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I_kwDOACgets58sLAM
| 3,565
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Add alias `VaspInputGenerator` for `VaspInputSet`
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[] | 2024-01-20T07:55:22
| 2024-02-23T10:52:37
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2024-02-23T10:52:37Z
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MEMBER
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My decision is that I have no problems with having an alias called VaspInputGenerator. But VASPInputSet will not be deprecated. Let's be pragmatic - there are many things we probably want to rename. But deprecation of classes/methods creates headaches and unless there is an actual practical benefit, i.e., a large change in functionality or the API, these should not be done.
_Originally posted by @shyuep in https://github.com/materialsproject/pymatgen/issues/3484#issuecomment-1838877706_
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PR_kwDOACgets5knvKI
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Alias `VaspInputSet` to `VaspInputGenerator`
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[
"Thanks @janosh !\r\nI would add the aliases to the subclasses too. For the base VaspInputSet, it's almost never used directly so it would not clarify things for the users. I can do that and make a PR to your vasp-input-gen-alias. I think it would be useful to add some explanations or note on this in the documentation. I will see to add this somewhere, at least in the API docstrings somewhere, maybe also somewhere in the main documentation, but I don't think there is anything (yet) about the io sets there.",
"> I can do that and make a PR to your vasp-input-gen-alias. I think it would be useful to add some explanations or note on this in the documentation\r\n\r\nplease, doc improvements are always welcome!\r\n\r\n> I would add the aliases to the subclasses too.\r\n\r\nthere are 23 subclasses that inherit from `VaspInputSet` via `DictSet`. not sure we need aliases for all of them. but only adding it for some seems inconsistent. not sure what's best",
"@davidwaroquiers this PR is conflicting now so I'm leaning towards resolving and merging now. you can then make a subsequent PR straight to `master`"
] | 2024-01-20T07:59:28
| 2024-02-23T11:28:01
|
2024-02-23T10:52:37Z
|
MEMBER
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To accomodate `atomate2` terminology.
Closes #3565.
@utf @davidwaroquiers Let me know if this serves your purpose and if you think more changes along similar lines would make sense.
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I_kwDOACgets58s51l
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Vulnerability Disclosure
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[
"Hi @SteakEnthusiast, thanks for getting in touch. I have enabled [private vulnerability reporting](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing-information-about-vulnerabilities/privately-reporting-a-security-vulnerability) for this repo, which should allow you to create a private fork directly. Does this work for you?",
"Perfect, thanks!"
] | 2024-01-20T16:31:17
| 2024-01-21T00:38:35
|
2024-01-21T00:38:35Z
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NONE
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Dear Maintainers,
I've identified a potential security issue that can arise from parsing arbitrary user input with the Pymatgen library. To securely address this, I am requesting that a [temporary private fork](https://docs.github.com/en/code-security/security-advisories/working-with-repository-security-advisories/collaborating-in-a-temporary-private-fork-to-resolve-a-repository-security-vulnerability) is created. This will allow us to discuss and resolve the issue without needing to publicly disclose a proof of concept before a patch can be made.
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PR_kwDOACgets5ku8gV
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Lazy import `pandas` in `Structure.as_dataframe()` to improve startup speed
|
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[] | 2024-01-22T15:12:18
| 2024-01-22T16:13:29
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2024-01-22T16:13:28Z
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MEMBER
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Closes #3563.
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PR_kwDOACgets5kvXfO
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Fix highly-nested parens when formula parsing in `Composition`
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[] | 2024-01-22T16:14:37
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2024-01-22T16:27:52Z
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Closes #3559.
9896133d3 fix highly-nested formula parsing in Composition
aca351cb4 add failure cases from gh-3559 as tests
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PR_kwDOACgets5kwkxD
| 3,570
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Add test for `NEBAnalysis.get_plot()`
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[] | 2024-01-22T19:35:30
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2024-01-22T19:49:31Z
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MEMBER
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closes #3523.
doesn't look like anything's actually broken in #3523 but still good to add a test.
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PR_kwDOACgets5kyf6h
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Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates
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[] | 2024-01-23T03:44:01
| 2024-02-08T14:47:02
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2024-02-08T14:47:02Z
|
CONTRIBUTOR
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> added by @janosh: breaking because of changes in [64c37be](https://github.com/materialsproject/pymatgen/pull/3572/commits/64c37be1b1ef82d7ed7d7e1766d2c347ffcfbd9d). SubstrateAnalyzer was poorly designed, requiring the user to know to call `SubstrateAnalyzer.calculate` before `SubstrateAnalyzer.generate_surface_vectors`. calling `SubstrateAnalyzer().generate_surface_vectors` alone would raise due to missing attributes `film` and `substrate`.
This change is to help the users to be capable to track the real film vectors and substrate vectors expressed in their own original crystal coordinates. This is important when they make interface structures because they need to figure out the exact crystal vectors in along the a, b, c vectors in the supercell
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PR_kwDOACgets5k1L2r
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Return `self` in `SiteCollection` spin/oxi state add/remove methods
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[] | 2024-01-23T12:22:30
| 2024-01-26T12:41:15
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2024-01-23T12:38:18Z
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MEMBER
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b06a0adbb return `self` in `SiteCollection.remove_oxidation_states()`
185711cd0 `test_remove_oxidation_states()` `assert struct_out is struct_specie`
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PR_kwDOACgets5k2HZz
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Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer
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[] | 2024-01-23T14:45:54
| 2024-01-23T19:36:26
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2024-01-23T19:23:17Z
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CONTRIBUTOR
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## Summary
The ordering property of the CollinearMagneticStructureAnalyzer class is set depending on the `total_magnetization = abs(sum(magmoms))`. Due to floating point imprecision, the sum of magmoms can adapt values close to zero instead of zero. This can, for example, lead to collinear AFM structures being misclassified as FiM.
This was resolved by replacing `if total_magnetization > 0` with `if not isclose(total_magnetization, 0, abs_tol=1e-8)`.
A test to determine the magnetic ordering of MAGNDATA entry 1.62 (CuO) which would have failed with the previous code was added.
Source mcif:
https://www.cryst.ehu.es/magndata/index.php?index=1.62
doi: 10.1088/0022-3719/21/15/023
## Open questions
@janosh
1. Is an absolute tolerance of `abs_tol=1e-8` a reasonable choice for "being close to zero" here?
2. I included a test file (tests/files/magnetic.example.CuO.mcif) from MAGNDATA because this was also done for magnetic.example.NiO.mcif - hope this is okay?
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PR_kwDOACgets5k3fwX
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`tests/io/aims` use `numpy.testing.assert_allclose` and `pytest.MonkeyPatch`
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[] | 2024-01-23T17:55:12
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2024-01-24T05:49:04Z
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MEMBER
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for better error msgs and auto-reverted side-effects resp.
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PR_kwDOACgets5k7jTA
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Add tests for the New Vasp input sets
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[
"Hi @utf, I have a quick question here: is there any particular reason for skipping `ENCUT` in INCAR (set as None) in `MITMDSet` and `MPMDSet`?\r\nhttps://github.com/materialsproject/pymatgen/blob/7e0c8f4ddea72367c2059865b0fa8cf8681663ea/pymatgen/io/vasp/sets.py#L2409\r\nhttps://github.com/materialsproject/pymatgen/blob/7e0c8f4ddea72367c2059865b0fa8cf8681663ea/pymatgen/io/vasp/sets.py#L2482\r\n\r\nThe default settings in `MVLNPTMDSet` look more reasonable to me if someone just wants to manually run an MD wo workflow and grab some snapshots from a single run.\r\nhttps://github.com/materialsproject/pymatgen/blob/7e0c8f4ddea72367c2059865b0fa8cf8681663ea/pymatgen/io/vasp/sets.py#L2559",
"@Zhuoying, I didn't change the behaviour of the input sets. I just updated the implementation. E.g., for the two input sets you mentioned, see the old implementation where ENCUT was also removed from the input set.\r\n\r\n- `MITMDSet`: https://github.com/materialsproject/pymatgen/blob/36e289cfb73572f54aef5528333673a4d969279b/pymatgen/io/vasp/sets.py#L2602\r\n- `MPMDSet`: https://github.com/materialsproject/pymatgen/blob/36e289cfb73572f54aef5528333673a4d969279b/pymatgen/io/vasp/sets.py#L2691\r\n\r\nI would highlight that the point of these tests is to ensure that the output of the new input set implementation is the same as the output of the old implementations.",
"thanks @Zhuoying! more tests are always appreciated! is this ready for review?",
"@janosh Yeah, it is ready to review now. Pytest code coverage for `pymatgen/io/vasp/sets.py ` improved from 93% to 95%.\r\nThe two failing checks are not related to this PR. Please let me know if you have any comments.\r\nFor other `io.vasp` modules (`inputs, outputs, optics`), I may submit new PRs for them later if needed. \r\nThanks.\r\n```\r\nName Stmts Miss Cover\r\n--------------------------------------------------\r\npymatgen/io/vasp/__init__.py 3 0 100%\r\npymatgen/io/vasp/help.py 35 35 0%\r\npymatgen/io/vasp/inputs.py 1071 109 90%\r\npymatgen/io/vasp/optics.py 186 18 90%\r\npymatgen/io/vasp/outputs.py 2350 211 91%\r\npymatgen/io/vasp/sets.py 1204 65 95%\r\n--------------------------------------------------\r\nTOTAL 4849 438 91%\r\n```",
"Yes, thanks a lot for these efforts!",
"This is great, thanks very much @Zhuoying "
] | 2024-01-24T09:44:00
| 2024-01-31T19:08:30
|
2024-01-31T09:36:56Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- Follow #3484, add tests and clean up test_sets.py
## Todos
- Add more MD and NED-related tests
- Fix lints
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR #3574
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"> They could also be affected by the error described in PR https://github.com/materialsproject/pymatgen/pull/3574 - do you think it's a good idea to add a threshold here as well?\r\n\r\nwhat would change based on the threshold? setting `self.total_magmoms` and `self.magnetization` to exactly 0 when below the threshold?\r\n\r\ncould you add a test case that passes a custom `threshold_ordering` and verifies different behavior?",
"> > They could also be affected by the error described in PR #3574 - do you think it's a good idea to add a threshold here as well?\r\n> \r\n> what would change based on the threshold? setting `self.total_magmoms` and `self.magnetization` to exactly 0 when below the threshold?\r\n\r\nYes - if, for example, a database is scanned for structures with zero magnetization based on `self.magnetization` the imprecision issue could be relevant. but i don't know if this important enough to be included?",
"> > > They could also be affected by the error described in PR #3574 - do you think it's a good idea to add a threshold here as well?\r\n> > \r\n> > \r\n> > what would change based on the threshold? setting `self.total_magmoms` and `self.magnetization` to exactly 0 when below the threshold?\r\n> \r\n> Yes - if, for example, a database is scanned for structures with zero magnetization based on `self.magnetization` the imprecision issue could be relevant. but i don't know if this important enough to be included?\r\n\r\nI would not change the data that is stored on the object. I think this would be unexpected behavior. If someone needs this, they will implement it themself"
] | 2024-01-24T13:47:58
| 2024-01-25T06:13:58
|
2024-01-25T06:13:58Z
|
CONTRIBUTOR
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## Summary
A parameter threshold_ordering was added to CollinearMagneticStructureAnalyzer below which the total magnetization is treated as zero when defining the magnetic ordering.
@JaGeo @janosh `self.total_magmoms = sum(magmoms)` and `self.magnetization = sum(magmoms) / structure.volume` are defined before processing the input magmoms. They could also be affected by the error described in PR #3574 - do you think it's a good idea to add a threshold here as well?
|
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Q-Chem 6.1.1 breaks the `QCOutput` parser in many ways
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[] | 2024-01-24T18:07:14
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MEMBER
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### Python version
Python 3.11.x
### Pymatgen version
2023.12.18
### Operating system version
_No response_
### Current behavior
The `QCOutput` file parser does not parse a lot of the data in Q-Chem 6.1.1 output files because various lines have been changed. For instance, the "final_energy" property is not being parsed properly because the "Total energy in the final basis set line" is not present. There are other items missing. An immediately obvious one is the "single_point_job" entry is blank for a single point job. I am sure there are others.
### Expected Behavior
The final energy and other properties should be parsed.
### Minimal example
```python
from pymatgen.io.qchem.outputs import QCOutput
data = QCOutput("wB97X-v.out.txt").data
print(data["final_energy"])
print(data["single_point_job"])
```
### Relevant files to reproduce this bug
[wB97X-V.out.txt](https://github.com/materialsproject/pymatgen/files/14042110/wB97X-V.out.txt)
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I_kwDOACgets59Gqwx
| 3,579
|
Is it OK to use the periodic table JSON data in my own library?
|
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[
"Feel free to use it. But pls acknowledge pymatgen and its development team. Also, I would just caution that we periodically update the json file to fix errors, add more properties, etc. "
] | 2024-01-24T19:03:04
| 2024-01-24T19:46:58
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2024-01-24T19:46:58Z
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NONE
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Hello,
Thanks for all of your work on such an important library.
I'm currently working on a Rust project intended to be spiritually similar to pymatgen, but reimagined for a a different language and goals. (It's open-source as well.) I'd like to keep rough API compatibility where possible, though, and so if possible I'd like to use the `pymatgen/core/periodic_table.json` data in my own library to ensure that there aren't subtle numerical differences that might cause headaches for users familiar with pymatgen. To be clear, Rust is different enough that the code will be essentially a full rewrite, so the only thing I'm intending to copy wholesale is the numerical data, which is mostly found through references to begin with as far as I'm aware.
A reading of the MIT license and the attributions within the code seem to indicate that this is allowed with attribution, but I thought it'd be appropriate to ask here. Is there any issue with use of the periodic table data with proper attribution? Are there issues I should be aware of when adapting the data to my own code?
Thanks for your time.
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PR_kwDOACgets5k_SU_
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Support parsing of "final_energy" in Q-Chem 6.1.1
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[] | 2024-01-24T19:34:03
| 2024-01-25T06:36:56
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2024-01-25T06:07:14Z
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MEMBER
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## Summary
This PR enables proper parsing of "final_energy" in Q-Chem 6.1.1 with `QCOutput` while maintaining backwards compatability. Partially addresses, but does not fully close, #3578.
CC: @samblau, @espottesmith, @rkingsbury
@janosh --- the error seems unrelated and is in `main`.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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`QCOutput` should parse the full Q-Chem version
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[] | 2024-01-24T20:05:17
| 2024-01-25T03:41:26
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MEMBER
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|
### Feature Requested
Right now, the Q-Chem `QCOutput` parser has a very rudimentary way of getting the version and only reports the major version, e.g. "6" instead of "6.1.1". It should report the full version. Note that 6.0 is reported as "6.0" and not "6.0.0".
```python
from pymatgen.io.qchem.outputs import QCOutput
data = QCOutput("...").data
print(data["version"])
```
### Proposed Solution
The string to try to capture is the version in something like "Q-Chem 6.1.1 for Intel X86 EM64T Linux".
### Relevant Information
_No response_
|
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I_kwDOACgets59IizU
| 3,582
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Visualization
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[
"when i first tried `StructureVis` 1-2 years ago i got the same behavior. not sure when it was last working. bug fix PRs welcome!",
"I've discovered that the issue is two-fold.\r\n\r\n1) I failed to read the documentation correctly and didn't realize that I needed to use the **set_structure** function on the newly created StructureVis object to actually give it something to render. That was why it was just showing a blank white window. My script should have been written like this.\r\n\r\n```Python\r\nfrom pymatgen.vis.structure_vtk import StructureVis\r\nfrom pymatgen.core import Structure\r\n\r\nstructure = Structure.from_file(\"Ca2CuO3.cif\")\r\nvis = StructureVis()\r\nvis.set_structure(structure)\r\n\r\nvis.show()\r\n```\r\n\r\n2) However, this script also errors out because of the **add_polyhedron** function in the structure_vtk module which gets called because `show_polyhedron = True` by default. When trying to figure out how to color the polyhedron, the module tries to make the polyhedron the same color as the center atom, but when the occupations of the center atom are fractional it will use the color of the center atom with the highest occupation.\r\n\r\n```Python\r\n if color == \"element\":\r\n # If partial occupations are involved, the color of the specie with\r\n # the highest occupation is used\r\n max_occu = 0.0\r\n for specie, occu in center.species.items():\r\n if occu > max_occu:\r\n max_specie = specie\r\n max_occu = occu\r\n color = [i / 255 for i in self.el_color_mapping[max_specie.symbol]]\r\n ac.GetProperty().SetColor(color)\r\n else:\r\n ac.GetProperty().SetColor(color)\r\n```\r\n\r\nThe main issue here is that the \"color\" variable is an array of fractional rgb values (ex: [1,0,0]), and I can't seem to find where this comparison against a string \"element\" comes from or why that was used. This can be solved relatively easily by either setting `show_polyhedron = False` when creating the StructureVis object, or by changing the condition to `if len(center.species.items()) > 1:`.\r\n\r\nI don't have a lot of experience contributing to open source projects on github but I can try to submit a bug fix PR in the next couple days.",
"Update, I actually may have misrepresented the issue slightly. It doesn't actually have anything to do with whether the center atom has multiple occupations or not, it all just comes down to that check of `if color == \"element\":` and that at no point in the code does color ever seem to be stored as a string. I don't think the proposed solution should be any different though.",
"Yes, I donβt know that this is actively used. I would usually point people towards Crystal Toolkit since it has native support for `Structure` visualisation in Jupyter etc., however itβs in need of some updated documentation.",
"This issue was never resolved. Why is it closed?"
] | 2024-01-25T01:19:50
| 2025-04-01T13:05:36
|
2024-01-25T23:58:09Z
|
CONTRIBUTOR
|
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### Python version
Python 3.11.0
### Pymatgen version
2023.12.18
### Operating system version
CentOS Linux 8
### Current behavior
I am attempting to visualize a crystal structure using the structure_vtk module. However, it just opens up a blank white window.
### Expected Behavior
I would like to be able to visualize a pymatgen structure object, without having to drag and drop over to a different software. I want something that works with a plain old python script and doesn't require using a jupyter notebook. I would like to avoid making my own jank, ugly visualizations with matplotlib.
### Minimal example
```Python
from pymatgen.vis.structure_vtk import StructureVis
from pymatgen.core import Structure
structure = Structure.from_file("Ca2CuO3.cif")
vis = StructureVis(structure)
vis.show()
```
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets59Nb6P
| 3,583
|
Enable use of square brackets when parsing string formulas in Composition
|
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[
"Thanks. Solution 2 has been implemented"
] | 2024-01-25T15:48:46
| 2024-01-25T15:55:51
|
2024-01-25T15:55:38Z
|
CONTRIBUTOR
|
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### Feature Requested
Square brackets are used in formulas to denote coordination complexes, e.g. as in (NH4)2[FeCl5(H2O)].
At the moment, when instantiating a Composition object from a single string, _parse_formula() only searches for substrings in round brackets.
`match = re.search(r"\(([^\(\)]+)\)\s*([\.e\d]*)", formula)` https://github.com/materialsproject/pymatgen/blob/c0c40dd714e8e68fdb17e2d92b76f8e341e8a87a/pymatgen/core/composition.py#L561
Parsing strings like "(NH4)2[FeCl5(H2O)]" throws a `ValueError: [] is an invalid formula!` at the moment.
I suggest a modification of _parse_formula() to also enable the use of square brackets in formula strings.
### Proposed Solution
Either the regular expressions in #L561 and #L570 could be modified or square brackets could simply be replaced by round brackets at the beginning of _parse_formula(), similar to the handling of metallofullerenes (https://github.com/materialsproject/pymatgen/blob/c0c40dd714e8e68fdb17e2d92b76f8e341e8a87a/pymatgen/core/composition.py#L546)
### Relevant Information
_No response_
|
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|
Pymatgen cannot appropriately parse CIF file download from Materials Project
|
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[
"I find it the `get_structure()` returns primitive cell, but the precision loss seems non-trivial"
] | 2024-01-26T02:00:57
| 2024-01-26T07:15:33
|
2024-01-26T07:15:33Z
|
NONE
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### Python version
3.11.4
### Pymatgen version
2023.10.11
### Operating system version
Windows 11
### Current behavior
if I want to parse the "mp-13.cif" (whose content is attached at the end), I use:
```Python
parser = CifParser(fname)
lattice = parser.get_structures()[0].lattice
a, b, c, alpha, beta, gamma = lattice.a, lattice.b, lattice.c, lattice.alpha, lattice.beta, lattice.gamma
```
This will return a, b, c and alpha, beta, gamma as:
```python
2.47780913, 2.4778130300000005, 2.4811049668007565, 109.44477568919714, 109.44495554289662, 109.46983668
```
```
# generated using pymatgen
data_Fe
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 2.47781303
_cell_length_b 2.47780913
_cell_length_c 4.05429521
_cell_angle_alpha 90.00003845
_cell_angle_beta 90.00031951
_cell_angle_gamma 109.46983668
_symmetry_Int_Tables_number 1
_chemical_formula_structural Fe
_chemical_formula_sum Fe2
_cell_volume 23.46816847
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe0 1 0.50000002 0.50000008 0.49999999 1
Fe Fe1 1 0.99999998 0.99999992 0.00000001 1
```
### Expected Behavior
should be consistent with original parsed file
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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Breaking: remove single-use `PolarizationLattice` which inherited from `Structure` (antipattern)
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[] | 2024-01-26T07:29:40
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2024-01-26T08:43:33Z
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MEMBER
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5c1df065a breaking: remove PolarizationLattice which inherited from Structure (antipattern) and refactor get_same_branch_polarization_data()
e17322125 rename d|s vars
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I_kwDOACgets59VH5E
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`Vasprun` parser raises a `FileNotFoundError` when searching for POTCARs with pymatgen 2024.1.26
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[
"Thanks @Andrew-S-Rosen! If anyone else encounters this issue while using this release of pymatgen, please note that using `Vasprun(\"./vasprun.xml\")` should correctly parse the POTCAR in the current (relative) working directory.\r\n\r\nFixed (hopefully) in #3587 ",
"Thanks! As a note, this workaround isn't possible when using several external codes depending on Pymatgen. For instance, Custodian by default will call `Vasprun(\"vasprun.xml\")` somewhere I believe. In any case, your PR should fix it."
