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dump_h5md.cpp
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Wed, Nov 6, 19:33

dump_h5md.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.
Contributing author: Pierre de Buyl (KU Leuven)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <limits.h>
#include "ch5md.h"
#include "dump_h5md.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "output.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "version.h"
using namespace LAMMPS_NS;
#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
/** Scan common options for the dump elements
*/
static int element_args(int narg, char **arg, int *every)
{
int iarg=0;
while (iarg<narg) {
if (strcmp(arg[iarg], "every")==0) {
if (narg<2) return -1;
*every = atoi(arg[iarg+1]);
iarg+=2;
} else {
break;
}
}
return iarg;
}
/* ---------------------------------------------------------------------- */
DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg<6) error->all(FLERR,"Illegal dump h5md command");
if (binary || compressed || multifile || multiproc)
error->all(FLERR,"Invalid dump h5md filename");
if (domain->triclinic!=0)
error->all(FLERR,"Invalid domain for dump h5md. Only triclinic domains supported.");
size_one = 6;
sort_flag = 1;
sortcol = 0;
format_default = NULL;
flush_flag = 0;
unwrap_flag = 0;
datafile_from_dump = -1;
author_name=NULL;
every_dump = force->inumeric(FLERR,arg[3]);
every_position = every_image = -1;
every_velocity = every_force = every_species = -1;
every_charge = -1;
do_box=true;
create_group=true;
bool box_is_set, create_group_is_set;
box_is_set = create_group_is_set = false;
int iarg=5;
int n_parsed, default_every;
size_one=0;
if (every_dump==0) default_every=0; else default_every=1;
while (iarg<narg) {
if (strcmp(arg[iarg], "position")==0) {
every_position=default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_position);
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
iarg += n_parsed;
size_one+=domain->dimension;
} else if (strcmp(arg[iarg], "image")==0) {
if (every_position<0) error->all(FLERR, "Illegal dump h5md command");
iarg+=1;
size_one+=domain->dimension;
every_image = every_position;
} else if (strcmp(arg[iarg], "velocity")==0) {
every_velocity = default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_velocity);
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
iarg += n_parsed;
size_one+=domain->dimension;
} else if (strcmp(arg[iarg], "force")==0) {
every_force = default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_force);
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
iarg += n_parsed;
size_one+=domain->dimension;
} else if (strcmp(arg[iarg], "species")==0) {
every_species=default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_species);
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
iarg += n_parsed;
size_one+=1;
} else if (strcmp(arg[iarg], "charge")==0) {
if (!atom->q_flag)
error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
every_charge = default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_charge);
if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
iarg += n_parsed;
size_one+=1;
} else if (strcmp(arg[iarg], "file_from")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
if (box_is_set||create_group_is_set)
error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
if (idump == output->ndump) error->all(FLERR,"Cound not find dump_modify ID");
datafile_from_dump = idump;
do_box=false;
create_group=false;
iarg+=2;
} else if (strcmp(arg[iarg], "box")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
box_is_set = true;
if (strcmp(arg[iarg+1], "yes")==0)
do_box=true;
else if (strcmp(arg[iarg+1], "no")==0)
do_box=false;
else
error->all(FLERR, "Illegal dump h5md command");
iarg+=2;
} else if (strcmp(arg[iarg], "create_group")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
create_group_is_set = true;
if (strcmp(arg[iarg+1], "yes")==0)
create_group=true;
else if (strcmp(arg[iarg+1], "no")==0) {
create_group=false;
}
else
error->all(FLERR, "Illegal dump h5md command");
iarg+=2;
} else if (strcmp(arg[iarg], "author")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
if (author_name==NULL) {
author_name = new char[strlen(arg[iarg])+1];
strcpy(author_name, arg[iarg+1]);
} else {
error->all(FLERR, "Illegal dump h5md command: author argument repeated");
}
iarg+=2;
} else {
error->all(FLERR, "Invalid argument to dump h5md");
}
}
// allocate global array for atom coords
bigint n = group->count(igroup);
natoms = static_cast<int> (n);
