Atoman - analysis and visualisation of atomistic simulations

License and copying

Developed by Chris Scott
Copyright 2015 Loughborough University
Released under the MIT license, see "LICENSE.md" for details.

Requirements

This code requires Python to run. Currently Python 2.7, 3.2+ should work. Atoman depends on a number of Python libraries, a C and C++ compiler (tested with gcc and g++) and also some other optional software.

Python modules

This is a list of third-party python modules that this code requires to run. They can be installed in a variety of ways, such as with MacPorts, pip, apt-get or similar.

Required:

• NumPy
• SciPy
• Matplotlib
• PySide
• Pillow
• VTK - version 7.0 or later required for Python 3
• Sphinx
• sphinx_rtd_theme
• nose (testing)
• setuptools

Optional:

• Paramiko - for loading files via the SFTP file browser
• pyhull - for computing facet areas of convex hulls

Other software

In order to be able to use all features the following programmes should be installed:

• POV-Ray (for offline rendering of images; looks better)
• Ffmpeg (for creating movies; sequencer and rotator)

If these are not installed in default system locations you can set the paths to where they are installed in the preferences dialog in the GUI.

Installation

You can either build the code in-place or install it into the Python site-packages directory, for example within a virtualenv.

In both cases you should first copy the config file: cp setup.cfg.example setup.cfg and add/edit any relevant sections. There are some comments in the file to help with selecting the options.

You need to choose one of the following two methods for installing the software.

In-place build

Build the documentation (includes inplace build of extensions):

python setup.py build_sphinx

and verify the tests run with no errors:

python setup.py test

Then you can add the /path/to/Atoman directory to you PYTHONPATH and run python -m atoman from anywhere to run the software.

Installing to Python site-packages

Build the documentation (includes inplace build of extensions):

python setup.py build_sphinx

and verify the tests run with no errors:

python setup.py test

Then run:

python setup.py build
python setup.py install

If you are not using a virtual environment you may need to sudo the last (install) command.

Following this you should be able to run python -m atoman from anywhere to run the software. Alternatively you could use the atoman command to run the software.

Building application (Mac OS X)

On Mac OS X you can build a .app application using PyInstaller. Simply change to the pyinstaller/ directory and run ./build.sh (you may need to edit the path to pyinstaller.py).