This is designed to help researchers to perform diffusion analysis from ab inito molecular dynamic (AIMD) simulations. It contains some useful python classes which can be integrated into your python analysis code, and one easy-to-use executable python script which can perform diffusion analysis on the terminal without further modification.
The executable python script (script/analyze_aimd.py) has two main functions:
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Analyze diffusion properties from AIMD calculations at one single temperature.
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Analyze diffusion properties from AIMD calculations at multiple temperatures.
More information can be found by the behind code after you install the library
analyze_aimd -h analyze_aimd diffusivity -h analyze_aimd arrhenius -h
If you use this library, please cite the following papers:
He, Xingfeng, Yizhou Zhu, Alexander Epstein, and Yifei Mo. "Statistical variances
of diffusional properties from ab initio molecular dynamics simulations."
npj Computational Materials 4, no. 1 (2018): 18.
http://dx.doi.org/10.1038/s41524-018-0074-y
He, Xingfeng, Yizhou Zhu, and Yifei Mo. "Origin of fast ion diffusion in super-ionic
conductors." Nature communications 8 (2017): 15893.
http://dx.doi.org/10.1038/ncomms15893
Mo, Yifei, Shyue Ping Ong, and Gerbrand Ceder. "First principles study of the Li10GeP2S12
lithium super ionic conductor material." Chemistry of Materials 24, no. 1 (2011): 15-17.
http://dx.doi.org/10.1021/cm203303y
Ong, Shyue Ping, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher,
Shreyas Cholia, Dan Gunter, Vincent L. Chevrier, Kristin A. Persson, and Gerbrand Ceder.
"Python Materials Genomics (pymatgen): A robust, open-source python library for materials
analysis." Computational Materials Science 68 (2013): 314-319.
https://doi.org/10.1016/j.commatsci.2012.10.028
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Install all dependency and this library
python setup.py install
if you have no root access, you may need to use
python setup.py install --user
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Try to import python classes in your python console
from aimd.diffusion import DiffusivityAnalyzer, ErrorAnalysisFromDiffusivityAnalyzer, \ ArreheniusAnalyzer
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The setup.py will automatically create an executable file analyze_aimd into your PATH. Try to call it from terminal and read the documentations:
analyze_aimd -h analyze_aimd diffusivity -h analyze_aimd arrhenius -h
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Use the provided test files to perform diffusion analysis.
a. go to the folder aimd/tests/tests_files/latp_md
b. run in terminal
analyze_aimd diffusivity Li+ RUN_ 10 29 3.2
c. You can ignore the warning msgs. You will get the diffusion results. The diffusivity is ~7.6e-5 cm^2/s, conductivity is ~583 mS/cm
d. go to folder aimd/tests/tests_files/arrhenius
e. run in terminal
analyze_aimd arrhenius D_T.csv -p POSCAR -T 300 -s Li+ analyze_aimd arrhenius D_T.csv -p POSCAR -T 300 -s Li+ --plot
f. You will get the arrhenius relationship of LATP. The conductivity at 300K is predicted to be ~1.08 mS/cm, Ea is ~0.258 eV +- 0.017 eV. If your x11 windows settings are correct or you are at local computer, you will have a plot window pop up to show the arrhenius relationship for cmd with -plot option.
We also generated standalong executable binary file for script/analyze_aimd.py, which can be found at the release page: https://github.com/mogroupumd/aimd/releases . The binary file included Python interpreter and all dependencies required by the analyze_aimd.py. Thus the user can run the packaged script without installing a Python interpreter or any other modules. The user documentations is same as in the https://github.com/mogroupumd/aimd#install-and-testing-steps
Python library aimd is released under the MIT License. The terms of the license are as follows:
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