py21cmfast

The py21cmfast package.

Submodules

Attributes

DATA_PATH

__version__

config

Classes

AngularLightconer

Angular lightcone slices constructed from rectlinear coevals.

AstroOptions

Options for the ionization routines which enable/disable certain modules.

AstroParams

Astrophysical parameters.

BrightnessTemp

A class containing the brightness temperature box.

CacheConfig

A configuration object that specifies whether a certain field should be cached.

CosmoParams

Cosmological parameters (with defaults) which translates to a C struct.

HaloBox

A class containing all gridded halo properties.

HaloCatalog

A class containing all fields related to halos.

InitialConditions

A class representing an InitialConditions C-struct.

InputParameters

A class defining a collection of InputStruct instances.

IonizedBox

A class containing all ionized boxes.

LightCone

A full Lightcone with all associated evolved data.

MatterOptions

Structure containing options which affect the matter field (ICs, perturbedfield, halos).

OutputCache

An object that manages cache files from 21cmFAST simulations.

PerturbedField

A class containing all perturbed field boxes.

PerturbedHaloCatalog

A class to hold a HaloCatalog whose coordinates are in real (Eulerian) space.

RectilinearLightconer

The class rectilinear lightconer.

RunCache

An object that specifies all cache files that should/can exist for a full run.

SimulationOptions

Structure containing broad simulation options.

TsBox

A class containing all spin temperature boxes.

XraySourceBox

A class containing the filtered sfr grids.

Functions

brightness_temperature(*, ionized_box, perturbed_field)

Compute a coeval brightness temperature box.

compute_halo_grid(*, redshift, initial_conditions[, ...])

Compute grids of halo properties from a catalogue.

compute_initial_conditions(*, inputs)

Compute initial conditions.

compute_ionization_field(*, perturbed_field, ...[, ...])

Compute an ionized box at a given redshift.

compute_luminosity_function(*, redshifts, inputs[, ...])

Compute a the luminosity function over a given number of bins and redshifts.

compute_rms(classy_output[, kind, redshifts, ...])

Compute the root-mean-square of a field at given redshifts.

compute_spin_temperature(*, initial_conditions, ...[, ...])

Compute spin temperature boxes at a given redshift.

compute_tau(*, redshifts, global_xHI, inputs[, z_re_HeII])

Compute the optical depth to reionization under the given model.

compute_xray_source_field(*, initial_conditions, ...)

Compute filtered grid of SFR for use in spin temperature calculation.

configure_logging()

Configure logging for the '21cmFAST' logger.

construct_fftw_wisdoms(*, use_fftw_wisdom)

Construct all necessary FFTW wisdoms.

create_params_from_template(template_name, **kwargs)

Construct the required InputStruct instances for a run from a given template.

determine_halo_catalog(*, redshift[, inputs, ...])

Find a halo list, given a redshift.

generate_lightcone(*, lightconer, inputs[, ...])

Create a generator function for a lightcone run.

get_logspaced_redshifts(min_redshift, z_step_factor, ...)

Compute a sequence of redshifts to evolve over that are log-spaced.

list_templates()

Return a list of the available templates.

perturb_field(*, redshift[, inputs])

Compute a perturbed field at a given redshift.

perturb_halo_catalog(*, initial_conditions[, inputs, ...])

Given a halo list, perturb the halos for a given redshift.

read_inputs(group[, safe])

Read the InputParameters from a cache file.

read_output_struct(path[, group, struct, safe])

Read an output struct from an HDF5 file.

run_classy(**kwargs)

Run CLASS with specified input parameters.

run_lightcone(**kwargs)

Run a lightcone simulation and return the final lightcone object.

setup_photon_cons(initial_conditions[, inputs])

Set up the photon non-conservation correction.

write_output_to_hdf5(output, path[, group, mode])

Write an output struct in standard HDF5 format.

write_template(inputs, template_file[, mode])

Write a set of input parameters to a template file.

