README.rst

Automated Forcefield Optimization Extension

Auto-FOX is a library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters. Further details are provided in the documentation.

Currently implemented

This package is a work in progress; the following functionalities are currently implemented:

• The MultiMolecule class, a class designed for handling and processing potential energy surfaces. (1)
• A multi-XYZ reader. (2)
• A radial and angular distribution generator (RDF & ADF). (3)
• A root mean squared displacement generator (RMSD). (4)
• A root mean squared fluctuation generator (RMSF). (5)
• Tools for describing shell structures in, e.g., nanocrystals or dissolved solutes. (6)
• A Monte Carlo forcefield parameter optimizer. (7)

Using Auto-FOX

• An input file with some basic examples is provided in the FOX.examples directory.
• An example MD trajectory of a CdSe quantum dot is included in the FOX.data directory.
  • The absolute path + filename of aforementioned trajectory can be retrieved as following:

>>> from FOX import example_xyz

• Further examples and more detailed descriptions are available in the documentation.

Installation

Anaconda environments

• While not a strictly required, it stronly recomended to use the virtual environments of Anaconda.
  • Available as either Miniconda or the complete Anaconda package.
• Anaconda comes with a built-in installer; more detailed installation instructions are available for a wide range of OSs.
  • See the Anaconda documentation.
• Anaconda environments can be created, enabled and disabled by, respectively, typing:
  • Create environment: conda create -n FOX -c conda-forge python pip
  • Enable environment: conda activate FOX
  • Disable environment: conda deactivate

Installing Auto-FOX

• If using Conda, enable the environment: conda activate FOX
• Install Auto-FOX with PyPi: pip install auto-FOX --upgrade
• Congratulations, Auto-FOX is now installed and ready for use!

Optional dependencies

• The plotting of data produced by Auto-FOX requires Matplotlib. Matplotlib is distributed by both PyPi and Anaconda:
  • Anaconda: conda install --name FOX -y -c conda-forge matplotlib
  • PyPi: pip install matplotlib
• Construction of the angular distribution function in parallel requires DASK.
  • Anaconda: conda install -name FOX -y -c conda-forge dask
• RDKit is required for a number of .psf-related recipes.
  • Anaconda: conda install -name FOX -y -c conda-forge rdkit
  • PyPi: pip install rdkit