{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Reading and writing Cosmology objects\n",
"\n",
"In this notebook, we show a few usage examples for how to read and write `Cosmology` objects to disk."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from pyccl import Cosmology"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"A cosmology including parameters and associated data (e.g. distances,\n",
" power spectra).\n",
"\n",
" .. note:: Although some arguments default to `None`, they will raise a\n",
" ValueError inside this function if not specified, so they are not\n",
" optional.\n",
"\n",
" .. note:: The parameter ``Omega_g`` can be used to set the radiation density\n",
" (not including relativistic neutrinos) to zero. Doing this will\n",
" give you a model that is physically inconsistent since the\n",
" temperature of the CMB will still be non-zero.\n",
"\n",
" .. note:: After instantiation, you can set parameters related to the\n",
" internal splines and numerical integration accuracy by setting\n",
" the values of the attributes of\n",
" :obj:`Cosmology.cosmo.spline_params` and\n",
" :obj:`Cosmology.cosmo.gsl_params`. For example, you can set\n",
" the generic relative accuracy for integration by executing\n",
" ``c = Cosmology(...); c.cosmo.gsl_params.INTEGRATION_EPSREL = 1e-5``.\n",
" See the module level documentation of `pyccl.core` for details.\n",
"\n",
" Args:\n",
" Omega_c (:obj:`float`): Cold dark matter density fraction.\n",
" Omega_b (:obj:`float`): Baryonic matter density fraction.\n",
" h (:obj:`float`): Hubble constant divided by 100 km/s/Mpc; unitless.\n",
" A_s (:obj:`float`): Power spectrum normalization. Exactly one of A_s\n",
" and sigma_8 is required.\n",
" sigma8 (:obj:`float`): Variance of matter density perturbations at\n",
" an 8 Mpc/h scale. Exactly one of A_s and sigma_8 is required.\n",
" n_s (:obj:`float`): Primordial scalar perturbation spectral index.\n",
" Omega_k (:obj:`float`): Curvature density fraction.\n",
" Defaults to 0.\n",
" Omega_g (:obj:`float`): Density in relativistic species\n",
" except massless neutrinos. The default of `None` corresponds\n",
" to setting this from the CMB temperature. Note that if a non-`None`\n",
" value is given, this may result in a physically inconsistent model\n",
" because the CMB temperature will still be non-zero in the\n",
" parameters.\n",
" Neff (:obj:`float`): Effective number of massless\n",
" neutrinos present. Defaults to 3.044.\n",
" m_nu (:obj:`float` or `array`):\n",
" Mass in eV of the massive neutrinos present. Defaults to 0.\n",
" If a sequence is passed, it is assumed that the elements of the\n",
" sequence represent the individual neutrino masses.\n",
" mass_split (:obj:`str`): Type of massive neutrinos. Should\n",
" be one of 'single', 'equal', 'normal', 'inverted'. 'single' treats\n",
" the mass as being held by one massive neutrino. The other options\n",
" split the mass into 3 massive neutrinos. Ignored if a sequence is\n",
" passed in m_nu. Default is 'normal'.\n",
" w0 (:obj:`float`): First order term of dark energy equation\n",
" of state. Defaults to -1.\n",
" wa (:obj:`float`): Second order term of dark energy equation\n",
" of state. Defaults to 0.\n",
" T_CMB (:obj:`float`): The CMB temperature today. The default of\n",
" is 2.725.\n",
" transfer_function (:obj:`str` or :class:`~pyccl.emulators.emu_base.EmulatorPk`):\n",
" The transfer function to use. Defaults to 'boltzmann_camb'.\n",
" matter_power_spectrum (:obj:`str` or :class:`~pyccl.emulators.emu_base.EmulatorPk`):\n",
" The matter power spectrum to use. Defaults to 'halofit'.\n",
" baryonic_effects (:class:`~pyccl.baryons.baryons_base.Baryons` or `None`):\n",
" The baryonic effects model to use. Options are `None` (no baryonic effects), or\n",
" a :class:`~pyccl.baryons.baryons_base.Baryons` object.\n",
" mg_parametrization (:class:`~pyccl.modified_gravity.modified_gravity_base.ModifiedGravity`\n",
" or `None`):\n",
" The modified gravity parametrization to use. Options are `None` (no MG), or\n",