Package Contents

py21cmfast.brightness_temperature(*, ionized_box, perturbed_field, spin_temp=None)[source]

Compute a coeval brightness temperature box.

Parameters:

  • ionized_box (IonizedBox) – A pre-computed ionized box.

  • perturbed_field (PerturbedField) – A pre-computed perturbed field at the same redshift as ionized_box.

  • spin_temp (TsBox, optional) – A pre-computed spin temperature, at the same redshift as the other boxes.

Returns:

BrightnessTemp instance.

Parameters:
Return type:

py21cmfast.wrapper.outputs.BrightnessTemp

py21cmfast.compute_halo_grid(*, redshift, initial_conditions, inputs=None, halo_catalog=None, previous_spin_temp=None, previous_ionize_box=None)[source]

Compute grids of halo properties from a catalogue.

At the moment this simply produces halo masses, stellar masses and SFR on a grid of HII_DIM. In the future this will compute properties such as emissivities which will be passed directly into ionize_box etc. instead of the catalogue.

Parameters:

  • initial_conditions (InitialConditions) – The initial conditions of the run.

  • inputs (InputParameters, optional) – The input parameters specifying the run.

  • halo_catalog (HaloCatalog, optional) – This contains all the dark matter haloes obtained if using a discrete halo model. This is a list of halo masses and coordinates for the dark matter halos.

  • previous_spin_temp (TsBox, optional) – The previous spin temperature box. Used for feedback when USE_MINI_HALOS==True

  • previous_ionize_box (IonizedBox or None) – An at the last timestep. Used for feedback when USE_MINI_HALOS==True

Returns:

HaloBox – An object containing the halo box data.

Other Parameters:

regenerate, write, cache – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.HaloBox

py21cmfast.compute_initial_conditions(*, inputs)[source]

Compute initial conditions.

Parameters:

  • inputs – The InputParameters instance defining the run.

  • regenerate (bool, optional) – Whether to force regeneration of data, even if matching cached data is found.

  • cache – An OutputCache object defining how to read cached boxes.

  • write – A boolean specifying whether we need to cache the box.

Returns:

InitialConditions

Parameters:

inputs (py21cmfast.wrapper.inputs.InputParameters)

Return type:

py21cmfast.wrapper.outputs.InitialConditions

py21cmfast.compute_ionization_field(*, perturbed_field, initial_conditions, inputs=None, previous_perturbed_field=None, previous_ionized_box=None, spin_temp=None, halobox=None)[source]

Compute an ionized box at a given redshift.

This function has various options for how the evolution of the ionization is computed (if at all). See the Notes below for details.

Parameters:

  • initial_conditions (InitialConditions instance) – The initial conditions.

  • inputs (InputParameters) – The input parameters specifying the run. Since this may be the first box to use the astro params/flags, it is needed when we have not computed a TsBox or HaloBox.

  • perturbed_field (PerturbedField) – The perturbed density field.

  • previous_perturbed_field (PerturbedField, optional) – An perturbed field at higher redshift. This is only used if USE_MINI_HALOS is included.

  • previous_ionize_box (IonizedBox or None) – An ionized box at higher redshift. This is only used if INHOMO_RECO and/or USE_TS_FLUCT are true. If either of these are true, and this is not given, then it will be assumed that this is the “first box”, i.e. that it can be populated accurately without knowing source statistics.

  • spin_temp (TsBox or None, optional) – A spin-temperature box, only required if USE_TS_FLUCT is True. If None, will try to read in a spin temp box at the current redshift, and failing that will try to automatically create one, using the previous ionized box redshift as the previous spin temperature redshift.

  • halobox (HaloBox or None, optional) – If passed, this contains all the dark matter haloes obtained if using the lagrangian source models. These are grids containing summed halo properties such as ionizing emissivity.

Returns:

IonizedBox – An object containing the ionized box data.

