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Spectral phonon relaxation time calculation tool by using normal mode analysis based on molecular dynamics
Calculate the spectral phonon relaxation time in solids based on molecular dynamics.
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Abstract
V1.2 Updates: Integrated the SED code into the LAMMPS package. Added a function so that the users can choose to skip the eigenvectors input. Resolved some bugs. Improved calculation efficiency. Opened the source code.
This tool allows users to calculate the spectral phonon relaxation time of most, theoretically all, pristine crystalline solids with available interatomic potentials. It is designed towards a broad application, users can upload any selfdefined structures/materials and use this tool to calculate the spectral phonon relaxation time. This tool is not limited to real materials, i.e., users can use this tool to simulate any artificial materials for special purposes. This tool is not only capable for 3D bulk materials, but also for most 1D and 2D materials and nanostructures such as nanowire, nanotube, nanoribbon, 2D sheet, 2D plate, etc. Its key input is the interatomic potential. For the nanostructures such as graphene/BN/MoS2/silicene/black phosphorus nanoribbon, carbon nanotube, Si nanowire, etc., and the complex structures such as Bi2Te3, Bi2Se3, SnSe, skutterudites, etc., the computation may be timeconsuming due to the large number of phonon branches. We expect this tool to pave the way towards an efficient investigation of phonon and thermal transport with applications in thermal management and thermoelectric energy conversion.
IMPORTANT NOTES:
1. The prebuilt structure works for graphene layer(s), graphite, CNT and ALL the cubic crystals. Users can easily use the "prebuilt structure" option in this tool. Users can build their own (real or artificial) cubiclattice materials by simply entering the information of the basis atoms. The prebuilt cubic crystals are suitable for ALL the fcc, bcc, and simple cubic crystals, including IV group simple substances (C, Si, Ge, etc); IIIV binary compounds (cBN, cBP, cBAs, AlP, AlAs, GaN, GaP, GaAs, etc.); common metals (Al, Au, Cu, Ag, Ti, Li, Na, etc.); and other materials (Ar, CdTe, PbTe, etc.).
2. The builtin interatomic potentials for graphene layer(s), graphite, CNT, Diamond, Si, Ge, SiC, Ar, CdTe, PbTe are available. For those materials you can choose to use the builtin potentials or use userdefined potentials. For the other materials, users must input/upload the interatomic potentials by themselves.
3. For the noncubiclattice materials, users can uncheck the "prebuilt structure" option, and upload the coordinate file and the potential file by themselves using the guidance in the tool. Please read carefully the description of each input slot in this case since this tool has a strict requirement on the format of input files. More example input files can be found in the supporting document.
4. Please upload the eigenvectors obtained elsewhere (e.g. GULP) by yourself. Since the Lorentzian fitting of phonon spectral energy density is done automatically for all the phonon branches, eigenvectors are needed to separate the branches (T Feng, B Qiu, X Ruan, Anharmonicity and necessity of phonon eigenvectors in the phonon normal mode analysis, Journal of Applied Physics 117 (19), 195102, 2015). This tool will be developed to compute the eigenvectors by itself finally, but now this function is still not stable.
5. This tool can automatically fit the spectral energy density functions of all the phonon branches as Lorentzian functions to obtain the phonon frequencies and relaxation times. In the results, if you are not satisfied with the AUTO Lorentzian fitting, you DO NOT need to run the whole long simulation again. Instead, you can download the spectral energy data files, and fit them as you needed in our another independent tool: Lorentzian fitting tool for phonon spectral energy density: (https://nanohub.org/tools/lorentzfit). There you can change the fitting parameters to obtain the best fit of each branch's spectral energy density separately.
6. If the users are not aware of eigenvectors, please uncheck the eigenvector option, and the tool will use a matrix composed of nkpoints 3n*3n identity matrices as the eigenvectors. In this case, the total SED cannot be automatically fitted well as individual Lorentz functions. The users need to manually fit them by using a Lorentzian fitting tool. We have provided a tool here: Lorentzian fitting tool for phonon spectral energy density: (https://nanohub.org/tools/lorentzfit).
7. The MD simulation may take a long time, depending on the domain size and MD steps you assign.
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The work was partially supported by the National Science Foundation (Award No. 1150948) and the DefenseAdvanced Research ProjectsAgency (Award No. HR00111520037).
Bio
Tianli Feng feng55@purdue.edu
Xiulin Ruan ruan@purdue.edu
Credits
We thank Bo Qiu and Prabhakar Marepalli for sharing some codes.
If you use this tool and publish your results, please support our work by citing our work.
References
T Feng, B Qiu, X Ruan, Anharmonicity and necessity of phonon eigenvectors in the phonon normal mode analysis, Journal of Applied Physics 117 (19), 195102, 2015.
B Qiu, H Bao, G Zhang, Y Wu, X Ruan, Molecular dynamics simulations of lattice thermal conductivity and spectral phonon mean free path of PbTe: Bulk and nanostructures, Computational Materials Science 53 (1), 278285, 2012.
T Feng, X Ruan, Prediction of spectral phonon mean free path and thermal conductivity with applications to thermoelectrics and thermal management: a review, Journal of Nanomaterials 2014, 206370 (2014).
Tianli Feng; Xiulin Ruan (2015), "Lorentzian fitting tool for phonon spectral energy density," https://nanohub.org/resources/lorentzfit. (DOI: 10.4231/D31Z41T8N).
Cite this work
Researchers should cite this work as follows:

T Feng, B Qiu, X Ruan, Anharmonicity and necessity of phonon eigenvectors in the phonon normal mode analysis, Journal of Applied Physics 117 (19), 195102, 2015.