ProbabilityDensityAnalysis results in strange chargcar

[thienbinh92]

Hello,
I get a strange result from ProbabilityDensityAnalysis. Li and transition metal layers are not arranged like POSCAR/CONTCAR. Here is the code I use:
file = ["tem-1000/out_vasprun.xml"]
analyzer = DiffusionAnalyzer.from_files(file, specie="Li", smoothed=False)
structure = analyzer.structure
trajectories = [s.frac_coords for s in analyzer.get_drift_corrected_structures()]
pda = ProbabilityDensityAnalysis(structure, trajectories, species="Li")
pda.to_chgcar("CHGCAR.vasp")
I attach vasprun file below. Hope that someone help me to check.

[AIMD.zip](https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/files/8717660/AIMD.zip)

[JiQi535]

@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.

[thienbinh92]

@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?

[JiQi535]

@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.

[thienbinh92]

@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.

[JiQi535]

@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.

[thienbinh92]

@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.