Parameters:
Return type:

py21cmfast.wrapper.outputs.IonizedBox

Notes

Typically, the ionization field at any redshift is dependent on the evolution of xHI up until that redshift, which necessitates providing a previous ionization field to define the current one. If neither the spin temperature field, nor inhomogeneous recombinations (specified in flag options) are used, no evolution needs to be done. If the redshift is beyond Z_HEAT_MAX, previous fields are not required either.

py21cmfast.compute_luminosity_function(*, redshifts, inputs, nbins=100, mturnovers=None, mturnovers_mini=None, component='both')[source]

Compute a the luminosity function over a given number of bins and redshifts.

Parameters:

  • redshifts (array-like) – The redshifts at which to compute the luminosity function.

  • inputs (InputParameters) – The input parameters defining the simulation run.

  • nbins (int, optional) – The number of luminosity bins to produce for the luminosity function.

  • mturnovers (array-like, optional) – The turnover mass at each redshift for massive halos (ACGs). Only required when USE_MINI_HALOS is True.

  • mturnovers_mini (array-like, optional) – The turnover mass at each redshift for minihalos (MCGs). Only required when USE_MINI_HALOS is True.

  • component (str, {‘both’, ‘acg’, ‘mcg}) – The component of the LF to be calculated.

Returns:

  • Muvfunc (np.ndarray) – Magnitude array (i.e. brightness). Shape [nredshifts, nbins]

  • Mhfunc (np.ndarray) – Halo mass array. Shape [nredshifts, nbins]

  • lfunc (np.ndarray) – Number density of haloes corresponding to each bin defined by Muvfunc. Shape [nredshifts, nbins].

Parameters:

  • redshifts (collections.abc.Sequence[float])

  • inputs (py21cmfast.wrapper.inputs.InputParameters)

  • nbins (int)

  • mturnovers (numpy.ndarray | None)

  • mturnovers_mini (numpy.ndarray | None)

  • component (Literal['both', 'acg', 'mcg'])

Return type:

tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]

py21cmfast.compute_rms(classy_output, kind='d_m', redshifts=0, smoothing_radius=0)[source]

Compute the root-mean-square of a field at given redshifts.

Parameters:

  • classy_output (classy.Class) – An object containing all the information from the CLASS calculation.

  • kind (str, optioanl) – The type of field for which the rms shall be computed. Options are:

    • “d_b”, “d_cdm”, “d_m”: density field of baryons, cold dark matter, or all matter (including massive neutrinos).

    • “v_b”, “v_cdm”: magnitude of the velocity vector field of baryons or CDM (this is gauge dependent).

    • “v_cb”: magnitude of the relative velocity vector field between baryons and CDM (this is gauge independent).

    Default is “d_m”.

  • redshifts (np.array or a float, optional) – The redshifts at which the rms shall be computed. Default is 0.

  • smoothing_radius (float, optional) – If non-zero, the field will be smoothed with a top hat filter (in real space) with comoving radius that is set to R_smooth. Can also be passed as type ‘astropy.units.quantity.Quantity’ with length unit. Default is 0.

Returns:

rms (np.array) – Array of the rms of the desired field at the given redshifts.

Parameters:

  • classy_output (classy.Class)

  • kind (str)

  • redshifts (collections.abc.Sequence[float])

  • smoothing_radius (float)

Return type:

collections.abc.Sequence[float]

py21cmfast.compute_spin_temperature(*, initial_conditions, perturbed_field, inputs=None, xray_source_box=None, previous_spin_temp=None, cleanup=False)[source]

Compute spin temperature boxes at a given redshift.

See the notes below for how the spin temperature field is evolved through redshift.

Parameters:

  • initial_conditions (InitialConditions) – The initial conditions

  • inputs (InputParameters) – The input parameters specifying the run. Since this will be the first box to use the astro params/flags when SOURCE_MODEL=’E-INTEGRAL’ and USE_TS_FLUCT=True.

