def _parse_parameter_file(self):
# Read all parameters.
simu = self._read_log_simu()
param = self._read_parameter()
# Set up general information.
self.filename_template = self.parameter_filename
self.file_count = 1
self.parameters.update(param)
self.particle_types = ('halos')
self.particle_types_raw = ('halos')
# Set up geometrical information.
self.refine_by = 2
self.dimensionality = 3
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(self.dimensionality, "int32") * nz
self.domain_left_edge = np.array([0.0, 0.0, 0.0])
# Note that boxsize is in Mpc but particle positions are in kpc.
self.domain_right_edge = np.array([simu['boxsize']] * 3) * 1000
self.periodicity = (True, True, True)
# Set up cosmological information.
self.cosmological_simulation = 1
self.current_redshift = param['z']
self.omega_lambda = simu['lambda0']
self.omega_matter = simu['omega0']
cosmo = Cosmology(hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda)
self.current_time = cosmo.lookback_time(param['z'], 1e6).in_units('s')
def _parse_parameter_file(self):
with open(self.parameter_filename, "rb") as f:
hvals = fpu.read_cattrs(f, header_dt)
hvals.pop("unused")
self.dimensionality = 3
self.refine_by = 2
self.unique_identifier = \
int(os.stat(self.parameter_filename)[stat.ST_CTIME])
prefix = ".".join(self.parameter_filename.rsplit(".", 2)[:-2])
self.filename_template = "%s.%%(num)s%s" % (prefix, self._suffix)
self.file_count = len(glob.glob(prefix + ".*" + self._suffix))
# Now we can set up things we already know.
self.cosmological_simulation = 1
self.current_redshift = (1.0 / hvals['scale']) - 1.0
self.hubble_constant = hvals['h0']
self.omega_lambda = hvals['Ol']
self.omega_matter = hvals['Om']
cosmo = Cosmology(hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda)
self.current_time = cosmo.lookback_time(self.current_redshift,
1e6).in_units("s")
self.periodicity = (True, True, True)
self.particle_types = ("halos")
self.particle_types_raw = ("halos")
self.domain_left_edge = np.array([0.0, 0.0, 0.0])
self.domain_right_edge = np.array([hvals['box_size']] * 3)
self.domain_dimensions = np.ones(3, "int32")
self.parameters.update(hvals)
def _parse_parameter_file(self):
with open(self.parameter_filename, "rb") as f:
hvals = fpu.read_cattrs(f, header_dt)
hvals.pop("unused")
self.dimensionality = 3
self.refine_by = 2
prefix = ".".join(self.parameter_filename.rsplit(".", 2)[:-2])
self.filename_template = f"{prefix}.%(num)s{self._suffix}"
self.file_count = len(glob.glob(prefix + ".*" + self._suffix))
# Now we can set up things we already know.
self.cosmological_simulation = 1
self.current_redshift = (1.0 / hvals["scale"]) - 1.0
self.hubble_constant = hvals["h0"]
self.omega_lambda = hvals["Ol"]
self.omega_matter = hvals["Om"]
cosmo = Cosmology(
hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda,
)
self.current_time = cosmo.lookback_time(self.current_redshift,
1e6).in_units("s")
self.periodicity = (True, True, True)
self.particle_types = "halos"
self.particle_types_raw = "halos"
self.domain_left_edge = np.array([0.0, 0.0, 0.0])
self.domain_right_edge = np.array([hvals["box_size"]] * 3)
self.domain_dimensions = np.ones(3, "int32")
self.parameters.update(hvals)
def _set_code_unit_attributes(self):
# First try to set units based on parameter file
if self.cosmological_simulation:
mu = self.parameters.get("dMsolUnit", 1.0)
self.mass_unit = self.quan(mu, "Msun")
lu = self.parameters.get("dKpcUnit", 1000.0)
# In cosmological runs, lengths are stored as length*scale_factor
self.length_unit = self.quan(lu, "kpc") * self.scale_factor
density_unit = self.mass_unit / (self.length_unit / self.scale_factor) ** 3
if "dHubble0" in self.parameters:
# Gasoline's internal hubble constant, dHubble0, is stored in
# units of proper code time
self.hubble_constant *= np.sqrt(G * density_unit)
# Finally, we scale the hubble constant by 100 km/s/Mpc
self.hubble_constant /= self.quan(100, "km/s/Mpc")
