This package interfaces ase, lammps, phonopy, alamode, thirdorder.py, Fourthorder.py and quippy for phonon calulations, written by Xin Qian (CU Boulder, MIT, HUST, current contant: xinqian21@hust.edu.cn).
API_Phonons is developed to make it easy to extract force constants and phononic properties of any empirical or machine learning potentials, or from AIMD data. The API_*.py files contains functions for interfacing different packages such as phonopy, lammps, phono3py, ShengBTE etc, and phonon properties can be easily calculated. The function name should be self-explanatory. API_Phonons also provided examples for computing harmonic/thirdorder/fourth force constants, dielectric tensor, high temperature dispersions, linewidths and thermal conductivity. Allen-Feldman's quantum theory for thermal transport in disordered materials and the extended quasi-harmonic green-kubo method is also included in this package.
If you find this package useful, please cite one of the following papers:
Xin Qian and Ronggui Yang, Phys. Rev. B 98, 224108 (2018)
Xin Qian, Shenyou Peng, Xiaobo Li, Yujie Wei, Ronggui Yang, Materials Today Physics 10, 100140 (2019)
In general, one needs to use gcc, gfortran, Cython compilers and parallel libs if necessary.
Currently, this package is based on the following packages:
ase 3.20.1: https://wiki.fysik.dtu.dk/ase/
phonopy 2.7.1 by A. Togo: https://phonopy.github.io/phonopy
lammps (24 Aug 2020) by Sandia National Lab: https://lammps.sandia.gov/doc/Install_tarball.html
quippy & GAP by A. Brtok and Csanyi et al.: https://libatoms.github.io/GAP/installation.html
ALM 2.0.0 by Tadano: https://alm.readthedocs.io/en/develop/
thirorder.py 1.1.0 by Prof. Wu Li and Prof. Mingo: http://www.shengbte.org/downloads
Fourthorder.py by Dr.Tianli Feng and Prof. Xiulin Ruan et al.: https://github.com/FourPhonon/FourPhonon
Please check the mannuals for each package installing/compiling them. Other python libraries such as matscipy and numba are also required, which is usually provided if you use anaconda.
Both thirdorder.py & Fourthorder.py needs to be added to PYTHONPATH for import.
It is recommended to compile using gcc and python 3.8 for the quippy packages. Certain versions of intel compilers would generate segmentation fault for quippy, when call quippy.potential.Potential objects' calculate function.
To have proper plot of phonon bandstructures, it's also recommended to install latex support. For ubuntu linux system just do:
apt-get install texlive-latex-recommended
The python executable bandplot is used to export band.yaml files to text, new version of phonopy-bandplot by phonopy doesn't have this function anymore, but using bandplot requires phonopy installed.
When compiling lammps as python library, remember to do the following:
cd lib/python
cp Makefile.lammps.python3 Makefile.lammps
cd ../src
make yes-python
make foo mode=shared
Then add lammps to the envoronment variable PYTHONPATH.
Codes and scripts for computing spectral energy density from MD trajectories. See the readme.md in the folder for further details.
In the folder Example_Scripts/, I provide several example files on how to use this package for phonon simulations:
I provided a soap based machine learning potential for NaCl. With the LD_quipGap_phonopy_NAC.py computes the harmonic force constants (FC2), while thirorder_gap.py computes third order anharmonic force constants (FC3). The usage of thirdorder_gap.py is the same as thirdorder_vasp.py for ShengBTE, execute with:
python3 thirdorder_gap.py [na] [nb] [nc] [cutoff(nm)]|-[n] GAP_potential_file <br />
where the parameters in [] need to be specified. Parameters named na nb and nc are the supercell dimensions, followed by cutoff radius or -n where -n is the number of nearest neighbors. There are also parallelized scripts for fc3 calculation such as thirdorder_gap_mp.py, compute using:
python3 thirdorder_gap_mp.py [na] [nb] [nc] [cutoff(nm)]|-[n] [Nprocesses] [GAP_potential_file]
Similarly, fourthorder force constants can also be extracted using:
python3 fourthorder_gap_mp.py [na] [nb] [nc] [cutoff(nm)]|-[n] [Nprocesses] [GAP_potential_file]
The jupyter notebook script then computes the dielectric function.
for perturbated snapshots.
This is a fairly simple example for computing phonon dispersion of hcp-phase of Zr.
This folder shows how temperature stablized phonon dispersion of bcc-Zr, which is dynamically unstable at 0K. Also included a script for relaxing cell structures. quippy potential objects can set as ase calculators using atom.set_calculator(). Then the cell can be relaxed using optimize module from ase.
The file RandDisps_SelfConsist_FC2_FC3.py and RandDisps_SelfConsit_FC2_GAP_ALM.py give examples on how to self-consistently compute second and thirdorder force constants. I first use the finite displacement method, and obtain the first generation of eigenvectors. Then I used the new set of FC2, FC3, eigenvectors to generate snapshots. This process is iterated. Convergence can usually be achieved after ~ 5 iterations.
A simple example of how to generate an inteface or gap using ase package.
A simple example of how to compute radial distribution function g(r).
An example of computing amorphous silicon thermal conductivity using Allen-Feldman Theory.
Compute the thermal conductivity of EIM NaCl using quasi-harmonic Green Kubo relations (quantum version). phono3py needs to be activated to obtain phonon linewidths. The velocity matrix operators are computed the same way in the Allen-Feldman model.
This gives example how we can interface lammps and phonopy to perform lattice dynamics based on the EIM potential supported by lammps. Thirdorder.py and Fourthorder.py are implemented with lammps code for computing FC3 and FC4.
This example uses Alamode to compute force constants, based on DFT data of energy and forces of random snapshots The random snapshots are generated based on this paper: Phys. Rev. B 95, 014302, 2017 by Olle Hellman.
These two folders implemented the code to randomly generate snapshots, using the Olle Hellman's stochastic method, which can be used as training datasets for TDEP, similar to AIMD snapshots.
This output eigenvector files in the GULP format.