pyC\(^2\)Ray Parameter File

Here, we will illustrate the content of pyC\(^2\)Ray parameter file and how you can extend it to add more astrophysical models and variables.

import pyc2ray as pc2r
import numpy as np, yaml
import matplotlib.pyplot as plt

import astropy.units as u

The variables employed in a pyC\(^2\)Ray run are defined in a YAML file, e.g. parameters.yml. The variables are grouped in cathegories and the basic requirement are:

• Grid: Parameters to set up the simulation volume (e.g. boxsize, mesh-size,

• Material: Initial properties of physical quantities in the simulation volume (neutral fraction, temperature and density)

• CGS: Miscellaneous physical constant (do not require modification).

• Abundaces: Cosmological element abundances (do not require modification).

• Photo: Control parameters for the photo-ionization rate and the proprieties of the sources.

• BlackBodySource: Parameters for the Black Body source (standard source model).

• Cosmology: Cosmological paramerters, at the moment only standard \(\Lambda\)CDM is implemented.

• Output: Paths of the input/output directories.

• Raytracing: Parameters for the raytracing, the only tunable parameter is the source batch size (see :math:S` source_batch_size.ipynb <source_batch_size.ipynb>`__ tutorial).

Based on the need of your simulation, you can add new cathegories. For instance, in the :math:S` make_sim.ipynb <make_sim.ipynb>`__ tutorial, we will have a look at the Sources and Sinks cathegories for the source and sink models that are already implemented in pyC\(^2\)Ray.

paramfile = 'parameters.yml'

with open(paramfile,'r') as f:
    params = yaml.load(f, yaml.CSafeLoader)

print(params.keys())

dict_keys(['Grid', 'Material', 'CGS', 'Abundances', 'Photo', 'Sinks', 'BlackBodySource', 'Cosmology', 'Output', 'Raytracing'])

Most of the cathegories do not require any substantial modification as these are standard value, for instance the group CGS contain miscellaneous defined physical constants.

params['CGS']

{'albpow': -0.7,
 'bh00': 2.59e-13,
 'alcpow': -0.672,
 'eth0': 13.598,
 'ethe0': 24.587,
 'ethe1': 54.416,
 'xih0': 1.0,
 'fh0': 0.83,
 'colh0_fact': 1.3e-08}

# ionizing energy [eV] of hydrogen
print('Ionizing energy for HI:', params['CGS']['eth0'] * u.eV)

# energy of the first ionization of helium [eV]
print('Ionizing energy for HeI:', params['CGS']['ethe0'] * u.eV)

# energy of the second ionization of helium [eV]
print('Ionizing energy for HeII', params['CGS']['ethe1'] * u.eV)

Ionizing energy for HI: 13.598 eV
Ionizing energy for HeI: 24.587 eV
Ionizing energy for HeII 54.416 eV

On the other hand, you are required to modify the I/O directories in the Output cathegory or the cosmological parameter, Cosmology.

params['Output']

{'results_basename': './test_results/',
 'inputs_basename': './',
 'sources_basename': './',
 'density_basename': './',
 'logfile': 'pyC2Ray.log'}

params['Cosmology']

{'cosmological': 0,
 'h': 0.6766,
 'Omega0': 0.30966,
 'Omega_B': 0.04897,
 'cmbtemp': 2.7255,
 'zred_0': 9.0}