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pypico 3.3.0

Quickly compute the CMB powerspectra and matter transfer functions.

Installation

To install PICO, download and extract the archive, and from the top folder run:

python setup.py build
python setup.py install [--user]

or, if you have PIP installed, you can automatically download PICO and install it in one command with:

pip install pypico [--user] [--upgrade]

Install notes

  • If you don’t have root access, the --user option installs PICO in your home directly.
  • The --upgrade option forces the newest version to be installed.
  • easy_install does not currently work.

Requirements

  • Python 2.7.X
  • NumPy (>=1.6.1)
  • SciPy (>=0.10.1)

Troubleshooting

To submit bug reports please use https://github.com/marius311/pypico/issues.

Usage

Once you have PICO installed, to do anything you’ll need some data files which actually contain interpolated data. You can find them on the PICO website at https://sites.google.com/a/ucdavis.edu/pico/download.

After that, PICO is used from the Python shell. Typical usage starts by loading a PICO data file:

>> import pypico
>> pico = pypico.load_pico("example_pico_file.dat")

To show accepted input parameters call:

>> pico.inputs()

and to show outputted quantities call:

>> pico.outputs()

Finally, to run PICO call:

>> result = pico.get(outputs, **inputs)

where outputs is a list of outputs you actually want (or leave it unspecified to calculate all outputs), and **inputs is a dictionary of parameter values with keys for each input returned above. The return value result is a dictionary with a key corresponding to each output you requested.

Usage Notes

  • Each PICO datafile is trained on a particular region of parameter space, generally one large enough to be relevant for typical analyses. If PICO is called for a set of parameters outside this range, a CantUsePICO error will be raised, and you should use CAMB instead. If you are running an MCMC chain, this can slow you down significantly before the chain is burned in. To remedy this, set force=True to force PICO to return results even outside its training region. The results won’t be guaranteed to be accurate, but will likely be good enough to get your chain to converge to the region where PICO is accurate.

  • The PICO convention for multipole indexing is that an array entry arr[l] corresponds to the l-th multiple. Since Python is 0-indexed, this means the first entry in an array is the 0-th multiple.

  • The specification pico.get(outputs, **inputs) means get can be called in several ways, including:

    >> pico.get(param1=val1, params2=val2)
    >> pico.get(**{'param1':val1, 'param2':val2})
    >> pico.get(**dict(param1=val1, param2=val2))
    >> pico.get(param1=val1, **{'param2':val2})
    
  • Certain data files may contain a set of example input values which can be accessed with:

    >> pico.example_inputs()
    

Calling PICO from C/C++/Fortran

PICO can be called from C/C++ and Fortran.

C/C++ Interface

To call PICO from C/C++, you should include the following two header files:

#include <python.h>
#include "pico.h"

Documentation for the functions defined in pico.h can be found in the pico.pyx file.

Fortran Interface

To call PICO from Fortran, you should use the following module:

use fpico

Documentation for the functions in the fpico module can be found in the fpico_interface.f90 file.

  • Note that the Fortran interface is built on C, and to ensure integer/real byte-sizes are the same between Fortran and C, independent of compiler, they are defined by hand as fpreal and fpint in fpico_interface.f90 and pico.pyx.

Compiling and Linking

When you installed PICO, a static library libpico.a was created. To link your code against this library, PICO provides an easy way to get include and link flags on your platform. To print out the necessary flags, call:

python -c "import pypico; print pypico.get_include()"
python -c "import pypico; print pypico.get_link()"

You should put these calls directly in your Makefile via:

$(shell python -c "import pypico; print pypico.get_link()")

The fortran interface file fpico_interface.f90 should be recompiled each time along side your program, as it must use the same Fortran compiler. The location of this file can be accessed from your Makefile via:

$(shell python -c "import pypico; print pypico.get_folder()")/fpico_interface.f90

Using PICO with CosmoMC

As of Apr 2014, partial PICO support is built into CosmoMC. See http://cosmologist.info/cosmomc/ for instructions.

Using PICO in place of CAMB

If you have a code which currently calls CAMB_GetResults, its easy to swap in PICO_GetResults which uses PICO instead (and falls back on the CAMB version for parameters ouside of the PICO training region).

To install the CAMB plugin:

  • Copy plugins/camb/pico_camb.f90 to the folder containing your code
  • In your Makefile, make sure pico_camb.f90 gets compiled and pico_camb.o gets included in your executable.
  • Add a call fpico_load(file) to load a PICO datafile.
  • Replace CAMB_GetResults with PICO_GetResults
  • Add use pico_camb wherever you need PICO_GetResults
  • Compile your code, making sure to use the correct include/link flags (see Compiling and Linking).

Known Issues

  • -fast with Intel Fortran does not work in some cases.

Authors

PICO is written by Marius Millea (feel free to send questions/comments to mmillea@ucdavis.edu). The CosmoMC plugin was largely written by Antony Lewis and Silvia Galli. PICO was originally created by Chad Fendt and Ben Wandelt (see http://arxiv.org/abs/0712.0194)

 
File Type Py Version Uploaded on Size
pypico-3.3.0.tar.gz (md5) Source 2014-05-01 57KB
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