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########################################### 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:

.. code:: python

>>> 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 <https://docs.anaconda.com/anaconda/install/>_.
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