FixPhonon

 FixPhonon implements the method to evaluate the phonon dispersion directly from molecular dynamics simulations. The basic algorithm is to construct the dynamical matrices by observing the displacement fluctuations. For details, check the documents of the project.

The implemented method enables one to evaluate the phonon dispersion under finite temperature/pressures without turning to the usual quasi-harmonic procedure. The code presented here needs to work along with LAMMPS, an open-source molecular dynamics simulation package; it is now distributed with LAMMPS as a user-contributed package, thus making use of the features from LAMMPS.

A post-processing code, phana, is also provided (A compiled version which should work under Ubuntu system can be downloaded here,), helping to analyze the result, which is written as binary files by fix-phonon. External libraries CLapack, Tricubic, and/or SPGLIB are needed by the post-processing code, which can be downloaded from their respective website; please check their respective websites for the correct citations of these libraries.

The post-processing code is driven by menu, one can follow its menu step by step to fulfill your task. The header of the generated files should be enough to explain the meaning of each column.

A variant of fix-phonon, dump2phonon, is also available, which measures the dynamical matrices based on MD trajectories, with which one can measure the phonons based on any MD code besides LAMMPS.

All publications using fix-phonon or dump2phonon are asked to cite the following paper(s):

1. L.T. Kong, Phonon dispersion measured directly from molecular dynamics simulations, Computer Physics Communications 182(10):2201-2207, 2011.

When the tricubic method provided in the post-processing code is used, please cite its original documents; and if Monkhost-Pack mesh is used in phonon density of states or vibrational thermal property evaluations, the original documents from SPGLIB are also suggested to be cited.

When the post-processing code is used to evaluate the local phonon density of state, one is suggested to refer to and/or cite the following articles:

2. L.T. Kong and L.J. Lewis, Surface diffusion coefficients: Substrate dynamics matters, Phys. Rev. B 77, 165422 (2008).

3. C. Hudon, R. Meyer, and L.J. Lewis, Low-frequency vibrational properties of nanocrystalline materials: Molecular dynamics simulations of two-dimensional systems, Phys. Rev. B 76, 045409 (2007).

If the real space Green's function method is used to evaluate the local phonon density of states (it only works if your primitive cell has a large number of atoms; but in this case, Fix-Phonon will be rather inefficient.), one is also suggested to refer to and/or cite the following article:

4. Z. Tang and N. R. Aluru, Calculation of thermodynamic and mechanical properties of silicon nanostructures using the local phonon density of states, Phys. Rev. B 74, 235441 (2006).

Any bug found, please feel free to drop a line to: konglt(at)sjtu.edu.cn.  

The FixPhonon project is supported by the Science and Technology Commission of Shanghai Municipality (10ZR1415800), Shanghai Pujiang Program (10PJ1405900), and National Natural Science Foundation of China (51001073).  

Author: Ling-Ti Kong, konglt_AT_sjtu.edu.cn.