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abelcarreras / DynaPhoPy

Phonon anharmonicity analysis from molecular dynamics
http://abelcarreras.github.io/DynaPhoPy/
MIT License
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Maxwell-Boltzmann distribution analysis does not fit well #2

Closed wenlibin02 closed 7 years ago

wenlibin02 commented 7 years ago

Dear Abel Carreras,

I installed the dynaphopy package and tested the Si example you gave in the doc. VASP was used for the testing, with 1E4 MD steps at 800 K. Then I ran the dynaphopy script in interactive mode, using the OUTCAR produced by VASP calculation. The Maxwell-Boltzmann distribution analysis plotted a graph and printed a fitting temperature (2022.4 K), but I found the fitting curve deviated too much from the data, as shown below. pipefile

I tried to change the number of MD steps used for analysis by specifying -n parameter, i.e. -n 8000 or -n 5000, resulting in exactly the same fitting results. It seems it did not really fit the data at all.

More Information on my setup: 1) dynaphopy: install using pip today (2017 07 21) 2) Debian system, with updated numpy and scipy packages

abelcarreras commented 7 years ago

That's strange. How many atoms did you use in the supercell? Have you tried reading the XDATCAR instead? (remember to set the time step using -ts flag) What do you obtain for the atomic displacements distribution calculation?

wenlibin02 commented 7 years ago

@abelcarreras I used nearly the same configuration as the Si example in the doc of DynaPhoPy. I just tested using the XDATCAR, and found the velocity fitted well. Then I tried using different number of steps: -n 5000 and `-n 2000, giving slightly different temperatures fluctuating around 800 K. That means XDATCAR gave the correct results for Maxwell-Boltzmann distribution fitting. The same tests using OUTCAR always give 2022.4 K, no matter how many MD steps I specified.

Except the difference in Maxwell-Boltzmann distribution analysis,

I used VASP 5.3.3 for the MD calculation.

abelcarreras commented 7 years ago

Ok, I see. I will check the OUTCAR parser. I use a slightly different version of VASP so maybe something changed in the OUTCAR file. The differences may also be due to the precision. The XDATCAR has more precision than the OUTCAR. I recommend to read the trajectory always from the XDATCAR file. In the future I plan to drop the OUTCAR parser support. Thanks a lot for the feedback I will revise the OUTCAR parser and the online manual.

wenlibin02 commented 7 years ago

Thank you for your reply. Your code is really nice.