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examples
fafoom
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COPYING.LESSER.txt
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README.md
fafoom_manual.pdf

README.md

Fafoom - Flexible algorithm for optimization of molecules

Fafoom is a tool for sampling the conformational space of organic molecules. Fafoom is intended to work with FHI-aims (Fritz Haber Institute ab initio molecular simulations package).

News

  • the paper "First-principles molecular structure search with a genetic algorithm" is now published in Journal of Chemical Information and Modeling; DOI: 10.1021/acs.jcim.5b00243

  • a new branch targeting the implementation of a further degree of freedom ('orientation') has been created

Requirements

  • functionality of the tool:

    • Python (used for testing: 2.7.6)
    • Numpy (used for testing: 1.8.2)
    • RDKit (used for testing: Release_2015_03_1)
  • first-principles methods:

    • (recommended) FHI-aims (Fritz Haber Institute ab initio molecular simulations package)
    • (alternative) NWChem (NWChem: Open Source High-Performance Computational Chemistry)
    • (alternative) ORCA (- An ab initio, DFT and semiempirical SCF-MO package -)

How to use

1) Clone the fafoom repository
git clone https://github.com/adrianasupady/fafoom
2) Export the fafoom directory to you PYTHONPATH
3) In python:
import fafoom

Example of usage

An implementation of a genetic algorithm is provided in the examples folder. Depending on the used parameter file following genetic algorithm based searches can be run:

  • parameters_aims.txt for first-principles (FHI-aims required)
  • parameters_ff.txt for force fields (force fields accessed from RDKit)
  • parameters_nwchem.txt for first-principles via NWChem (NWChem required)
  • parameters_orca.txt for first-principles via ORCA (ORCA required)

Get familiar with the provided manual to learn more about the tool and the parameters.

Outlook

Development goals:

  • flexible formulation of the scoring function, e.g. allowing for optimizing a user-defined property
  • adding more kinds of degrees of freedom, e.g. orientation of a molecule
  • adding wrappers for different molecular simulations packages

Comments, feedback or development contributions are always welcome!

License

Fafoom is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Fafoom is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with fafoom. If not, see http://www.gnu.org/licenses/.

Copyright 2015 Adriana Supady