] | 2024-01-26T18:22:58
| 2024-01-28T18:51:30
|
2024-01-28T18:51:30Z
|
MEMBER
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### Python version
3.11
### Pymatgen version
2024.1.26
### Operating system version
Ubuntu
### Current behavior
Do the following in a completed folder containing a VASP run.
```Python
from pymatgen.io.vasp.outputs import Vasprun
Vasprun('vasprun.xml')
```
```python
File /scratch/network/asrosen/software/miniconda/envs/quacc/lib/python3.10/site-packages/pymatgen/i
o/vasp/outputs.py:296, in Vasprun.__init__(self, filename, ionic_step_skip, ionic_step_offset, pars
e_dos, parse_eigen, parse_projected_eigen, parse_potcar_file, occu_tol, separate_spins, exception_o
n_bad_xml)
293 self.nionic_steps = len(self.ionic_steps)
295 if parse_potcar_file:
--> 296 self.update_potcar_spec(parse_potcar_file)
297 self.update_charge_from_potcar(parse_potcar_file)
299 if self.incar.get("ALGO") not in ["CHI", "BSE"] and not self.converged and self.parameters.
get("IBRION") != 0:
File /scratch/network/asrosen/software/miniconda/envs/quacc/lib/python3.10/site-packages/pymatgen/i
o/vasp/outputs.py:1054, in Vasprun.update_potcar_spec(self, path)
1046 def update_potcar_spec(self, path):
1047 """
1048 Args:
1049 path: Path to search for POTCARs
(...)
1052 Potcar spec from path.
1053 """
-> 1054 if potcar := self.get_potcars(path):
1055 self.potcar_spec = [
1056 {"titel": sym, "hash": ps.md5_header_hash, "summary_stats": ps._summary_stats}
1057 for sym in self.potcar_symbols
1058 for ps in potcar
1059 if ps.symbol == sym.split()[1]
1060 ]
File /scratch/network/asrosen/software/miniconda/envs/quacc/lib/python3.10/site-packages/pymatgen/i
o/vasp/outputs.py:1010, in Vasprun.get_potcars(self, path)
1007 else:
1008 search_path = os.path.split(self.filename)[0] if path is True else str(path)
1009 potcar_paths = [
-> 1010 f"{search_path}/{fn}" for fn in os.listdir(search_path) if fn.startswith("POTCAR")
and ".spec" not in fn
1011 ]
1013 for potcar_path in potcar_paths:
1014 try:
FileNotFoundError: [Errno 2] No such file or directory: ''
```
Here are the files in my directory (can share over Slack since POTCAR is proprietary).
```
AECCAR0 CHGCAR IBZKPT OSZICAR POTCAR vasp.out
AECCAR1 CONTCAR INCAR OUTCAR POTCAR.orig vaspout.h5
AECCAR2 custodian.json INCAR.orig PCDAT PROCAR vasprun.xml
ase-sort.dat DOSCAR KPOINTS POSCAR REPORT WAVECAR
CHG EIGENVAL KPOINTS.orig POSCAR.orig std_err.txt XDATCAR
```
Likely introduced in #3491.
### Expected Behavior
The `Vasprun` should correctly identify the POTCAR file in the present working directory.
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PR_kwDOACgets5lMivG
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Fix `Vasprun.get_potcars` search method; tweak fake POTCARs
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[] | 2024-01-26T21:07:13
| 2024-01-29T19:27:04
|
2024-01-28T07:45:29Z
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CONTRIBUTOR
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The main change here is to correct the `update_potcar_spec` method of `Vasprun` found by @Andrew-S-Rosen in issue #3586. Specifying `Vasprun("vasprun.xml")` would not find POTCARs, but specifying the leading `Vasprun("./vasprun.xml")` would. That has been corrected.
Other fixes:
- Add test for this behavior, `io/test_outputs.TestVasprun.test_parse_potcar_cwd_relative`
- Update potcar scrambling to ensure that scrambled POTCARs have same TITELs as originals. A "FAKE" comment still exists in the scrambled POTCARs to show that they're gobbled, but this is no longer parsed into `PotcarSingle.TITEL`
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Super slow import times on `2024.1.26`
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[
"A new version was released that should fix it. It is due to a bug introduced in monty."
] | 2024-01-27T01:04:19
| 2024-01-27T05:42:17
|
2024-01-27T05:42:17Z
|
MEMBER
|
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### Python version
3.11.7
### Pymatgen version
2024.1.26
### Operating system version
Windows 11, Ubuntu
### Current behavior
```
conda create --name test python=3.11
pip install pymatgen
conda activate test
```
```Python
from pymatgen.io.vasp.outputs import Vasprun
```
Running the above after a clean install in an otherwise clean conda environment takes a *super* long time. I stopped timing it after waiting 2.5 minutes.
@esoteric-ephemera has observed similar behavior.
### Expected Behavior
It to not take several minutes.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5lNPhT
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Fix text formatting in `bug_report.yaml`
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[] | 2024-01-27T01:07:25
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2024-01-27T02:25:20Z
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MEMBER
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The "Current behavior" section is formatted as Python code by default, which is super annoying since it should be text (and you don't see the Python formatting until after you post). I fixed it.
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I_kwDOACgets59XKci
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String representation of Spin enum
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[
"Changing the `__repr__` would be a safer option than changing `__str__` if we want something more readable."
] | 2024-01-27T04:54:12
| 2024-02-14T00:29:08
|
CONTRIBUTOR
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Should the string representations for `Spin.up`/`Spin.down` be "up" and "down" respectively?
https://github.com/materialsproject/pymatgen/blob/ac8a7e9cd93ba9f7afeaced45dc28af6d4e151d4/pymatgen/electronic_structure/core.py#L29-L30
Similar to `OrbitalType`:
https://github.com/materialsproject/pymatgen/blob/ac8a7e9cd93ba9f7afeaced45dc28af6d4e151d4/pymatgen/electronic_structure/core.py#L42-L43
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PR_kwDOACgets5lP7VH
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Use `name` instead of `value` in `Spin.__str__`
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[
"Thank @janosh! I was thinking of contributing myself and was waiting for comments from maintainers if this is a change that is required. No worries, I will try to fix the failed test here and open a PR to `fix-gh-3590` :)",
"thanks @R1j1t. i think this change makes sense which is why i wanted to make a PR to see how much it would break. the `Spin.from_str` method can be made backward compatible to handle both the old and new serialization (\"up\"/\"down\" vs \"1\"/\"-1\"). but of course, it's still a breaking change in that JSON documents (e.g. for DOS and band structure objects) in existing databases will become inhomogeneous. old ones will have \"1\"/\"-1\" as keys for spin projections, new ones \"up\"/\"down\". this is not a change to commit to lightly and will require community discussion.",
"@shyuep what's your stance here? keep serializing `Spin.up`/`Spin.down` as 1/-1 or change to `\"up\"`/`\"down\"`? we could also choose `\"Spin.up\"`/`\"Spin.down\"` to be even more explicit",
"> @shyuep what's your stance here? keep serializing Spin.up/Spin.down as 1/-1 or change to \"up\"/\"down\"? we could also choose \"Spin.up\"/\"Spin.down\" to be even more explicit\r\n\r\nResponding to this: we should definitely keep the existing 1/-1. We should absolutely not make changes to how things are serialized unless absolutely necessary.\r\n\r\nUltimately, good arguments could be made for a different value here, but at this point it's an aesthetic choice. Changing it would not bring a clear benefit, but would introduce a lot of potential data incompatibilities or chores for downstream users, as noted:\r\n\r\n> but of course, it's still a breaking change in that JSON documents (e.g. for DOS and band structure objects) in existing databases will become inhomogeneous",
"I would definitely not do this. It is purely aesthetic. ",
"I can't entirely agree with the argument that it is not required because it's an aesthetic change. Choices like these make the outputs more readable. However, I completely understand that it is a significant change. Hence, it will have a much lower priority. ",
"It is not about required or not. It is a balance between the value of the change and the headache it will create for the community. "
] | 2024-01-28T07:56:48
| 2024-09-08T21:18:47
|
2024-02-26T14:59:07Z
|
MEMBER
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Closes #3590.
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Adding FHI-aims inputs developers
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[] | 2024-01-29T17:20:27
| 2024-01-30T06:21:52
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2024-01-30T06:21:52Z
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CONTRIBUTOR
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## Summary
Adding the FHI-aims developers to the developers list
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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Add interface to icet SQS tools through SQSTransformation
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[
"Hi @esoteric-ephemera, full support!\r\n\r\nThis is a very sensible addition, since it's in-line with existing transformation functionality. I would be happy to merge. The code itself looks fairly complete, is there anything left to be done?\r\n\r\nDon't forget to modify `setup.py`/`requirements-optional.txt` to add `icet` as an optional dependency. This will make sure it gets tested in CI, and will also make it easier for people to install.",
"Thanks @mkhorton! Maybe nothing more to add on the pymatgen side, you might want to wait to merge until [this icet issue](https://gitlab.com/materials-modeling/icet/-/issues/614) is resolved\r\n\r\nI've had to install from git and lightly modify icet to get it running, but it works quite well besides that",
"also, we can use GH's draft PR feature instead of prefixing PR titles with `[WIP]` as it's commonly forgotten to remove once PR is ready",
"> is the draft status on this PR to wait for the above? otherwise lgtm\r\n\r\nIt might take a bit to get a new version of icet released so let's move forward with it. The draft was for that issue and the resolution of failing tests"
] | 2024-01-30T17:05:37
| 2024-02-29T19:12:01
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2024-02-21T19:53:13Z
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CONTRIBUTOR
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In a recent PR #3541, @mkhorton pointed out the existence of another SQS generation tool already natively in python, icet. This has nice features that complement the ATAT MCSQS interface already in PMG, namely generation of SQS by enumeration of all possible supercells.
This is possible for smaller supercells, and guarantees that you get the "optimal" SQS for a given supercell size (when feasible).
This PR adds:
- An interface to icet through `io.icet`
- Access to icet's enumeration and Monte Carlo features through `transformations.advanced_transformations.SQSTransformation`
- Tests for the icet features in `SQSTransformation`
Looking to get feedback on if people think these are sensible additions, or if they belong somewhere else (like atomate2), or if there are features that should be added.
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I_kwDOACgets59svBH
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Issue when using pymatgen to plot dos
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[
"you can zip your `vasprun.xml` and upload the compressed version. without it, we can't repro your error.",
"i just realized your calling `python dos.ipynb`. I don't think that's supposed to work. You run the notebook through Jupyter, not with Python."
] | 2024-01-30T22:12:13
| 2024-01-31T10:51:48
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2024-01-31T10:51:48Z
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NONE
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### Python version
Python 3.10.9
### Pymatgen version
2024.1.27
### Operating system version
linux? bridges2
### Current behavior
this is my `ipynb` file:
```py
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
import matplotlib.pyplot as plt
v = Vasprun('./vasprun.xml')
cdos = v.complete_dos
dos = cdos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(dos)
plotter.show(xlim=[-10, 5], ylim=[-25, 25])
plt.savefig('spd_dos.png')
Output:
Traceback (most recent call last):
File "/ocean/projects/che170038p/zyang1/ZrO/3rdbest/3rdbest_str/DOS/dos.ipynb", line 5, in <module>
"execution_count": null,
NameError: name 'null' is not defined
```
### Expected Behavior
### Minimal example
```Python
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
import matplotlib.pyplot as plt
v = Vasprun('./vasprun.xml')
cdos = v.complete_dos
dos = cdos.get_spd_dos()
plotter = DosPlotter()
plotter.add_dos_dict(dos)
plotter.show(xlim=[-10, 5], ylim=[-25, 25])
plt.savefig('uo2_spd_dos.png')
```
### Relevant files to reproduce this bug
not able to upload vasprun.xml file
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I_kwDOACgets59uXBF
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tribchem: "Fixing" some issues in pymatgen.
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[] | 2024-01-31T05:19:25
| 2024-01-31T05:26:16
|
CONTRIBUTOR
|
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In [README.md](https://gitlab.com/triboteam/tribchem/-/blob/master/README.md?ref_type=heads) of tribchem, I noticed the following description [here](https://gitlab.com/triboteam/tribchem#fixing-some-issues-in-pymatgen):
> "Fixing" some issues in pymatgen
>
> In our installation, we encountered an error due to partial incompatibility of the old Materials Project API within the pymatgen package. Here is the suggested fix.
> The user should go to line 177 of the file <path_virtual_env>/lib/python3.8/site-packages/pymatgen/ext/matproj.py and find:
>
> self.preamble = SETTINGS.get("PMG_MAPI_ENDPOINT",https://materialsproject.org/rest/v2)
>
> Then, replace the URL address with the legacy one: https://legacy.materialsproject.org/rest/v2
It bothers me. Is this a bug in pymatgen?
See [here](https://matsci.org/t/tribchem-fixing-some-issues-in-atomate/53304) for the related discussion.
Regards,
Zhao
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PR_kwDOACgets5lmp1t
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|
Switch macOS wheel building to new M1 runners
|
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[] | 2024-01-31T18:27:07
| 2024-01-31T19:37:36
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2024-01-31T19:37:35Z
|
MEMBER
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This PR switches building the macOS wheel to [GitHub's just-announced free and much faster M1 hardware](https://github.blog/changelog/2024-01-30-github-actions-introducing-the-new-m1-macos-runner-available-to-open-source). My understanding is the compiled wheel will still be universal, i.e. run on M1 and Intel Macs.
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I_kwDOACgets592vIa
| 3,597
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Compare two descriptions of crystal structures to see if the have the same underlying structure.
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[
"It is called the StructureMatcher. We have had this since ages ago...",
"So, you mean that [my following code](https://github.com/romankempt/hetbuilder/issues/9#issuecomment-1920466398) is exactly for the purpose discussed here, am I right?\r\n\r\n```python\r\n$ cat pymatgen_compare_structures.py \r\nimport sys\r\nfrom ase.io import read\r\nfrom pymatgen.io.ase import AseAtomsAdaptor\r\nfrom pymatgen.analysis.structure_matcher import StructureMatcher\r\n\r\ndef compare_structures(path1, path2):\r\n # Read the constructure\r\n structure1 = read(path1)\r\n structure2 = read(path2)\r\n\r\n # Convert ASE to Pymatgen structure\r\n s1 = AseAtomsAdaptor.get_structure(structure1)\r\n s2 = AseAtomsAdaptor.get_structure(structure2)\r\n\r\n # Initialize the StructureMatcher\r\n matcher = StructureMatcher()\r\n\r\n # Compare the structures\r\n are_similar = matcher.fit(s1, s2)\r\n\r\n print(\"Do the structures have the same underlying structure?\", are_similar)\r\n\r\nif __name__ == \"__main__\":\r\n if len(sys.argv) != 3:\r\n print(\"Usage: script.py path_to_structure1 path_to_structure2\")\r\n else:\r\n path1, path2 = sys.argv[1], sys.argv[2]\r\n compare_structures(path1, path2)\r\n\r\n$ python pymatgen_compare_structures.py C12H14Mg7N6O14_18.00_degree_0.in C12H14Mg7N6O14_19.00_degree_0.in\r\nDo the structures have the same underlying structure? True\r\n```",
"Yes",
"I think there should be a more efficient implementation for such a job via tools like [CARAT](https://github.com/lbfm-rwth/carat) as a starting point. The core idea and first step is to determine the orientation preserving affine isomorphic transformation between two space groups, as described on page 35 [here](https://www.math.ru.nl/~souvi/krist_09/cryst.pdf):\r\n\r\n\r\n\r\nBased on the above results, we can further determine the mapping correspondences in terms of atomic positions, number, and types within the unit cells of the two structures. Thereby, ultimately ascertaining whether the given two crystal structures are symmetrically equivalent.\r\n\r\nBTW, I recently released the [CrystKit](https://github.com/hongyi-zhao/CrystKit) package which can also solve the isomorphism problem between space groups, but it's based on [GAP](https://www.gap-system.org/) and cannot work with float, aka, real numbers easily.",
"The idea here is to not use spacegroups as a criteria for matching. Matching spacegroups is an easy problem. \r\n\r\nIn any case, if you have a more efficient or more accurate implementation, we are always happy to receive a PR. ",
">The idea here is to not use spacegroups as a criteria for matching. \r\n\r\nThis is because the implementation method of `StructureMatcher` takes into account a wider range of situations. However, for very large supercells, the approach implemented here may be inefficient and may not even work successfully. On the other hand, if we want to search and compare a large number of crystal structures, the efficiency of the method implemented here is also a bottleneck.\r\n\r\n>Matching spacegroups is an easy problem.\r\n\r\nAgreed. Although more computational work is required to determine whether two crystal structures are symmetry equivalent, a good starting point is to determine the isomorphism of space groups.\r\n\r\n>In any case, if you have a more efficient or more accurate implementation, we are always happy to receive a PR.\r\n\r\nNot at the moment, but what I've described above is a general idea for such a job.\r\n\r\nP.S. Another tool that can do this type of job is [critic2](https://aoterodelaroza.github.io/critic2/examples/example_13_01_strcompare/)."
] | 2024-02-01T04:12:29
| 2024-02-11T04:35:44
|
2024-02-01T04:53:01Z
|
CONTRIBUTOR
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I'm not sure if pymatgen can do the job as implemented in [XtalComp](https://github.com/allisonvacanti/XtalComp): Compare two descriptions of crystal structures to see if they have the same underlying structure.
See [here](https://github.com/romankempt/hetbuilder/issues/9#issuecomment-1920466398) for the related discussion. Any tips will be helpful.
Regards,
Zhao
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PR_kwDOACgets5luUMI
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Rename `master` branch to `main`
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[
"I have said no to this before and I will not say it again. Do not merge this. ",
"there's no cost to being consistent with majority of repos but clear benefits by reducing mental burden",
"Agree with @janosh here, regardless of views on other factors, consistency has its benefits. 2 to 1?"
] | 2024-02-01T16:35:52
| 2024-02-01T21:49:51
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2024-02-01T16:39:03Z
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MEMBER
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I_kwDOACgets5-I4Vu
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`PBE_64` configured via pmg doesn't work with pymatgen.
