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DynaPhoPy

Phonon anharmonic properties from Molecular Dynamics

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Introduction

Dynaphopy allows to calculate anharmonic phonon linewidhts and frequency shifts using the mode descomposition technique. To do that it uses a VASP or LAMMPS Molecular Dynamics (MD) trajectory and projects it onto a set of harmonic phonon modes obtained by Phonopy. Afterwards the power spectrum is calculated usign Fourier transform or Maximum Entropy Method (MEM) and the peaks are fitted to Lorentzian functions to extract the phonon anharmonic properties.
The theoretical background in which this software is based on is summarized in the following work. If you use this software please cite it:

  • A. Carreras, A. Togo, I. Tanaka, DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations, Computer Physics Communications (2017). (Journal link, arXiv link).

    Main features

  • Phonon anharmonic frequencies
  • Phonon linewidths
  • Boltzmann distribution analysis
  • Visualize harmonic phonon modes
  • Atomic displacements distribution
  • Finite temperature renormalized force constants
  • Thermal properties
  • Thermal ellipsoids

    Installation instructions

    1. Check requeriments

      2. Python 2.7 or higher
      Phonopy 1.9.6 or higher (http://phonopy/sourceforge.net)
      numpy
      matplotlib
      scipy
      h5py
      seekpath (optional)
      pyfftw (optional)
      OpenMP (optional)

    2. Download

      3. Download source code and unzip it into the installation directory.
      Old releases available here

    3. Configure and install

      4. Run setup.py script using python to install

      $ python setup.py install —-user

      Executable scripts are placed in script folder. Optionally you can either add this folder to $PATH environment variable or copy(or link) them to /home/user/bin directory. Refere to your OS documentation for detailed information.

      To compile with OpenMP support use setup_openmp.py

      $ python setup_openmp.py install —-user
      Note: To compile DynaPhoPy C extensions with OpenMP on MACOSX/OSX use gcc compiler instead of clang.

    Usage and description

    1. How to use
    2. Features description
    3. Advanced features
    4. Examples
    5. Troubleshooting

    Authors and Contributors

    This software has been developed by Abel Carreras Conill.
    Also I would like to thank Dr. Atsushi Togo, developer of phonopy, for his support and advices during the development of this software. You can visit his profile at @atztogo

    License

    This software is distributed as open source under the MIT License (MIT)
    Copyright (c) 2014 Abel Carreras Conill

    Contact & support

    If you have any trouble or question related to this software, please feel free to contact to

    Abel Carreras Conill ([email protected])
    Department of Materials Science and Engineering, Kyoto University
    Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan