A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
Project description
Automated Forcefield Optimization Extension 0.10.2
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_xyzFurther 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.
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
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