21cmFAST 3.0.2.dev0

Refactor FFTW wisdom creation to be a python callable function

Updated the radiation source model: (i) all radiation fields including X-rays, UV ionizing, Lyman Werner and Lyman alpha are considered from two seperated population namely atomic-cooling (ACGs) and minihalo-hosted molecular-cooling galaxies (MCGs); (ii) the turn-over masses of ACGs and MCGs are estimated with cooling efficiency and feedback from reionization and lyman werner suppression (Qin et al. 2020). This can be switched on using new flag_options USE_MINI_HALOS.

Updated kinetic temperature of the IGM with fully ionized cells following equation 6 of McQuinn (2015) and partially ionized cells having the volume-weightied temperature between the ionized (volume: 1-xHI; temperature T_RE ) and neutral components (volume: xHI; temperature: temperature of HI). This is stored in IonizedBox as temp_kinetic_all_gas. Note that Tk in TsBox remains to be the kinetic temperature of HI.

Tests: many unit tests, and also some regression tests.

CLI: run 21cmFAST boxes from the command line, query the cache database, and produce plots for standard comparison runs.

Documentation: Jupyter notebook demos and tutorials, FAQs, installation instructions.

Plotting routines: a number of general plotting routines designed to plot coeval and lightcone slices.

New power spectrum option (POWER_SPECTRUM=5) that uses a CLASS-based transfer function. WARNING: If POWER_SPECTRUM==5 the cosmo parameters cannot be altered, they are set to the Planck2018 best-fit values for now (until CLASS is added): (omegab=0.02237, omegac= 0.120, hubble=0.6736 (the rest are irrelevant for the transfer functions, but in case: A_s=2.100e-9, n_s=0.9649, z_reio = 11.357)

New user_params option USE_RELATIVE_VELOCITIES, which produces initial relative velocity cubes (option implemented, but not the actual computation yet).

Configuration management.

global params now has a context manager for changing parameters temporarily.

Vastly improved error handling: exceptions can be caught in C code and propagated to Python to inform the user of what’s going wrong.

Ability to write high-level data (Coeval and Lightcone objects) directly to file in a simple portable format.

POWER_SPECTRUM option moved from global_params to user_params.

Default cosmology updated to Planck18.

Updated the ionizing source model: (i) the star formation rates and ionizing escape fraction are scaled with the masses of dark matter halos and (ii) the abundance of active star forming galaxies is exponentially suppressed below the turn-over halo mass, M_{turn}, according to a duty cycle of exp(−M_{turn}/M_{h}), where M_{h} is a halo mass.

Removed the mean free path parameter, R_{mfp}. Instead, directly computes inhomogeneous, sub-grid recombinations in the intergalactic medium following the approach of Sobacchi & Mesinger (2014)

Code ‘redshift_interpolate_boxes.c’ to interpolate between comoving cubes, creating comoving light cone boxes.

Enabled openMP threading for SMP machines. You can specify the number of threads (for best performace, do not exceed the number of processors) in INIT_PARAMS.H. You do not need to have an SMP machine to run the code. NOTE: YOU SHOULD RE-INSTALL FFTW to use openMP (see INSTALL file)

Included a threaded driver file ‘drive_zscroll_reion_param.c’ set-up to perform astrophysical parameter studies of reionization

Included explicit support for WDM cosmologies; see COSMOLOGY.H. The prescription is similar to that discussed in Barkana+2001; Mesinger+2005, madifying the (i) transfer function (according to the Bode+2001 formula; and (ii) including the effective pressure term of WDM using a Jeans mass analogy. (ii) is approximated with a sharp cuttoff in the EPS barrier, using 60* M_J found in Barkana+2001 (the 60 is an adjustment factor found by fitting to the WDM collapsed fraction).

A Gaussian filtering step of the PT fields to perturb_field.c, in addition to the implicit boxcar smoothing. This avoids having”empty” density cells, i.e. delta=-1, with some small loss in resolution. Although for most uses delta=-1 is ok, some Lya forest statistics do not like it.

Added treatment of the risidual electron fraction from X-ray heating when computing the ionization field. Relatedly, modified Ts.c to output all intermediate evolution boxes, Tk and x_e.

Added a missing factor of Omega_b in Ts.c corresponding to eq. 18 in MFC11. Users who used a previous version should note that their results just effecively correspond to a higher effective X-ray efficiency, scaled by 1/Omega_baryon.

Normalization optimization to Ts.c, increasing performace on arge resolution boxes

GSL interpolation error in kappa_elec_pH for GSL versions > 1.15

Typo in macro definition, which impacted the Lya background calculation in v1.11 (not applicable to earlier releases)

Outdated filename sytax when calling gen_size_distr in drive_xHIscroll

Redshift scrolling so that drive_logZscroll_Ts.c and Ts.c are in sync.

Output format to avoid FFT padding for all boxes

Filename conventions to be more explicit.

Small changes to organization and structure

Wrapper functions mod_fwrite() and mod_fread() in Cosmo_c_progs/misc.c, which should fix problems with the library fwrite() and fread() for large files (>4GB) on certain operating systems.

Included print_power_spectrum_ICs.c program which reads in high resolution initial conditions and prints out an ASCII file with the associated power spectrum.

Parameter in Ts.c for the maximum allowed kinetic temperature, which increases stability of the code when the redshift step size and the X-ray efficiencies are large.

Oversight adding support for a Gaussian filter for the lower resolution field.