def _nuclei_density(field, data):
ftype = field.name[0]
element = field.name[1][:field.name[1].find("_")]
nuclei_mass_field = "%s_nuclei_mass_density" % element
if (ftype, nuclei_mass_field) in data.ds.field_info:
return (data[(ftype, nuclei_mass_field)] /
ChemicalFormula(element).weight /
data.ds.units.physical_constants.amu_cgs)
metal_field = "%s_metallicity" % element
if (ftype, metal_field) in data.ds.field_info:
return (data[ftype, "density"] * data[(ftype, metal_field)] /
ChemicalFormula(element).weight /
data.ds.units.physical_constants.amu_cgs)
field_data = np.zeros_like(data[ftype,
"%s_number_density" %
data.ds.field_info.species_names[0]])
for species in data.ds.field_info.species_names:
nucleus = species
if "_" in species:
nucleus = species[:species.find("_")]
# num is the number of nuclei contributed by this species.
num = _get_element_multiple(nucleus, element)
# Since this is a loop over all species existing in this dataset,
# we will encounter species that contribute nothing, so we skip them.
if num == 0:
continue
field_data += num * data[ftype, "%s_number_density" % species]
return field_data
def test_default_species_fields():
ds = data_dir_load(sloshing)
sp = ds.sphere("c", (0.2, "unitary"))
amu_cgs = ds.units.physical_constants.amu_cgs
mueinv = 1.0 * _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
mueinv *= sp["index", "ones"]
mueinv += 2.0 * _primordial_mass_fraction["He"] / ChemicalFormula(
"He").weight
mupinv = _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
mupinv *= sp["index", "ones"]
muainv = _primordial_mass_fraction["He"] / ChemicalFormula("He").weight
muainv *= sp["index", "ones"]
mueinv2 = sp["gas", "El_number_density"] * amu_cgs / sp["gas", "density"]
mupinv2 = sp["gas", "H_p1_number_density"] * amu_cgs / sp["gas", "density"]
muainv2 = sp["gas", "He_p2_number_density"] * amu_cgs / sp["gas",
"density"]
assert_allclose_units(mueinv, mueinv2)
assert_allclose_units(mupinv, mupinv2)
assert_allclose_units(muainv, muainv2)
assert_equal(sp["gas", "H_p1_number_density"], sp["gas",
"H_nuclei_density"])
assert_equal(sp["gas", "He_p2_number_density"], sp["gas",
"He_nuclei_density"])
def _default_nuclei_density(field, data):
ftype = field.name[0]
element = field.name[1][: field.name[1].find("_")]
amu_cgs = data.ds.units.physical_constants.amu_cgs
if element == "El":
# This assumes full ionization!
muinv = 1.0 * _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
muinv += 2.0 * _primordial_mass_fraction["He"] / ChemicalFormula("He").weight
else:
muinv = _primordial_mass_fraction[element] / ChemicalFormula(element).weight
return data[ftype, "density"] * muinv / amu_cgs
def _default_nuclei_density(field, data):
ftype = field.name[0]
element = field.name[1][: field.name[1].find("_")]
amu_cgs = data.ds.units.physical_constants.amu_cgs
if element == "El":
# This is for determining the electron number density.
# If we got here, this assumes full ionization!
muinv = 1.0 * _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
muinv += 2.0 * _primordial_mass_fraction["He"] / ChemicalFormula("He").weight
else:
# This is for anything else besides electrons
muinv = _primordial_mass_fraction[element] / ChemicalFormula(element).weight
return data[ftype, "density"] * muinv / amu_cgs
def _create_number_density_func(ftype, species):
formula = ChemicalFormula(species)
weight = formula.weight # This is in AMU
weight *= amu_cgs
def _number_density(field, data):
return data[ftype, "%s_density" % species] \
/ weight
return _number_density
def _create_number_density_func(ftype, species):
formula = ChemicalFormula(species)
def _number_density(field, data):
weight = formula.weight # This is in AMU
weight *= data.ds.units.physical_constants.amu_cgs
return data[ftype, "%s_density" % species] \
/ weight
return _number_density
def test_formulas():
for formula, components, charge in _molecules:
f = ChemicalFormula(formula)
w = sum(n * periodic_table[e].weight for e, n in components)
assert_equal(f.charge, charge)
assert_equal(f.weight, w)
for (n, c1), (e, c2) in zip(components, f.elements):
assert_equal(n, e.symbol)
assert_equal(c1, c2)
def setup_species_fields(registry, ftype="gas", slice_info=None):
for species in registry.species_names:
# These are all the species we should be looking for fractions or
# densities of.
if (ftype, f"{species}_density") in registry:
func = add_species_field_by_density
elif (ftype, f"{species}_fraction") in registry:
func = add_species_field_by_fraction
else:
# Skip it
continue
func(registry, ftype, species)