if (every_position>=0)
memory->create(dump_position,domain->dimension*natoms,"dump:position");
if (every_image>=0)
memory->create(dump_image,domain->dimension*natoms,"dump:image");
if (every_velocity>=0)
memory->create(dump_velocity,domain->dimension*natoms,"dump:velocity");
if (every_force>=0)
memory->create(dump_force,domain->dimension*natoms,"dump:force");
if (every_species>=0)
memory->create(dump_species,natoms,"dump:species");
if (every_charge>=0)
memory->create(dump_charge,natoms,"dump:charge");
openfile();
ntotal = 0;
}
/* ---------------------------------------------------------------------- */
DumpH5MD::~DumpH5MD()
{
if (every_position>=0) {
memory->destroy(dump_position);
if (me==0) {
h5md_close_element(particles_data.position);
if (do_box)
h5md_close_element(particles_data.box_edges);
}
}
if (every_image>=0) {
memory->destroy(dump_image);
if (me==0) h5md_close_element(particles_data.image);
}
if (every_velocity>=0) {
memory->destroy(dump_velocity);
if (me==0) h5md_close_element(particles_data.velocity);
}
if (every_force>=0) {
memory->destroy(dump_force);
if (me==0) h5md_close_element(particles_data.force);
}
if (every_species>=0) {
memory->destroy(dump_species);
if (me==0) h5md_close_element(particles_data.species);
}
if (every_charge>=0) {
memory->destroy(dump_charge);
if (me==0) h5md_close_element(particles_data.charge);
}
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::init_style()
{
if (sort_flag == 0 || sortcol != 0)
error->all(FLERR,"Dump h5md requires sorting by atom ID");
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::openfile()
{
char *group_name;
int group_name_length;
int dims[2];
char *boundary[3];
for (int i=0; i<3; i++) {
boundary[i] = new char[9];
if (domain->periodicity[i]==1) {
strcpy(boundary[i], "periodic");
} else {
strcpy(boundary[i], "none");
}
}
if (me == 0) {
if (datafile_from_dump<0) {
if (author_name==NULL) {
datafile = h5md_create_file(filename, "N/A", NULL, "lammps", LAMMPS_VERSION);
} else {
datafile = h5md_create_file(filename, author_name, NULL, "lammps", LAMMPS_VERSION);
}
group_name_length = strlen(group->names[igroup])+1;
group_name = new char[group_name_length];
strcpy(group_name, group->names[igroup]);
if (create_group) {
particles_data = h5md_create_particles_group(datafile, group_name);
} else {
particles_data.group = h5md_open_particles_group(datafile.particles, group_name);
}
delete [] group_name;
dims[0] = natoms;
dims[1] = domain->dimension;
if (every_position>0) {
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
}
if (every_image>0)
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
if (every_velocity>0)
particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_force>0)
particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_species>0)
particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
if (every_charge>0) {
particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
}
} else {
DumpH5MD* other_dump;
other_dump=(DumpH5MD*)output->dump[datafile_from_dump];
datafile = other_dump->datafile;
group_name_length = strlen(group->names[igroup]);
group_name = new char[group_name_length];
strcpy(group_name, group->names[igroup]);
if (create_group) {
particles_data = h5md_create_particles_group(datafile, group_name);
} else {
particles_data = other_dump->particles_data;
}
dims[0] = natoms;
dims[1] = domain->dimension;
if (every_position>0) {
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
}
if (every_image>0)
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
if (every_velocity>0)
particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_force>0)
particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_species>0)
particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
if (every_charge>0) {
particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
}
}
}
if (author_name!=NULL) delete [] author_name;
for (int i=0; i<3; i++) {
delete [] boundary[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::write_header(bigint nbig)
{
return;
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::pack(tagint *ids)
{
int m,n;
tagint *tag = atom->tag;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *species = atom->type;
double *q = atom->q;
imageint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int dim=domain->dimension;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (every_position>=0) {
int ix = (image[i] & IMGMASK) - IMGMAX;
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int iz = (image[i] >> IMG2BITS) - IMGMAX;
if (unwrap_flag == 1) {