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"I noticed the following code snippet:\r\nhttps://github.com/materialsproject/pymatgen/blob/9ef132a9dcc3307ce2638b7b85aeef44abf08680/pymatgen/io/vasp/inputs.py#L1595-L1612\r\n\r\nIt indicates that in my example, the `psp_resources` directory must be populated as follows:\r\n```shell\r\n$ ls ~/Public/hpc/vasp/pot/psp_resources \r\nPOT_LDA_PAW_64 POT_PAW_PBE_64\r\n```\r\nBut the `PMG_DEFAULT_FUNCTIONAL: PBE_64` setting in `~/.pmgrc.yaml` still doesn't take effect. Therefore, I finally manually set it in the code:\r\n\r\n```python\r\n$ grep -Ev '^[ ]*(#|$)' pmg-potcar.py \r\nfrom mp_api.client import MPRester\r\nfrom pymatgen.io.vasp.sets import MPRelaxSet\r\nwith MPRester() as mpr:\r\n structure = mpr.get_structure_by_material_id(\"mp-2469\")\r\nrelax_set = MPRelaxSet(structure)\r\nrelax_set.user_potcar_functional = \"PBE_64\" # Specifically designate the POTCAR functional as PBE_64\r\ntry:\r\n potcar_symbols = relax_set.potcar_symbols\r\n print(\"Successfully prepared POTCAR metadata with PBE_64 functional. Here are the symbols:\")\r\n print(potcar_symbols)\r\nexcept Exception as e:\r\n print(f\"Error occurred while attempting to prepare POTCAR metadata: {e}\") \r\n\r\n$ python pmg-potcar.py \r\nRetrieving MaterialsDoc documents: 100%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 1/1 [00:00<00:00, 13573.80it/s]\r\nSuccessfully prepared POTCAR metadata with PBE_64 functional. Here are the symbols:\r\n['Cd', 'S']\r\n```\r\n",
"That's wonderful input for reproducing an issue and I think you're going towards the right direction. By setting up the `functional` tag as `PBE_64` you specify the functional, and the POTCAR directory is then parsed as `\"POT_PAW_PBE_64\"` according to: https://github.com/materialsproject/pymatgen/blob/9ef132a9dcc3307ce2638b7b85aeef44abf08680/pymatgen/io/vasp/inputs.py#L1595-L1612\r\n\r\nTherefore `pymatgen` should be looking for your POTCAR under `POT_PAW_PBE_64` of your `$PMG_VASP_PSP_DIR`, however in the case of `MPRelaxSet` the functional setting is overwritten to `PBE` by `MPRelaxSet.yaml`:\r\nhttps://github.com/materialsproject/pymatgen/blob/e9dff45383ae712d627ef4321eedc0992d99aa07/pymatgen/io/vasp/MPRelaxSet.yaml#L83\r\n\r\nas defined in:https://github.com/materialsproject/pymatgen/blob/e9dff45383ae712d627ef4321eedc0992d99aa07/pymatgen/io/vasp/sets.py#L1206-L1221",
"Thanks, @hongyi-zhao and @DanielYang59. You can see in the exception thrown by PMG:\r\n```You do not have the right POTCAR with functional='PBE' and symbol='Cd'```\r\nthe point that @DanielYang59 made: because the call to `user_potcar_functional` is made after the set class is instantiated, `MPRelaxSet().potcar_functional` retains its default value, \"PBE\".\r\n\r\nTo use the \"PBE_64\" pseudopotentials, you just need to change these lines:\r\n```\r\nrelax_set = MPRelaxSet(structure)\r\nrelax_set.user_potcar_functional = \"PBE_64\" # Specifically designate the POTCAR functional as PBE_64\r\n```\r\nto `relax_set = MPRelaxSet(structure, user_potcar_functional = \"PBE_64\")`",
"Thanks for the input @esoteric-ephemera! My bad, forgot to mention the fix.",
"> https://github.com/materialsproject/pymatgen/blob/9ef132a9dcc3307ce2638b7b85aeef44abf08680/pymatgen/io/vasp/inputs.py#L1595-L1612\r\n\r\nTo improve the clarity and memorability of the functional_dir dictionary's key-value pairings, a more intuitive approach may be to restructure this data in a way that organizes the pseudopotentials by their general category (like PBE or LDA), and then within those categories, differentiate by specific attributes (like version and hash presence). This could improve readability and make it easier for users to understand the relationship between a key and its value.\r\n\r\nLet's refactor the given functional_dir into a more structured format:\r\n\r\n# Structured Pseudopotential Directory\r\n\r\nFor better organization and clarity, we'll group by type (e.g., PBE, LDA) and then detail each variant within these groups. This nesting allows for intuitive navigation and understanding of pseudopotentials' versions and additional properties.\r\n```python\r\nfunctional_dir = {\r\n \"PBE\": {\r\n \"default\": \"POT_GGA_PAW_PBE\",\r\n \"versions\": {\r\n \"52\": {\r\n \"path\": \"POT_GGA_PAW_PBE_52\",\r\n \"with_hash\": \"POTPAW_PBE_52\"\r\n },\r\n \"54\": {\r\n \"path\": \"POT_GGA_PAW_PBE_54\",\r\n \"with_hash\": \"POTPAW_PBE_54\"\r\n },\r\n \"64\": \"POT_PAW_PBE_64\"\r\n }\r\n },\r\n \"LDA\": {\r\n \"default\": \"POT_LDA_PAW\",\r\n \"versions\": {\r\n \"52\": {\r\n \"path\": \"POT_LDA_PAW_52\",\r\n \"with_hash\": \"POTPAW_LDA_52\"\r\n },\r\n \"54\": {\r\n \"path\": \"POT_LDA_PAW_54\",\r\n \"with_hash\": \"POTPAW_LDA_54\"\r\n },\r\n \"64\": \"POT_LDA_PAW_64\"\r\n }\r\n },\r\n \"PW91\": \"POT_GGA_PAW_PW91\",\r\n \"LDA_US\": \"POT_LDA_US\",\r\n \"PW91_US\": \"POT_GGA_US_PW91\",\r\n \"Perdew_Zunger81\": \"POT_LDA_PAW\"\r\n}\r\n```\r\n \r\n# Accessing the Data\r\n\r\nTo facilitate accessing this restructured data, let's write a helper function. This function aims to navigate through the new structure smoothly, allowing us to request pseudopotentials by their type, optionally specifying a version and whether we prefer the version with a hash.\r\n\r\n```python\r\ndef get_pseudopotential_path(method, version=None, with_hash=False):\r\n potcar_data = functional_dir.get(method)\r\n\r\n if isinstance(potcar_data, dict):\r\n if \"default\" in potcar_data:\r\n if version is None:\r\n return potcar_data[\"default\"]\r\n else:\r\n version_info = potcar_data[\"versions\"].get(version)\r\n if isinstance(version_info, dict):\r\n return version_info.get(\"with_hash\" if with_hash else \"path\")\r\n else:\r\n return version_info # Direct path for versions without additional properties\r\n return potcar_data # Direct path for methods without versions\r\n```\r\n\r\n \r\n# Example Usage\r\n\r\nThis example demonstrates how to use the get_pseudopotential_path function to access various pseudopotential paths in the new, more structured directory.\r\n\r\n```python\r\n# Access the default PBE pseudopotential\r\nprint(get_pseudopotential_path(\"PBE\"))\r\n\r\n# Access PBE version 52, without hash\r\nprint(get_pseudopotential_path(\"PBE\", version=\"52\"))\r\n\r\n# Access PBE version 54, with hash\r\nprint(get_pseudopotential_path(\"PBE\", version=\"54\", with_hash=True))\r\n\r\n# Access PW91 without worrying about versions or hash\r\nprint(get_pseudopotential_path(\"PW91\"))\r\n```\r\n\r\n \r\n# Summary\r\n\r\nBy grouping the pseudopotentials by the functional form and further organizing the versions and hash options within these groups, this revamped structure aims to enhance clarity, making it easier for both users and developers to navigate and understand the relationships between different pseudopotentials. The provided get_pseudopotential_path function complements this structured approach by offering flexible access to the desired paths.",
"Hi @hongyi-zhao, you're welcome to submit a PR to make these changes. This would introduce breaking changes to the structure of `PotcarSingle`.\r\n\r\nFor me, a nested dict is less easily interpreted than the current `{key : value}` implementation of `PotcarSingle.functional_dir`, but this is up to personal preference.",
"@esoteric-ephemera Objectively speaking, I don't think my proposal above is all that great. I would even prefer to directly use these keys as the corresponding directory names. That would be more straightforward. I wonder why the original developers decided to create such a somewhat troublesome dictionary to map these directory names.",
"I personally think @hongyi-zhao's proposal is much easier to read for a person but harder to access the value from the code, as one might need multiple keys. Meanwhile from [The Zen of Python](https://peps.python.org/pep-0020/#the-zen-of-python) (though one should not take it too seriously) there is `Flat is better than nested.`. So I might personally prefer a flat version, especially when changing it would be breaking.",
"@DanielYang59 Therefore, the flattest version is a list, not a dictionary."
] | 2024-02-03T05:37:49
| 2024-02-08T14:02:38
|
2024-02-06T03:18:27Z
|
CONTRIBUTOR
|
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I'm using the latest version of PAW potentials released by the VASP team but failed to let Pymatgen select them correctly. See my following configuration done via pmg:
```shell
$ cat ~/.pmgrc.yaml
PMG_DEFAULT_FUNCTIONAL: PBE_64
PMG_MAPI_KEY: <my-mapi-key>
PMG_VASP_PSP_DIR: /home/werner/Public/hpc/vasp/pot/psp_resources
$ ls -R ~/Public/hpc/vasp/pot/psp_resources
/home/werner/Public/hpc/vasp/pot/psp_resources:
potpaw_LDA_64 potpaw_PBE_64
/home/werner/Public/hpc/vasp/pot/psp_resources/potpaw_LDA_64:
POTCAR.Ac.gz POTCAR.Br_sv_GW.gz POTCAR.Fe.gz POTCAR.Hf.gz POTCAR.Mg_sv.gz POTCAR.O_s_GW.gz POTCAR.Rh_sv_GW.gz POTCAR.Te.gz
POTCAR.Ag_GW.gz POTCAR.B_s.gz POTCAR.Fe_pv.gz POTCAR.Hf_pv.gz POTCAR.Mn_GW.gz POTCAR.O_s.gz POTCAR.Rn_d_GW.gz POTCAR.Te_sv_GW.gz
POTCAR.Ag.gz POTCAR.Ca_pv.gz POTCAR.Fe_sv_GW.gz POTCAR.Hf_sv_GW.gz POTCAR.Mn.gz POTCAR.Os.gz POTCAR.Rn.gz POTCAR.Th.gz
POTCAR.Ag_pv.gz POTCAR.Ca_sv_GW.gz POTCAR.Fe_sv.gz POTCAR.Hf_sv.gz POTCAR.Mn_pv.gz POTCAR.Os_pv.gz POTCAR.Rn_sv_GW.gz POTCAR.Th_s.gz
POTCAR.Ag_sv_GW.gz POTCAR.Ca_sv.gz POTCAR.F_GW.gz POTCAR.Hg.gz POTCAR.Mn_sv_GW.gz POTCAR.Os_sv_GW.gz POTCAR.Ru.gz POTCAR.Ti.gz
POTCAR.Al_GW.gz POTCAR.Cd_GW.gz POTCAR.F_GW_new.gz POTCAR.Hg_sv_GW.gz POTCAR.Mn_sv.gz POTCAR.Pa.gz POTCAR.Ru_pv.gz POTCAR.Ti_pv.gz
POTCAR.Al.gz POTCAR.Cd.gz POTCAR.F.gz POTCAR.H_GW.gz POTCAR.Mo.gz POTCAR.Pa_s.gz POTCAR.Ru_sv_GW.gz POTCAR.Ti_sv_GW.gz
POTCAR.Al_sv_GW.gz POTCAR.Cd_sv_GW.gz POTCAR.F_h_GW.gz POTCAR.H.gz POTCAR.Mo_pv.gz POTCAR.Pb_d_GW.gz POTCAR.Ru_sv.gz POTCAR.Ti_sv.gz
POTCAR.Am.gz POTCAR.Ce_GW.gz POTCAR.F_h.gz POTCAR.H_h_GW.gz POTCAR.Mo_sv_GW.gz POTCAR.Pb_d.gz POTCAR.Sb_d_GW.gz POTCAR.Tl_d_GW.gz
POTCAR.Ar_GW.gz POTCAR.Ce.gz POTCAR.Fr_sv.gz POTCAR.H_h.gz POTCAR.Mo_sv.gz POTCAR.Pb.gz POTCAR.Sb_GW.gz POTCAR.Tl_d.gz
POTCAR.Ar.gz POTCAR.Ce_h.gz POTCAR.F_s.gz POTCAR.H_s.gz POTCAR.Na.gz POTCAR.Pb_sv_GW.gz POTCAR.Sb.gz POTCAR.Tl.gz
POTCAR.As_d.gz POTCAR.C_GW.gz POTCAR.Ga_d_GW.gz POTCAR.I_GW.gz POTCAR.Na_pv.gz POTCAR.Pd_GW.gz POTCAR.Sb_sv_GW.gz POTCAR.Tl_sv_GW.gz
POTCAR.As_GW.gz POTCAR.C_GW_new.gz POTCAR.Ga_d.gz POTCAR.I.gz POTCAR.Na_sv_GW.gz POTCAR.Pd.gz POTCAR.Sc.gz POTCAR.U.gz
POTCAR.As.gz POTCAR.C.gz POTCAR.Ga_GW.gz POTCAR.In_d_GW.gz POTCAR.Na_sv.gz POTCAR.Pd_pv.gz POTCAR.Sc_sv_GW.gz POTCAR.U_s.gz
POTCAR.As_sv_GW.gz POTCAR.C_h_GW.gz POTCAR.Ga.gz POTCAR.In_d.gz POTCAR.Nb_pv.gz POTCAR.Pd_sv_GW.gz POTCAR.Sc_sv.gz POTCAR.V.gz
POTCAR.At_d_GW.gz POTCAR.C_h.gz POTCAR.Ga_h.gz POTCAR.In.gz POTCAR.Nb_sv_GW.gz POTCAR.P_GW.gz POTCAR.Se_GW.gz POTCAR.V_pv.gz
POTCAR.At.gz POTCAR.Cl_GW.gz POTCAR.Ga_sv_GW.gz POTCAR.In_sv_GW.gz POTCAR.Nb_sv.gz POTCAR.P.gz POTCAR.Se.gz POTCAR.V_sv_GW.gz
POTCAR.At_sv_GW.gz POTCAR.Cl.gz POTCAR.Ge_d_GW.gz POTCAR.Ir.gz POTCAR.Ne_GW.gz POTCAR.P_h.gz POTCAR.Se_sv_GW.gz POTCAR.V_sv.gz
POTCAR.Au_GW.gz POTCAR.Cl_h.gz POTCAR.Ge_d.gz POTCAR.Ir_sv_GW.gz POTCAR.Ne.gz POTCAR.Po_d_GW.gz POTCAR.S_GW.gz POTCAR.W.gz
POTCAR.Au.gz POTCAR.Cm.gz POTCAR.Ge_GW.gz POTCAR.I_sv_GW.gz POTCAR.Ne_s_GW.gz POTCAR.Po_d.gz POTCAR.S.gz POTCAR.W_sv_GW.gz
POTCAR.Au_sv_GW.gz POTCAR.Co_GW.gz POTCAR.Ge.gz POTCAR.K_pv.gz POTCAR.N_GW.gz POTCAR.Po.gz POTCAR.S_h.gz POTCAR.W_sv.gz
POTCAR.Ba_sv_GW.gz POTCAR.Co.gz POTCAR.Ge_h.gz POTCAR.Kr_GW.gz POTCAR.N_GW_new.gz POTCAR.Po_sv_GW.gz POTCAR.Si_GW.gz POTCAR.Xe_GW.gz
POTCAR.Ba_sv.gz POTCAR.Co_pv.gz POTCAR.Ge_sv_GW.gz POTCAR.Kr.gz POTCAR.N.gz POTCAR.Pt_GW.gz POTCAR.Si.gz POTCAR.Xe.gz
POTCAR.Be_GW.gz POTCAR.Co_sv_GW.gz POTCAR.H1.25.gz POTCAR.K_sv_GW.gz POTCAR.N_h_GW.gz POTCAR.Pt.gz POTCAR.Si_sv_GW.gz POTCAR.Xe_sv_GW.gz
POTCAR.Be.gz POTCAR.Co_sv.gz POTCAR.H1.33.gz POTCAR.K_sv.gz POTCAR.N_h.gz POTCAR.Pt_pv.gz POTCAR.Sn_d_GW.gz POTCAR.Y_sv_GW.gz
POTCAR.Be_sv_GW.gz POTCAR.Cr.gz POTCAR.H1.5.gz POTCAR.La_GW.gz POTCAR.Ni_GW.gz POTCAR.Pt_sv_GW.gz POTCAR.Sn_d.gz POTCAR.Y_sv.gz
POTCAR.Be_sv.gz POTCAR.Cr_pv.gz POTCAR.H1.66.gz POTCAR.La.gz POTCAR.Ni.gz POTCAR.Pu.gz POTCAR.Sn.gz POTCAR.Zn_GW.gz
POTCAR.B_GW.gz POTCAR.Cr_sv_GW.gz POTCAR.H1.75.gz POTCAR.La_s.gz POTCAR.Ni_pv.gz POTCAR.Pu_s.gz POTCAR.Sn_sv_GW.gz POTCAR.Zn.gz
POTCAR.B_GW_new.gz POTCAR.Cr_sv.gz POTCAR.H.25.gz POTCAR.Li_AE_GW.gz POTCAR.Ni_sv_GW.gz POTCAR.Ra_sv.gz POTCAR.Sr_sv_GW.gz POTCAR.Zn_sv_GW.gz
POTCAR.B.gz POTCAR.C_s_GW.gz POTCAR.H.33.gz POTCAR.Li_GW.gz POTCAR.Np.gz POTCAR.Rb_pv.gz POTCAR.Sr_sv.gz POTCAR.Zr_sv_GW.gz
POTCAR.B_h.gz POTCAR.C_s.gz POTCAR.H.42.gz POTCAR.Li.gz POTCAR.Np_s.gz POTCAR.Rb_sv_GW.gz POTCAR.Ta.gz POTCAR.Zr_sv.gz
POTCAR.Bi_d_GW.gz POTCAR.Cs_sv_GW.gz POTCAR.H.58.gz POTCAR.Li_sv_GW.gz POTCAR.N_s_GW.gz POTCAR.Rb_sv.gz POTCAR.Ta_pv.gz
POTCAR.Bi_d.gz POTCAR.Cs_sv.gz POTCAR.H.5.gz POTCAR.Li_sv.gz POTCAR.N_s.gz POTCAR.Re.gz POTCAR.Ta_sv_GW.gz
POTCAR.Bi_GW.gz POTCAR.Cu_GW.gz POTCAR.H.66.gz POTCAR.Mg_GW.gz POTCAR.O_GW.gz POTCAR.Re_pv.gz POTCAR.Tc.gz
POTCAR.Bi.gz POTCAR.Cu.gz POTCAR.H.75.gz POTCAR.Mg.gz POTCAR.O_GW_new.gz POTCAR.Re_sv_GW.gz POTCAR.Tc_pv.gz
POTCAR.Bi_sv_GW.gz POTCAR.Cu_pv.gz POTCAR.H_AE.gz POTCAR.Mg_pv_GW.gz POTCAR.O.gz POTCAR.Rh_GW.gz POTCAR.Tc_sv_GW.gz
POTCAR.Br_GW.gz POTCAR.Cu_sv_GW.gz POTCAR.He_GW.gz POTCAR.Mg_pv.gz POTCAR.O_h_GW.gz POTCAR.Rh.gz POTCAR.Tc_sv.gz
POTCAR.Br.gz POTCAR.Fe_GW.gz POTCAR.He.gz POTCAR.Mg_sv_GW.gz POTCAR.O_h.gz POTCAR.Rh_pv.gz POTCAR.Te_GW.gz
/home/werner/Public/hpc/vasp/pot/psp_resources/potpaw_PBE_64:
POTCAR.Ac.gz POTCAR.Ca_sv.gz POTCAR.Eu_3.gz POTCAR.He_AE.gz POTCAR.Mg.gz POTCAR.O_h_GW.gz POTCAR.Rh_GW.gz POTCAR.Tc_pv.gz
POTCAR.Ag_GW.gz POTCAR.Cd_GW.gz POTCAR.Eu.gz POTCAR.He_GW.gz POTCAR.Mg_pv_GW.gz POTCAR.O_h.gz POTCAR.Rh.gz POTCAR.Tc_sv_GW.gz
POTCAR.Ag.gz POTCAR.Cd.gz POTCAR.Eu_h.gz POTCAR.He.gz POTCAR.Mg_pv.gz POTCAR.O_s_GW.gz POTCAR.Rh_pv.gz POTCAR.Tc_sv.gz
POTCAR.Ag_pv.gz POTCAR.Cd_sv_GW.gz POTCAR.Fe_GW.gz POTCAR.Hf.gz POTCAR.Mg_sv_GW.gz POTCAR.O_s.gz POTCAR.Rh_sv_GW.gz POTCAR.Te_GW.gz
POTCAR.Ag_sv_GW.gz POTCAR.Ce_3.gz POTCAR.Fe.gz POTCAR.Hf_pv.gz POTCAR.Mg_sv.gz POTCAR.Os.gz POTCAR.Rn_d_GW.gz POTCAR.Te.gz
POTCAR.Al_GW.gz POTCAR.Ce_GW.gz POTCAR.Fe_pv.gz POTCAR.Hf_sv_GW.gz POTCAR.Mn_GW.gz POTCAR.Os_pv.gz POTCAR.Rn.gz POTCAR.Te_sv_GW.gz
POTCAR.Al.gz POTCAR.Ce.gz POTCAR.Fe_sv_GW.gz POTCAR.Hf_sv.gz POTCAR.Mn.gz POTCAR.Os_sv_GW.gz POTCAR.Rn_sv_GW.gz POTCAR.Th.gz
POTCAR.Al_sv_GW.gz POTCAR.Ce_h.gz POTCAR.Fe_sv.gz POTCAR.Hg.gz POTCAR.Mn_pv.gz POTCAR.Pa.gz POTCAR.Ru.gz POTCAR.Th_s.gz
POTCAR.Am.gz POTCAR.Cf.gz POTCAR.F_GW.gz POTCAR.Hg_sv_GW.gz POTCAR.Mn_sv_GW.gz POTCAR.Pa_s.gz POTCAR.Ru_pv.gz POTCAR.Ti.gz
POTCAR.Ar_GW.gz POTCAR.C_GW.gz POTCAR.F_GW_new.gz POTCAR.H_GW.gz POTCAR.Mn_sv.gz POTCAR.Pb_d_GW.gz POTCAR.Ru_sv_GW.gz POTCAR.Ti_pv.gz
POTCAR.Ar.gz POTCAR.C_GW_new.gz POTCAR.F.gz POTCAR.H_GW_new.gz POTCAR.Mo.gz POTCAR.Pb_d.gz POTCAR.Ru_sv.gz POTCAR.Ti_sv_GW.gz
POTCAR.As_d.gz POTCAR.C.gz POTCAR.F_h_GW.gz POTCAR.H.gz POTCAR.Mo_pv.gz POTCAR.Pb.gz POTCAR.Sb_d_GW.gz POTCAR.Ti_sv.gz
POTCAR.As_GW.gz POTCAR.C_h_GW.gz POTCAR.F_h.gz POTCAR.H_h_GW.gz POTCAR.Mo_sv_GW.gz POTCAR.Pb_sv_GW.gz POTCAR.Sb_GW.gz POTCAR.Tl_d_GW.gz
POTCAR.As.gz POTCAR.C_h.gz POTCAR.Fr_sv.gz POTCAR.H_h.gz POTCAR.Mo_sv.gz POTCAR.Pd_GW.gz POTCAR.Sb.gz POTCAR.Tl_d.gz
POTCAR.As_sv_GW.gz POTCAR.Cl_GW.gz POTCAR.F_s.gz POTCAR.Ho_3.gz POTCAR.Na.gz POTCAR.Pd.gz POTCAR.Sb_sv_GW.gz POTCAR.Tl.gz
POTCAR.At_d_GW.gz POTCAR.Cl.gz POTCAR.Ga_d_GW.gz POTCAR.Ho.gz POTCAR.Na_pv.gz POTCAR.Pd_pv.gz POTCAR.Sc.gz POTCAR.Tl_sv_GW.gz
POTCAR.At.gz POTCAR.Cl_h.gz POTCAR.Ga_d.gz POTCAR.Ho_h.gz POTCAR.Na_sv_GW.gz POTCAR.Pd_sv_GW.gz POTCAR.Sc_sv_GW.gz POTCAR.Tm_3.gz
POTCAR.At_sv_GW.gz POTCAR.Cm.gz POTCAR.Ga_GW.gz POTCAR.H_s.gz POTCAR.Na_sv.gz POTCAR.P_GW.gz POTCAR.Sc_sv.gz POTCAR.Tm.gz
POTCAR.Au_GW.gz POTCAR.Co_GW.gz POTCAR.Ga.gz POTCAR.I_GW.gz POTCAR.Nb_pv.gz POTCAR.P.gz POTCAR.Se_GW.gz POTCAR.Tm_h.gz
POTCAR.Au.gz POTCAR.Co.gz POTCAR.Ga_h.gz POTCAR.I.gz POTCAR.Nb_sv_GW.gz POTCAR.P_h.gz POTCAR.Se.gz POTCAR.U.gz
POTCAR.Au_sv_GW.gz POTCAR.Co_pv.gz POTCAR.Ga_sv_GW.gz POTCAR.In_d_GW.gz POTCAR.Nb_sv.gz POTCAR.Pm_3.gz POTCAR.Se_sv_GW.gz POTCAR.U_s.gz
POTCAR.Ba_sv_GW.gz POTCAR.Co_sv_GW.gz POTCAR.Gd_3.gz POTCAR.In_d.gz POTCAR.Nd_3.gz POTCAR.Pm.gz POTCAR.S_GW.gz POTCAR.V.gz
POTCAR.Ba_sv.gz POTCAR.Co_sv.gz POTCAR.Gd.gz POTCAR.In.gz POTCAR.Nd.gz POTCAR.Pm_h.gz POTCAR.S.gz POTCAR.V_pv.gz
POTCAR.Be_GW.gz POTCAR.Cr.gz POTCAR.Gd_h.gz POTCAR.In_sv_GW.gz POTCAR.Nd_h.gz POTCAR.Po_d_GW.gz POTCAR.S_h.gz POTCAR.V_sv_GW.gz
POTCAR.Be.gz POTCAR.Cr_pv.gz POTCAR.Ge_d_GW.gz POTCAR.Ir.gz POTCAR.Ne_GW.gz POTCAR.Po_d.gz POTCAR.Si_GW.gz POTCAR.V_sv.gz
POTCAR.Be_sv_GW.gz POTCAR.Cr_sv_GW.gz POTCAR.Ge_d.gz POTCAR.Ir_sv_GW.gz POTCAR.Ne.gz POTCAR.Po.gz POTCAR.Si.gz POTCAR.W.gz
POTCAR.Be_sv.gz POTCAR.Cr_sv.gz POTCAR.Ge_GW.gz POTCAR.I_sv_GW.gz POTCAR.Ne_s_GW.gz POTCAR.Po_sv_GW.gz POTCAR.Si_sv_GW.gz POTCAR.W_sv_GW.gz
POTCAR.B_GW.gz POTCAR.C_s_GW.gz POTCAR.Ge.gz POTCAR.K_pv.gz POTCAR.N_GW.gz POTCAR.Pr_3.gz POTCAR.Sm_3.gz POTCAR.W_sv.gz
POTCAR.B_GW_new.gz POTCAR.C_s.gz POTCAR.Ge_h.gz POTCAR.Kr_GW.gz POTCAR.N_GW_new.gz POTCAR.Pr.gz POTCAR.Sm.gz POTCAR.Xe_GW.gz
POTCAR.B.gz POTCAR.Cs_sv_GW.gz POTCAR.Ge_sv_GW.gz POTCAR.Kr.gz POTCAR.N.gz POTCAR.Pr_h.gz POTCAR.Sm_h.gz POTCAR.Xe.gz
POTCAR.B_h_GW.gz POTCAR.Cs_sv.gz POTCAR.H1.25.gz POTCAR.K_sv_GW.gz POTCAR.N_h_GW.gz POTCAR.Pt_GW.gz POTCAR.Sn_d_GW.gz POTCAR.Xe_sv_GW.gz
POTCAR.B_h.gz POTCAR.Cu_GW.gz POTCAR.H1.33.gz POTCAR.K_sv.gz POTCAR.N_h.gz POTCAR.Pt.gz POTCAR.Sn_d.gz POTCAR.Yb_2.gz
POTCAR.Bi_d_GW.gz POTCAR.Cu.gz POTCAR.H1.5.gz POTCAR.La_GW.gz POTCAR.Ni_GW.gz POTCAR.Pt_pv.gz POTCAR.Sn.gz POTCAR.Yb_3.gz
POTCAR.Bi_d.gz POTCAR.Cu_pv.gz POTCAR.H1.66.gz POTCAR.La.gz POTCAR.Ni.gz POTCAR.Pt_sv_GW.gz POTCAR.Sn_sv_GW.gz POTCAR.Yb.gz
POTCAR.Bi_GW.gz POTCAR.Cu_sv_GW.gz POTCAR.H1.75.gz POTCAR.La_s.gz POTCAR.Ni_pv.gz POTCAR.Pu.gz POTCAR.Sr_sv_GW.gz POTCAR.Yb_h.gz
POTCAR.Bi.gz POTCAR.Dy_3.gz POTCAR.H.25.gz POTCAR.Li_AE_GW.gz POTCAR.Ni_sv_GW.gz POTCAR.Pu_s.gz POTCAR.Sr_sv.gz POTCAR.Y_sv_GW.gz
POTCAR.Bi_sv_GW.gz POTCAR.Dy.gz POTCAR.H.33.gz POTCAR.Li_GW.gz POTCAR.Np.gz POTCAR.Ra_sv.gz POTCAR.Ta.gz POTCAR.Y_sv.gz
POTCAR.Br_GW.gz POTCAR.Dy_h.gz POTCAR.H.42.gz POTCAR.Li.gz POTCAR.Np_s.gz POTCAR.Rb_pv.gz POTCAR.Ta_pv.gz POTCAR.Zn_GW.gz
POTCAR.Br.gz POTCAR.Er_2.gz POTCAR.H.58.gz POTCAR.Li_sv_GW.gz POTCAR.N_s_GW.gz POTCAR.Rb_sv_GW.gz POTCAR.Ta_sv_GW.gz POTCAR.Zn.gz
POTCAR.Br_sv_GW.gz POTCAR.Er_3.gz POTCAR.H.5.gz POTCAR.Li_sv.gz POTCAR.N_s.gz POTCAR.Rb_sv.gz POTCAR.Tb_3.gz POTCAR.Zn_sv_GW.gz
POTCAR.B_s.gz POTCAR.Er.gz POTCAR.H.66.gz POTCAR.Lu_3.gz POTCAR.O_GW.gz POTCAR.Re.gz POTCAR.Tb.gz POTCAR.Zr_sv_GW.gz
POTCAR.Ca_pv.gz POTCAR.Er_h.gz POTCAR.H.75.gz POTCAR.Lu.gz POTCAR.O_GW_new.gz POTCAR.Re_pv.gz POTCAR.Tb_h.gz POTCAR.Zr_sv.gz
POTCAR.Ca_sv_GW.gz POTCAR.Eu_2.gz POTCAR.H_AE.gz POTCAR.Mg_GW.gz POTCAR.O.gz POTCAR.Re_sv_GW.gz POTCAR.Tc.gz
```
The test script is as follows:
```python
$ cat test-pmg-potcar.py
from pymatgen.ext.matproj import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet
# No need to specify the API key, assuming it's configured via the .pmgrc.yaml file
with MPRester() as mpr:
# Requesting structure data for CdS from the Materials Project
structure = mpr.get_structure_by_material_id("mp-2469")
# Initializing MPRelaxSet with the obtained structure, this will prepare the necessary input files for VASP calculation
relax_set = MPRelaxSet(structure)
