inonchiu/hmf

Python halo mass function calculator

hmf

The halo mass function calculator

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 http://hmf.icrar.org.

Documentation

You can find the documentation at http://hmf.readthedocs.org

Attribution

Please cite Murray, Power and Robotham (2013) if you find this code useful in your research.

License

Copyright (c) 2014, Steven Murray.

See LICENSE.txt for details.

HISTORY

1.8.0 - February 2, 2015

Added better WDM models Separated WDM models from main class for extendibility Enhanced caching to deal with subclassing Added SharpK and SharpKEllipsoid filters and overhauled filter system. Minor bugfixes

1.7.1 - January 28, 2015

Added warning to docstring of _dlnsdlnm and n_eff for non-physical oscillations.

1.7.0 - October 28, 2014

Modified get_hmf to be more general Moved get_hmf and related functions to "functional.py" Very much updated fitting routines, in class structure Made fitting_functions more flexible and model-like.

1.6.2 - September 16, 2014

Fixed bug in Behroozi fit which caused an infinite recursion Better Singleton labelling in get_hmf New HALOFIT option for original co-oefficients from Smith+03 Much cleaning of mass function integrations. New separate module for it. IMPORTANT: Removal of nltm routine altogether, as it is inconsistent. IMPORTANT: mltm now called rho_ltm, and mgtm called rho_gtm IMPORTANT: Definition of rho_ltm now assumes all mass is in halos. Tests fixed for new cumulants. Behroozi-specific modifications moved to Behroozi class New property _fit which is the actual class for mf_fit

1.6.1 - September 8, 2014

Fixed "transfer" property Updates fixed for transfer_fit Updates fixed for nu Better get_hmf function Fixed cache bug where unexecuted branches caused some properties to be misinterpreted Fixed bug in CAMB transfer options, where defaults would overwrite user-given values (introduced in 1.6.0) Fixed dependence on transfer_options Fixed typo in Tinker10 fit at z = 0

1.6.0 - August 19, 2014

Completely re-worked caching module to be easier to code and faster. New Tinker10 fit (Tinker renamed Tinker08, but Tinker still available) Fixed all tests. Better Cosmology class -- more input combinations available.

1.5.0 - May 08, 2014

Introduced _cache module Extracts all caching logic to a separate module which defines decorators -- much simpler coding!

1.4.5 - January 24, 2014

Fixed a bug on updating delta_c Added Behroozi alias to fits Added get_hmf function to tools.py -- easy iteration over models! Added hmf script which provides cmd-line access to most functionality. Changed kmax and k_per_logint back to have transfer__ prefix. Changed default kmax and k_per_logint values a little higher for accuracy.

1.4.4 - January 23, 2014

Fixed a bug in the Tinker function (log was meant to be log10)

-- thanks to Sebastian Bocquet for pointing this out!

Updated this README Made updating Cosmology simpler. Added ability to change the default cosmology parameters Fixed a bug in updating n and sigma_8 on their own (introduced in 1.4.0) Fixed a bug when using a file for the transfer function.

1.4.3 - January 10, 2014

Changed license in setup

1.4.2 - January 10, 2014

Mocked imports of cosmolopy for setup Cleaner imports of cosmolopy

1.4.1 - January 10,2014

Updated setup requirements and fixed a few tests

1.4.0 - January 10, 2014

Upgraded API once more. Now Perturbations --> MassFunction Added transfer.py which handles all k-based quantities Upgraded docs significantly.

1.3.1 - January 06, 2014

Fixed bug in transfer read-in introduced in 1.3.0

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.