def create_hdf5_data_sample(self, filename, schema_val, datas, time_list):
hdf5_file = h5py.File(filename, 'w')
# header
header_group = hdf5_file.create_group('lattice_info')
hcp = HCPLattice()
hcp.load_schema_value(schema_val)
hcp_dset = header_group.create_dataset('HCP_group', (2, ),
hcp.get_lattice_schema())
hcp_dset.attrs['lattice_type'] = hcp.get_lattice_type()
hcp_dset[0] = schema_val
#for dummy lattice info
voxelRadius = 1.0e-10
theNormalizedVoxelRadius = 0.5
hcp_dset[1] = (2, (1.5, 0.9, 0.4), voxelRadius,
theNormalizedVoxelRadius)
simple = SimpleLattice()
simple_dset = header_group.create_dataset('Simple_group', (1, ),
simple.get_lattice_schema())
simple_dset.attrs['lattice_type'] = simple.get_lattice_type()
simple_dset[0] = (3, (1.0, 1.0, 1.0), voxelRadius,
theNormalizedVoxelRadius)
# set data
data_group = hdf5_file.create_group('data')
for time, data in zip(time_list, datas):
time_group = data_group.create_group(str(time))
time_group.attrs['t'] = time
# pattern 1
time_dset = time_group.create_dataset('particles', (len(data), ),
hcp.get_partilce_schema())
for i, record in enumerate(data):
nindex = record[0] + hcp.get_theStartCoord()
time_dset[i] = (nindex, record[1], record[2])
# set species
self.create_species(hdf5_file)
hdf5_file.close()
def create_hdf5_data_sample(self, filename, schema_val, datas, time_list):
hdf5_file = h5py.File(filename, "w")
# header
header_group = hdf5_file.create_group("lattice_info")
hcp = HCPLattice()
hcp.load_schema_value(schema_val)
hcp_dset = header_group.create_dataset("HCP_group", (2,), hcp.get_lattice_schema())
hcp_dset.attrs["lattice_type"] = hcp.get_lattice_type()
hcp_dset[0] = schema_val
# for dummy lattice info
voxelRadius = 1.0e-10
theNormalizedVoxelRadius = 0.5
hcp_dset[1] = (2, (1.5, 0.9, 0.4), voxelRadius, theNormalizedVoxelRadius)
simple = SimpleLattice()
simple_dset = header_group.create_dataset("Simple_group", (1,), simple.get_lattice_schema())
simple_dset.attrs["lattice_type"] = simple.get_lattice_type()
simple_dset[0] = (3, (1.0, 1.0, 1.0), voxelRadius, theNormalizedVoxelRadius)
# set data
data_group = hdf5_file.create_group("data")
for time, data in zip(time_list, datas):
time_group = data_group.create_group(str(time))
time_group.attrs["t"] = time
# pattern 1
time_dset = time_group.create_dataset("particles", (len(data),), hcp.get_partilce_schema())
for i, record in enumerate(data):
nindex = record[0] + hcp.get_theStartCoord()
time_dset[i] = (nindex, record[1], record[2])
# set species
self.create_species(hdf5_file)
hdf5_file.close()