try:
# Attempting to access the POTCAR
potcar = relax_set.potcar
print("Successfully retrieved the POTCAR. Here are some details:")
print(potcar)
except Exception as e:
print(f"Error occurred while attempting to retrieve the POTCAR: {e}")
```
The test result is as follows:
```shell
$ python test-pmg-potcar.py
/home/werner/.pyenv/versions/datasci/lib/python3.11/site-packages/mp_api/client/mprester.py:182: UserWarning: mpcontribs-client not installed. Install the package to query MPContribs data, or construct pourbaix diagrams: 'pip install mpcontribs-client'
warnings.warn(
Retrieving MaterialsDoc documents: 100%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 1/1 [00:00<00:00, 12905.55it/s]
Error occurred while attempting to retrieve the POTCAR: You do not have the right POTCAR with functional='PBE' and symbol='Cd' in your PMG_VASP_PSP_DIR='/home/werner/Public/hpc/vasp/pot/psp_resources'. Paths tried: ['/home/werner/Public/hpc/vasp/pot/psp_resources/POT_GGA_PAW_PBE/POTCAR.Cd', '/home/werner/Public/hpc/vasp/pot/psp_resources/POT_GGA_PAW_PBE/Cd/POTCAR']
```
Some additional info:
```shell
(datasci) werner@X10DAi:~$ pip list | grep pymatgen
pymatgen 2024.1.27
pymatgen-db 2023.7.18
[notice] A new release of pip is available: 23.3.1 -> 23.3.2
[notice] To update, run: python3.11 -m pip install --upgrade pip
(datasci) werner@X10DAi:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.3 LTS
Release: 22.04
Codename: jammy
```
However, according to the guidance [here](https://pymatgen.org/installation.html#potcar-setup), I can't see where I went wrong in my configuration. Any tips/comments would be helpful.
Regards,
Zhao
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PR_kwDOACgets5l9X9D
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Minor update to avoid deprecation warning
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[] | 2024-02-04T22:29:38
| 2024-02-05T06:02:07
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2024-02-05T06:02:07Z
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This is just a _tiny_ update to avoid the newly-added deprecation warnings for `get_vasp_input()`.
`get_vasp_input()` is still used in `DictSet.write_input()`, but should be changed to `get_input_set()` in line with the deprection warning (as implemented here).
PS: The recent updates to the VASP sets code is very nice @utf!
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VASP IO `copy()` methods
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[
"Thanks @janosh! Question for @shyuep: @janosh and I were discussing if it makes more sense to define the `self.copy` method for `MSONable` - do you think it makes more sense to define the `copy` method for specific classes that inherit from `MSONable`, or for `MSONable` itself?",
"Depends on how general the copy method is. If it is generic and uses the MSONAble capabilities to do the copy, then it makes sense.",
"Just an addendum that when I say \"makes sense\", it means it makes sense for any MSONable class, not just VASP io related stuff."
] | 2024-02-05T06:37:40
| 2024-02-08T09:36:06
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2024-02-08T09:36:05Z
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MEMBER
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as pointed out by @esoteric-ephemera, calling `.copy()` on VASP IO classes like `Incar` and `VaspInput` returns a dict rather than a new instance of the class as most users would expect. this PR adds explicit `copy()` methods to minimize user surprise.
@esoteric-ephemera that mixin snippet i sent doesn't work as the `__init__` signatures of IO classes are too different. for the record, we considered defining
```py
class CopyableMixin:
def copy(self):
return type(self)(self)
```
and making all Vasp IO classes inherit from it
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2024-02-05T19:26:07Z
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CONTRIBUTOR
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updates:
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I_kwDOACgets5-VPF3
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Vasprun get_potcars fails if no explicit directories in file path
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[
"Thanks @bfield1, this is a duplicate of #3586, and should be fixed in #3587. Can you pip install from git and see if this issue is resolved (`pip install git+https://github.com/materialsproject/pymatgen.git`)?",
"@esoteric-ephemera Ah, yes, the latest development version of pymatgen fixes this. In my haste I must have forgotten to check the existing issues for this bug. Apologies for the bother.",
"No worries I'm glad to hear this is fixed!"
] | 2024-02-05T21:34:50
| 2024-02-06T19:15:01
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2024-02-06T18:59:51Z
|
CONTRIBUTOR
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### Python version
3.9.18
### Pymatgen version
2024.1.27
### Operating system version
MacOS 13.6.4
### Current behavior
When loading a Vasprun using a 'vasprun.xml' file in the present working directory (i.e. `Vasprun('vasprun.xml')`), it throws a FileNotFoundError when it attempts to `get_potcar`. The traceback is below.
Specifically, in `get_potcar`, it uses `os.path.split` to get the directory of the filename. But in this case, that is an empty string. The code then fails in the next line, when it attempts to evaluate `os.listdir('')`.
If I instead call `Vasprun('./vasprun.xml')` or `Vasprun('vasprun.xml', parse_potcar_file=False)` the code runs without error.
```python3
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[2], line 1
----> 1 Vasprun('vasprun.xml')
File ~/anaconda3/envs/ifermi/lib/python3.9/site-packages/pymatgen/io/vasp/outputs.py:296, in Vasprun.__init__(self, filename, ionic_step_skip, ionic_step_offset, parse_dos, parse_eigen, parse_projected_eigen, parse_potcar_file, occu_tol, separate_spins, exception_on_bad_xml)
293 self.nionic_steps = len(self.ionic_steps)
295 if parse_potcar_file:
--> 296 self.update_potcar_spec(parse_potcar_file)
297 self.update_charge_from_potcar(parse_potcar_file)
299 if self.incar.get("ALGO") not in ["CHI", "BSE"] and not self.converged and self.parameters.get("IBRION") != 0:
File ~/anaconda3/envs/ifermi/lib/python3.9/site-packages/pymatgen/io/vasp/outputs.py:1054, in Vasprun.update_potcar_spec(self, path)
1046 def update_potcar_spec(self, path):
1047 """
1048 Args:
1049 path: Path to search for POTCARs
(...)
1052 Potcar spec from path.
1053 """
-> 1054 if potcar := self.get_potcars(path):
1055 self.potcar_spec = [
1056 {"titel": sym, "hash": ps.md5_header_hash, "summary_stats": ps._summary_stats}
1057 for sym in self.potcar_symbols
1058 for ps in potcar
1059 if ps.symbol == sym.split()[1]
1060 ]
File ~/anaconda3/envs/ifermi/lib/python3.9/site-packages/pymatgen/io/vasp/outputs.py:1010, in Vasprun.get_potcars(self, path)
1007 else:
1008 search_path = os.path.split(self.filename)[0] if path is True else str(path)
1009 potcar_paths = [
-> 1010 f"{search_path}/{fn}" for fn in os.listdir(search_path) if fn.startswith("POTCAR") and ".spec" not in fn
1011 ]
1013 for potcar_path in potcar_paths:
1014 try:
FileNotFoundError: [Errno 2] No such file or directory: ''
```
### Expected Behavior
`Vasprun.get_potcar` should be able to handle the case where `self.filename` is a relative path with no directories.
This could be done by adding a line `if search_path == '': search_path = None`. This will then work as expected, because `os.listdir(None)` acts as if the argument were the present working directory.
### Minimal example
In a directory containing a `vasprun.xml` file...
```Python
from pymatgen.io.vasp.outputs import Vasprun
Vasprun('vasprun.xml')
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets5-Wb2K
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|
Bug on DiscretizeOccupanciesTransformation
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[] | 2024-02-06T02:27:04
| 2024-02-06T02:27:04
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NONE
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### Python version
Python 3.11.5
### Pymatgen version
2023.12.18
### Operating system version
_No response_
### Current behavior
Class DiscretizeOccupanciesTransformation in transformation/standard_transformation doesn't work correctly. discretize is not performed.
### Expected Behavior
It return the input structure including old species
species = [dict(sp) for sp in structure.species_and_occu]
for sp in species:
for k in sp:
old_occ = sp[k]
new_occ = float(Fraction(old_occ).limit_denominator(self.max_denominator))
if self.fix_denominator:
new_occ = around(old_occ * self.max_denominator) / self.max_denominator
if round(abs(old_occ - new_occ), 6) > self.tol:
raise RuntimeError("Cannot discretize structure within tolerance!")
sp[k] = new_occ
return Structure(structure.lattice, species, structure.frac_coords)
Below code might return the structure as expected
species = [dict(sp) for sp in structure.species_and_occu]
new_species = []
for sp in species:
for k in sp:
old_occ = sp[k]
new_occ = float(Fraction(old_occ).limit_denominator(self.max_denominator))
if self.fix_denominator:
print('aaa')
new_occ = around(old_occ * self.max_denominator) / self.max_denominator
if round(abs(old_occ - new_occ), 6) > self.tol:
raise RuntimeError("Cannot discretize structure within tolerance!")
sp[k] = new_occ
new_species.append(sp)
return Structure(structure.lattice, new_species, structure.frac_coords)
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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Bump nokogiri from 1.15.3 to 1.16.2 in /docs
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[
"CI doesn't trigger on file changes in `docs/`"
] | 2024-02-06T03:37:24
| 2024-02-12T05:45:32
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2024-02-12T05:45:07Z
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CONTRIBUTOR
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Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.15.3 to 1.16.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/releases">nokogiri's releases</a>.</em></p>
<blockquote>
<h2>v1.16.2 / 2024-02-04</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to address CVE-2024-25062. See <a href="https://github.com/sparklemotion/nokogiri/security/advisories/GHSA-xc9x-jj77-9p9j">GHSA-xc9x-jj77-9p9j</a> for more information.</li>
</ul>
<h3>Dependencies</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to <a href="https://gitlab.gnome.org/GNOME/libxml2/-/releases/v2.12.5">v2.12.5</a> from v2.12.4. (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
</ul>
<hr />
<p>sha256 checksums:</p>
<pre><code>69ba15d2a2498324489ed63850997f0b8f684260114ea81116d3082f16551d2d nokogiri-1.16.2-aarch64-linux.gem
6a05ce42e3587a40cf8936ece0beaa5d32922254215d2e8cf9ad40588bb42e57 nokogiri-1.16.2-arm-linux.gem
c957226c8e36b31be6a3afb8602e2128282bf8b40ea51016c4cd21aa2608d3f8 nokogiri-1.16.2-arm64-darwin.gem
122652bfc338cd8a54a692ac035e245e41fd3b8283299202ca26e7a7d50db310 nokogiri-1.16.2-java.gem
7344b5072ca69fc5bedb61cb01a3b765b93a27aae5a2a845c2ba7200e4345074 nokogiri-1.16.2-x64-mingw-ucrt.gem
a2a5e184a424111a0d5b77947986484920ad708009c667f061e8d02035c562dd nokogiri-1.16.2-x64-mingw32.gem
833efddeb51a6c2c9f6356295623c2b2e0d50050d468695c59bd929162953323 nokogiri-1.16.2-x86-linux.gem
e67fc0418dffaff9dc8b1dc65f0605282c3fee9488832d0223b620b4319e0b53 nokogiri-1.16.2-x86-mingw32.gem
5def799e5f139f21a79d7cf71172313a7b6fb0e4b2a31ab9bd5d4ad305994539 nokogiri-1.16.2-x86_64-darwin.gem
5b146240ac6ec6c40fd4367623e74442bca45a542bd3282b1d4d18b07b8e5dfe nokogiri-1.16.2-x86_64-linux.gem
68922ee5cde27497d995c46f2821957bae961947644eed2822d173daf7567f9c nokogiri-1.16.2.gem
</code></pre>
<h2>v1.16.1 / 2024-02-03</h2>
<h3>Dependencies</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to <a href="https://gitlab.gnome.org/GNOME/libxml2/-/releases/v2.12.4">v2.12.4</a> from v2.12.3. (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>[CRuby] <code>XML::Reader</code> defaults the encoding to UTF-8 if it's not specified in either the document or as a method parameter. Previously non-ASCII characters were serialized as NCRs in this case. <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/2891">#2891</a> (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
<li>[CRuby] Restored support for compilation by GCC versions earlier than 4.6, which was broken in v1.15.0 (540e9aee). <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3090">#3090</a> (<a href="https://github.com/adfoster-r7"><code>@βadfoster-r7</code></a>)</li>
<li>[CRuby] Patched upstream libxml2 to allow parsing HTML5 in the context of a namespaced node (e.g., foreign content like MathML). [#3112, <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3116">#3116</a>] (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
<li>[CRuby] Fixed a small memory leak in libgumbo (HTML5 parser) when the maximum tree depth limit is hit. [#3098, <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3100">#3100</a>] (<a href="https://github.com/stevecheckoway"><code>@βstevecheckoway</code></a>)</li>
</ul>
<hr />
<p>sha256 checksums:</p>
<pre><code>a541f35e5b9798a0c97300f9ee18f4217da2a2945a6d5499e4123b9018f9cafc nokogiri-1.16.1-aarch64-linux.gem
6b82affd195000ab2f9c36cc08744ec2d2fcf6d8da88d59a2db67e83211f7c69 nokogiri-1.16.1-arm-linux.gem
</tr></table>
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md">nokogiri's changelog</a>.</em></p>
<blockquote>
<h2>v1.16.2 / 2024-02-04</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to address CVE-2024-25062. See <a href="https://github.com/sparklemotion/nokogiri/security/advisories/GHSA-xc9x-jj77-9p9j">GHSA-xc9x-jj77-9p9j</a> for more information.</li>
</ul>
<h3>Dependencies</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to <a href="https://gitlab.gnome.org/GNOME/libxml2/-/releases/v2.12.5">v2.12.5</a> from v2.12.4. (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
</ul>
<h2>v1.16.1 / 2024-02-03</h2>
<h3>Dependencies</h3>
<ul>
<li>[CRuby] Vendored libxml2 is updated to <a href="https://gitlab.gnome.org/GNOME/libxml2/-/releases/v2.12.4">v2.12.4</a> from v2.12.3. (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>[CRuby] <code>XML::Reader</code> defaults the encoding to UTF-8 if it's not specified in either the document or as a method parameter. Previously non-ASCII characters were serialized as NCRs in this case. <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/2891">#2891</a> (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
<li>[CRuby] Restored support for compilation by GCC versions earlier than 4.6, which was broken in v1.15.0 (540e9aee). <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3090">#3090</a> (<a href="https://github.com/adfoster-r7"><code>@βadfoster-r7</code></a>)</li>
<li>[CRuby] Patched upstream libxml2 to allow parsing HTML5 in the context of a namespaced node (e.g., foreign content like MathML). [#3112, <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3116">#3116</a>] (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</li>
<li>[CRuby] Fixed a small memory leak in libgumbo (HTML5 parser) when the maximum tree depth limit is hit. [#3098, <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3100">#3100</a>] (<a href="https://github.com/stevecheckoway"><code>@βstevecheckoway</code></a>)</li>
</ul>
<h2>v1.16.0 / 2023-12-27</h2>
<h3>Notable Changes</h3>
<h4>Ruby</h4>
<p>This release introduces native gem support for Ruby 3.3.</p>
<p>This release ends support for Ruby 2.7, for which <a href="https://www.ruby-lang.org/en/downloads/branches/">upstream support ended 2023-03-31</a>.</p>
<h4>Pattern matching</h4>
<p>This version marks <em>official support</em> for the pattern matching API in <code>XML::Attr</code>, <code>XML::Document</code>, <code>XML::DocumentFragment</code>, <code>XML::Namespace</code>, <code>XML::Node</code>, and <code>XML::NodeSet</code> (and their subclasses), originally introduced as an experimental feature in v1.14.0. (<a href="https://github.com/flavorjones"><code>@βflavorjones</code></a>)</p>
<p>Documentation on what can be matched:</p>
<ul>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/Attr.html?h=deconstruct#method-i-deconstruct_keys"><code>XML::Attr#deconstruct_keys</code></a></li>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/Document.html?h=deconstruct#method-i-deconstruct_keys"><code>XML::Document#deconstruct_keys</code></a></li>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/Namespace.html?h=deconstruct+namespace#method-i-deconstruct_keys"><code>XML::Namespace#deconstruct_keys</code></a></li>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/Node.html?h=deconstruct#method-i-deconstruct_keys"><code>XML::Node#deconstruct_keys</code></a></li>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/DocumentFragment.html?h=deconstruct#method-i-deconstruct"><code>XML::DocumentFragment#deconstruct</code></a></li>
<li><a href="https://nokogiri.org/rdoc/Nokogiri/XML/NodeSet.html?h=deconstruct#method-i-deconstruct"><code>XML::NodeSet#deconstruct</code></a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/673756fdd69d1036874b7d7250cc38a51fd4d7b8"><code>673756f</code></a> version bump to v1.16.2</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/74ffd67a8efb9972657e5c4625fd8419bbccbe06"><code>74ffd67</code></a> dep: update libxml to 2.12.5 (branch v1.16.x) (<a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3122">#3122</a>)</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/0d4018dc7009580659c101fc41efb3babcfec229"><code>0d4018d</code></a> dep: update libxml2 to v2.12.5</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/f33a25f4378df33912ebc6b4ebc0f9e8e80ddfa8"><code>f33a25f</code></a> dep: remove patch from <a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3112">#3112</a> which has been released upstream</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/e99416896a182bc520a7940bbe286ec33597ab2b"><code>e994168</code></a> version bump to v1.16.1</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/77ea2f228c20e79c848ca2906813ea5b5010281b"><code>77ea2f2</code></a> dev: add files to manifest ignore list</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/756f27c6b7a23294d84bdcca5e03a639d0dd7421"><code>756f27c</code></a> build(deps): bump actions/{download,upload}-artifact from 3 to 4</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/464f8d41eb73ca9c6dae0b366afcf5f4e8bff342"><code>464f8d4</code></a> .gitignore: clangd-related files</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/2beeb960691df28dd5ebf828192c65b60250670f"><code>2beeb96</code></a> doc: update CHANGELOG</li>
<li><a href="https://github.com/sparklemotion/nokogiri/commit/a26536d7a41fd40c52940e165bb5a4f6b4c39662"><code>a26536d</code></a> fix: apply upstream patch for in-context parsing (<a href="https://redirect.github.com/sparklemotion/nokogiri/issues/3116">#3116</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/sparklemotion/nokogiri/compare/v1.15.3...v1.16.2">compare view</a></li>
</ul>
</details>
<br />
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You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/materialsproject/pymatgen/network/alerts).
