n",nbonds);
fprintf(fp,"%d bond types\n",atom->nbondtypes);
}
if (atom->nangles || atom->nangletypes) {
fprintf(fp,BIGINT_FORMAT " angles\n",nangles);
fprintf(fp,"%d angle types\n",atom->nangletypes);
}
if (atom->ndihedrals || atom->ndihedraltypes) {
fprintf(fp,BIGINT_FORMAT " dihedrals\n",atom->ndihedrals);
fprintf(fp,"%d dihedral types\n",atom->ndihedraltypes);
}
if (atom->nimpropers || atom->nimpropertypes) {
fprintf(fp,BIGINT_FORMAT " impropers\n",atom->nimpropers);
fprintf(fp,"%d improper types\n",atom->nimpropertypes);
}
}
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->wd_header)
for (int m = 0; m < modify->fix[i]->wd_header; m++)
modify->fix[i]->write_data_header(fp,m);
fprintf(fp,"\n");
fprintf(fp,"%-1.16e %-1.16e xlo xhi\n",domain->boxlo[0],domain->boxhi[0]);
fprintf(fp,"%-1.16e %-1.16e ylo yhi\n",domain->boxlo[1],domain->boxhi[1]);
fprintf(fp,"%-1.16e %-1.16e zlo zhi\n",domain->boxlo[2],domain->boxhi[2]);
if (domain->triclinic)
fprintf(fp,"%-1.16e %-1.16e %-1.16e xy xz yz\n",
domain->xy,domain->xz,domain->yz);
}
/* ----------------------------------------------------------------------
proc 0 writes out any type-based arrays that are defined
------------------------------------------------------------------------- */
void WriteData::type_arrays()
{
if (atom->mass) {
double *mass = atom->mass;
fprintf(fp,"\nMasses\n\n");
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
}
}
/* ----------------------------------------------------------------------
proc 0 writes out force field info
------------------------------------------------------------------------- */
void WriteData::force_fields()
{
if (force->pair && force->pair->writedata) {
if (pairflag == II) {
fprintf(fp,"\nPair Coeffs # %s\n\n", force->pair_style);
force->pair->write_data(fp);
} else if (pairflag == IJ) {
fprintf(fp,"\nPairIJ Coeffs # %s\n\n", force->pair_style);
force->pair->write_data_all(fp);
}
}
if (force->bond && force->bond->writedata && atom->nbondtypes) {
fprintf(fp,"\nBond Coeffs # %s\n\n", force->bond_style);
force->bond->write_data(fp);
}
if (force->angle && force->angle->writedata && atom->nangletypes) {
fprintf(fp,"\nAngle Coeffs # %s\n\n", force->angle_style);
force->angle->write_data(fp);
}
if (force->dihedral && force->dihedral->writedata && atom->ndihedraltypes) {
fprintf(fp,"\nDihedral Coeffs # %s\n\n", force->dihedral_style);
force->dihedral->write_data(fp);
}
if (force->improper && force->improper->writedata && atom->nimpropertypes) {
fprintf(fp,"\nImproper Coeffs # %s\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
// max_size = 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;
fprintf(fp,"\nAtoms # %s\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
// max_size = 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;
fprintf(fp,"\nVelocities\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_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
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;
fprintf(fp,"\nBonds\n\n");
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
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;
fprintf(fp,"\nAngles\n\n");
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
// max_size = 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 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;
fprintf(fp,"\nDihedrals\n\n");
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
// max_size = 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 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;
fprintf(fp,"\nImpropers\n\n");
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 Mth section of data file owned by Fix ifix
------------------------------------------------------------------------- */
void WriteData::fix(int ifix, int mth)
{
// communication buffer for Fix info
int sendrow,ncol;
modify->fix[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
modify->fix[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;
modify->fix[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;
modify->fix[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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