Comments (6)
@thienbinh92 Can you explain more why you say "Li and transition metal layers are not arranged like POSCAR/CONTCAR"?
From my check, the CHGCAR.vasp from ProbabilityDensityAnalysis has the same atom coordinates as that of the initial structure in the AIMD snapshots you attached. I added structure.to("cif","AIMD_01.cif")
to your code and compared AIMD_01.cif and CHGCAR.vasp.
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@JiQi535 Do you get "AIMD_01.cif" from vasprun.xml?
I found that the orders of elements in vasprun file (Li Co O 24 36 72) and in CHGCAR.vasp (Co Li O 36 24 72) are not the same. Here is from vasprun file:
Here is CHGCAR.vasp generated from ProbabilityDensityAnalysis:
charge.zip
Since the code defines incorrectly element order, may it result in wrong MSD and diffusivity?
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@thienbinh92 Yes, I got the AIMD_01.cif from vasprun.xml. The structure it contains should be equivalent to the initial structure of AIMD, instead of structure in CONTCAR.
With the code you provided, I generated one CHAGCAR.vasp file that does not have the problem you described.
CHGCAR.vasp.zip
I believe what you are reporting is related to a solved issue. Please update your package with git pull
and pip install .
, then the issue should be solved.
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@JiQi535 I am not clear on how to upgrade. So I have just uninstalled pymatgen-analysis-diffusion and re-install with the command pip install pymatgen-analysis-diffusion
. It still works incorrectly.
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@thienbinh92 You can update it with the below codes and try again:
pip uninstall pymatgen-analysis-diffusion
git pull https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion
cd pymatgen-analysis-diffusion; pip install .
@shyuep Hi Shyue Ping, I think it may be necessary to update the release on pypi, as the bug described in issue #125 has been fixed.
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@JiQi535 Thanks a lot. I downloaded and its result looks good.
PS: git pull
does not work on my laptop. but git clone https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion
works well.
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Related Issues (20)
- Finite rounding in endpoint structure creation HOT 1
- How to obtain the .npy file or .json file HOT 1
- how to obtain the .npy and .json file HOT 1
- Error with get_arrhenius_plot HOT 1
- Possible bug in RadialDistributionFunction HOT 3
- vasprun.xml generated with ML-MD can't be read HOT 1
- Issue with MSD HOT 5
- DiffusionAnalyzer will fail if there is no framework ions HOT 1
- setting n_jobs != 1 raises ValueError: not enough values to unpack (expected 3, got 2)
- [Bug]: pretty_plot() gives error due to the breaking change of pymatgen HOT 4
- [Bug]: Website Access Issue: Materials Virtual Lab pymatgen-diffusion Guide HOT 1
- [Bug]: analyzer.get_msd_plot failed HOT 2
- [Bug]: get_arrhenius_plot() failed HOT 3
- [Bug]: get_arrhenius_plot() fails in pymatgen-analysis-diffusion/pymatgen/analysis/diffusion /analyzer.py
- [Bug]: ValueError: zero-size array to reduction operation maximum which has no identity
- [Bug]: msd, arrhenius and van hove plotting functions are not working! HOT 3
- [Bug]: msd, arrhenius and van hove plotting functions are not working again after v2024.6.24 release! HOT 1
- [Bug]: v2024.6.25 pypi installation doesn't install analyzer.py and init HOT 1
- [Bug]: van_hove analysis 3d plot function doesnt work! HOT 1
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