</details>
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I_kwDOACgets5-dgKG
| 3,607
|
Line mode and reciprocal density bug int MPHSEBSSet
|
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[
"Hi @fraricci, thanks for bringing this up. \r\n\r\nIn the older version of `MPHSEBSSet`, setting `user_kpoints_settings={\"reciprocal_density\":100}` wouldn't have any effect. It was simply ignored.\r\n\r\nIn the new version of the input sets, the `user_kpoints_settings` is strictly respected. In this case you are only asking for uniform k-points, hence no line mode k-points none are generated. If you want to produce line mode k-points you'd have to do:\r\n\r\n```python\r\nmpset = MPHSEBSSet(\r\n st, \r\n mode=\"Line\",\r\n user_kpoints_settings={\"reciprocal_density\":100, \"zero_weighted_line_density\": 20}\r\n)\r\n```\r\n\r\nThe reason for this is that I wanted to always respect `user_*_settings`. If for some reason you want to use the rest of the HSE line mode settings but with a uniform mesh, then this should be possible. This is in contrast to the older input sets where `user_kpoints_settings` was completely ignored in `MPHSEBSSet`.\r\n\r\nThe recommendation is to simply configure everything using the init parameters, which will configure the k-points for you. For completeness, these are:\r\n\r\n```python\r\nMPHSEBSSet(\r\n reciprocal_density=50, # controls density of weighted uniform mesh for all modes\r\n kpoints_line_density=20, # controls density of zero weighted line k-points for mode=line\r\n zero_weighted_reciprocal_density=100 # controls density of zero weighted uniform for mode=uniform_dense\r\n)\r\n```",
"Hi @utf , thanks for the explanation here.\r\n\r\nThough, I still find this behavior a little obscure for these reasons:\r\n1) If I want to use the `user_kpoints_setting` I need to set all the keys and not just the one I want to change. Shouldn't just take the rest from the init params?\r\n2) Apparently, when only a single key is set, `reciprocal_density` in this case, the mode is changed internally and not transparently.\r\n3) The key `zero_weighted_line_density` spells differently from the init param `kpoints_line_density` but they represent the same thing. Shouldn't be called the same? This is something I found also in other sets...\r\n\r\nAnyway, I agree the best way is to just use the init parameters."
] | 2024-02-06T21:04:20
| 2024-02-08T17:29:21
|
CONTRIBUTOR
|
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### Python version
python 3.11
### Pymatgen version
2024.1.27
### Operating system version
_No response_
### Current behavior
In: `mpset = MPHSEBSSet(st, mode="Line",reciprocal_density=100)`
Out: Correct list of kpoints
In: `mpset = MPHSEBSSet(st, mode="Line",user_kpoints_settings={"reciprocal_density":100})`
Out:
```
pymatgen with grid density = 1239 / number of atoms
0
Gamma
2 2 2
```
### Expected Behavior
In: `mpset = MPHSEBSSet(st, mode="Line",user_kpoints_settings={"reciprocal_density":100})`
Out: Correct list of kpoints
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets5mTAGO
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chore: fix a typo
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[] | 2024-02-07T19:04:23
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2024-02-07T19:10:47Z
|
CONTRIBUTOR
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## Summary
Fixes: fix a funny typo that I encountered while working with the package
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PR_kwDOACgets5mTEsV
| 3,610
|
Add `SiteCollection.reduced_formula` property
|
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[] | 2024-02-07T19:18:13
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2024-02-07T19:33:41Z
|
MEMBER
|
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just a convenience method to shorten frequently occurring
```py
struct.composition.reduced_formula -> struct.reduced_formula
```
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PR_kwDOACgets5mWOhC
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|
Add `Entry.(formula|reduced_formula)`
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[] | 2024-02-08T08:46:16
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2024-02-08T09:01:01Z
|
MEMBER
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similar to #3610 but for `Entry`
4e094cb78 add properties formula and reduced_formula to Entry
b342ab1b6 refactor
86180a0d9 Add tests for formula and reduced formula properties
1bb9af8a9 composition.reduced_formula -> reduced_formula
115d45e65 composition.formula -> formula
|
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I_kwDOACgets5-sE2t
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Should we let the `StructureMatcher` method work at the affine space group classification level instead of the crystallographic space group classification level?
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[
"this sounds interesting and i can see why you might want to allow only orientation-preserving rotations. but i don't have enough background to say why the current behavior was chosen in the first place. potentially there were reasons i'm unaware of. hoping others with more context can chime in",
"Is this the same issue encountered [here](http://aflowlib.org/prototype-encyclopedia/enantiomorph_info.html) with judging equivalence of structures with enantiomorphic space groups?",
"@mkhorton Yes. This is the exact case in a 3-dimensional space. But in higher dimensions, this is a more complicated problem to solve and I have given a [gap implementation](https://github.com/hongyi-zhao/CrystKit/blob/e4816b6292ad11361342115b560aa4fdd175bb7f/gap/CrystKit.gi#L1055) based on [the algorithm](https://doi.org/10.1107/S0108767303004161) suggested by Bernd.",
"I think it is best to consider that once you get to this kind of granularity of equivalence, the deviations in total energies may be below the threshold of chemical accuracy [1](https://doi.org/10.1016/0375-9601(79)90647-9) [2](https://www.pnas.org/doi/full/10.1073/pnas.96.8.4252)- even by the standards of the highest levels of theory. \r\n\r\nWith that said, there are in fact very important observable differences in chiral crystals. Circular dichroism and (reciprocal space) topology being two properties that are sensitive to such symmetries. [3](https://www.mdpi.com/1996-1944/15/17/5812)\r\n\r\nSolving this problem is incredibly interesting, but I am unsure how much it will benefit the users of pymatgen, especially if this routine incurs additional additional computational overhead. And naturally, this new feature will require additional maintenance that requires a niche expertise. \r\n\r\nI think the best thing, which might actually help address #2593 , is to diversify the routines offered in StructureMatcher ? It would allow for the users to determine what degree of specificity they really care about and perhaps that can reduce the computational load if they are looking for a course grain matching. \r\n\r\nBut I suppose we have to wonder if readily available solutions exist elsewhere, then does pymatgen bear this responsibility? ",
"thanks @wladerer, that's a lot of helpful context! π \r\n\r\n> I think the best thing, which might actually help address https://github.com/materialsproject/pymatgen/issues/2593, is to diversify the routines offered in StructureMatcher?\r\n\r\ni'm open to that. sounds like that's the most actionable way forward to address #2593 and potentially even this issue"
] | 2024-02-08T15:40:13
| 2024-02-22T12:20:19
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CONTRIBUTOR
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See my following testing:
```python
$ python ./pymatgenStructureMatcher.py 5/POSCAR 6/POSCAR -s0.53 -l 0.01 -a5
Structures are similar: True
Transformation Information:
(array([[ 1, 0, 0],
[ 0, -1, 0],
[ 0, 1, 1]]), array([-4.07660017e-17, -4.16198382e-01, 3.28125000e-01]), [3, 58, 59, 60, 33, 8, 0, 1, 56, 12, 13, 68, 25, 70, 71, 63, 10, 11, 21, 22, 23, 24, 15, 44, 36, 37, 20, 30, 49, 32, 7, 34, 35, 27, 28, 47, 48, 40, 41, 42, 43, 26, 18, 19, 46, 39, 31, 50, 51, 52, 53, 45, 38, 29, 64, 4, 5, 6, 61, 62, 54, 55, 2, 66, 67, 14, 69, 16, 17, 9, 57, 65, 75, 102, 77, 78, 79, 80, 72, 73, 101, 93, 85, 86, 87, 88, 98, 81, 91, 83, 84, 94, 95, 96, 97, 89, 90, 82, 92, 76, 103, 104, 105, 106, 107, 99, 100, 74, 144, 145, 146, 138, 139, 140, 147, 148, 149, 141, 142, 143, 123, 124, 125, 108, 109, 110, 126, 127, 128, 111, 112, 113, 129, 130, 131, 114, 115, 116, 117, 118, 119, 132, 133, 134, 120, 121, 122, 135, 136, 137, 186, 187, 188, 174, 175, 176, 189, 190, 191, 177, 178, 179, 159, 160, 161, 150, 151, 152, 153, 154, 155, 162, 163, 164, 156, 157, 158, 165, 166, 167, 180, 181, 182, 168, 169, 170, 183, 184, 185, 171, 172, 173])
```
As you can see, according to the [Classification systems](https://en.wikipedia.org/wiki/Space_group#Classification_systems) of the space group, the `StructureMatcher` method implemented currently works at the affine space group classification level instead of the crystallographic space group classification level, aka, it permits the non-proper rotation which doesn't preserve [orientation](https://en.wikipedia.org/wiki/Orientation_(mathematics)).
But as Bernd pointed out [here](https://www.math.ru.nl/~souvi/krist_09/cryst.pdf) on page 35, as shown below:
> Since crystals occur in physical space and physical space can only be transformed by orientation preserving mappings, space groups are only regarded as equivalent if they are conjugate by an orientation preserving affine mapping, i.e. by an affine mapping that has linear part with positive determinant.
So, should we let the `StructureMatcher` method work at the affine space group classification level instead of the crystallographic space group classification level?
Attached are all the test files mentioned above. Please check them.
[test_StructureMatcher.zip](https://github.com/materialsproject/pymatgen/files/14211296/test_StructureMatcher.zip)
See [here](https://github.com/materialsproject/pymatgen/issues/3597) for the related discussion.
Regards,
Zhao
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PR_kwDOACgets5mcc1f
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Fix URL joining in OptimadeRester
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[] | 2024-02-09T04:29:38
| 2024-02-21T08:05:23
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2024-02-09T15:08:10Z
|
CONTRIBUTOR
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## Summary
Major changes:
- fix 1:
- Fix URL joining in OptimadeRester. The original os.path.join function is not the correct function to use for joining URLs. It's designed for joining file paths, and its behavior depends on the operating system. On Windows, it uses a backslash (\) as the separator, while on Unix-based systems, it uses a forward slash (/).
- This is a small fix, so no tests were added to 'test_optimade.py'
- This fix should resolve the issue reported at: https://matsci.org/t/could-not-retrieve-information-from-optimade/39469
## Todos
None
## Checklist
- [N/A] Google format doc strings added. Check with `ruff`.
- [N/A] Type annotations included. Check with `mypy`.
- [N/A] Tests added for new features/fixes.
- [N/A] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Add missing parameters to `MPSCANRelaxSet.yaml`
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[] | 2024-02-09T05:10:20
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2024-02-09T05:11:35Z
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MEMBER
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Add missing `MPSCANRelaxSet.yaml` parameters and alphabetize
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"@esoteric-ephemera --- I see the thumbs up. Does that mean this is good to go, or are you still planning to review this? ",
"Looks good to me. I think `ISMEAR` was probably omitted since this was intended to be set dynamically based on gap. I have no objection to include a default value.\r\n\r\nI believe there was also some talk about switching `LREAL` to False, but this might require a separate, updated input set, since it would technically break compatibility with the published input set.",
"@Andrew-S-Rosen thanks for putting this together! @mkhorton, yeah for the new input sets, putting them in a separate PR would be good. I'll reach out to the foundation soonish with that",
"Great, thank you both! I also agree that some minor modifications should be made but that will be elsewhere.\n\n@shyuep, I think we have the necessary blessings for this one. ",
"@janosh should I update the hash? ",
"yes please"
] | 2024-02-09T05:18:52
| 2024-02-16T13:46:40
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2024-02-16T13:40:33Z
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Tagging @esoteric-ephemera for review, @utf for context, and @shyuep & @mkhorton as code owners of the MP sets.
This PR ensures that the `MPSCANRelaxSet.yaml` in Pymatgen matches the [`BaseMPR2SCANRelaxSet.yaml`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/vasp/sets/BaseMPR2SCANRelaxSet.yaml) used in Atomate2 (and thereby, in MP production calculations). Namely, the `MPSCANRelaxSet.yaml` in pymatgen was missing the "sensible defaults" added by @esoteric-ephemera, which includes: `ISMEAR: 0`, `KSPACING: 0.22`, `SIGMA: 0.05`. Everything else is just a reordering for alphabetization purposes.
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Create a `CODEOWNERS`
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[
"Ah, you beat me to making a comment, @shyuep. It looks like only those with write permissions to the repo are valid as `CODEOWNERS`, so it can't just me an arbitrary contributor. Feel free to remove my name under the ASE line.",
"I can grant you write permissions.",
"Sure, that works too. π ",
"I was very excited about this feature before seeing the 2nd comment. π
",
"@JaGeo I am happy to add you as a codeowner. For lobster?",
"@shyuep , thank you! This would be great, yes!"
] | 2024-02-09T20:11:41
| 2024-02-21T08:06:12
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2024-02-09T20:13:03Z
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This PR adds a `CODEOWNERS` file (details [here](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners#about-code-owners)) that will automatically request a review from the specified code owner when a corresponding file is edited. Notably, the PR can still be merged without their review, but hopefully this will help keep folks informed for codes they have heavily developed and rely on daily.
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Revert back `TransformedStructure.__getattr__`
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"(`black` was updated recently to the 2024 stable style. We'll probably be seeing a bunch of these trivial changes across the repo unless someone decides to run `black .` on the whole thing)",
"@mjwen apologies for causing this bug and thanks for the fix! π \r\n\r\nwe now have a test case to guard against this in 0eb6d10\r\n\r\n> Others are formatting by pre-commit.\r\n\r\ni assume you mean by your editor config? our pre-commit config no longer runs `black`"
] | 2024-02-09T21:03:44
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## Summary
Fix a recursion bug when using TransformedStructure.final_structure. Revert it back it original implementation. See example bug here: https://github.com/materialsproject/atomate2/issues/707
Only the codes around line 90 of pymatgen/alchemy/materials.py are updated. Others are formatting by pre-commit.
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I_kwDOACgets5-9H0R
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Finding the Lowest Energy Stacking Configuration for Two Layers with Specific Miller Indices Using Pymatgen.
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[
"This is better for the discussion section of pymatgen, but I will leave some resources here and maybe someone (or yourself) could close this\r\n\r\nThe pymatgen [analysis.interfaces](https://pymatgen.org/pymatgen.analysis.interfaces.html) module could help you with input generation and structure matching (maybe), but I doubt there are any routines built in that will do everything you are looking for\r\n\r\nThis paper could be of use to you\r\nhttps://joss.theoj.org/papers/10.21105/joss.05886\r\n\r\nAnd slightly less relevant, but still a nice paper\r\nhttps://www.sciencedirect.com/science/article/abs/pii/S0022311523003690#bib0028\r\n\r\nYou may also look at DFT-CP by the Frederickson group. They have some interesting insights into how \"chemical pressure\" influences interlayer stacking\r\nhttps://pubs.acs.org/doi/pdf/10.1021/ja300685j\r\n\r\nBest of luck"
] | 2024-02-12T11:38:04
| 2024-03-02T07:15:54
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2024-03-02T07:15:54Z
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CONTRIBUTOR
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Dear Pymatgen Development Team,
I am currently exploring the theoretical aspects of heterostructures formed by two different single layers, each defined by specific Miller indices. A pivotal component of my study is identifying the stacking configuration between these layers that manifests the lowest energy, thereby elucidating the consequential electronic and structural traits.
In my quest to achieve this objective, I have come across several methodologies that appear promising for implementation within my research framework:
- Computing Cell of Non-identical Displacement (CNID), which is a sublattice of [Displacement Shift Complete (DSC)](https://www.tf.uni-kiel.de/matwis/amat/def_en/kap_7/backbone/r7_1_3.html): This approach, implemented in [interface_master](https://github.com/nmdl-mizo/interface_master), focuses on evaluating different displacements to ascertain the optimal alignment of two layers constituting the interface.
- Wyckoff Position-Based Method: Implemented in [Hetero2d](https://github.com/cmdlab/Hetero2d), this method leverages Wyckoff positions to facilitate the search for the energetically most favorable stacking configurations between two-dimensional materials.
Given the aforementioned methods and Pymatgen's extensive capabilities in manipulating and analyzing crystal structures, I am reaching out to inquire if Pymatgen encompasses functionalities akin to these approaches, or if there exist recommended workflows that could seamlessly integrate such methodologies for efficiently identifying the lowest energy stacking configuration between two specified layers.
I look forward to your guidance and suggestions.
