Automated Forcefield Optimization Extension 0.7.4¶
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.
- 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 --name FOX python=3.7
- Enable environment:
conda activate FOX
- Disable environment:
conda deactivate
- Create environment:
Installing Auto-FOX¶
- If using Conda, enable the environment:
conda activate FOX
- Install Auto-FOX with PyPi:
pip install git+https://github.com/nlesc-nano/auto-FOX@master --upgrade
- Congratulations, Auto-FOX is now installed and ready for use!
Optional dependencies¶
- Use of the FOX.monte_carlo module requires h5py.
Note: h5py is not distrbuted via PyPi:
- Anaconda:
conda install --name FOX -y -c conda-forge h5py
- Anaconda:
- 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
- Anaconda:
- Construction of the angular distribution function in parallel requires DASK.
- Anaconda:
conda install -name FOX -y -c conda-forge dask
- Anaconda: