yossibokorbleile / topologicalmaterialanalysis

README

TopologicalMaterialAnalysis is a Python application to analyse topological structures in materials. It can be used via a graphical user interface or a command line interface. It was developed in conjunction with the Glass Structure and Mechanics Group, Aalborg Unviersity.

Currently, you need the following Python packages to be installed:

• PySimpleGUI
• ASE
• Pandas
• Numpy
• SciPy
• Dionysus
• Diode
• Oineus
• Plotly Express
• colour
• • any i have forgotten

You will also need to ensure tkinter, CGAL, oneTBB are installed.

Documentation

The full documentation is built using doxygen, which you will need to install if you want to build the documentation locally. This README contains a quick start guide, and the documentation shouldn't be necessary unless you encounter erros, or wish to contribute to the application.

To build the documentation locally, run

doxygen

in the top-level repository directory. Then, the HTML documents will be generated in Documentation/html. doxygen also builds LaTeX documentation, which is in Documentation/latex which needs to be compiled. Do to so, run

make

in Documentation/latex.

Running the GUI:

Once you have all the packages installed and are in your python environment of choice, navigate to the GUI directory, and from a terminal (on Mac/Linux) or Command prompt(?) (Windows), run

src/ToMA.py

You can then select from 3 different modes: single, multi and batch. Using the GUI should be pretyy self-explanatory from here.

Running the CLI:

To run the CLI, use

src/ToMA.py -i c -s $SETTINGSFILE -n $SETTINGSNAME

The SETTINGSFILE should be an .ini file, and each section corresponds to a set of variables. Depending on what mode is being used, the contents of the section will differ a little bit. Each section needs to contain a variable MODE which can have values single, multi, or batch. All three modes also need information about the structure settings to use, which are also stored in an .ini file. This structure file can also be used to load structures when using the GUI. For information on formating the structure file, see Structure files

Settings for single mode

Structure files