Best Regards,
Zhao
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Adds support for an `MSONAtoms` class that's an `MSONable` form of an ASE `Atoms` object
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[
"MSONAbleAtoms is a mouthful.How about just call it AtomsM?",
"> MSONAbleAtoms is a mouthful.How about just call it AtomsM?\n\nMy personal opinion is that descriptive is better than concise. It's not immediately clear what an `AtomsM` means at a glance. Having it be unambiguous is particularly helpful with type hinting, among other things.\n\nThat said, I agree it's somewhat long. I'm open to other alternatives.",
"I would also vote for MSONAbleAtoms or something descriptive. ",
"Then MSONAtoms? ",
"Works for me. I'll make the change when I'm at my laptop. ",
"@mkhorton Good question. I have spent a fair bit of time on this module to ensure that it is lossless, and there are back-and-forth tests for this as well. If you spot an edge case, please let me know and I will patch it! ",
"> Or are some attributes potentially lost?\r\n\r\n@mkhorton there's no remaining known loss of information during `Atoms`<->`Structure` round trips. many edge cases were reported in the past which have all been addressed, most recently in\r\n\r\nhttps://github.com/materialsproject/pymatgen/pull/3359\r\nhttps://github.com/materialsproject/pymatgen/pull/3338\r\nhttps://github.com/materialsproject/pymatgen/pull/3270\r\nhttps://github.com/materialsproject/pymatgen/pull/3151\r\n\r\nunknown remaining edge cases are possible but likely rare",
"Thanks @Andrew-S-Rosen . This is great!",
"I just pushed a change that ensures MSONAtoms is returned by from_dict. This is supposed to be the case. Otherwise it loses functionality with deserializaation.\r\n"
] | 2024-02-13T06:26:40
| 2024-02-22T14:26:57
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2024-02-14T13:22:20Z
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## Summary
Here, I introduce the `MSONAtoms` class, which is simply an `MSONable` version of the ASE `Atoms` object, introducing an `.as_dict()` and `from_dict()` method that uses ASE's JSON encode/decoder to do the serialization. By default, the object returned from `ASEAtomsAdaptor.get_atoms()` is now an `MSONableAtoms` object. The original `Atoms` class can be returned via the `msonable=False` keyword argument, although this should rarely be needed in practice since the functionality of `MSONAtoms` is otherwise identical to `Atoms`. This is a follow-up to https://github.com/materialsvirtuallab/monty/pull/619.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets5mukNM
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Refactors + types + fix doc string returns to use Google format
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nothing to see here π
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Improve INCAR tag check
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[
"I did some research and found [typeguard](https://pypi.org/project/typeguard/) seems to be what we're looking for. \r\nFor example:\r\n```python\r\nfrom typeguard import check_type, CollectionCheckStrategy\r\n\r\n\r\ncheck_type(\r\n value=[1, \"hi\"], expected_type=list[int],\r\n collection_check_strategy=CollectionCheckStrategy.ALL_ITEMS\r\n)\r\n\r\ncheck_type(\r\n value=[1, \"hi\"], expected_type=list[int, int],\r\n collection_check_strategy=CollectionCheckStrategy.ALL_ITEMS\r\n)\r\n\r\ncheck_type(\r\n value=[1, \"hi\"], expected_type=eval(\"list[int, int]\"),\r\n collection_check_strategy=CollectionCheckStrategy.ALL_ITEMS\r\n)\r\n```\r\n\r\nHowever there are still some concerns to address:\r\n1. Is it essentially necessary to add an extra dependency `typeguard` to `pymatgen`\r\n2. I currently don't know any better approach to cast string to object (`\"list\"` to `list`) than `eval`, but in our case the source is internal (from file `incar_parameters.json`), so it should not lead to any securify issues\r\n3. type check each item might incur a performance penalty (https://github.com/agronholm/typeguard/issues/418#issuecomment-1817515059), thus we would need to discuss the necessity of this and have a switch for strict mode (check every item or just check the first item, where check first item of a collection is the default for `typeguard`).\r\n",
"Can you give me some advice on this @janosh? Do you think it's necessary to have an item-wise type check for INCAR tags (and might need to include an extra dependency `typeguard`)? Or should we stick to a more general type check (`list` instead of `list[int, int, int]` for instance). Thanks for any input in advance.",
"> Do you think it's necessary to have an item-wise type check for INCAR tags (and might need to include an extra dependency `typeguard`)?\r\n\r\ni think adding `typeguard` as a dependency just for this is a tall ask. i'm guessing @shyuep will be strongly against.\r\nunless there's a strong selling point i would also lean against",
"> i think adding `typeguard` as a dependency just for this is a tall ask. i'm guessing @shyuep will be strongly against. unless there's a strong selling point i would also lean against\r\n\r\nYes I was thinking the same, adding a dependency to be used only once would be too much overhead. Actually this should be questions:\r\n- Do you think it would be necessary to perform item-wise check for INCAR tags (or just keep current more general type checking)? @janosh I'm pretty unsure and worried about the potential performance penalty here.\r\n- If so, including an extra dependency should certainly be discouraged. I would see if I could find another way around.",
"> Do you think it would be necessary to perform item-wise check for INCAR tags\r\n\r\ni don't think so. i don't remember a lot of GitHub issues about this.",
"> i don't think so. i don't remember a lot of GitHub issues about this.\r\n\r\nLet's keep the type checking unchanged then, and implement more careful checking when necessary. This PR should be good for review now @janosh . Thanks a lot!",
"Guess this PR get forgotten... Can you please review this @janosh ? Thanks.",
"Thanks for reviewing @janosh "
] | 2024-02-13T10:02:04
| 2024-02-24T15:01:09
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2024-02-24T14:59:43Z
|
CONTRIBUTOR
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## Summary
Some legacy from #3539.
- Clean up INCAR parameters recording file `incar_parameters.json` to separate types and values.
- Clean up INCAR checking mechanism accordingly.
## TODOs
Enable checking of more complex type annotations like `LATTICE_CONSTRAINTS : Sequence[bool, bool, bool])` suggested by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3539#discussion_r1471615138.
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Error when initializing Vasprun when LDAUL/J or MAGMOM exception triggers
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[] | 2024-02-13T13:31:12
| 2024-02-13T18:52:38
|
CONTRIBUTOR
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### Python version
Python 3.10.13
### Pymatgen version
2023.12.18
### Operating system version
Mint 20
### Current behavior
I wasn't sure where to post this as it triggered when `VasprunXMLValidator` from `custodian` checked a job and found issues with the LDAU parameters in the `vasprun.xml`. I feel like the issue belongs here as the simplest fix is done through pymatgen. The issue is when `custodian` tries to initialize a `Vasprun` object in the `VasprunXMLValidator().check()` by simply calling `Vasprun("vasprun.xml")`, and can not correctly parse some of the values in the XML and tries to parse the INCAR instead. This is done through [_parse_from_incar](https://github.com/materialsproject/pymatgen/blob/ea3173711ad130d0d8f09c02e6342777274a6320/pymatgen/io/vasp/outputs.py#L115) which when given simply `"vasprun.xml"`, sets `dirname` to `os.path.dirname(filename)`, which is an empty string since the file is in current working directory. `os.listdir(dirname)` in the following line then raises a `FileNotFoundError` and the `check()` method of the validator incorrectly returns `True`.
The simplest fix would be to change [dirname = os.path.dirname(filename)](https://github.com/materialsproject/pymatgen/blob/ea3173711ad130d0d8f09c02e6342777274a6320/pymatgen/io/vasp/outputs.py#L117) to `dirname = os.path.dirname(filename) or '.'`.
The other fix would be to change the `vrun = Vasprun('vasprun.xml')` in the `try` block in `VasprunXMLValidator().check()` of `custodian` to use the full path instead.
If you think this is the correct place to apply the fix, I can do a PR, otherwise I go to the `custodian` repo :)
### Expected Behavior
I think the reason this evaded attention was because this unexpected parsing of LDAU and/or MAGMOM from `vasprun.xml` is kind of rare, and the reason tests pass is because they always use the full path of `vasprun.xml`, in which case this doesn't happen. Only when `vasprun.xml` is used directly as in the case of `VasprunXMLValidator`, we get an exception. Even though `_parse_v_parameters` in `pymatgen.io.vasp.outputs` explicitly states that the `filename` should be the fullpath of vasprun.xml, I personally see no reason why `Vasprun` should fail when initialized in the same path as the `vasprun.xml`.
### Minimal example
_No response_
### Relevant files to reproduce this bug
I have a vasprun.xml that can reproduce this error but it's rather large (~90MB). I can upload it if anyone wants to take a look, though.
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PR_kwDOACgets5m1dd1
| 3,623
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Return `self` from all `SiteCollection/Structure/Molecule` in-place modification methods
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[] | 2024-02-14T09:23:09
| 2024-02-14T09:45:32
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2024-02-14T09:45:32Z
|
MEMBER
|
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Non-breaking change but makes for a more functional API since modification methods can now be chained.
E.g. frequent use case of loading a file from disk/memory and directly applying an in-place modification previously required 2 lines:
```py
struct = Structure.from_file("path/to/file")
struct.add_oxidation_state_by_guess()
```
but can now be shortened to
```py
struct = Structure.from_file("path/to/file").add_oxidation_state_by_guess()
```
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Breaking `Lobsterenv` improvements
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[
"@JaGeo , Tagging you here. Let us know if you have any suggestions on this change π ",
"From my side, this is fine. A breaking change is probably okay here as not many people are using LobsterEnv directly"
] | 2024-02-14T12:56:55
| 2024-04-10T05:58:22
|
2024-02-18T05:49:25Z
|
CONTRIBUTOR
|
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# Todo
- [x] Adapt LobsterNeighbours to work using pymatgen objects instead of file path
- [x] Rename args to use lowercase
- [x] Add test for new functionality of working with pymatgen objects
- [ ] Align lightstructure environment output to match other types
- [ ] Add test for adapted lightstructure environment outputs
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PR_kwDOACgets5m3hpf
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Fixed Incar object to allow for ML_MODE vasp tag
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[] | 2024-02-14T14:33:20
| 2024-02-15T16:16:15
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2024-02-15T16:16:15Z
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CONTRIBUTOR
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Fixed Incar object to allow for ML_MODE vasp tag which does not want to have capitalized values (train, run, ...). By default, pymatgen capitalizes the values of the INCAR tags (e.g. "ALGO = Fast", even if you set incar["ALGO"] = "fast"). This is not working for the ML_MODE tag.
Also fixed (i.e. ignored specific mypy code) random mypy errors in files that were not touched ...
## Summary
Major changes:
- Allow the use of ML_MODE tag in INCAR (not capitalizing, lowering instead)
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I_kwDOACgets5_OnTi
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CifParser check() method does not account for different site multiplicities
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[
"Mentioned this in PR #3628"
] | 2024-02-14T14:55:17
| 2024-02-23T10:37:39
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2024-02-23T10:37:39Z
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CONTRIBUTOR
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### Python version
3.10.0
### Pymatgen version
2024.2.8 or master
### Operating system version
_No response_
### Current behavior
The check() method of the CifParser class performs checks on the compositions reported in both cif and Structure object parsed from cif. Besides other things, it is checked if the relative stochiometry from cif and structure are the same.
If the cif file is missing both the keys `_chemical_formula_sum` and `_chemical_formula_structural`, `cif_formula` is constructed from the atom types of all crystallographically unique sites in the structure:
https://github.com/materialsproject/pymatgen/blob/098b2a9663d889f766458a4c7283c3d776e3913a/pymatgen/io/cif.py#L1345
However, if the site multiplicities differ within the structure, the formula of the Structure object will have a different relative stochiometry. This leads to a `UserWarning: Incorrect stoichiometry` even if the cif file is not faulty.
### Expected Behavior
No `UserWarning` to be raised for the below mentioned example.
In my opinion, checking the relative stochiometry should be skipped if both `_chemical_formula_sum` and `_chemical_formula_structural` are not present in the cif. To obtain the true stochiometry (including multiplicities) from the cif without these keys, its symmetry operations would need to be applied as it is also done for constructing the Structure object - therefore, this would no longer be a sanity check (?).
### Minimal example
```Python
from pymatgen.io.cif import CifParser
import warnings
warnings.filterwarnings("error")
struct = CifParser("path-to-example-cif").parse_structures(primitive=True)[0]
```
### Relevant files to reproduce this bug
The bug can be for example reproduced with the mcif file of MAGNDATA entry 0.296:
https://www.cryst.ehu.es/magndata/index.php?this_label=0.296
This structure contains three crystallographically unique Cu sites, out of which two each have a site multiplicity of 2 and one has a multiplicity of 4. The site multiplicity of all unique anion sites is also 4. This results in a warning:
`UserWarning: Incorrect stoichiometry:
CIF={'Cu': 3.0, 'Cl': 1.0, 'O': 3.0}
PMG={'Cu': 8.0, 'Cl': 4.0, 'O': 12.0}
ratios={'Cl': 4.0, 'O': 4.0, 'Cu': 2.6666666666666665}`
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Lobster io improvements
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[
"Hi @JaGeo , I made this changes as per our prep to update our schema in atomate2.",
"Thank you!\r\n\r\n@naik-aakash , could you add tests for from_dict as well? And, doesn't monty already implement as_dict. Why do you need to implement this yourself?",
"Just to add @naik-aakash and I will discuss this and then update the PR. ",
"Hello,\r\n\r\n\r\nIf I may, here are some possibly useful comments.\r\n\r\n\r\nI would avoid having the filename in the init, but only have the data itself and have a from_file method that reads in.\r\nExample for Charge object:\r\n\r\n```py\r\nclass Charge(MSONable):\r\n def __init__(self, atomlist, types, mulliken, loewdin):\r\n self.atomlist = atomlist\r\n self.types= types\r\n self.mulliken= mulliken\r\n self.loewdin= loewdin\r\n\r\n @classmethod\r\n def from_file(cls, filename: str = \"CHARGE.lobster\"):\r\n with zopen(filename, mode=\"rt\") as file:\r\n data = file.read().split(\"\\n\")[3:-3]\r\n if len(data) == 0:\r\n raise OSError(\"CHARGES file contains no data.\")\r\n\r\n atomlist: list[str] = []\r\n types: list[str] = []\r\n mulliken: list[float] = []\r\n loewdin: list[float] = []\r\n for line in data:\r\n sp = line.split()\r\n atomlist.append(sp[1] + sp[0])\r\n types.append(sp[1])\r\n mulliken.append(float(sp[2]))\r\n loewdin.append(float(sp[3]))\r\n return cls(atomlist=atomlist, types=types, mulliken=mulliken, loewdin=loewdin)\r\n\r\n @property\r\n def num_atoms(self)\r\n return len(self.atomlist)\r\n```\r\n\r\nSuch an organization of the object is usually cleaner than init with filenames (which are actually not exactly compatible with MSONable, which is probably why @naik-aakash needed to reimplement as_dict). For standard MSONable to work, the init method should only set the attributes and do nothing else no \"post-processing\" of the arguments passed to init ideally.\r\n\r\nThen indeed you don't need to implement as_dict and from_dict in principle.\r\n\r\nAlso I would avoid having capitalized attributes (herabove mulliken instead of Mulliken), otherwise you may think it's a class.\r\n\r\nSame applies to the other objects of course. I don't know if it's possible or easy to change for you on the packages/scripts using these but I would say it would improve the lobster io if it is possible.\r\n\r\nBest\r\n\r\n",
"Thanks, @davidwaroquiers !",
"Some first thoughts from my side.\r\n\r\nIt would be good to keep the breaking changes minimal as these classes are used by other people. Thus, I am not sure if implementing a from_file method at this point is a good idea.\r\n\r\nVasp output io implements the classes similarily. And I think I took them as an example when I initially started with this development, e.g., https://github.com/materialsproject/pymatgen/blob/098b2a9663d889f766458a4c7283c3d776e3913a/pymatgen/io/vasp/outputs.py#L143\r\n\r\nIn any case, if we implement an as_dict method, the from_dict one needs to work. \r\n\r\nAnd, we can rename the property names but I would suggest to add a deprecation warning then. I agree that I did not follow naming conventions very well when I initially implemented these classes. Might take some time to correct all of these issues.\r\n\r\n\r\n",
"My answer sounds a bit too direct. Sorry for this. I\r\nn any case, the suggestions are very helpful but we need to keep a balance between correcting all poor design choices from some years ago, consistency with other code parts and few breaking changes. ",
"No offense taken @JaGeo ;)\r\nI fully agree there is a trade-of to take into account when making backward incompatible changes.\r\nNevertheless, I also tend to compare with other (much more used) packages, such as numpy, matplotlib, pandas, pydantic and many others, which did (recently) huge changes with big backward incompatible changes. While I agree it was (and still is for some of these changes) annoying to adapt the codes, scripts and the like, I believe these changes made sense as they were all adding value: cleaner api, more standardized usage, removal of weird (or wrong) methods/features, easier development of new features, more modularity, ...\r\nAnyway, I'm currently not a user of lobster (nor a user or developer of lobster_io) and you should decide what's best for the lobster community.\r\nAs for the vasp io, I believe it is the same trade-off, with a larger user base. The choices made 10-15 years ago for these seemed good at the time and now we are living with these choices, which will probably not change unless a big backward incompatible refactoring happens all at once (not in any current plan of pymatgen I believe).\r\n\r\nBest,",
"Thank you @davidwaroquiers , for your suggestions. They were certainly insightful and would be nice to keep in mind when implementing new stuff here on.",
"Hi @JaGeo , I have adapted Charge class now, without introducing breaking change am able to get as_dict and from_dict working out of the box without having to define it myself. If you think this is fine, will add a similar approach to other classes as well.\r\n\r\nNote: Will add deprecation warning for renamed attributes , I just want to know if you think this approach is fine. π ",
"fwiw, i had the same thought as @davidwaroquiers and was planning to make similar comments but they've already been discussed so feel free to merge",
"@janosh , great thanks. \r\n\r\nIs there any io class that you would recommend to model other io classes after? Might be helpful for future implementations. I think we have very different strategies depending on the io module at the moment.",
"good question! maybe the recently added FHI-aims IO modules? e.g.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0f474f67bd4f5a2cfc6abcc5e44c921308669c72/pymatgen/io/aims/outputs.py#L30-L50\r\n\r\nthe `io.res` module also has pretty good code quality. e.g. `ResProvider` and `AirssProvider`\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0f474f67bd4f5a2cfc6abcc5e44c921308669c72/pymatgen/io/res.py#L323-L353\r\n\r\n`io.vasp` uses `InputFile` and similar classes feel a bit \"boilerplatey\" so i wouldn't always model after `io.vasp` even though it's widely used\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0f474f67bd4f5a2cfc6abcc5e44c921308669c72/pymatgen/io/core.py#L48"
] | 2024-02-14T16:16:38
| 2024-02-21T08:07:55
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2024-02-15T15:25:44Z
|
CONTRIBUTOR
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# Todo
Make MSONable
- [x] Charge
- [x] Sitepotential
- [x] Grosspop
- [x] Bandoverlap
- [x] MadelungEngeries
- [x] Icohplist
- [x] Update tests
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Modified CifParser.check() as one possible solution for issue #3626
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[
"~~If you are okay with this approach i could adapt the 2 cif tests that are failing now (and for example add a formula key so the checks are not skipped).~~ (Modifying the tests no longer necessary as other checks than for relative stoichiometry were reincluded in case of missing formula keys)",
"Thanks @kaueltzen for pointing this out! I like your solution of warning that the stoichiometry check couldn't be accomplished - the fallback I added originally clearly isn't robust enough in general\r\n\r\nAdding a test for this (using the magnetic cif you sent with the issue) would be great to move this forward",
"Thank you for your quick replies! I added a test both for skipping the relative stoichiometry check and appending a warning in the case of missing formula keys. There was already a test file in pymatgen, Li10GeP2S12.cif, that matched the criteria (it has no formula keys and sites with different multiplicities and occupancies)."
] | 2024-02-16T13:40:31
| 2024-02-23T10:49:43
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2024-02-22T18:09:32Z
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CONTRIBUTOR
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closes #3626. `CifParser.check()` raises a `UserWarning: Incorrect stoichiometry` for a cif, if
- the keys `_chemical_formula_sum` and `_chemical_formula_structural` are missing and
- crystallographic sites have different multiplicities
For the relative stoichiometry to be checked correctly, the site multiplicities would have to be included by applying the cif's symmetry operations to the crystallographically unique sites (like for construction for the structure).
As this would be no longer a sanity check, i propose skipping the relative stoichiometry check in this case (but still including all the other checks for valid elements etc.).
For the case of skipping the relative stoichiometry check, i appended a message to `self.warnings`, but I'm not sure if there are better ways to handle this case.
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POTCAR setup instructions should be made clearer
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[
"I imagine this is covered in the [POTCAR setup](https://pymatgen.org/installation.html#potcar-setup) section of the docs, but it is not written clearly enough for me to understand.\r\n\r\n- What is `<MY_PSP>`? It is not defined anywhere.\r\n- Why should there need to be reconfiguring of my POTCAR directory anyway? Shouldn't I be able to just set `PMG_VASP_PSP_DIR` to the directory of my POTCARs as-downloaded from VASP without further modification?\r\n\r\nHistorically, I have always just renamed my pseudos to `POT_GGA_PAW_PBE_54`, but this is sufficiently bothersome that I wanted to open an issue.\r\n",
"The functional directory is specified in PotcarSingle. The setup is in cli/pmg_potcar.py. The reason why this setup was done in the past is because VASP can arbitrarily change their directory structure or names (as you have just encountered). But we configure the directories in a standard way. ",
"Thanks for the reply, @shyuep. I think the [docs](https://pymatgen.org/installation.html#potcar-setup) should be updated to be clearer for clueless people like me because I could not figure out what `pmg config -p <EXTRACTED_VASP_POTCAR> <MY_PSP>` was supposed to correspond to (and hence why I always just manually did it in the past). I'll open a PR to clarify this."
] | 2024-02-16T21:08:53
| 2024-02-17T05:04:38
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2024-02-17T05:04:37Z
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### Python version
3.10+
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
Currently, when Pymatgen searches for a pseudopotential, it has a default set of paths it looks in. For instance, if we look for the PBE_54 pseudos and symbol Al, Pymatgen will search as follows:
```
OSError: You do not have the right POTCAR with functional='PBE_54' and symbol='Al' in your
PMG_VASP_PSP_DIR='/home/rosen/software/vasp/pseudos'. Paths tried:
['/home/rosen/software/vasp/pseudos/POT_GGA_PAW_PBE_54/POTCAR.Al',
'/home/rosen/software/vasp/pseudos/POT_GGA_PAW_PBE_54/Al/POTCAR']
```
However, for quite a while now, VASP has been using `potpaw_LDA.54` and `potpaw_PBE.54` as the folder names. We should really add these as defaults so users don't have to deal with modifying this. The same folder structure is used in the v64 pseudos as well.
To be clear, this is the expected path:
```
VASP_PSP_DIR/potpaw_PBE.54/Al/POTCAR
```
### Expected Behavior
Pymatgen should register pseudos out-of-the-box.
### Minimal example
```python
from pymatgen.io.vasp.inputs import Potcar
Potcar(["Al"],functional="PBE_54")
```
### Relevant files to reproduce this bug
_No response_
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Make the POTCAR setup instructions clearer
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Closes #3629. I have always found the POTCAR setup instructions to be incredibly confusing, in part because some parts were never defined (e.g. `<MY_PSP>`) and in other parts because things are quite out-of-sync with the POTCAR structure offered by VASP as of the last several years. This is an attempt to make it clearer.
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I_kwDOACgets5_jHHZ
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`bader_analysis_from_path` misusing `_get_filepath` and hence not finding input VASP files
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[
"Thanks a lot for the fast and clean fix! @janosh "
] | 2024-02-17T09:12:06
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I'm quite sure that this PR is causing the "bader_analysis_from_path" method to fail for any of its usage. I'm confused how could this PR pass the tests without failing.
The problematic line is line 455 in this PR and now line 451 in the latest pymatgen. The method is now looking for CHGCAR in the "Could not find CHGCAR!" folder path...
I think the tests and this code should be corrected.
https://github.com/materialsproject/pymatgen/blob/5514ff5418b23da809b23056ea876c0a4c244c96/pymatgen/command_line/bader_caller.py#L438-L452
_Originally posted by @JiQi535 in https://github.com/materialsproject/pymatgen/pull/3458#pullrequestreview-1886487793_
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Fix `bader_analysis_from_path` using warning as file path and reinstate test
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closes #3631.
