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lammps/lib/ch5md/src/ch5md.c
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ch5md.c
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/* This file is part of ch5md
* Copyright (C) 2013-2015 Pierre de Buyl
* All rights reserved.
*
* This software may be modified and distributed under the terms
* of the BSD license. See the LICENSE file for details.
*/
#include "hdf5.h"
#include "ch5md.h"
#include <string.h>
#include <stdlib.h>
#define MIN_CHUNK 10
#define MAX_CHUNK 256
#define MAX_RANK 5
h5md_file h5md_create_file (const char *filename, const char *author, const char *author_email, const char *creator, const char *creator_version)
{
h5md_file file;
hid_t g, g1;
hid_t a, s, t;
hsize_t dims[1];
file.version[0] = 1;
file.version[1] = 0;
file.id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
g = H5Gcreate(file.id, "h5md", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
dims[0] = 2;
s = H5Screate_simple(1, dims, NULL);
a = H5Acreate(g, "version", H5T_NATIVE_INT, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, H5T_NATIVE_INT, file.version);
H5Aclose(a);
H5Sclose(s);
s = H5Screate(H5S_SCALAR);
g1 = H5Gcreate(g, "author", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, strlen(author));
a = H5Acreate(g1, "name", t, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, t, author);
H5Aclose(a);
H5Tclose(t);
if (NULL!=author_email) {
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, strlen(author_email));
a = H5Acreate(g1, "author_email", t, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, t, author_email);
H5Aclose(a);
H5Tclose(t);
}
H5Gclose(g1);
g1 = H5Gcreate(g, "creator", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, strlen(creator));
a = H5Acreate(g1, "name", t, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, t, creator);
H5Aclose(a);
H5Tclose(t);
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, strlen(creator_version));
a = H5Acreate(g1, "version", t, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, t, creator_version);
H5Aclose(a);
H5Tclose(t);
H5Gclose(g1);
file.particles = H5Gcreate(file.id, "particles", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
file.observables = H5Gcreate(file.id, "observables", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
file.parameters = H5Gcreate(file.id, "parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
return file;
}
int h5md_close_file(h5md_file file) {
H5Gclose(file.particles);
H5Gclose(file.observables);
H5Gclose(file.parameters);
H5Fclose(file.id);
return 0;
}
hid_t h5md_open_file (const char *filename)
{
hid_t file;
hid_t g;
hid_t a, s;
hsize_t dims[1];
int version[2];
int version_ok;
file = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
g = H5Gopen(file, "h5md", H5P_DEFAULT);
version_ok = false;
dims[0] = 2;
a = H5Aopen(g, "version", H5P_DEFAULT);
s = H5Aget_space(a);
if (!(H5Sis_simple(s)>0)) {
printf("H5MD version is not a simple dataspace");
H5Sclose(s);
H5Aclose(a);
H5Gclose(g);
H5Fclose(file);
} else {
if (H5Sget_simple_extent_ndims(s)==1) {
H5Sget_simple_extent_dims(s, dims, NULL);
if (dims[0]==2) {
H5Aread(a, H5T_NATIVE_INT, version);
if ( (version[0]==1) && (version[1]==0) ) {version_ok = true;}
}
}
}
H5Aclose(a);
H5Sclose(s);
H5Gclose(g);
if (!version_ok) H5Fclose(file);
return file;
}
h5md_particles_group h5md_create_particles_group(h5md_file file, const char *name)
{
h5md_particles_group group;
group.group = H5Gcreate(file.particles, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