buf[m++] = (x[i][0] + ix * xprd);
buf[m++] = (x[i][1] + iy * yprd);
if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
} else {
buf[m++] = x[i][0];
buf[m++] = x[i][1];
if (dim>2) buf[m++] = x[i][2];
}
if (every_image>=0) {
buf[m++] = ix;
buf[m++] = iy;
if (dim>2) buf[m++] = iz;
}
}
if (every_velocity>=0) {
buf[m++] = v[i][0];
buf[m++] = v[i][1];
if (dim>2) buf[m++] = v[i][2];
}
if (every_force>=0) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
if (dim>2) buf[m++] = f[i][2];
}
if (every_species>=0)
buf[m++] = species[i];
if (every_charge>=0)
buf[m++] = q[i];
ids[n++] = tag[i];
}
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::write_data(int n, double *mybuf)
{
// copy buf atom coords into global array
int m = 0;
int dim = domain->dimension;
int k = dim*ntotal;
int k_image = dim*ntotal;
int k_velocity = dim*ntotal;
int k_force = dim*ntotal;
int k_species = ntotal;
int k_charge = ntotal;
for (int i = 0; i < n; i++) {
if (every_position>=0) {
for (int j=0; j<dim; j++) {
dump_position[k++] = mybuf[m++];
}
if (every_image>=0)
for (int j=0; j<dim; j++) {
dump_image[k_image++] = mybuf[m++];
}
}
if (every_velocity>=0)
for (int j=0; j<dim; j++) {
dump_velocity[k_velocity++] = mybuf[m++];
}
if (every_force>=0)
for (int j=0; j<dim; j++) {
dump_force[k_force++] = mybuf[m++];
}
if (every_species>=0)
dump_species[k_species++] = mybuf[m++];
if (every_charge>=0)
dump_charge[k_charge++] = mybuf[m++];
ntotal++;
}
// if last chunk of atoms in this snapshot, write global arrays to file
if (ntotal == natoms) {
if (every_dump>0) {
write_frame();
ntotal = 0;
} else {
write_fixed_frame();
}
}
}
/* ---------------------------------------------------------------------- */
int DumpH5MD::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"unwrap") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpH5MD::write_frame()
{
int local_step;
double local_time;
double edges[3];
local_step = update->ntimestep;
local_time = local_step * update->dt;
edges[0] = boxxhi - boxxlo;
edges[1] = boxyhi - boxylo;
edges[2] = boxzhi - boxzlo;
if (every_position>0) {
if (local_step % (every_position*every_dump) == 0) {
h5md_append(particles_data.position, dump_position, local_step, local_time);
h5md_append(particles_data.box_edges, edges, local_step, local_time);
if (every_image>0)
h5md_append(particles_data.image, dump_image, local_step, local_time);
}
} else {
if (do_box) h5md_append(particles_data.box_edges, edges, local_step, local_time);
}
if (every_velocity>0 && local_step % (every_velocity*every_dump) == 0) {
h5md_append(particles_data.velocity, dump_velocity, local_step, local_time);
}
if (every_force>0 && local_step % (every_force*every_dump) == 0) {
h5md_append(particles_data.force, dump_force, local_step, local_time);
}
if (every_species>0 && local_step % (every_species*every_dump) == 0) {
h5md_append(particles_data.species, dump_species, local_step, local_time);
}
if (every_charge>0 && local_step % (every_charge*every_dump) == 0) {
h5md_append(particles_data.charge, dump_charge, local_step, local_time);
}
}
void DumpH5MD::write_fixed_frame()
{
double edges[3];
int dims[2];
char *boundary[3];
for (int i=0; i<3; i++) {
boundary[i] = new char[9];
if (domain->periodicity[i]==1) {
strcpy(boundary[i], "periodic");
} else {
strcpy(boundary[i], "none");
}
}
dims[0] = natoms;
dims[1] = domain->dimension;
edges[0] = boxxhi - boxxlo;
edges[1] = boxyhi - boxylo;
edges[2] = boxzhi - boxzlo;
if (every_position==0) {
particles_data.position = h5md_create_fixed_data_simple(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, dump_position);
h5md_create_box(&particles_data, dims[1], boundary, false, edges, NULL);
if (every_image==0)
particles_data.image = h5md_create_fixed_data_simple(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, dump_image);
}
if (every_velocity==0)
particles_data.velocity = h5md_create_fixed_data_simple(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, dump_velocity);
if (every_force==0)
particles_data.force = h5md_create_fixed_data_simple(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, dump_force);
if (every_species==0)
particles_data.species = h5md_create_fixed_data_simple(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, dump_species);
if (every_charge==0) {
particles_data.charge = h5md_create_fixed_data_simple(particles_data.group, "charge", 1, dims, H5T_NATIVE_INT, dump_charge);
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
}
for (int i=0; i<3; i++) {
delete [] boundary[i];
}
}

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