mesnardo/snake

Collection of Python scripts to generate and post-process results

Snake

A collection of Python modules to post-process the numerical solution of simulations run with one of the following software:

• PetIBM
• cuIBM
• IBAMR
• OpenFOAM

Installation

Dependencies (last tested)

• Python-2.7 or Python-3.5
• Numpy-1.11.1
• Scipy-0.17.1
• Matplotlib-1.5.3
• Pandas-0.19.2

To install the specific version of these packages we recommend using either conda.

To create a new environment for using snake with Python-3.5 with conda you can do the following:

> conda create -n snakepy35 python=3.5 numpy scipy matplotlib pandas
> source activate snakepy35

or with Python-2.7:

> conda create -n snakepy27 python=2.7 numpy scipy matplotlib pandas
> source activate snakepy27

Optional

• PETSc-3.7.4 (for PetIBM post-processing; only the Python scripts are needed)
• VisIt-2.12.1 (IBAMR post-processing)
• OpenFOAM-2.3.1 and ThirdParty-2.3.1 (for OpenFOAM post-processing)

Install snake using git

> git clone https://github.com/mesnardo/snake.git
> cd snake
> python setup.py install
> export SNAKE=$PWD

Install snake using a specific release

> VERSION="X.X.X"
> wget https://github.com/mesnardo/snake/archive/v${VERSION}.tar.gz
> mkdir snake-${VERSION}
> tar -xzf v${VERSION}.tar.gz -C snake-${VERSION} --strip-components=1
> rm -f v${VERSION}.tar.gz
> cd snake-${VERSION}
> python setup.py install
> export SNAKE=$PWD

where X.X.X defines the version number to use.

Notes

Some of the modules call the environment variable $SNAKE defined as the local directory of the snake repository. The variable can be set by adding the following line to your .bashrc or .bash_profile file:

> export SNAKE="/path/to/snake/directory"

The module for PetIBM calls the environment variable $PETSC_DIR defined as the local directory of PETSc. The variable can be set by adding the following line to your .bashrc or .bash_profile file:

> export PETSC_DIR="/path/to/petsc/directory"

Some examples to post-process the numerical solution from the four codes are provided in the examples folder.

Suggestions and bug-fix are welcome. Contact: [email protected]

snake's Issues

[Python 3] New API change to the use of color_cycler

In Python 3, it seems matplotlib has removed the old usage of color_cycler like what is at line 118 in logSummaryReader.py.

According to the suggested new API usage, line 118 in logSummaryReader.py should be modified to

color_cycle = ax._get_lines.prop_cycler

And line 126 in the same file should be modified correspondingly to:

... color=next(color_cycle)['color'], ...

Also, line 20 in mesnardo.mplstyle is deprecated in Python 3, though it has not been deleted yet. The new usage is:

axes.prop_cycle : cycler('color', 
    ['348ABD', '7A68A6', 'A60628', '467821', 'CF4457', '188487', 'E24A33'])