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I_kwDOACgets5_l3gB
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`BadInputSetWarning` should not be raised for ISMEAR = 0 relaxations with metals if SIGMA is small
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[] | 2024-02-17T21:59:47
| 2024-02-21T14:56:34
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2024-02-21T14:56:33Z
|
MEMBER
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### Python version
3.10+
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
In [this part](https://github.com/materialsproject/pymatgen/blob/ff45527caf5de3bc76ed859bab0d978cab38972d/pymatgen/io/vasp/sets.py#L746-L753) of `pymatgen.io.vasp.sets.py`, a `BadInputSetWarning` is raised if a relaxation is done on a likely metal with ISMEAR < 1. However, there is no issue with doing a relaxation of a metal with ISMEAR = 0 if you have a sufficiently small SIGMA.
As quoted in the VASP manual:
> If you have no a priori knowledge of your system, for instance, if you do not know whether your system is an insulator, semiconductor or metal then always use Gaussian smearing ISMEAR=0 in combination with a small [SIGMA](https://www.vasp.at/wiki/index.php/SIGMA)=0.03-0.05.
### Expected Behavior
The warning should only be raised if either: a) ISMEAR < 0; b) ISMEAR = 0 and SIGMA > 0.05.
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets5nMp9a
| 3,634
|
Modify `BadInputSetWarning` logic for relaxations of a likely metal
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[] | 2024-02-17T22:04:14
| 2024-02-23T11:25:24
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2024-02-21T14:56:32Z
|
MEMBER
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Closes #3633. Relaxing a metal with ISMEAR = 0 is fine, as noted in the VASP manual, provided SIGMA is sufficiently small (< 0.05 is the recommendation in the VASP manual).
> If you have no a priori knowledge of your system, for instance, if you do not know whether your system is an insulator, semiconductor or metal then always use Gaussian smearing ISMEAR=0 in combination with a small [SIGMA](https://www.vasp.at/wiki/index.php/SIGMA)=0.03-0.05.
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PR_kwDOACgets5nU_2_
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Speeding up `get_nn_info` in local_env.py
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[] | null |
[
"Awesome. Thanks! I recently tried the minimum distance method for an amorphous structure π
... \r\nAnd it took forever. ",
"@ftherrien thanks, much appreciated! the failing test here looks like maybe this doesn't handle translations correctly? shifting the `I` atom by a full $a$ lattice vector shouldn't make a difference.\r\n\r\n```py\r\nTestCrystalNN.test_shifted_sites _______________________\r\n\r\nself = <tests.analysis.test_local_env.TestCrystalNN testMethod=test_shifted_sites>\r\n\r\n def test_shifted_sites(self):\r\n cnn = CrystalNN()\r\n \r\n sites = [[0.0, 0.2, 0.2], [0, 0, 0]]\r\n struct = Structure([7, 0, 0, 0, 7, 0, 0, 0, 7], [\"I\"] * len(sites), sites)\r\n bonded_struct = cnn.get_bonded_structure(struct)\r\n \r\n sites_shifted = [[1.0, 0.2, 0.2], [0, 0, 0]]\r\n struct_shifted = Structure([7, 0, 0, 0, 7, 0, 0, 0, 7], [\"I\"] * len(sites_shifted), sites_shifted)\r\n bonded_struct_shifted = cnn.get_bonded_structure(struct_shifted)\r\n \r\n> assert len(bonded_struct.get_connected_sites(0)) == len(bonded_struct_shifted.get_connected_sites(0))\r\nE assert 1 == 2\r\n```",
"@janosh the auto-merge was cancelled FYI",
"I have merged now, @janosh , as you approved it already.",
"Thanks y'all!"
] | 2024-02-19T20:41:25
| 2024-02-20T18:23:08
|
2024-02-20T17:49:16Z
|
CONTRIBUTOR
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`_get_image` and `_get_original_site` do not need to recompute site and index when `site` is a `PeriodicNeighbor` which has them as attributes.
When there are several sites, this makes a significant difference on speed for `get_nn_info`
Alternative implementation would have been `try/except` and `hasattr`. `try/except` is much slower when most of the sites are not `PeriodicNeighbor`.
## Summary
Major changes:
- feature: image and site index are not recomputed when they are already an attribute of the site
|
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`pymatgen.io.res` - compatibility issue with the AIRSS package.
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[
"pinging @stefsmeets in case you know a good fix (of course no obligation to respond)",
"Sure, I can have a look at this next week."
] | 2024-02-20T14:35:48
| 2024-03-05T14:07:30
|
2024-03-05T14:07:30Z
|
NONE
|
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### Python version
Python 3.10.8
### Pymatgen version
2023.11.12
### Operating system version
_No response_
### Current behavior
When there is nothing in REMS, a blank line appears between the blank line TITL and CELL.
### Expected Behavior
When there is nothing in REMS, CELL must come after TITL without any blank line.
Also, when we do `cat *.res`, we must be able to concatenate the res files without overlapping lines.
### Minimal example
When I run `cat*.res` for res files generated using ResIO, it for some reason concatenates END and TITL into a single line.
```
TITL mp-976411-mp-1398010 0.00 80.2525 -7.62450 0.000000 0.000000 (P6_3/mmc) n - 1
REM Retrieved from Materials Project
REM material_id = mp-976411
REM task_id = mp-1398010
REM run_type = GGA
CELL 1.00000 3.07107 3.07107 9.82536 90.00000 90.00000 120.00001
LATT -1
SFAC Li
Li 1 0.00000000 0.00000000 0.00000000 1.000000 0.00
Li 2 0.33333300 0.66666700 0.25000000 1.000000 -0.00
Li 3 0.00000000 0.00000000 0.50000000 1.000000 0.00
Li 4 0.66666700 0.33333300 0.75000000 1.000000 -0.00
ENDTITL mp-976411-mp-1976760 0.00 81.4633 -9.52327 0.000000 0.000000 (P6_3/mmc) n - 1
REM Retrieved from Materials Project
REM material_id = mp-976411
REM task_id = mp-1976760
REM run_type = R2SCAN
CELL 1.00000 3.03439 3.03439 10.21621 90.00000 90.00000 120.00001
LATT -1
SFAC Li
Li 1 0.00000000 -0.00000000 0.00000100 1.000000 0.00
Li 2 0.33333300 0.66666500 0.25000000 1.000000 0.00
Li 3 0.00000000 -0.00000000 0.49999900 1.000000 0.00
Li 4 0.66666800 0.33333300 0.75000000 1.000000 0.00
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5nhePb
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Fix Lobsterenv Bug
|
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[
"Thanks! Can you add a test to catch future regressions?",
"> Thanks! Can you add a test to catch future mistakes?\r\n\r\nYes, just added one now",
"Hi @janosh , can a new release of Pymatgen be made please? As this is bug breaks our LobsterPy package https://github.com/JaGeo/LobsterPy/pull/232 \r\n\r\nSorry for the inconvenience.",
"> Hi @janosh , can a new release of Pymatgen be made please? \r\n\r\nwe just had one today so i'd prefer to accumulate a few more changes before the next release",
"@janosh , this currently prevents our on-going JOSS review for LobsterPy. We could use the latest master branch from pymatgen for the release but it's not exactly best practice.",
"i see. let's also get in https://github.com/materialsproject/pymatgen/pull/3593 (awaiting OP) and then we can release",
"@janosh Thanks! ",
"[v2024.2.23](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.23) should be on PyPI in ~1h.",
"> [v2024.2.23](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.23) should be on PyPI in ~1h.\r\n\r\nThanks π "
] | 2024-02-21T13:22:45
| 2024-03-13T18:02:01
|
2024-02-21T15:04:38Z
|
CONTRIBUTOR
|
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# Bug
The charges read from file are not assigned
# Fix
Fix the erroneous if else condition introduced during #3624
# Todo
- [x] Add test
|
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I_kwDOACgets5_-O6J
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how to load an MD from LAMMPS into a Trajectory object?
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[] | 2024-02-21T15:20:00
| 2024-02-24T09:07:40
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2024-02-24T09:07:40Z
|
NONE
|
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Good afternoon,
I am quite new to using Lammps for my MDs and I am struggling to load my MD data into a pymatgen trajectory. I am studying diffusion in a crystal. Currently I have my MD trajectory in an xyz file but it would be possible for me to use other common outputs from LAMMPS if that's easier.
Thanks in advance!
|
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PR_kwDOACgets5njTqw
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[BugFix] Subclass Construction Locpot<:VolumetricData
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[
"No problem! The test I added passes with the new code but not the old code."
] | 2024-02-21T17:15:06
| 2024-02-23T11:28:26
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2024-02-21T19:43:13Z
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CONTRIBUTOR
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## Subclass Construction Locpot<:VolumetricData
The constructor signature for `Locpot` is different from the parent.
This makes it hard to write general code to handle different kinds of `VolumetricData` objects.
Just adding a `**kwarg` there should work.
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VASP noncollinear Wavecar read error
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[
"No errors were found after commenting out the following lines (starting at 4345)\r\n\r\n```python\r\n if len(self.Gpoints[ink]) != nplane and 2 * len(self.Gpoints[ink]) != nplane:\r\n raise ValueError(\r\n f\"Incorrect {vasp_type=}. Please open an issue if you are certain this WAVECAR\"\r\n \" was generated with the given vasp_type.\"\r\n )\r\n```\r\nAnd produced the expected cube file. \r\n\r\nI will investigate more over the weekend"
] | 2024-02-22T08:30:34
| 2024-02-22T08:34:03
|
CONTRIBUTOR
|
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### Python version
Python 3.11.7
### Pymatgen version
Version: 2023.11.12
### Operating system version
Red Hat Enterprise Linux 8.8
### Current behavior
similar to #1995
```
vsh wavecar WAVECAR -k 130 -b 84 85 -S CONTCAR -o both_bands_gamma.vasp -p --vasp-type ncl --prec accurate
Traceback (most recent call last):
File "/p/home/wladerer/.pyenv/versions/3.11.7/bin/vsh", line 8, in <module>
sys.exit(main())
^^^^^^
File "/p/home/wladerer/.execs/vsh/vsh/cli.py", line 23, in main
command.run(args)
File "/p/home/wladerer/.execs/vsh/vsh/scripts/wavecar.py", line 207, in run
func(args)
File "/p/home/wladerer/.execs/vsh/vsh/scripts/wavecar.py", line 54, in generate_parchg
wave = Wavecar(args.input, vasp_type=args.vasp_type, precision=args.prec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/home/wladerer/.pyenv/versions/3.11.7/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 4354, in __init__
raise ValueError(
ValueError: Incorrect vasp_type='ncl'. Please open an issue if you are certain this WAVECAR was generated with the given vasp_type.
```
### Expected Behavior
My goal was to create a cube file from a specific kpoint and band, so I anticipated that the script would run and produce an output file.
### Minimal example
```Python
from pymatgen.io.vasp.outputs import Wavecar
wave = Wavecar("WAVECAR", vasp_type="ncl", precision="accurate")
```
### Relevant files to reproduce this bug
I have included some basic [wavecar info](https://github.com/materialsproject/pymatgen/files/14370962/wavecar_info.txt), the
[verbose ](https://github.com/materialsproject/pymatgen/files/14370964/verbose.log) output of the Wavecar __init__ method,
the [kpoints file](https://github.com/materialsproject/pymatgen/files/14370965/kpoints.txt) and the
[incar](https://github.com/materialsproject/pymatgen/files/14370966/incar.txt) file
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|
Is it possible to reduce the size of `tests` directory?
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[
"I support the gzipping effort @DanielYang59!",
"I guess someone just needs to go ahead and do it. We discussed it before. I compressed some cohp files a while ago but one can surely do more. \r\n",
"Everyone, we don't need to revisit this again. Gzipping can be done. But it is not going to help because Git already gzips prior to transmitting changes. The only people who have to deal with a large tests directory are the developers, who really need the test files anyway. Everyone else just pip installs and the wheels and a few Mb in size. Do not conflate the repo size with the install size. They are two different matters.",
"Yes, surely.\r\n\r\nIf someone wants to develop somewhere without much storage, it might still be beneficial to gzip. I guess no one would mind if someone goes ahead and does this. ",
"Sure. But as far as I know, even the lowest level machines nowadays have storage 500Gb and above.....",
"Thanks a lot for everyone's helpful discussion here. I would go ahead to compress these files and see how everything goes."
] | 2024-02-22T08:30:48
| 2024-02-23T01:33:02
|
2024-02-22T16:55:40Z
|
CONTRIBUTOR
|
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### Feature Requested
During a recent clone I noticed the total repo size is pretty big at around 1.9 GB in total, where (sorted and only show the largest several)
```bash
959M tests
868M .git
49M docs
16M pymatgen
11M cmd_line
9.4M dev_scripts
```
While in `tests`:
```bash
898M files
47M analysis
13M io
568K electronic_structure
344K core
```
And in `files`:
```bash
139M molecules
59M vasprun.xml.dfpt.ionic
55M boltztrap
42M vasprun.lvel.Si2H.xml
42M cohp
38M vasprun.xml.pbesol_vdw
38M vasprun.xml.pbesol
36M vasprun.xml.nonlm
33M neb_analysis
30M path_finder
29M bader
20M C_48_bandstructure.json
17M surface_tests
15M lifepo4.xml
14M vasprun.xml.int_Te_SOC.gz
13M vasprun.xml.sc_overflow
13M vasprun.xml
13M Zr_Vasprun
13M CHGCAR.Fe3O4
12M vasprun.xml.hse06
12M chgden
11M vasprun.xml.lobster.spin
11M chemenv
8.7M WAVEDERF.Si
8.3M grid_data_files
8.2M nmr
7.8M nwchem
7.4M boltztrap2
6.8M OUTCAR.stopped
6.8M CHGCAR.Fe3O4_ref
6.3M absorption
6.0M OUTCAR
```
### Proposed Solution
A simply `gzip` seems to reduce the file size by over 90%:
```bash
59M ./vasprun.xml.dfpt.ionic
4.4M ./vasprun.xml.dfpt.ionic.tgz
```
Or reuse some test files wherever possible?
I'm wondering if we have any plan to compress the test files a bit? Thanks.
|
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PR_kwDOACgets5nnkLO
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Remove properties from abivars dict as this breaks the interface withβ¦
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[
"we can make a new release once this and #3645 is merged."
] | 2024-02-22T08:43:36
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2024-02-23T10:31:08Z
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CONTRIBUTOR
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Hi @janosh , is it possible to merge this fix and make a new release of Pymatgen
as this bug breaks the interface with Abinit? Thanks
|
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Importing Trajectory from pymatgen.core.trajectory gives an NameError on latest release (2024.2.20)
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[
"See #3644 (if you want a quick workaround just `pip install ase`)",
"Thank you for the workaround suggestion!\r\n\r\nClosing this as duplicate of #3644 "
] | 2024-02-22T13:57:44
| 2024-02-23T07:01:34
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2024-02-23T07:01:33Z
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CONTRIBUTOR
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### Python version
3.11
### Pymatgen version
2024.2.20
### Operating system version
Any Linux
### Current behavior
Importing gives a NameError:
```
from pymatgen.core.trajectory import Trajectory as PymatgenTrajectory
/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/site-packages/pymatgen/core/trajectory.py:19: in <module>
from pymatgen.io.ase import AseAtomsAdaptor
/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/site-packages/pymatgen/io/ase.py:44: in <module>
class MSONAtoms(Atoms, MSONable):
E NameError: name 'Atoms' is not defined
```
### Expected Behavior
I expect the import to be successful. It works on all versions before 2024.2.20
### Minimal example
```Python
Python 3.11.7 (main, Dec 4 2023, 18:10:11) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pymatgen.core.trajectory import Trajectory
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/vikko/local_projects/GEMDAT/.venv/lib/python3.11/site-packages/pymatgen/core/trajectory.py", line 19, in <module>
from pymatgen.io.ase import AseAtomsAdaptor
File "/home/vikko/local_projects/GEMDAT/.venv/lib/python3.11/site-packages/pymatgen/io/ase.py", line 44, in <module>
class MSONAtoms(Atoms, MSONable):
^^^^^
NameError: name 'Atoms' is not defined
```
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6AGW6a
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Can no longer import some modules without having ASE installed
|
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[
"Also just a comment that I would've expected this to be picked up by a linter; for me `Atoms is possible unbound` is flagged up by pyright but perhaps mypy is less picky as configured?",
"I noticed the same issue while trying to export XRD pattern for example [here](https://next-gen.materialsproject.org/materials/mp-728693?chemsys=Ni-Co-C-N-O-H#properties) with `mp_api` with the following demo code:\r\n```python\r\nfrom mp_api.client import MPRester\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\n\r\nwith MPRester(api_key=\"<enter your api key>\") as mpr:\r\n # first retrieve the relevant structure\r\n structure = mpr.get_structure_by_material_id(\"mp-728693\")\r\n\r\n# important to use the conventional structure to ensure\r\n# that peaks are labelled with the conventional Miller indices\r\nsga = SpacegroupAnalyzer(structure)\r\nconventional_structure = sga.get_conventional_standard_structure()\r\n\r\n# this example shows how to obtain an XRD diffraction pattern\r\n# these patterns are calculated on-the-fly from the structure\r\ncalculator = XRDCalculator(wavelength=\"CuKa\")\r\npattern = calculator.get_pattern(conventional_structure)\r\n```\r\n\r\nThe `ImportError` is captured in https://github.com/materialsproject/pymatgen/blob/57842a7969577e5959fb8c2086724d7ec6f47e47/pymatgen/io/ase.py#L25-L34\r\n\r\nSo no explicit error like `no module named ase` is raised.\r\n"
] | 2024-02-22T14:04:10
| 2024-02-23T10:18:21
|
2024-02-23T10:18:21Z
|
CONTRIBUTOR
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### Python version
3.11.7
### Pymatgen version
2024.2.20
### Operating system version
Any
### Current behavior
I observed this in a fresh virtual environment when trying to install and use `mp_api`. Before #3619 (or related follow-up commits, can't tell) you were able to import the AseAtomsAdaptor without an error, even if you didn't have ASE installed. This was changed by the creation of the `MSONAtoms` class which uses `Atoms` via inheritance and thus is loaded at import time.
Example as posted in https://github.com/materialsproject/pymatgen/pull/3619#discussion_r1499283539
```python
>>> from mp_api.client.mprester import MPRester
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/mp_api/client/__init__.py", line 8, in <module>
from .mprester import MPRester
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/mp_api/client/mprester.py", line 10, in <module>
from emmet.core.electronic_structure import BSPathType
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/emmet/core/electronic_structure.py", line 11, in <module>
from pymatgen.analysis.magnetism.analyzer import (
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/pymatgen/analysis/magnetism/__init__.py", line 5, in <module>
from pymatgen.analysis.magnetism.analyzer import (
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/pymatgen/analysis/magnetism/analyzer.py", line 24, in <module>
from pymatgen.transformations.advanced_transformations import MagOrderingTransformation, MagOrderParameterConstraint
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/pymatgen/transformations/advanced_transformations.py", line 33, in <module>
from pymatgen.io.ase import AseAtomsAdaptor
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-mp-api/lib/python3.11/site-packages/pymatgen/io/ase.py", line 44, in <module>
class MSONAtoms(Atoms, MSONable):
^^^^^
NameError: name 'Atoms' is not defined
```
### Expected Behavior
The module should still be importable in cases where `ase` is not available, as it was before.
### Minimal example
```Python
python -m venv .venv
. .venv/bin/activate
pip install pymatgen
$ python -c "from pymatgen.analysis.magnetism.analyzer import *"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-pymatgen/lib/python3.11/site-packages/pymatgen/analysis/magnetism/__init__.py", line 5, in <module>
from pymatgen.analysis.magnetism.analyzer import (
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-pymatgen/lib/python3.11/site-packages/pymatgen/analysis/magnetism/analyzer.py", line 24, in <module>
from pymatgen.transformations.advanced_transformations import MagOrderingTransformation, MagOrderParameterConstraint
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-pymatgen/lib/python3.11/site-packages/pymatgen/transformations/advanced_transformations.py", line 33, in <module>
from pymatgen.io.ase import AseAtomsAdaptor
File "/home/mevans/repos/re2fractive/re2fractive/experiments/2_featurizing_refractive_index_data/.venv-pymatgen/lib/python3.11/site-packages/pymatgen/io/ase.py", line 44, in <module>
class MSONAtoms(Atoms, MSONable):
^^^^^
NameError: name 'Atoms' is not defined
```
which runs correctly if you `pip install pymatgen==2024.2.8`.