# If we leave it as a YTQuantity, the cosmology object
# used below will add units back on.
self.hubble_constant = self.hubble_constant.to_value("")
else:
mu = self.parameters.get("dMsolUnit", 1.0)
self.mass_unit = self.quan(mu, "Msun")
lu = self.parameters.get("dKpcUnit", 1.0)
self.length_unit = self.quan(lu, "kpc")
# If unit base is defined by the user, override all relevant units
if self._unit_base is not None:
for my_unit in ["length", "mass", "time"]:
if my_unit in self._unit_base:
my_val = self._unit_base[my_unit]
my_val = (
self.quan(*my_val)
if isinstance(my_val, tuple)
else self.quan(my_val)
)
setattr(self, f"{my_unit}_unit", my_val)
# Finally, set the dependent units
if self.cosmological_simulation:
cosmo = Cosmology(
hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda,
)
self.current_time = cosmo.lookback_time(self.current_redshift, 1e6)
# mass units are rho_crit(z=0) * domain volume
mu = (
cosmo.critical_density(0.0)
* (1 + self.current_redshift) ** 3
* self.length_unit ** 3
)
self.mass_unit = self.quan(mu.in_units("Msun"), "Msun")
density_unit = self.mass_unit / (self.length_unit / self.scale_factor) ** 3
# need to do this again because we've modified the hubble constant
self.unit_registry.modify("h", self.hubble_constant)
else:
density_unit = self.mass_unit / self.length_unit ** 3
if not hasattr(self, "time_unit"):
self.time_unit = 1.0 / np.sqrt(density_unit * G)
def _parse_parameter_file(self):
hvals = self._get_hvals()
self.dimensionality = 3
self.refine_by = 2
self.parameters["HydroMethod"] = "sph"
self.unique_identifier = \
int(os.stat(self.parameter_filename)[stat.ST_CTIME])
# Set standard values
# We may have an overridden bounding box.
if self.domain_left_edge is None and hvals['BoxSize'] != 0:
self.domain_left_edge = np.zeros(3, "float64")
self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
self.domain_dimensions = np.ones(3, "int32")
self.periodicity = (True, True, True)
self.cosmological_simulation = 1
try:
self.current_redshift = hvals["Redshift"]
except KeyError:
# Probably not a cosmological dataset, we should just set
# z = 0 and let the user know
self.current_redshift = 0.0
only_on_root(
mylog.info, "Redshift is not set in Header. Assuming z=0.")
try:
self.omega_lambda = hvals["OmegaLambda"]
self.omega_matter = hvals["Omega0"]
self.hubble_constant = hvals["HubbleParam"]
except KeyError:
# If these are not set it is definitely not a cosmological dataset.
self.omega_lambda = 0.0
self.omega_matter = 1.0 # Just in case somebody asks for it.
# Hubble is set below for Omega Lambda = 0.
# According to the Gadget manual, OmegaLambda will be zero for
# non-cosmological datasets. However, it may be the case that
# individuals are running cosmological simulations *without* Lambda, in
# which case we may be doing something incorrect here.
# It may be possible to deduce whether ComovingIntegration is on
# somehow, but opinions on this vary.
if self.omega_lambda == 0.0:
only_on_root(
mylog.info, "Omega Lambda is 0.0, so we are turning off Cosmology.")
self.hubble_constant = 1.0 # So that scaling comes out correct
self.cosmological_simulation = 0
self.current_redshift = 0.0
# This may not be correct.
self.current_time = hvals["Time"]
else:
# Now we calculate our time based on the cosmology, because in
# ComovingIntegration hvals["Time"] will in fact be the expansion
# factor, not the actual integration time, so we re-calculate
# global time from our Cosmology.
cosmo = Cosmology(hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda)
self.current_time = cosmo.lookback_time(self.current_redshift, 1e6)
only_on_root(mylog.info, "Calculating time from %0.3e to be %0.3e seconds",
hvals["Time"], self.current_time)
self.parameters = hvals
prefix = os.path.abspath(
os.path.join(os.path.dirname(self.parameter_filename),
os.path.basename(self.parameter_filename).split(".", 1)[0]))
if hvals["NumFiles"] > 1:
self.filename_template = "%s.%%(num)s%s" % (prefix, self._suffix)
else:
self.filename_template = self.parameter_filename
self.file_count = hvals["NumFiles"]