  • perturbed_field (PerturbedField, optional) – If given, this field will be used, otherwise it will be generated. To be generated, either initial_conditions and redshift must be given, or simulation_options, cosmo_params and redshift. By default, this will be generated at the same redshift as the spin temperature box. The redshift of perturb field is allowed to be different than redshift. If so, it will be interpolated to the correct redshift, which can provide a speedup compared to actually computing it at the desired redshift.

  • xray_source_box (XraySourceBox, optional) – When using a lagrangian source model, this box specifies the filtered sfr and xray emissivity at all redshifts/filter radii required by the spin temperature algorithm.

  • previous_spin_temp (TsBox or None) – The previous spin temperature box. Needed when we are beyond the first snapshot

Returns:

TsBox – An object containing the spin temperature box data.

Other Parameters:

regenerate, write, cache – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.TsBox

py21cmfast.compute_tau(*, redshifts, global_xHI, inputs, z_re_HeII=3.0)[source]

Compute the optical depth to reionization under the given model.

Parameters:

  • redshifts (array-like) – Redshifts defining an evolution of the neutral fraction.

  • global_xHI (array-like) – The mean neutral fraction at redshifts.

  • inputs (InputParameters) – Defines the input parameters of the run

  • z_re_HeII (float, optional) – The redshift at which helium reionization occurs.

Returns:

tau (float) – The optical depth to reionization

Raises:

ValueError : – If redshifts and global_xHI have inconsistent length or if redshifts are not in ascending order.

Parameters:
Return type:

float

py21cmfast.compute_xray_source_field(*, initial_conditions, hboxes, redshift)[source]

Compute filtered grid of SFR for use in spin temperature calculation.

This will filter over the halo history in annuli, computing the contribution to the SFR density

If no halo field is passed one is calculated at the desired redshift as if it is the first box.

Parameters:

  • initial_conditions (InitialConditions) – The initial conditions of the run. The user and cosmo params

  • hboxes (Sequence of HaloBox instances) – This contains the list of Halobox instances which are used to create this source field

Returns:

XraySourceBox – An object containing x ray heating, ionisation, and lyman alpha rates.

Other Parameters:

regenerate, write, cache – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.XraySourceBox

py21cmfast.configure_logging()[source]

Configure logging for the ‘21cmFAST’ logger.

py21cmfast.construct_fftw_wisdoms(*, use_fftw_wisdom)[source]

Construct all necessary FFTW wisdoms.

Parameters:

USE_FFTW_WISDOM (bool) – Whether we are interested in having FFTW wisdoms.

Parameters:

use_fftw_wisdom (bool)

Return type:

int

py21cmfast.create_params_from_template(template_name, **kwargs)[source]

Construct the required InputStruct instances for a run from a given template.

Parameters:

template_name (str,) – defines the name/alias of the native template (see templates/manifest.toml for a list) alternatively, is the path to a TOML file containing tables titled [CosmoParams], [SimulationOptions], [AstroParams] and [AstroOptions] with parameter settings

Other Parameters:

  • Any other parameter passed is considered to be a name and

  • value of a parameter in any of the `InputStruct` subclasses,

  • and will be used to over-ride the template values.

Returns:

input_dict (dict containing:) –

cosmo_paramsCosmoParams

Instance containing cosmological parameters

simulation_optionsSimulationOptions

Instance containing general run parameters

simulation_optionsMatterOptions

Instance containing general run flags and enums

astro_paramsAstroParams

Instance containing astrophysical parameters

astro_optionsAstroOptions

Instance containing astrophysical flags and enums

Parameters:

template_name (str | pathlib.Path | collections.abc.Sequence[str | pathlib.Path])

Return type:

dict[str, dict[str, Any]]

py21cmfast.determine_halo_catalog(*, redshift, inputs=None, initial_conditions, descendant_halos=None)[source]

Find a halo list, given a redshift.

