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_pspace(self, filename, schema_val, datas,
time_list):
"""
Create particle-space sample data using lattice-space data.
CAUTION: The coordinate of particle-space data is different
from lattices-space data slightly.
"""
hdf5_file = h5py.File(filename, 'w')
# calculate world size
hcp = HCPLattice()
hcp.load_schema_value(schema_val)
wsize = hcp.get_world_sizes()
voxelRadius = 1.0e-10
sca = voxelRadius * 2.0
# particle schema for paricle space.
pschema = \
[
('id', 'u8',),
('species_id', 'u8',),
('position', 'f8', (3,))
]
# set data
data_group = hdf5_file.create_group('data')
data_group.attrs['world_size'] = max(wsize)
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), ),
pschema)
for i, record in enumerate(data):
nindex = record[0] + hcp.get_theStartCoord()
co = hcp.coord2point(nindex)
wrec = (nindex, record[1], (co[0] * sca, co[1] * sca,
co[2] * sca))
time_dset[i] = wrec
# set species
self.create_species_pspace(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()
def create_hdf5_data_sample_pspace(self, filename, schema_val, datas, time_list):
"""
Create particle-space sample data using lattice-space data.
CAUTION: The coordinate of particle-space data is different
from lattices-space data slightly.
"""
hdf5_file = h5py.File(filename, "w")
# calculate world size
hcp = HCPLattice()
hcp.load_schema_value(schema_val)
wsize = hcp.get_world_sizes()
voxelRadius = 1.0e-10
sca = voxelRadius * 2.0
# particle schema for paricle space.
pschema = [("id", "u8"), ("species_id", "u8"), ("position", "f8", (3,))]
# set data
data_group = hdf5_file.create_group("data")
data_group.attrs["world_size"] = max(wsize)
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),), pschema)
for i, record in enumerate(data):
nindex = record[0] + hcp.get_theStartCoord()
co = hcp.coord2point(nindex)
wrec = (nindex, record[1], (co[0] * sca, co[1] * sca, co[2] * sca))
time_dset[i] = wrec
# set species
self.create_species_pspace(hdf5_file)
hdf5_file.close()
def calc_row_col_lay(schema_val):
hcp_tmp = HCPLattice()
hcp_tmp.load_schema_value(schema_val)
row_col_lay = (hcp_tmp._theRowSize, hcp_tmp._theColSize, hcp_tmp._theLayerSize)
return row_col_lay
def calc_row_col_lay(schema_val):
hcp_tmp = HCPLattice()
hcp_tmp.load_schema_value(schema_val)
row_col_lay = (hcp_tmp._theRowSize, hcp_tmp._theColSize,
hcp_tmp._theLayerSize)
return row_col_lay
