cclib
                   Parsers and algorithms for
                    computational chemists

      Noel O’Boyle,1 Adam ...
Overview of cclib

  • cclib is a programming library which
      – contains parsers for output files of
        computati...
Why is cclib needed?
  • Analysis methods are available only to users of
    certain packages
     – Morokuma energy decom...
Parsers
  • ADF, GAMESS (US), Gaussian, PC
    GAMESS (GAMESS-UK, Jaguar, Molpro)
  • Useful information for algorithms
  ...
Algorithms
  • Population analysis algorithms
     – Mulliken, C2, Mayer's bond orders
  • We are currently working on
   ...
Development
  • Follows Open Source development model
     – Subversion, wiki, mailing lists, bug tracker
  • Follows best...
cclib
                Parsers and algorithms for
                 computational chemists


        Noel O’Boyle, Adam Tend...
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cclib - parsers and algorithms for computational chemists

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cclib - parsers and algorithms for computational chemists

  1. 1. cclib Parsers and algorithms for computational chemists Noel O’Boyle,1 Adam Tenderholt2, Mehdi Bounouar3 1 Unilever Centre for Molecular Science Informatics 2 Dept. of Chemistry, Stanford University 3 Technical University of Munich Acknowledgements: Dr. John Mitchell, Cambridge http://cclib.sf.net baoilleach@gmail.com
  2. 2. Overview of cclib • cclib is a programming library which – contains parsers for output files of computational chemistry codes – includes several algorithms for analysing results • cclib is written in Python • cclib is Open Source (LGPL) http://cclib.sf.net baoilleach@gmail.com
  3. 3. Why is cclib needed? • Analysis methods are available only to users of certain packages – Morokuma energy decomposition (implemented in GAMESS) – Charge Decomposition Analysis (Frenking's code only reads Gaussian output files) • Keeps up to date with new versions of packages • Allows chemists to focus on algorithms • Makes implementation of algorithms independent of proprietary software http://cclib.sf.net baoilleach@gmail.com
  4. 4. Parsers • ADF, GAMESS (US), Gaussian, PC GAMESS (GAMESS-UK, Jaguar, Molpro) • Useful information for algorithms – overlap matrix, molecular orbital coefficients, (basis set coefficients, Hessian) • Useful information for visualisation – coordinates, vibrational frequencies, electronic transitions • Currently used by GaussSum and PyMOlyze http://cclib.sf.net baoilleach@gmail.com
  5. 5. Algorithms • Population analysis algorithms – Mulliken, C2, Mayer's bond orders • We are currently working on – Calculation of the electron density – Calculation of the Cartesian displacement matrix • We intend to implement – Bader's Atoms in Molecules – Frenking's Charge Decomposition Analysis – Hirshfeld Population Analysis http://cclib.sf.net baoilleach@gmail.com
  6. 6. Development • Follows Open Source development model – Subversion, wiki, mailing lists, bug tracker • Follows best practice for Python – Cheesecake index, pylint • Extensive use of unit tests and regression tests (test-driven development) – Parsers developed on example log files and the result must agree with the other parsers – Modified to cope with real-life problem cases http://cclib.sf.net baoilleach@gmail.com
  7. 7. cclib Parsers and algorithms for computational chemists Noel O’Boyle, Adam Tenderholt, Mehdi Bounouar Thank you... ...and new developers welcome! http://cclib.sf.net baoilleach@gmail.com
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