Parameters:

  • redshift (float) – The redshift at which to determine the halo list.

  • initial_conditions (InitialConditions instance) – The initial conditions fields (density, velocity).

  • descendant_halos (HaloCatalog instance, optional) – The halos that form the descendants (i.e. lower redshift) of those computed by this function. If this is not provided, we generate the initial stochastic halos directly in this function (and progenitors can then be determined by these).

Returns:

HaloCatalog

Other Parameters:

regenerate, write, cache – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.HaloCatalog

py21cmfast.generate_lightcone(*, lightconer, inputs, initial_conditions=None, include_dvdr_in_tau21=True, apply_rsds=False, n_rsd_subcells=4, cleanup=True, write=_cache, cache=_ocache, regenerate=True, progressbar=False, lightcone_filename=None)[source]

Create a generator function for a lightcone run.

This is generally the easiest and most efficient way to generate a lightcone, though it can be done manually by using the lower-level functions which are called by this function.

Parameters:

  • lightconer (Lightconer) – This object specifies the dimensions, redshifts, and quantities required by the lightcone run

  • inputs (InputParameters) – This object specifies the input parameters for the run, including the random seed

  • initial_conditions (InitialConditions, optional) – If given, the user and cosmo params will be set from this object, and it will not be re-calculated.

  • include_dvdr_in_tau21 (bool, optional) – If True, velocity gradient corrections to the 21cm optical depth will be applied. See Mao+ 2012. Default is True.

  • apply_rsds (bool, optional) – If True, all output lightcones will be transformed from real space to redshift space, according to the peculiar velocity fields. See Mao+ 2012. Default is False.

  • n_rsd_subcells (int, optional) – The number of subcells into which each cell is divided when redshift space distortions are applied. Becomes relevant only if apply_rsds is True. Default is False.

  • cleanup (bool, optional) – A flag to specify whether the C routine cleans up its memory before returning. Typically, if spin_temperature is called directly, you will want this to be true, as if the next box to be calculate has different shape, errors will occur if memory is not cleaned. Note that internally, this is set to False until the last iteration.

  • progressbar (bool, optional) – If True, a progress bar will be displayed throughout the simulation. Defaults to False.

  • lightcone_filename – The filename to which to save the lightcone. The lightcone is returned in memory, and can be saved manually later, but including this filename will save the lightcone on each iteration, which can be helpful for checkpointing.

Returns:

  • lightcone (LightCone) – The lightcone object.

  • coeval_callback_output (list) – Only if coeval_callback in not None.

Other Parameters:

regenerate, write, direc, hooks – See docs of initial_conditions() for more information.

Parameters:
py21cmfast.get_logspaced_redshifts(min_redshift, z_step_factor, max_redshift)[source]

Compute a sequence of redshifts to evolve over that are log-spaced.

Parameters:

  • min_redshift (float)

  • z_step_factor (float)

  • max_redshift (float)

Return type:

tuple[float]

py21cmfast.list_templates()[source]

Return a list of the available templates.

Return type:

list[dict]

py21cmfast.perturb_field(*, redshift, inputs=None, initial_conditions)[source]

Compute a perturbed field at a given redshift.

Parameters:

  • redshift (float) – The redshift at which to compute the perturbed field.

  • initial_conditions (InitialConditions instance) – The initial conditions.

Returns:

PerturbedField

Other Parameters:

regenerate, write, cache – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.PerturbedField

Examples

>>> initial_conditions = compute_initial_conditions()
>>> field7 = perturb_field(7.0, initial_conditions)
>>> field8 = perturb_field(8.0, initial_conditions)

The user and cosmo parameter structures are by default inferred from the initial_conditions.

py21cmfast.perturb_halo_catalog(*, initial_conditions, inputs=None, previous_spin_temp=None, previous_ionize_box=None, halo_catalog)[source]

Given a halo list, perturb the halos for a given redshift.

