fc["H3plus_density"][:] = tiny_number * fc["density"]
fc["HCOplus_density"][:] = tiny_number * fc["density"]
fc["HeHplus_density"][:] = tiny_number * fc["density"]
fc["CH3plus_density"][:] = tiny_number * fc["density"]
fc["CH4plus_density"][:] = tiny_number * fc["density"]
fc["CH5plus_density"][:] = tiny_number * fc["density"]
fc["O2Hplus_density"][:] = tiny_number * fc["density"]
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc.calculate_hydrogen_number_density()
# then begin collapse
# evolve density and temperature according to free-fall collapse
data = evolve_freefall_metal(fc,
final_metallicity,
final_time,
dtmax=dtmax)
######### METALLICITY CONVERGENCE PLOTS ###################
pyplot.loglog(data["time"],
(np.divide(data["O_density"],
(data["O_density"] + data["Water_density"] +
data["OH_density"] + data["O2_density"]))),
label='O',
color='maroon',
#fc["de"][:] = (fc["HII"][:] + fc["Cplus_density"][:] + fc["OHplus_density"][:] + fc["Oplus_density"][:] + fc["O2plus_density"][:] + fc["COplus_density"][:]) * fc["density"]
fc["de"][:] = 1.e-4 * fc["density"]
fc["HeI"][:] = 8.333e-2 * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units / \
fc.calculate_mean_molecular_weight() / \
(my_chemistry.Gamma - 1.0)
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["n_H"][:] = fc.calculate_hydrogen_number_density()
# timestepping safety factor
safety_factor = 0.1
# evolve density and temperature according to free-fall collapse
data = evolve_freefall(fc, final_density, safety_factor=safety_factor)
#fH2 data!
logfH2_df = pd.DataFrame({
"log(n_H)":
np.log10(data["n_H"]),
"log(fH2)":
np.log10(data["H2I"] / (data["HDI"] + data["HM"] + data["HI"] +
data["HII"] + data["H2I"] + data["H2II"]))
})