# setting initial conditions init_array = np.ones(NCELLS) * density init_values = dict() init_values["H_1"] = (1 - X) * init_array init_values['H_2'] = X * init_array init_values['H_m0'] = init_array * tiny init_values['He_1'] = init_array * tiny init_values['He_2'] = init_array * tiny init_values['He_3'] = init_array * tiny init_values['H2_1'] = init_array * tiny init_values['H2_2'] = init_array * tiny init_values['de'] = init_array * 0.0 # update and calculate electron density and etc with the handy functions total_density = primordial.calculate_total_density(init_values) init_values = primordial.convert_to_mass_density(init_values) init_values['de'] = primordial.calculate_free_electrons(init_values) init_values['density'] = primordial.calculate_total_density(init_values) number_density = primordial.calculate_number_density(init_values) # set up initial temperatures values used to define ge init_values['T'] = temperature # calculate ge (very crudely, no H2 help here) gamma = 5.0 / 3.0 init_values['ge'] = ((temperature * number_density * kboltz) / (init_values['density'] * mh * (gamma - 1))) # Write the initial conditions file # IF you need to use the Makefile, and c-library # you will have to specified the library_path
print(s, type(s)) if start_neutral: for s in ion_by_ion.required_species: if getattr(s, 'free_electrons', -1) == 0: init_values[s.name] = init_array.copy() else: init_values[s.name] = X * init_array # Scale to solar abundances if s.name not in ['de', 'ge']: ion_name = s.name.lower() ion = ch.ion(ion_name, temperature=init_values['T']) init_values[s.name] *= ion.Abundance init_values['de'][:] = 1e-30 init_values = ion_by_ion.convert_to_mass_density(init_values) else: # start CIE for s in sorted(ion_by_ion.required_species): if s.name != 'ge': if s.name == 'de': continue else: ion_name = s.name.lower() ion = ch.ion(ion_name, temperature=init_values['T']) print(ion_name) ion.ioneqOne() # this calcuate the equilirbium abundance @ T # however this attr is not defined for fully ionized species... # fix that later, take this as 1 for now first
init_array = np.ones(NCELLS) * density init_values = dict() init_values['OII'] = X * init_array init_values['OIII'] = init_array * X init_values['OIV'] = init_array * X init_values['OV'] = init_array * X init_values['OVI'] = init_array * X init_values['OVII'] = init_array * X init_values['OVIII'] = init_array * X init_values['OIX'] = init_array * X init_values['de'] = init_array * 0.0 total_density = oxygen.calculate_total_density(init_values, ("OI", )) init_values["OI"] = init_array.copy() - total_density init_values = oxygen.convert_to_mass_density(init_values) init_values['de'] = oxygen.calculate_free_electrons(init_values) init_values['density'] = oxygen.calculate_total_density(init_values) number_density = oxygen.calculate_number_density(init_values) # set up initial temperatures values used to define ge init_values['T'] = temperature # calculate ge (very crudely, no H2 help here) gamma = 5.0 / 3.0 init_values['ge'] = ((temperature * number_density * kboltz) / (init_values['density'] * mh * (gamma - 1))) # Write the initial conditions file oxygen.write_solver("oxygen", output_dir=".")
init_values['I2_1'] = 8.0e-8 * init_array * (126 * 2) init_values['H2O_1'] = 1.0 * init_array * (18) init_values['HOIO_1'] = 9.0e-11 * init_array * (126 + 32 + 1) init_values['IO3m_0'] = 0.01 * init_array * (1 + 16 * 3) init_values['O2_1'] = 2.5e3 * init_array * (16 * 2) init_values['CH2_COOH2_1'] = 0.0015 * init_array * (12 + 2 + (12 + 16 * 2 + 1) * 2) init_values['CHI_COOH2_1'] = 1.0e-20 * init_array * (12 + 126 + (12 + 16 * 2 + 1) * 2) init_values["H2O2_1"] = 0.33 * init_array * (2 + 16) * 2 print(new.required_species) total_density = new.calculate_total_density(init_values) init_values = new.convert_to_mass_density(init_values) init_values['de'] = new.calculate_free_electrons(init_values) init_values['density'] = init_array # new.calculate_total_density(init_values) number_density = new.calculate_number_density(init_values) # set up initial temperatures values used to define ge init_values['T'] = temperature # calculate ge (very crudely, no H2 help here) gamma = 5.0 / 3.0 init_values['ge'] = ((temperature * number_density * kboltz) / (init_values['density'] * mh * (gamma - 1))) # Write the initial conditions file # IF you need to use the Makefile, and c-library # you will have to specified the library_path
init_array = np.ones(NCELLS) * density init_values = dict() init_values['us_H_1'] = init_array * X init_values['us_H2_1'] = init_array * X init_values['us_e_0'] = init_array * 0.0 print(init_values) #print sorted(umist.reactions.values()) for species in umist.required_species: if species.name not in init_values: init_values[species.name] = init_array * 0.0 total_density = umist.calculate_total_density(init_values) init_values = umist.convert_to_mass_density(init_values) init_values['us_e_0'] = umist.calculate_free_electrons(init_values) init_values['density'] = umist.calculate_total_density(init_values) number_density = umist.calculate_number_density(init_values) # set up initial temperatures values used to define ge init_values['T'] = temperature # calculate ge (very crudely, no H2 help here) gamma = 5.0 / 3.0 init_values['ge'] = ((temperature * number_density * kboltz) / (init_values['density'] * mh * (gamma - 1))) print(init_values) import pdb
start_neutral = False if start_neutral: init_values['OII'] = X * init_array init_values['OIII'] = init_array * X init_values['OIV'] = init_array * X init_values['OV'] = init_array * X init_values['OVI'] = init_array * X init_values['OVII'] = init_array * X init_values['OVIII'] = init_array * X init_values['OIX'] = init_array * X init_values['de'] = init_array * 0.0 total_density = combined.calculate_total_density(init_values, ("OI", )) init_values["OI"] = init_array.copy() - total_density init_values = combined.convert_to_mass_density(init_values) else: # start CIE import chianti.core as ch import chianti.util as chu for s in sorted(combined.required_species): if s.name != 'ge': if s.name == 'de': continue else: print s.name, s.number, s.free_electrons + 1 ion_name = chu.zion2name(np.int(s.number), np.int(s.free_electrons + 1)) ion = ch.ion(ion_name, temperature=init_values['T']) ion.ioneqOne()