chemreac 0.10.0

Python package for modeling chemical kinetics with diffusion and drift.

chemreac

chremreac is an open source library which aims to collect tools and utilities for modeling of chemical kinetics problems. It is primarily designed to be useful in the context of aqueous phase with external radiation fields (including advection/diffusion processes).

The (heavy) numerical processing is done in rountines written in C++ which have been wrapped in a Python interface using Cython.

Documentation

• Documentation for the latest stable release is found here: http://chemreac.github.io/chemreac/latest/

• and development documentation for the current master branch is found here: http://hera.physchem.kth.se/~chemreac/branches/master/html).

Installation

The easiest way to install chemreac (on linux) is to use conda:

$ conda install -c chemreac chemreac pytest

and you’re done! To check if chemreac is installed correctly you may run:

$ pytest --pyargs chemreac

which should run the test suite (all tests should pass or xfail). If you are using a special platform with non-standard math libraries you may need to compile your own pacakges. The “recipes” for the conda packages are kept here.

If you are not using the conda package manager you can still install chemreac from source. You will find the instructions for doing so below.

Building from source

Below you will find instructions for installation by building chemreac from source. You may also look in scripts/ folder for automated install scripts used on the continuous integration servers.

Prerequisites

Version numbers of dependencies indicate what has been tested:

• C++ compiler with C++11 support (e.g. GCC >= 4.8)

• LAPACK (provided by e.g. OpenBLAS)

• Sundials 2.6.2

• Python (2.7 or >=3.4)

In addition to the standard library provided by Python, a number of python packages are required (see setup.py), they are found on PyPI and are automatically installed when using pip.

For rendering the documentation you also need:

• Sphinx

• numpydoc

• sphinx_rtd_theme

to run all the tests you also need these tools:

• valgrind

• graphviz

• dot2tex

• pdflatex

Building and installing

Once non-python prerequisites are in installed, you may procede e.g. as:

$ git clone https://github.com/chemreac/chemreac.git
$ cd chemreac
$ pip install --user -e .[all]
$ ./scripts/run_tests.sh

the above procedure works on Ubuntu 14.04 for example.

To specify an alternative LAPACK lib, set the environment variable LLAPACK, e.g.:

$ LLAPACK=openblas python setup.py build_ext --inplace

The following environment variables are also supported by setup.py (defaults to “0”, enable by setting them to “1”):

Environament variable	Default	Action
WITH_OPENMP	0	Enable parallell evaluation of rhs and jac.
WITH_BLOCK_DIAG_ILU_DGETRF	0	Use unblocked version of dgetrf instead of LAPACK
WITH_BLOCK_DIAG_ILU_OPENMP	0	Evaluate LU decomposition of blocks in parallel
WITH_DATA_DUMPING	0	For debugging purposes only
WITH_DEBUG	0	For debugging purposes only

Enabling the first three is known to provide significant speed up for some scenarios (performance is system dependent, hence recommendations are not possible to give without benchmarking).

Tests

If you have py.test installed you may run the test suite on the installed package:

$ py.test --pyargs chemreac

All tests should pass (or xfail). If they do not, please file an issue.

Status

Both the correctness (continuous integration) and the performance (benchmarks) of the code base is monitored continuously.

Continuous integration

In order to minimize the risk of (re)introducing bugs into the code base, it is continuously built on a CI server:

Performace tracking

Benchmarks for tracking the performance of the library are kept at https://github.com/chemreac/chemreac-benchmarks

License

The source code is Open Source and is released under the very permissive “simplified (2-clause) BSD license”. See LICENSE.txt for further details. Contributors are welcome to suggest improvements at https://github.com/chemreac/chemreac

Author

Björn Dahlgren, contact:

• gmail address: bjodah