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Note: thermo will no longer be updated. Please see the gpyumd package for a more up-to-date Python interface for GPUMD.

thermo

This repository is a collection of structure and data processing functions geared towards calculating thermal properties from molecular dynamics simulations. The code is primarily designed to interface with GPUMD with some supporting LAMMPS code.

As of now, the development of the code reflects my needs as a researcher and the interface with GPUMD is far from complete. The code is also subject to change drastically with GPUMD as we determine permanant GPUMD features/formats. The releases page identifies which GPUMD release corresponds to each thermo release.

Documentation:

The latest version of the documentation (matches master branch) can be found here:

https://thermomd.readthedocs.io/en/latest/

Version specific documentation can be found in the release files by going to docs/build/html/. The index.html file is the root of the documentation.

Installation:

The current version of thermo has been moved to Python3 recently. Please create an issue if there are any bugs.

To install the most recent version, use the following command:

pip install git+https://github.com/AlexGabourie/thermo.git

This will install all of the dependencies and the thermo package in the virtual environment.

Installation issues:

• If pyfftw fails to install, run the following line to install it:

sudo apt-get install libfftw3-dev libfftw3-doc

• If you get an error like: 'Failed building wheel for subprocess32,' run the following:

sudo apt-get install python-dev