# Add aliases of X_p0_<field> to X_<field>.
# These are deprecated and will be removed soon.
if ChemicalFormula(species).charge == 0:
alias_species = species.split("_")[0]
if (ftype, f"{alias_species}_density") in registry:
continue
add_deprecated_species_aliases(registry, "gas", alias_species, species)
add_nuclei_density_fields(registry, ftype)
def setup_species_fields(registry, ftype = "gas", slice_info = None):
# We have to check what type of field this is -- if it's particles, then we
# set particle_type to True.
particle_type = ftype not in registry.ds.fluid_types
for species in registry.species_names:
# These are all the species we should be looking for fractions or
# densities of.
if (ftype, "%s_density" % species) in registry:
func = add_species_field_by_density
elif (ftype, "%s_fraction" % species) in registry:
func = add_species_field_by_fraction
else:
# Skip it
continue
func(registry, ftype, species, particle_type)
# Adds aliases for all neutral species from their raw "MM_"
# species to "MM_p0_" species to be explicit.
# See YTEP-0003 for more details.
if (ChemicalFormula(species).charge == 0):
alias_species = "%s_p0" % species.split('_')[0]
add_species_aliases(registry, "gas", alias_species, species)
add_nuclei_density_fields(registry, ftype, particle_type=particle_type)
def test_default_species_fields():
# Test default case (no species fields)
ds = fake_random_ds(32)
sp = ds.sphere("c", (0.2, "unitary"))
mu = 0.5924489101195808
assert_allclose_units(mu * sp["index", "ones"],
sp["gas", "mean_molecular_weight"])
assert ("gas", "H_nuclei_density") not in ds.derived_field_list
assert ("gas", "He_nuclei_density") not in ds.derived_field_list
assert ("gas", "El_number_density") not in ds.derived_field_list
assert ("gas", "H_p1_number_density") not in ds.derived_field_list
assert ("gas", "He_p2_number_density") not in ds.derived_field_list
assert ("gas", "H_p0_number_density") not in ds.derived_field_list
assert ("gas", "He_p0_number_density") not in ds.derived_field_list
# Test fully ionized case
dsi = fake_random_ds(32, default_species_fields="ionized")
spi = dsi.sphere("c", (0.2, "unitary"))
amu_cgs = dsi.units.physical_constants.amu_cgs
mueinv = 1.0 * _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
mueinv *= spi["index", "ones"]
mueinv += 2.0 * _primordial_mass_fraction["He"] / ChemicalFormula(
"He").weight
mupinv = _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
mupinv *= spi["index", "ones"]
muainv = _primordial_mass_fraction["He"] / ChemicalFormula("He").weight
muainv *= spi["index", "ones"]
mueinv2 = spi["gas", "El_number_density"] * amu_cgs / spi["gas", "density"]
mupinv2 = spi["gas", "H_p1_number_density"] * amu_cgs / spi["gas",
"density"]
muainv2 = spi["gas", "He_p2_number_density"] * amu_cgs / spi["gas",
"density"]
assert_allclose_units(mueinv, mueinv2)
assert_allclose_units(mupinv, mupinv2)
assert_allclose_units(muainv, muainv2)
assert_equal(spi["gas", "H_p1_number_density"], spi["gas",
"H_nuclei_density"])
assert_equal(spi["gas", "He_p2_number_density"], spi["gas",
"He_nuclei_density"])
mu = 0.5924489101195808
assert_allclose_units(mu * spi["index", "ones"],
spi["gas", "mean_molecular_weight"])
# Test fully neutral case
dsn = fake_random_ds(32, default_species_fields="neutral")
spn = dsn.sphere("c", (0.2, "unitary"))
amu_cgs = dsn.units.physical_constants.amu_cgs
assert ("gas", "El_number_density") not in ds.derived_field_list
mupinv = _primordial_mass_fraction["H"] / ChemicalFormula("H").weight
mupinv *= spn["index", "ones"]
muainv = _primordial_mass_fraction["He"] / ChemicalFormula("He").weight
muainv *= spn["index", "ones"]
mupinv2 = spn["gas", "H_p0_number_density"] * amu_cgs / spn["gas",
"density"]
muainv2 = spn["gas", "He_p0_number_density"] * amu_cgs / spn["gas",
"density"]
assert_allclose_units(mueinv, mueinv2)
assert_allclose_units(mupinv, mupinv2)
assert_allclose_units(muainv, muainv2)
assert_equal(spn["gas", "H_p0_number_density"], spn["gas",
"H_nuclei_density"])
assert_equal(spn["gas", "He_p0_number_density"], spn["gas",
"He_nuclei_density"])
mu = 1.2285402715185552
assert_allclose_units(mu * spn["index", "ones"],
spn["gas", "mean_molecular_weight"])
def _default_nuclei_density(field, data):
ftype = field.name[0]
element = field.name[1][:field.name[1].find("_")]
return data[ftype, "density"] * _primordial_mass_fraction[element] / \
ChemicalFormula(element).weight / amu_cgs