return group;
}
h5md_element h5md_create_time_data(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, h5md_element *link)
{
h5md_element td;
hid_t spc, plist;
hsize_t dims[MAX_RANK], max_dims[MAX_RANK], chunks[MAX_RANK];
int i;
dims[0] = 0 ;
max_dims[0] = H5S_UNLIMITED ;
for (i=0; i<rank; i++) {
dims[i+1] = int_dims[i];
max_dims[i+1] = int_dims[i];
}
chunks[0] = 1 ;
if (MAX_CHUNK<int_dims[0]/4) {
chunks[1] = MAX_CHUNK;
} else {
chunks[1] = int_dims[0];
}
for (i=1; i<rank; i++) {
chunks[i+1]=int_dims[i];
}
td.group = H5Gcreate(loc, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (NULL==link) {
spc = H5Screate_simple( 1 , dims, max_dims);
plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(plist, 1, chunks);
td.time = H5Dcreate(td.group, "time", H5T_NATIVE_DOUBLE, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
td.step = H5Dcreate(td.group, "step", H5T_NATIVE_INT, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
H5Pclose(plist);
H5Sclose(spc);
td.link=NULL;
} else {
td.link = link;
H5Lcreate_hard(link->group, "step", td.group, "step", H5P_DEFAULT, H5P_DEFAULT);
H5Lcreate_hard(link->group, "time", td.group, "time", H5P_DEFAULT, H5P_DEFAULT);
}
spc = H5Screate_simple( rank+1 , dims, max_dims) ;
plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(plist, rank+1, chunks);
td.value = H5Dcreate(td.group, "value", datatype, spc, H5P_DEFAULT, plist, H5P_DEFAULT);
H5Pclose(plist);
H5Sclose(spc);
td.datatype = datatype;
td.is_time = true;
return td;
}
int h5md_close_element(h5md_element e)
{
if (!e.is_time) return 0;
if (e.link==NULL) {
H5Dclose(e.step);
H5Dclose(e.time);
}
H5Dclose(e.value);
H5Gclose(e.group);
return 0;
}
h5md_element h5md_create_fixed_data_simple(hid_t loc, const char *name, int rank, int int_dims[], hid_t datatype, void *data)
{
h5md_element fd;
hid_t spc;
hsize_t dims[H5S_MAX_RANK];
int i;
for (i=0; i<rank; i++) {
dims[i] = int_dims[i];
}
spc = H5Screate_simple(rank, dims, NULL);
fd.value = H5Dcreate(loc, name, datatype, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(spc);
H5Dwrite(fd.value, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
H5Dclose(fd.value);
fd.is_time = false;
return fd;
}
h5md_element h5md_create_fixed_data_scalar(hid_t loc, const char *name, hid_t datatype, void *data)
{
h5md_element fd;
hid_t spc;
spc = H5Screate(H5S_SCALAR);
fd.value = H5Dcreate(loc, name, datatype, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(spc);
H5Dwrite(fd.value, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
H5Dclose(fd.value);
fd.is_time = false;
return fd;
}
int h5md_extend_by_one(hid_t dset, hsize_t *dims) {
hid_t file_space;
int rank;
hsize_t maxdims[H5S_MAX_RANK];
// Get dataset information
file_space = H5Dget_space(dset);
rank = H5Sget_simple_extent_ndims(file_space);
if (rank > H5S_MAX_RANK) {
return CH5MD_RANK_ERROR;
}
H5Sget_simple_extent_dims(file_space, dims, maxdims);
H5Sclose(file_space);
// Extend dimensions by one
dims[0] = dims[0]+1;
H5Dset_extent(dset, dims);
return 0;
}
int h5md_append(h5md_element e, void *data, int step, double time) {
hid_t mem_space, file_space;
int i, rank;
hsize_t dims[H5S_MAX_RANK];
hsize_t start[H5S_MAX_RANK], count[H5S_MAX_RANK];
// If not a time-dependent H5MD element, do nothing
if (!e.is_time) return 0;
if (NULL==e.link) {
h5md_extend_by_one(e.step, dims);
// Define hyperslab selection
start[0] = dims[0]-1;
count[0] = 1;
// Select the hyperslab
file_space = H5Dget_space(e.step);
rank = H5Sget_simple_extent_ndims(file_space);
