pyflation 0.2.0

Pyflation is a Python package for calculating cosmological perturbations during an inflationary expansion of the universe.

Introduction

Pyflation is a Python package for calculating cosmological perturbations during inflationary expansion of the universe.

Once installed the modules in the pyflation package can be used to run simulations of different scalar field models of the early universe.

The main classes are contained in the cosmomodels module and include simulations of background fields and first order and second order perturbations. The sourceterm package contains modules required for the computation of the term required for the evolution of second order perturbations. The analysis package contains routines to calculate the first order First and Second order perturbations can be calculated for single field models but only first order perturbations can be evolved for multi-field models.

Alongside the Python package, the bin directory contains Python scripts which can run first and second order simulations. A helper script called “pyflation-qsubstart.py” sets up a full second order run (including background, first order and source calculations) to be used on queueing system which contains the “qsub” executable (e.g. a Rocks cluster).

Installation of the code is described in the INSTALL.txt file. The pyflation package can be installed as a normal Python package to the site-packages directory or each run of the code can be self-contained with code, results and logs all contained in a run directory.

The “pyflation-newrun.py” script creates a new run directory and populates it with the code and sub-directories which are required. In particular the file “provenence.log” in the “applogs” directory contains information about the version of the code and system libraries at the time of the creation of the run.

More information about Pyflation is available at the website http://pyflation.ianhuston.net.

Basic usage of the pyflation package

The pyflation package can be used independently of the scripts which run full first and second order calculations. If you have installed the package using the setup.py install command then it should be available by doing

> import pyflation

in an interactive Python session. If you have not installed the package then make sure that the path where the pyflation directory is located has been added to the PYTHONPATH variable.

The most important module in the package is cosmomodels. This contains the classes which drive first and second order evolution. To run a first order simulation with the default settings first import the cosmomodels module:

> from pyflation import cosmomodels as c

Here the module is aliased as c for convenience. Then create a new first order model using the FOCanonicalTwoStage class:

> m = c.FOCanonicalTwoStage()

You can inspect the attributes and methods of m in the usual way by using dir(m) or tab completion in the iPython environment.

To begin the first order run use:

> m.run()

The results are stored in m.yresult in raw form for all time steps. The value of the first order perturbations for all time steps are also labelled as m.dp1.

Basic Usage of Scripts

Assuming you have followed the instructions in INSTALL.txt to install the program either system-wide, locally, or in a contained directory, you can create a new run directory using the pyflation-newrun.py script.

If you have used the setup.py install command, the script should be somewhere on your PATH. If not you will need to prefix the following commands with the path to the pyflation-newrun.py script. To create a new run in the directory $HOME/pyflation-runs and call the run mynewrun run the pyflation-newrun.py script with the following options:

$ pyflation-newrun.py -d $HOME/pyflation-runs -n mynewrun

The script should create the directory (and any parent ones needed) and set up the file structure inside. Change to the run directory and look inside. The directories applogs, qsublogs, qsubscripts and results are created automatically and the run_config.py file is put inside the run directory. If you want the code to be copied in to the run directory please see the advanced options of the pyflation-newrun.py script.

The run_config.py file inside the run directory contains user changeable settings. In particular the choice of potential and k range to be used in the scripts is made here. The python classes used for the different stages of the evolution can also be changed in this file.

The script files are descriptively named. To begin a first order perturbation calculation use pyflation-firstorder.py. For each script the –help option will show all the options available. Simple operation uses the defaults in run_config.py for example

$ pyflation-firstorder.py

will run the first order code and store the result in the file specified in run_config.py, usually results/fo.hf5.

Description of available scripts

• The pyflation-newrun.py script creates a new run directory and the needed directories and files inside it. Options include the ability to copy the code into the new run directory to keep it contained.

• The pyflation-firstorder.py script runs background and first order perturbation simulations and saves the results, by default in results/fo.hf5.

• The pyflation-source.py script runs a full source term calculation using the first order results. This may take a long time especially if it is not executed in parallel. The options for this script include the location of the first order results file and simple assignment of task number in a parallel (or multiple serial) environment.

• The pyflation-srcmerge.py script will merge any separate source files, for example from a parallel run, into one main source file. Rudimentary checking of the existence of each time step is completed. One of the options to this script is to further merge the first order and source term results together. The new merged file is used as the input for the second order calculation.

• The pyflation-secondorder.py script uses the source term and first order results from the merged file to calculate the second order perturbation solution.

• The pyflation-combine.py script combines all the results from the first, source and second order runs into one final results file. In this file the timesteps from the second order run are used so only half the results of the first and source term calculations are stored. For this reason this file is more for ease of analysis then long term data storage.

• The pyflation-qsubstart.py script is used when the qsub queueing command is available. See the section “Using Qsub” below for more information.

Using Qsub

If you are running Pyflation in a cluster environment or somewhere with the qsub queueing system available, there is an extra pyflation-qsubstart.py script which will be useful. When you create a new run the file qsub-sh.template is created which holds a very general outline of a qsub run script. Change any of the options in the preliminary section to meet your needs. The length of runs and the number of task units can be set in run_config.py. When you run

$ pyflation-qsubstart.py

a new batch of qsub jobs will be created and submitted, running a full second order calculation. Please note that the full calculation make take some considerable time depending on the available computing power. The scripts which are submitted using qsub are available in the directory qsub-scripts. An additional src_individual.qsub script is useful if one of the tasks in the long source term calculation fails for some reason. To restart just one task with the same options as before use

$ qsub src_individual.qsub N

where N is the number of the task to restart.

Acknowledgements

This author of this software is supported by the Science & Technology Facilities Council under grant ST/G002150/1.

Author: Ian Huston For copyright and license information please see the LICENSE.txt file.

For installation information see the INSTALL.txt file.