Parameters:

  • initial_conditions (InitialConditions) – The initial conditions of the run. The user and cosmo params as well as the random seed will be set from this object.

  • halo_catalog (:class: ~HaloCatalog) – The halo catalogue in Lagrangian space to be perturbed.

Returns:

PerturbedHaloCatalog

Other Parameters:

regenerate, write, direc – See docs of initial_conditions() for more information.

Parameters:
Return type:

py21cmfast.wrapper.outputs.PerturbedHaloCatalog

Examples

Fill this in once finalised

py21cmfast.read_inputs(group, safe=True)[source]

Read the InputParameters from a cache file.

Parameters:

  • group (h5py.Group | Path | h5py.File) – A file, or HDF5 Group within a file, to read the input parameters from.

  • safe (bool, optional) – If in safe mode, errors will be raised if keys exist in the file that are not valid attributes of the InputParameters. Otherwise, only warnings will be raised.

Returns:

inputs (InputParameters) – The input parameters contained in the file.

Parameters:

  • group (h5py.Group | pathlib.Path | h5py.File)

  • safe (bool)

Return type:

py21cmfast.wrapper.inputs.InputParameters

py21cmfast.read_output_struct(path, group='/', struct=None, safe=True)[source]

Read an output struct from an HDF5 file.

Parameters:

  • path (Path) – The path to the HDF5 file.

  • group (str, optional) – A path within the HDF5 heirarchy to the top-level of the OutputStruct. This is usually the root of the file.

  • struct – A string specifying the kind of OutputStruct to read (e.g. InitialConditions). Generally, this does not need to be provided, as cache files contain just a single output struct.

  • safe – Whether to read the file in “safe” mode. If True, keys found in the file that are not valid attributes of the struct will raise an exception. If False, only a warning will be raised.

Returns:

OutputStruct – An OutputStruct that is contained in the cache file.

Parameters:

  • path (pathlib.Path)

  • group (str)

  • struct (str | None)

  • safe (bool)

Return type:

py21cmfast.wrapper.outputs.OutputStruct

py21cmfast.run_classy(**kwargs)[source]

Run CLASS with specified input parameters.

Parameters:

kwargs – Optional keywords to pass to CLASS.

Returns:

output (classy.Class) – An object containing all the information from the CLASS calculation.

Return type:

classy.Class

py21cmfast.run_lightcone(**kwargs)[source]

Run a lightcone simulation and return the final lightcone object.

This simply wraps generate_lightcone() and returns the final lightcone object after the generator has been exhausted. All parameters are passed directly to generate_lightcone().

Return type:

LightCone

py21cmfast.setup_photon_cons(initial_conditions, inputs=None, **kwargs)[source]

Set up the photon non-conservation correction.

First performs a simplified calibration simulation and saves its neutral fraction history, to be matched to the analytic expression from solving the filling factor ODE.

This matching can happen via a redshift adjustment, or an adjustment to the escape fraction power-law parameters

Parameters:

  • initial_conditions (InitialConditions,) – The InitialConditions instance to use for the photonconservation calculation

  • inputs (InputParameters, optional) – An InputParameters instance. If not given will taken from initial_conditions.

Other Parameters:

Any other parameters able to be passed to :func:`compute_initial_conditions`.

Parameters:
py21cmfast.write_output_to_hdf5(output, path, group=None, mode='w')[source]

Write an output struct in standard HDF5 format.

Parameters:

  • output – The OutputStruct to write.

  • path (Path) – The path to write the output struct to.

  • group (str, optional) – The HDF5 group into which to write the object. By default, this is the root.

  • mode (str) – The mode in which to open the file.

Parameters:
py21cmfast.write_template(inputs, template_file, mode='full')[source]

Write a set of input parameters to a template file.

Parameters:

  • inputs – The inputs to write to file.

  • template_file – The path of the output.

Parameters:
py21cmfast.DATA_PATH
py21cmfast.__version__[source]
py21cmfast.config