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
// Define hyperslab selection
start[0] = dims[0]-1;
count[0] = 1;
for (i=1 ; i<rank ; i++) {
start[i] = 0;
count[i] = dims[i];
}
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
H5Dwrite(e.step, H5T_NATIVE_INT, mem_space, file_space, H5P_DEFAULT, (void *)&step);
H5Sclose(file_space);
H5Sclose(mem_space);
h5md_extend_by_one(e.time, dims);
// Define hyperslab selection
start[0] = dims[0]-1;
count[0] = 1;
// Select the hyperslab
file_space = H5Dget_space(e.time);
rank = H5Sget_simple_extent_ndims(file_space);
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
// Define hyperslab selection
start[0] = dims[0]-1;
count[0] = 1;
for (i=1 ; i<rank ; i++) {
start[i] = 0;
count[i] = dims[i];
}
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
H5Dwrite(e.time, H5T_NATIVE_DOUBLE, mem_space, file_space, H5P_DEFAULT, (void *)&time);
H5Sclose(file_space);
H5Sclose(mem_space);
}
h5md_extend_by_one(e.value, dims);
// Select the hyperslab
file_space = H5Dget_space(e.value);
rank = H5Sget_simple_extent_ndims(file_space);
mem_space = H5Screate_simple(rank-1, dims+1, NULL);
// Define hyperslab selection
start[0] = dims[0]-1;
count[0] = 1;
for (i=1 ; i<rank ; i++) {
start[i] = 0;
count[i] = dims[i];
}
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
H5Dwrite(e.value, e.datatype, mem_space, file_space, H5P_DEFAULT, data);
H5Sclose(file_space);
H5Sclose(mem_space);
return 0;
}
int h5md_create_box(h5md_particles_group *group, int dim, char *boundary[], bool is_time, double value[], h5md_element *link)
{
hid_t spc, att, t;
hsize_t dims[1];
int int_dims[1];
int i;
size_t boundary_length, tmp;
//char *tmp_boundary;
// Create box group
group->box = H5Gcreate(group->group, "box", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// Create dimension attribute
spc = H5Screate(H5S_SCALAR);
att = H5Acreate(group->box, "dimension", H5T_NATIVE_INT, spc, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(att, H5T_NATIVE_INT, &dim);
H5Aclose(att);
H5Sclose(spc);
// Compute the size of the string type for boundary
dims[0] = dim;
boundary_length=0;
for (i=0; i<dim; i++) {
tmp = strlen(boundary[i])+1;
if (tmp>boundary_length) {
boundary_length=tmp;
}
}
char *tmp_boundary = malloc(dim*sizeof(char)*boundary_length);
for (i=0; i<dim; i++) {
strcpy((tmp_boundary+i*boundary_length), boundary[i]);
}
// Create boundary attribute
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, boundary_length);
spc = H5Screate_simple(1, dims, NULL);
att = H5Acreate(group->box, "boundary", t, spc, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(att, t, tmp_boundary);
free(tmp_boundary);
H5Aclose(att);
H5Sclose(spc);
H5Tclose(t);
// Create edges
// Check if the box is time-dependent or not
int_dims[0]=dim;
if (is_time) {
group->box_edges = h5md_create_time_data(group->box, "edges", 1, int_dims, H5T_NATIVE_DOUBLE, link);
} else {
if (NULL!=value) {
group->box_edges = h5md_create_fixed_data_simple(group->box, "edges", 1, int_dims, H5T_NATIVE_DOUBLE, value);
}
}
H5Gclose(group->box);
return 0;
}
int h5md_write_string_attribute(hid_t loc, const char *obj_name,
const char *att_name, const char *value)
{
hid_t obj;
hid_t s, t, a;
obj = H5Oopen(loc, obj_name, H5P_DEFAULT);
t = H5Tcopy(H5T_C_S1);
H5Tset_size(t, strlen(value));
s = H5Screate(H5S_SCALAR);
a = H5Acreate(obj, att_name, t, s, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(a, t, value);
H5Aclose(a);
H5Sclose(s);
H5Tclose(t);
H5Oclose(obj);
return 0;
}
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