hmf 1.3.0

===
hmf
===

.. image:: https://travis-ci.org/steven-murray/hmf.png?branch=master
:target: https://travis-ci.org/steven-murray/hmf

``hmf`` is a python application that provides a flexible and simple way to calculate the
Halo Mass Function for any input cosmology, redshift, dark matter model, virial
overdensity or several other variables. Addition of further variables should be simple.

It is also the backend to HMFcalc, the online HMF calculator at <hmf.icrar.org>


INSTALLATION
------------
1. Install pycamb:
>>> cd <Directory that pycamb source will live in>
>>> git clone https://github.com/steven-murray/pycamb
>>> cd pycamb
>>> [sudo] python setup.py install
2. >>> pip install hmf


USAGE
-----
hmf can be used interactively (for instance in ipython) or in a script.
To use interactively, in ipython do something like the following:

>>> from hmf import Perturbations
>>> pert = Perturbations()
>>> mass_func = pert.dndlnm
>>> mass_variance = pert.sigma
>>> ...

This will return a Sheth-Tormen mass function between 10^10 and 10^15 M_sun,
at redshift 0 for a default cosmology. Cosmological parameters may be passed
to the initialiser, ``Perturbations()``

To change the parameters (cosmological or otherwise), one should use the
`update()` method, if a Perturbations() object already exists. For example
>>> pert = Perturbations()
>>> pert.update(omegab = 0.05,z=10) #update baryon density and redshift
>>> cumulative_mass_func = pert.ngtm

Check the docstring of `Perturbations()` for all arguments allowed.


HISTORY
-------
1.3.0 - January 03, 2014
A few more documentation updates (especially tools.py)
Removed new_k_bounds function from tools.py
Added `w` parameter to cosmolopy dictionary in `cosmo.py`
Changed cosmography significantly to use cosmolopy in general
Fixed a pretty bad bug where updating h/H0 would crash the program if
only one of omegab/omegac was updated alongside it
Generally tidied up some of the update mechanisms.
API CHANGE: cosmography.py no longer exists -- I've chosen to utilise
cosmolopy more heavily here.
Added Travis CI usage
Fixed a compatibility issue with older versions of numpy in cumulative
functions

1.2.2 - December 10, 2013
Bug in "EH" transfer function call

1.2.1 - December 6, 2013
Small bugfixes to update() method

1.2.0 - December 5, 2013
Major documentation overhaul -- most docstrings are now in Sphinx/numpydoc format
Addition of cosmo module, which deals with the cosmological parameters in a cleaner way
Some tidying up of several functions.

1.1.10- October 29, 2013
Fixed bug in mltm property
Better updating -- checks if update value is actually different.
Now performs a check to see if mass range is inside fit range.

1.1.9 - October 4, 2013
Fixed some issues with n(<m) and M(<m) causing them to give NaN's

1.1.85- October 2, 2013
The normalization of the power spectrum now saved as an attribute (mostly
for use with the hod package... coming soon ;)

1.1.8 - September 19, 2013
Fixed small bug in SMT function which made it crash

1.1.7 - September 19, 2013
Updated "ST" fit to "SMT" fit to avoid confusion. "ST" is still available for now.
Now uses trapezoid rule for integration as it is faster.

1.1.6 - September 05, 2013
Modified comments to reflect parameters
Couple of bugfixes for fitting_functions.py
Included an option to use delta_halo as compared to critical rather than mean density (thanks to A. Vikhlinin and anonymous referree)
Fixed mass range of Tinker (thanks to J. Tinker and anonymous referee for this)

1.1.5 - September 03, 2013
Fixed bug in mgtm (thanks to J. Mirocha)
Fixed an embarrassing error in Reed07 fitting function
Fixed a bug in which dndlnm and its dependents (ngtm, etc..) were calculated wrong
if dndlog10m was called first.
Added a whole suite of tests against genmf that actually work
Fixed error in which for some choices of M, the whole extension in ngtm would be NAN and give error

1.1.4 - August 27, 2013
Added ability to change resolution in CAMB from hmf interface
(This requires a re-install of pycamb to the newest version on the fork)

1.1.3 - August 7, 2013
Added Behroozi Fit (thanks to P. Behroozi)

1.1.2 - July 02, 2013
Ability to calculate fitting functions to whatever mass you want (BEWARE!!)
Small bugfix

1.1.1 - July 02, 2013
Corrections to Watson fitting function from latest update on arXiv (thanks to W. Watson)
** Fixed units for k and transfer function ** (Thanks to A. Knebe)
Improved docstring for Perturbations class
Added Eisenstein-Hu fit to the transfer function

1.1.0 - June 27, 2013
Massive overhaul of structure
Now dependencies are tracked throughout the program, making updates even faster

1.0.10- June 24, 2013
Added dependence on Delta_vir to Tinker

1.0.9 - June 19, 2013
Fixed an error with an extra ln(10) in the mass function (quoted as dn/dlnM but actually outputting dn/dlog10M)

1.0.8 - June 19, 2013
Took out log10 from cumulative mass functions
Better cumulative mass function logic

1.0.6 - June 19, 2013
Fixed cumulative mass functions (extra factor of M was in there)

1.0.4 - June 6, 2013
Added Bhattacharya fitting function
Fixed concatenation of list and dict issue

1.0.2 - May 21, 2013
Fixed some warnings for non-updated variables passed to update()

1.0.1 - May 20, 2013
Added better warnings for non-updated variables passed to update()
Made default cosmology WMAP7

0.9.99- May 10, 2013
Added warning for k*R limits
Couple of minor bugfixes
**Important** Angulo fitting function corrected (arXiv version had a typo).

0.9.97- April 15, 2013
Urgent Bugfix for updating cosmology (for transfer functions)

0.9.96- April 11, 2013
Few bugfixes

0.9.95- April 09, 2013
Added cascading variable changes for optimization
Added this README
Added update() function to simply change parameters using cascading approach

0.9.9 - April 08, 2013
First version in its own package
Added pycamb integration
Removed fitting function from being a class variable
Removed overdensity form being a class variable

0.9.7 - March 18, 2013
Modified set_z() so it only does calculations necessary when z changes
Made calculation of dlnsdlnM in init since it is same for all z
Removed mean density redshift dependence

0.9.5 - March 10, 2013
The class has been in the works for almost a year now, but it currently
will calculate a mass function based on any of several fitting functions.