" a :class:`~pyccl.modified_gravity.modified_gravity_base.ModifiedGravity` object. \n",
" Currently, only :class:`~pyccl.modified_gravity.MuSigmaMG` is supported.\n",
" extra_parameters (:obj:`dict`): Dictionary holding extra\n",
" parameters. Currently supports extra parameters for CAMB.\n",
" Details described below. Defaults to None.\n",
" T_ncdm (:obj:`float`): Non-CDM temperature in units of photon\n",
" temperature. The default is 0.71611.\n",
"\n",
" Currently supported extra parameters for CAMB are:\n",
"\n",
" * `halofit_version`\n",
" * `HMCode_A_baryon`\n",
" * `HMCode_eta_baryon`\n",
" * `HMCode_logT_AGN`\n",
" * `kmax`\n",
" * `lmax`\n",
" * `dark_energy_model`\n",
"\n",
" Consult the CAMB documentation for their usage. These parameters are passed\n",
" in a :obj:`dict` to `extra_parameters` as::\n",
"\n",
" extra_parameters = {\"camb\": {\"halofit_version\": \"mead2020_feedback\",\n",
" \"HMCode_logT_AGN\": 7.8}}\n",
"\n",
" .. note :: If using camb to compute the non-linear power spectrum with HMCode\n",
" to include baryonic effects, you should not include any extra\n",
" baryonic effects (i.e. set `baryonic_effects=None`).\n",
" \n"
]
}
],
"source": [
"cosmo = Cosmology(Omega_c=0.25, Omega_b=0.05, sigma8=0.8, h=0.7, n_s=0.96)\n",
"print(cosmo.__doc__)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Serialization (writing parameters to disk)\n",
"\n",
"Cosmology objects can be saved to a YAML format using the `write_yaml` method. This format is not currently very robust -- the exact order of the parameters must be maintained or the object cannot be read back in."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Omega_c: 0.25\n",
"Omega_b: 0.05\n",
"h: 0.7\n",
"n_s: 0.96\n",
"sigma8: 0.8\n",
"A_s: null\n",
"Omega_k: 0.0\n",
"Omega_g: null\n",
"Neff: 3.044\n",
"m_nu: 0.0\n",
"mass_split: normal\n",
"w0: -1.0\n",
"wa: 0.0\n",
"T_CMB: 2.7255\n",
"T_ncdm: 0.71611\n",
"extra_parameters: {}\n",
"transfer_function: boltzmann_camb\n",
"matter_power_spectrum: halofit\n"
]
}
],
"source": [
"cosmo.write_yaml('example_params.yaml')\n",
"!cat example_params.yaml"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"## Deserialization (reading parameters from disk)\n",
"\n",
"The parameters can be read back in using the `read_yaml` *class method*. Note that this must be called on the `Cosmology` class itself, as shown below, and not an instance of the class."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"cosmo2 = Cosmology.read_yaml(\"example_params.yaml\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<pyccl.cosmology.Cosmology>\n",
"\tNeff = 3.044\n",
"\tOmega_b = 0.05\n",
"\tOmega_c = 0.25\n",
"\th = 0.7\n",
"\tn_s = 0.96\n",
"\tsigma8 = 0.8\n",
"\textra_parameters =\n",
"\tHASH_ACCURACY_PARAMS = 0xb6e46c24158c0e30\n"
]
}
],
"source": [
"print(cosmo2)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"This `Cosmology` object can then be used to obtain cosmological predictions. See the other examples in this directory, for example *Distance Calculations Example.ipynb* or the more comprehensive demo *SLAC Feb2018 Demo.ipynb*."
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using Python Pickle\n",
"\n",
"`Cosmology` objects are also pickle-able, to make them easy to store on disk and to pass around in MPI environments."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"import pickle\n",
"\n",
"with open('cosmo.pkl', 'wb') as fp:\n",
" pickle.dump(cosmo2, fp)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<pyccl.cosmology.Cosmology>\n",
"\tNeff = 3.044\n",
"\tOmega_b = 0.05\n",
"\tOmega_c = 0.25\n",
"\th = 0.7\n",
"\tn_s = 0.96\n",
"\tsigma8 = 0.8\n",
"\textra_parameters =\n",
"\tHASH_ACCURACY_PARAMS = 0xb6e46c24158c0e30\n"
]
}
],
"source": [
"with open('cosmo.pkl', 'rb') as fp:\n",
" cosmo3 = pickle.load(fp)\n",
"\n",
"print(cosmo3)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "ccl_dev",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.9"
}
},
"nbformat": 4,
"nbformat_minor": 2
}