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|
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:target: https://docs.python.org/3.7/
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##################################################
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:
.. 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``
.. _1: https://auto-fox.readthedocs.io/en/latest/3_multimolecule.html
.. _2: https://auto-fox.readthedocs.io/en/latest/5_xyz_reader.html
.. _3: https://auto-fox.readthedocs.io/en/latest/1_rdf.html
.. _4: https://auto-fox.readthedocs.io/en/latest/2_rmsd.html#root-mean-squared-displacement
.. _5: https://auto-fox.readthedocs.io/en/latest/2_rmsd.html#root-mean-squared-fluctuation
.. _6: https://auto-fox.readthedocs.io/en/latest/2_rmsd.html#discerning-shell-structures
.. _7: https://auto-fox.readthedocs.io/en/latest/4_monte_carlo.html
.. _8: https://www.youtube.com/watch?v=hFDcoX7s6rE
.. _documentation: https://auto-fox.readthedocs.io/en/latest/
.. _Miniconda: http://conda.pydata.org/miniconda.html
.. _Anaconda: https://www.anaconda.com/distribution/#download-section
.. _Matplotlib: https://matplotlib.org/
.. _FOX.data: https://github.com/nlesc-nano/auto-FOX/blob/master/FOX/data
.. _FOX.examples: https://github.com/nlesc-nano/auto-FOX/blob/master/FOX/examples/input.py
.. _DASK: https://dask.org/
.. _RDKit: https://www.rdkit.org/
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