Integrate LOBSTER apps into crystal toolkit - #459
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JaGeo
changed the title
StructureMoleculeComponent update
CohpAndDosComponent Features
Example rendered app
Todos (Will be worked on once app layout is finalized))
Open questions and things to improve
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@naik-aakash @JaGeo for this to be used on MP's site, we'll need any of the required outputs to be in the LobsterTaskDocument. The client will retrieve a LobsterTaskDocument and then use any fields, like (The client shouldn't depend on lobsterpy / need to call lobsterpy). Also to be clear, crystal toolkit shouldn't depend on emmet, but should use data that is available in the task document The method you implemented is OK to keep as a Can you double check that any data that is required for the app to work is included in the task document model? Any updates to the schema should be made against this branch in emmet (PR link) |
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Hi @esoteric-ephemera, thanks for the suggestion. I will look at the pinned emmet PR and raise a PR if I find anything is missing. I will also try to make the changes in the client in the PR soon. |
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| class CustomVasprun(Vasprun): |
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For this class, I would recommend against copying all of Vasprun.final_energy:
class CustomVasprun(Vasprun):
@property
def final_energy(self):
return float(super().final_energy)
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Hi @esoteric-ephemera , have one question. So, now the plan is that LobsterPy is already run as part of taskdoc generation, and we simply use the outputs from the taskdoc and render the app? I did it this way because, in our initial discussions, it was emphasized that Postprocessing should not be part of Taskdoc, but rather that this app should handle it. Curious about how the workflow pipeline would be now. Once I start with this, I can better comment on the emmet PR. |
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Any "heavy" post-processing, or post-processing which requires raw output files like vasprun.xml, should happen in the build process for your data. In the current pipeline, the lobster build would be Ex: all derived MP data is built from Light post-processing can occur in the app (e.g., the oxygen evolution graph drawing in the client) , but this should be Let me know if that makes sense! |
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Hi @esoteric-ephemera , I made the changes are requested to directly work with taskdoc inputs. Made some tweaks and added some more options to enable more interactive anaylsis. Here is screenshot of updated layout 
Also I have an additional code that can create such visualization using plotly and dash. Have attached a short video of it here Screencast.from.06.02.2026.17.03.33.webmI could not figure out to reuse the Let me know what you think? Also if this additional app is desired, It would be great if anyone can help with modifying |
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Thanks, @naik-aakash! Looking good and perhaps @minhsueh has suggestions on how to modify / work with existing components We can discuss this more, but would this ideally be included as a separate property tab for a material, or in a standalone app? |
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Hi @esoteric-ephemera , @minhsueh, I added the LobsterEnv analysis algorithm to Have also added a 
Also, not 100%: I didn't break anything in Tagging @JaGeo here just to keep in the loop |
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| struct = self.from_data(struct) | ||
| struct = _extract_structure_from_data(struct) |
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Do we need to replace the original code with _extract_structure_from_data here? These callbacks are for soap_analysis, soap_similarities, chemenv_analysis, and bondinggraph_analysis, so they shouldn’t use a structure-extraction function specific to the LOBSTER analysis.
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Seemed like this to me, because without it I could not make it work.
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I could not figure out how to do this best way. If you have ideas let me know or if you like to make changes in on this PR or other PR. Also not sure if my changes break anything as there are no specific test cases.
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Although _extract_structure_from_data falls back to returning the original data, I don't think we need to use it in soap_analysis, soap_similarities, chemenv_analysis, or bondinggraph_analysis, since those seem to be working correctly in the current production. We could keep _extract_structure_from_data specific to the LOBSTER components if needed.
Could you elaborate on what isn't working in your other local environment? I'm not sure I understand the issue.
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Hi @minhsueh , so if I do not use this function and try to initialize the app locally with data necessary for lobsterenv option. i.e the structure, icohplist, and charges Python objects in dict form, the chemenv and other options seem to give errors as they expect just the structure object without dict form.
We can see this issue using the added example localenv.py app from the repo and replacing the _extract_structure_from_data with the existing method (self.from_data) in soap_analysis, soap_similarities, chemenv_analysis, or bondinggraph_analysis. Maybe this makes things clearer. I apologize for not being very clear before with explaining the problem.
…y_graph with MoleculeGraph.from_empty_graph
…y_graph with MoleculeGraph.from_empty_graph
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| struct = self.from_data(struct) | ||
| struct = _extract_structure_from_data(struct) |
There was a problem hiding this comment.
Although _extract_structure_from_data falls back to returning the original data, I don't think we need to use it in soap_analysis, soap_similarities, chemenv_analysis, or bondinggraph_analysis, since those seem to be working correctly in the current production. We could keep _extract_structure_from_data specific to the LOBSTER components if needed.
Could you elaborate on what isn't working in your other local environment? I'm not sure I understand the issue.
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@naik-aakash My guess is that the LOBSTER analysis is taking longer than expected, causing the page to exceed the 30-second timeout. One suggestion before directly increasing the timeout: if you're able to reproduce the issue locally, try running the test in headed mode with python -m pytest --cov=crystal_toolkit --cov-report=xml --color=yes --webdriver Chrome --headed --slowmo 3000 crystal_toolkit/apps/examples/tests/test_lobsterenv.py |
Hi @minhsueh , I created a fresh new environment and installed the same dependencies as in the current CI workflow. It still seems to pass without any issues. The page seemed to load properly and navigate to the expected dropdown option "LobsterEnv" before running the assertions. No errors I could see. |
Seems now the test passed, not sure if it failed yesterday use to issues of github actions yesterday or now it passed cause of my changes here.. |
5 participants
This is the PR to integrate LOBSTER into the Crystal Toolkit.
See below for a detailed explanation of the PR by @naik-aakash !