21cmfast

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Added
~~~~~
* ``coeval_callback`` and ``coeval_callback_redshifts`` flags to the ``run_lightcone``.
Gives the ability to run arbitrary code on ``Coeval`` boxes.
* JOSS paper!
* ``get_fields`` classmethod on all output classes, so that one can easily figure out
what fields are computed (and available) for that class.

Fixed
~~~~~
* Only raise error on non-available ``external_table_path`` when actually going to use it.

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Fixed
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* Added prototype functions to enable compilation for some standard compilers on MacOS.

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Modifications to the internal code structure of 21cmFAST

Added
~~~~~
* Refactor FFTW wisdom creation to be a python callable function

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Complete overhaul of 21cmFAST, including a robust python-wrapper and interface,
caching mechanisms, and public repository with continuous integration. Changes
and equations for minihalo features in this version are found in

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All changes and equations for this version are found in https://arxiv.org/abs/1809.08995.

Changed
~~~~~~~

* 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)

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Added
~~~~~
- 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


Fixed
~~~~~
- 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.

Changed
~~~~~~~
- Output format to avoid FFT padding for all boxes
- Filename conventions to be more explicit.
- Small changes to organization and structure