Issues in calculating E_hull of matrials containing specific elements

[RyotaroOKabe]

I have difficulty in predicting energy above hull (E_hull) ad formation energy (E_form) using PatchedPhaseDiagram. After I defined ppd_mp (

matbench-discovery/data/wbm/compile_wbm_test_set.py

Line 543 in c9dc8ee

ppd_mp: PatchedPhaseDiagram = pickle.load(zip_file)

), I have tried calculating E_hull and E_form using the line below:

e_above_hull = ppd_mp.get_e_above_hull(cse, allow_negative=True)

The error message is:

ValueError: Unable to get decomposition for wbm-1-46 ComputedStructureEntry - La1 Yb1 Ag2  (LaYbAg2)

I also got an error from the line below:

e_form_ppd = ppd_mp.get_form_energy_per_atom(cse) - cse.correction_per_atom

The error message is:

KeyError: Element Yb

As much as I surveyed, pymatgen's phase diagram object cannot handle materials with elements like Yb and Rn. Is there any way we can use PatchedPhaseDiagram for all materials?

I used the following versions for this work:

Python 3.11.7
pymatgen==2024.2.23

[CompRhys]

when you load/make the ppd it should have attributes ppd.elements and ppd.el_refs I can't immediately think of what might be causing your issues so if you could post the output of those two attributes it would be helpful to explore this futher.

[RyotaroOKabe]

ppd_mp.el_refs.txt
ppd_mp.elements.txt
Here I attached the outputs of ppd_mp.elements and ppd_mp.el_refs as txt files. I followed the code build_phase_diagram.py and compile_wbm_test_set.py for building PatchedPhaseDiagram ppd_mp. Seems both of the outputs did not present Yb.

[janosh]

if you rerun the code that fetches all MP computes entries from the latest MP DB release (v2023.11.1), you won't get any Yb compounds. they were all deprecated due to a poor choice of Yb_2 pseudo-potential (see materialsproject/pymatgen#2969 for details). i'd recommend you use the compressed entries that were archived specifically for Matbench Discovery.

[janosh]

@esoteric-ephemera is planning to rerun all Yb-containing MP compounds with Yb_3 which when completed would allow you to build a new complete PatchedPhaseDiagram

[RyotaroOKabe]

Thanks. _ checked the archived data of Matbench Discovery v1.0.0 in the link you shared. So far, I could find only 2023-02-07-mp-computed-structure-entries.json.gz as the most up-to-date dataset of Entry objects. Should I refer to any other data?