def __init__(self,
filename,
dataset_type='openPMD',
storage_filename=None,
units_override=None):
# This defines which of the data sets are meshes (fields)
self.fluid_types += ('openPMD', )
# This defines which of the data sets are particles
self.particle_types = ["electrons", "ions", "all"]
self.particle_types = tuple(self.particle_types)
self.particle_types_raw = self.particle_types
# Opens a HDF5 file and stores its file handle in _handle
# All _handle objects refers to the file
self._handle = HDF5FileHandler(filename)
Dataset.__init__(self,
filename,
dataset_type,
units_override=units_override)
self.storage_filename = storage_filename
def __init__(self,
filename,
dataset_type='flash_particle_hdf5',
storage_filename=None,
units_override=None,
index_order=None,
index_filename=None,
unit_system="cgs"):
self.index_order = validate_index_order(index_order)
self.index_filename = index_filename
if self._handle is not None: return
self._handle = HDF5FileHandler(filename)
self.refine_by = 2
Dataset.__init__(self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system)
self.storage_filename = storage_filename
def __init__(
self,
filename,
dataset_type="athena_pp",
storage_filename=None,
parameters=None,
units_override=None,
unit_system="code",
default_species_fields=None,
magnetic_normalization="gaussian",
):
self.fluid_types += ("athena_pp", )
if parameters is None:
parameters = {}
self.specified_parameters = parameters
if units_override is None:
units_override = {}
self._handle = HDF5FileHandler(filename)
xrat = self._handle.attrs["RootGridX1"][2]
yrat = self._handle.attrs["RootGridX2"][2]
zrat = self._handle.attrs["RootGridX3"][2]
if xrat != 1.0 or yrat != 1.0 or zrat != 1.0:
self._index_class = AthenaPPLogarithmicIndex
self.logarithmic = True
else:
self._index_class = AthenaPPHierarchy
self.logarithmic = False
self._magnetic_factor = get_magnetic_normalization(
magnetic_normalization)
Dataset.__init__(
self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system,
default_species_fields=default_species_fields,
)
if storage_filename is None:
storage_filename = self.basename + ".yt"
self.storage_filename = storage_filename
def __init__(
self,
filename,
dataset_type="athena_pp",
storage_filename=None,
parameters=None,
units_override=None,
unit_system="code",
default_species_fields=None,
):
self.fluid_types += ("athena_pp",)
if parameters is None:
parameters = {}
self.specified_parameters = parameters
if units_override is None:
units_override = {}
self._handle = HDF5FileHandler(filename)
xrat = self._handle.attrs["RootGridX1"][2]
yrat = self._handle.attrs["RootGridX2"][2]
zrat = self._handle.attrs["RootGridX3"][2]
if xrat != 1.0 or yrat != 1.0 or zrat != 1.0:
self._index_class = AthenaPPLogarithmicIndex
self.logarithmic = True
else:
self._index_class = AthenaPPHierarchy
self.logarithmic = False
Dataset.__init__(
self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system,
default_species_fields=default_species_fields,
)
self.filename = filename
if storage_filename is None:
storage_filename = f"{filename.split('/')[-1]}.yt"
self.storage_filename = storage_filename
self.backup_filename = self.filename[:-4] + "_backup.gdf"
def __init__(
self,
filename,
dataset_type="openPMD",
storage_filename=None,
units_override=None,
unit_system="mks",
**kwargs,
):
self._handle = HDF5FileHandler(filename)
self.gridsize = kwargs.pop("open_pmd_virtual_gridsize", 10 ** 9)
self.standard_version = StrictVersion(self._handle.attrs["openPMD"].decode())
self.iteration = kwargs.pop("iteration", None)
self._set_paths(self._handle, path.dirname(filename), self.iteration)
Dataset.__init__(
self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system,
)
self.storage_filename = storage_filename
self.fluid_types += ("openPMD",)
try:
particles = tuple(
str(c)
for c in self._handle[self.base_path + self.particles_path].keys()
)
if len(particles) > 1:
# Only use on-disk particle names if there is more than one species
self.particle_types = particles
mylog.debug("self.particle_types: %s", self.particle_types)
self.particle_types_raw = self.particle_types
self.particle_types = tuple(self.particle_types)
except (KeyError, TypeError, AttributeError):
pass
def __init__(self,
filename,
dataset_type='chombo_hdf5',
storage_filename=None,
ini_filename=None,
units_override=None):
self.fluid_types += ("chombo", )
self._handle = HDF5FileHandler(filename)
self.dataset_type = dataset_type
self.geometry = "cartesian"
self.ini_filename = ini_filename
self.fullplotdir = os.path.abspath(filename)
Dataset.__init__(self,
filename,
self.dataset_type,
units_override=units_override)
self.storage_filename = storage_filename
self.cosmological_simulation = False
# These are parameters that I very much wish to get rid of.
self.parameters["HydroMethod"] = 'chombo'
self.parameters["DualEnergyFormalism"] = 0
self.parameters["EOSType"] = -1 # default
def __init__(
self,
filename,
dataset_type="flash_hdf5",
storage_filename=None,
particle_filename=None,
units_override=None,
unit_system="cgs",
default_species_fields=None,
):
self.fluid_types += ("flash", )
if self._handle is not None:
return
self._handle = HDF5FileHandler(filename)
self.particle_filename = particle_filename
if self.particle_filename is None:
# try to guess the particle filename
try:
self._particle_handle = HDF5FileHandler(
filename.replace("plt_cnt", "part"))
self.particle_filename = filename.replace("plt_cnt", "part")
mylog.info("Particle file found: %s",
self.particle_filename.split("/")[-1])
except OSError:
self._particle_handle = self._handle
else:
# particle_filename is specified by user
self._particle_handle = HDF5FileHandler(self.particle_filename)
# Check if the particle file has the same time
if self._particle_handle != self._handle:
part_time = self._particle_handle.handle.get("real scalars")[0][1]
plot_time = self._handle.handle.get("real scalars")[0][1]
if not np.isclose(part_time, plot_time):
self._particle_handle = self._handle
mylog.warning(
"%s and %s are not at the same time. "
"This particle file will not be used.",
self.particle_filename,
filename,
)
# These should be explicitly obtained from the file, but for now that
# will wait until a reorganization of the source tree and better
# generalization.
self.refine_by = 2
Dataset.__init__(
self,
filename,
dataset_type,
units_override=units_override,
unit_system=unit_system,
default_species_fields=default_species_fields,
)
self.storage_filename = storage_filename
self.parameters["HydroMethod"] = "flash" # always PPM DE
self.parameters["Time"] = 1.0 # default unit is 1...