### Relevant files to reproduce this bug
_No response_
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PR_kwDOACgets5np26z
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Guard `MSONAtoms` definition behind ASE package availability
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"> It would be nice to add a test or linter rule that would have caught the initial issue.\r\n\r\nthat π ",
"> > It would be nice to add a test or linter rule that would have caught the initial issue.\r\n> \r\n> that π\r\n\r\nAs opposed to a linter rule that only catches my fix ;)\r\n\r\n```\r\npymatgen/io/ase.py:64: error: Name \"MSONAtoms\" already defined on line 46 [no-redef]\r\nFound 1 error in 1 file (checked 279 source files)\r\n```",
"Makes sense. Thanks! ",
"I'm actually a bit confused why `mypy` passes in its current state on master... when I run locally following the same format as the CI (removing cache etc.) I get hundreds of errors (but not the one in question here interestingly :sweat_smile:)",
"> I'm actually a bit confused why `mypy` passes in its current state on master... when I run locally following the same format as the CI (removing cache etc.) I get hundreds of errors (but not the one in question here interestingly π
)\r\n\r\nIf anyone is interested, click details below... I guess the reason is that `mypy` is called in CI without any other dependencies installed, so will not check any third-party types (like numpy etc.). The `pre-commit` version of mypy is also skipped in the CI. Perhaps installing something like `types-all` would catch some of these without the overhead of reinstalling everything. \r\n\r\n<details>\r\n<summary>\r\nFound 788 errors in 81 files (checked 279 source files)\r\n</summary>\r\n\r\n```\r\n$ mypy pymatgen\r\npymatgen/util/coord.py:117: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[floating[Any]]]\", variable has type \"float\") [assignment]\r\npymatgen/util/coord.py:134: error: Argument 1 to \"zip\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]]\" [arg-type]\r\npymatgen/util/coord.py:134: error: Argument 1 to \"zip\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Any]\" [arg-type]\r\npymatgen/util/coord.py:134: error: Argument 2 to \"zip\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]]\" [arg-type]\r\npymatgen/util/coord.py:134: error: Argument 2 to \"zip\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Any]\" [arg-type]\r\npymatgen/util/coord.py:134: error: Argument \"key\" to \"sorted\" has incompatible type \"Callable[[tuple[Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]], Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]]], Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]]\"; expected \"Callable[[tuple[Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]], Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]]], Union[SupportsDunderLT[Any], SupportsDunderGT[Any]]]\" [arg-type]\r\npymatgen/util/coord.py:134: error: Incompatible return value type (got \"Union[int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]]]\", expected \"Union[SupportsDunderLT[Any], SupportsDunderGT[Any]]\") [return-value]\r\npymatgen/util/coord.py:139: error: Value of type variable \"SupportsRichComparisonT\" of \"min\" cannot be \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [type-var]\r\npymatgen/util/coord.py:139: error: If x = b'abc' then f\"{x}\" or \"{}\".format(x) produces \"b'abc'\", not \"abc\". If this is desired behavior, use f\"{x!r}\" or \"{!r}\".format(x). Otherwise, decode the bytes [str-bytes-safe]\r\npymatgen/util/coord.py:139: error: Value of type variable \"SupportsRichComparisonT\" of \"max\" cannot be \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [type-var]\r\npymatgen/util/coord.py:139: error: Argument 1 to \"min\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/util/coord.py:139: error: Argument 1 to \"max\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/util/coord.py:227: error: Incompatible return value type (got \"list[Never]\", expected \"ndarray[Any, Any]\") [return-value]\r\npymatgen/util/coord.py:273: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[floating[Any]]]\", variable has type \"float\") [assignment]\r\npymatgen/electronic_structure/core.py:146: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"Sequence[float]\") [assignment]\r\npymatgen/electronic_structure/core.py:148: error: No overload variant of \"__call__\" of \"_FloatOp\" matches argument type \"Sequence[float]\" [call-overload]\r\npymatgen/electronic_structure/core.py:148: note: Possible overload variants:\r\npymatgen/electronic_structure/core.py:148: note: def __call__(self, bool, /) -> floating[Any]\r\npymatgen/electronic_structure/core.py:148: note: def __call__(self, int, /) -> floating[Any]\r\npymatgen/electronic_structure/core.py:148: note: def __call__(self, float, /) -> floating[Any]\r\npymatgen/electronic_structure/core.py:148: note: def __call__(self, complex, /) -> complexfloating[Any, Any]\r\npymatgen/electronic_structure/core.py:148: note: def [_NBit2 <: NBitBase] __call__(self, Union[integer[_NBit2], floating[_NBit2]], /) -> floating[Union[Any, _NBit2]]\r\npymatgen/electronic_structure/core.py:425: error: Argument 1 to \"Magmom\" has incompatible type \"object\"; expected \"Union[float, Sequence[float], ndarray[Any, Any], Magmom]\" [arg-type]\r\npymatgen/core/lattice.py:364: error: Signature of \"from_dict\" incompatible with supertype \"MSONable\" [override]\r\npymatgen/core/lattice.py:364: note: Superclass:\r\npymatgen/core/lattice.py:364: note: @classmethod\r\npymatgen/core/lattice.py:364: note: def from_dict(cls, d: Any) -> Any\r\npymatgen/core/lattice.py:364: note: Subclass:\r\npymatgen/core/lattice.py:364: note: @classmethod\r\npymatgen/core/lattice.py:364: note: def from_dict(cls, dct: dict[Any, Any], fmt: Optional[str] = ..., **kwargs: Any) -> Any\r\npymatgen/core/lattice.py:1807: error: Argument 1 to \"append\" of \"list\" has incompatible type \"tuple[Any, float, int, tuple[Any, ...]]\"; expected \"tuple[ndarray[Any, Any], float, int, ndarray[Any, Any]]\" [arg-type]\r\npymatgen/symmetry/groups.py:124: error: Argument 1 to \"from_rotation_and_translation\" of \"SymmOp\" has incompatible type \"SymmOp\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/symmetry/groups.py:364: error: List item 0 has incompatible type \"SymmOp\"; expected \"ndarray[Any, Any]\" [list-item]\r\npymatgen/symmetry/groups.py:370: error: Argument 1 to \"append\" of \"list\" has incompatible type \"SymmOp\"; expected \"ndarray[Any, Any]\" [arg-type]\r\npymatgen/symmetry/groups.py:371: error: Incompatible return value type (got \"tuple[list[ndarray[Any, Any]], list[ndarray[Any, Any]]]\", expected \"tuple[list[ndarray[Any, Any]], list[SymmOp]]\") [return-value]\r\npymatgen/core/operations.py:491: error: \"SymmOp\" has no attribute \"time_reversal\" [attr-defined]\r\npymatgen/core/structure.py:343: error: Signature of \"__getitem__\" incompatible with supertype \"Sequence\" [override]\r\npymatgen/core/structure.py:343: note: Superclass:\r\npymatgen/core/structure.py:343: note: @overload\r\npymatgen/core/structure.py:343: note: def __getitem__(self, int, /) -> Any\r\npymatgen/core/structure.py:343: note: @overload\r\npymatgen/core/structure.py:343: note: def __getitem__(self, slice, /) -> Sequence[Any]\r\npymatgen/core/structure.py:343: note: Subclass:\r\npymatgen/core/structure.py:343: note: def __getitem__(self, Union[int, slice], /) -> Site\r\npymatgen/core/structure.py:684: error: Invalid index type \"Species\" for \"dict[Element, float]\"; expected type \"Element\" [index]\r\npymatgen/core/structure.py:837: error: Item \"Structure\" of \"Union[Structure, Molecule]\" has no attribute \"calc\" [union-attr]\r\npymatgen/core/structure.py:837: error: Item \"Molecule\" of \"Union[Structure, Molecule]\" has no attribute \"calc\" [union-attr]\r\npymatgen/core/structure.py:838: error: Item \"Structure\" of \"Union[Structure, Molecule]\" has no attribute \"dynamics\" [union-attr]\r\npymatgen/core/structure.py:838: error: Item \"Molecule\" of \"Union[Structure, Molecule]\" has no attribute \"dynamics\" [union-attr]\r\npymatgen/core/structure.py:1338: error: Argument 1 to \"SpacegroupAnalyzer\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:1359: error: Argument 1 to \"fit_anonymous\" of \"StructureMatcher\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:1359: error: Argument 2 to \"fit_anonymous\" of \"StructureMatcher\" has incompatible type \"Union[IStructure, Structure]\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:1360: error: Argument 1 to \"fit\" of \"StructureMatcher\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:1360: error: Argument 2 to \"fit\" of \"StructureMatcher\" has incompatible type \"Union[IStructure, Structure]\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:1434: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:1467: error: Incompatible types in assignment (expression has type \"Site\", variable has type \"PeriodicSite\") [assignment]\r\npymatgen/core/structure.py:1468: error: Argument 1 to \"distance\" of \"PeriodicSite\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/core/structure.py:1649: error: Incompatible types in assignment (expression has type \"list[Site]\", variable has type \"Optional[Sequence[PeriodicSite]]\") [assignment]\r\npymatgen/core/structure.py:1650: error: Value of type variable \"_SCT\" of \"ascontiguousarray\" cannot be \"float\" [type-var]\r\npymatgen/core/structure.py:1650: error: Item \"None\" of \"Optional[Sequence[PeriodicSite]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/core/structure.py:1867: error: Incompatible types in assignment (expression has type \"list[Site]\", variable has type \"Optional[Sequence[PeriodicSite]]\") [assignment]\r\npymatgen/core/structure.py:1872: error: Argument 1 to \"len\" has incompatible type \"Optional[Sequence[PeriodicSite]]\"; expected \"Sized\" [arg-type]\r\npymatgen/core/structure.py:1880: error: Value of type \"Optional[Sequence[PeriodicSite]]\" is not indexable [index]\r\npymatgen/core/structure.py:1906: error: Argument 1 to \"len\" has incompatible type \"Optional[Sequence[PeriodicSite]]\"; expected \"Sized\" [arg-type]\r\npymatgen/core/structure.py:1955: error: Incompatible types in assignment (expression has type \"list[Site]\", variable has type \"Optional[Sequence[PeriodicSite]]\") [assignment]\r\npymatgen/core/structure.py:1956: error: Item \"None\" of \"Optional[Sequence[PeriodicSite]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/core/structure.py:1966: error: Argument 2 to \"zip\" has incompatible type \"Optional[Sequence[PeriodicSite]]\"; expected \"Iterable[PeriodicSite]\" [arg-type]\r\npymatgen/core/structure.py:2158: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:2186: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:2594: error: List item 0 has incompatible type \"IStructure\"; expected \"Structure\" [list-item]\r\npymatgen/core/structure.py:2606: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/structure.py:2641: error: Argument 1 to \"structure_to_abivars\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2708: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:2735: error: Argument 1 to \"CifWriter\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2739: error: Argument 1 to \"CifWriter\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2743: error: Incompatible types in assignment (expression has type \"Poscar\", variable has type \"CifWriter\") [assignment]\r\npymatgen/core/structure.py:2743: error: Argument 1 to \"Poscar\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2757: error: Argument 1 to \"XSF\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2770: error: Argument 1 to \"Mcsqs\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2778: error: Argument 1 to \"Prismatic\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2796: error: Argument 1 to \"structure_to_str\" of \"ResIO\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2804: error: Incompatible types in assignment (expression has type \"AtomConfig\", variable has type \"CifWriter\") [assignment]\r\npymatgen/core/structure.py:2804: error: Argument 1 to \"AtomConfig\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:2893: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/core/structure.py:2896: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/structure.py:3003: error: Argument 1 to \"SpacegroupAnalyzer\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/core/structure.py:3098: error: Argument 1 to \"tuple\" has incompatible type \"list[Site]\"; expected \"Iterable[PeriodicSite]\" [arg-type]\r\npymatgen/core/structure.py:3482: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/core/structure.py:3482: error: Argument 1 to \"range\" has incompatible type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"SupportsIndex\" [arg-type]\r\npymatgen/core/structure.py:3483: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/core/structure.py:3483: error: Argument 1 to \"range\" has incompatible type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"SupportsIndex\" [arg-type]\r\npymatgen/core/structure.py:3693: error: Definition of \"__getitem__\" in base class \"SiteCollection\" is incompatible with definition in base class \"MutableSequence\" [misc]\r\npymatgen/core/structure.py:3848: error: \"Site\" has no attribute \"lattice\" [attr-defined]\r\npymatgen/core/structure.py:3975: error: \"PeriodicNeighbor\" has no attribute \"__iter__\" (not iterable) [attr-defined]\r\npymatgen/core/structure.py:3975: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/core/structure.py:3978: error: \"PeriodicNeighbor\" has no attribute \"__iter__\" (not iterable) [attr-defined]\r\npymatgen/core/structure.py:4011: error: Incompatible types in assignment (expression has type \"IMolecule\", variable has type \"Molecule\") [assignment]\r\npymatgen/core/structure.py:4041: error: \"Site\" has no attribute \"__iter__\"; maybe \"__str__\"? (not iterable) [attr-defined]\r\npymatgen/core/structure.py:4066: error: Incompatible types in assignment (expression has type \"list[PeriodicSite]\", variable has type \"list[Site]\") [assignment]\r\npymatgen/core/structure.py:4066: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/core/structure.py:4066: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/core/structure.py:4193: error: \"Site\" has no attribute \"frac_coords\" [attr-defined]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"float\") [operator]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"complex\") [operator]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"str\") [operator]\r\npymatgen/core/structure.py:4308: error: Unsupported operand types for * (\"Structure\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/core/structure.py:4308: note: Right operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/core/structure.py:4420: error: Incompatible return value type (got \"Union[Structure, Molecule, tuple[Union[Structure, Molecule], Union[Any, Any]]]\", expected \"Union[Structure, tuple[Structure, Union[Any, Any]]]\") [return-value]\r\npymatgen/core/structure.py:4461: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4463: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4465: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4469: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4471: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4475: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4479: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4483: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4487: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4491: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/structure.py:4499: error: Definition of \"__getitem__\" in base class \"SiteCollection\" is incompatible with definition in base class \"MutableSequence\" [misc]\r\npymatgen/core/structure.py:4886: error: Incompatible types in assignment (expression has type \"IMolecule\", variable has type \"Molecule\") [assignment]\r\npymatgen/core/structure.py:4947: error: Incompatible return value type (got \"Union[Structure, Molecule, tuple[Union[Structure, Molecule], Union[Any, Any]]]\", expected \"Union[Molecule, tuple[Molecule, Any]]\") [return-value]\r\npymatgen/util/plotting.py:179: error: Argument 1 to \"polyfit\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]]], bool, int, float, _NestedSequence[Union[bool, int, float]]]\" [arg-type]\r\npymatgen/util/plotting.py:179: error: Argument 2 to \"polyfit\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]]], bool, int, float, _NestedSequence[Union[bool, int, float]]]\" [arg-type]\r\npymatgen/util/plotting.py:180: error: Value of type variable \"SupportsRichComparisonT\" of \"min\" cannot be \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [type-var]\r\npymatgen/util/plotting.py:180: error: Argument 1 to \"linspace\" has incompatible type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]]], bool, int, float, _NestedSequence[Union[bool, int, float]]]\" [arg-type]\r\npymatgen/util/plotting.py:180: error: Argument 1 to \"min\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/util/plotting.py:180: error: Value of type variable \"SupportsRichComparisonT\" of \"max\" cannot be \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [type-var]\r\npymatgen/util/plotting.py:180: error: Argument 2 to \"linspace\" has incompatible type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]], _NestedSequence[_SupportsArray[dtype[Union[bool_, integer[Any], floating[Any]]]]], bool, int, float, _NestedSequence[Union[bool, int, float]]]\" [arg-type]\r\npymatgen/util/plotting.py:180: error: Argument 1 to \"max\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/util/plotting.py:360: error: Argument 1 to \"to_rgba\" of \"ScalarMappable\" has incompatible type \"Element\"; expected \"ndarray[Any, Any]\" [arg-type]\r\npymatgen/util/plotting.py:361: error: Argument 1 to \"_decide_fontcolor\" has incompatible type \"ndarray[Any, Any]\"; expected \"tuple[Any, ...]\" [arg-type]\r\npymatgen/util/plotting.py:456: error: Argument \"xy\" to \"annotate\" has incompatible type \"list[Any]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/util/plotting.py:457: error: Argument \"xy\" to \"annotate\" has incompatible type \"list[Any]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/util/plotting.py:458: error: Argument \"xy\" to \"annotate\" has incompatible type \"list[Any]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/util/plotting.py:538: error: Argument \"xy\" to \"annotate\" has incompatible type \"list[object]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/io/res.py:307: error: Argument 1 to \"_res_from_structure\" of \"ResWriter\" has incompatible type \"Union[Structure, ComputedStructureEntry]\"; expected \"Structure\" [arg-type]\r\npymatgen/io/res.py:307: error: Argument 1 to \"_res_from_entry\" of \"ResWriter\" has incompatible type \"Union[Structure, ComputedStructureEntry]\"; expected \"ComputedStructureEntry\" [arg-type]\r\npymatgen/io/res.py:370: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/io/common.py:58: error: \"ndarray[Any, Any]\" has no attribute \"items\"; maybe \"item\"? [attr-defined]\r\npymatgen/io/common.py:60: error: Need type annotation for \"data_aug\" [var-annotated]\r\npymatgen/io/ase.py:54: error: Signature of \"from_dict\" incompatible with supertype \"MSONable\" [override]\r\npymatgen/io/ase.py:54: note: Superclass:\r\npymatgen/io/ase.py:54: note: @classmethod\r\npymatgen/io/ase.py:54: note: def from_dict(cls, d: Any) -> Any\r\npymatgen/io/ase.py:54: note: Subclass:\r\npymatgen/io/ase.py:54: note: def from_dict(d) -> MSONAtoms\r\npymatgen/io/ase.py:281: error: \"Structure\" has no attribute \"calc\" [attr-defined]\r\npymatgen/io/ase.py:350: error: Argument \"cls\" to \"get_structure\" of \"AseAtomsAdaptor\" has incompatible type \"type[Molecule]\"; expected \"type[Structure]\" [arg-type]\r\npymatgen/io/ase.py:363: error: \"Structure\" has no attribute \"set_charge_and_spin\" [attr-defined]\r\npymatgen/io/ase.py:365: error: Incompatible return value type (got \"Structure\", expected \"Molecule\") [return-value]\r\npymatgen/io/vasp/inputs.py:134: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/io/vasp/inputs.py:134: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/io/vasp/inputs.py:137: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/io/vasp/inputs.py:443: error: Argument 1 to \"append\" of \"list\" has incompatible type \"list[Any]\"; expected \"ndarray[Any, Any]\" [arg-type]\r\npymatgen/io/abinit/abiobjects.py:234: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[Any]\") [assignment]\r\npymatgen/electronic_structure/dos.py:1263: error: Argument 3 to \"CompleteDos\" has incompatible type \"dict[Site, dict[Orbital, dict[Spin, Any]]]\"; expected \"Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\" [arg-type]\r\npymatgen/electronic_structure/dos.py:1279: error: Invalid index type \"Site\" for \"Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/electronic_structure/dos.py:1409: error: Argument 3 to \"LobsterCompleteDos\" has incompatible type \"dict[Site, dict[Any, dict[Spin, Any]]]\"; expected \"Mapping[PeriodicSite, Mapping[Orbital, Mapping[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\" [arg-type]\r\npymatgen/analysis/structure_matcher.py:949: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/analysis/phase_diagram.py:426: error: Set comprehension has incompatible type Set[Union[Element, Species, DummySpecies]]; expected Set[Element] [misc]\r\npymatgen/analysis/phase_diagram.py:607: error: \"Entry\" has no attribute \"name\" [attr-defined]\r\npymatgen/analysis/phase_diagram.py:695: error: No overload variant of \"zip\" matches argument types \"Simplex\", \"Any\" [call-overload]\r\npymatgen/analysis/phase_diagram.py:695: note: Possible overload variants:\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co] __new__(cls) -> zip[Any]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co, _T1] __new__(cls, Iterable[_T1], /) -> zip[tuple[_T1]]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co, _T1, _T2] __new__(cls, Iterable[_T1], Iterable[_T2], /) -> zip[tuple[_T1, _T2]]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co, _T1, _T2, _T3] __new__(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], /) -> zip[tuple[_T1, _T2, _T3]]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co, _T1, _T2, _T3, _T4] __new__(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], /) -> zip[tuple[_T1, _T2, _T3, _T4]]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co, _T1, _T2, _T3, _T4, _T5] __new__(cls, Iterable[_T1], Iterable[_T2], Iterable[_T3], Iterable[_T4], Iterable[_T5], /) -> zip[tuple[_T1, _T2, _T3, _T4, _T5]]\r\npymatgen/analysis/phase_diagram.py:695: note: def [_T_co] __new__(cls, Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], Iterable[Any], /, *iterables: Iterable[Any]) -> zip[tuple[Any, ...]]\r\npymatgen/analysis/phase_diagram.py:828: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"list[Entry]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/analysis/phase_diagram.py:828: error: Argument \"elements\" to \"PhaseDiagram\" has incompatible type \"list[Union[Element, Species, DummySpecies]]\"; expected \"Sequence[Element]\" [arg-type]\r\npymatgen/analysis/phase_diagram.py:929: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"set[Union[Entry, Any]]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/analysis/phase_diagram.py:1614: error: Set comprehension has incompatible type Set[Union[Element, Species, DummySpecies]]; expected Set[Element] [misc]\r\npymatgen/analysis/phase_diagram.py:1757: error: Invalid index type \"frozenset[Union[Element, Species]]\" for \"dict[frozenset[Element], PhaseDiagram]\"; expected type \"frozenset[Element]\" [index]\r\npymatgen/analysis/phase_diagram.py:1982: error: \"PDEntry\" has no attribute \"decomposition\" [attr-defined]\r\npymatgen/analysis/phase_diagram.py:2176: error: Argument 1 to \"get_form_energy_per_atom\" of \"PhaseDiagram\" has incompatible type \"Entry\"; expected \"PDEntry\" [arg-type]\r\npymatgen/analysis/phase_diagram.py:2278: error: Item \"None\" of \"Union[Any, Figure, None]\" has no attribute \"show\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2280: error: Item \"Axes\" of \"Union[Any, Axes]\" has no attribute \"show\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2296: error: Item \"SubFigure\" of \"Union[Any, Figure, SubFigure, None]\" has no attribute \"set_size_inches\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2296: error: Item \"None\" of \"Union[Any, Figure, SubFigure, None]\" has no attribute \"set_size_inches\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2297: error: Item \"SubFigure\" of \"Union[Any, Figure, SubFigure, None]\" has no attribute \"savefig\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2297: error: Item \"None\" of \"Union[Any, Figure, SubFigure, None]\" has no attribute \"savefig\" [union-attr]\r\npymatgen/analysis/phase_diagram.py:2300: error: Item \"Axes\" of \"Union[Any, Axes]\" has no attribute \"write_image\" [union-attr]\r\npymatgen/symmetry/kpath.py:926: error: Incompatible types in assignment (expression has type \"Composition\", variable has type \"list[Composition]\") [assignment]\r\npymatgen/symmetry/kpath.py:928: error: Argument 1 to \"index\" of \"list\" has incompatible type \"list[Composition]\"; expected \"Union[str, Element, Species, DummySpecies]\" [arg-type]\r\npymatgen/symmetry/kpath.py:931: error: Argument 1 to \"append\" of \"list\" has incompatible type \"list[Composition]\"; expected \"Union[str, Element, Species, DummySpecies]\" [arg-type]\r\npymatgen/io/cif.py:1123: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/io/cif.py:1129: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/electronic_structure/bandstructure.py:742: error: Argument 1 to \"append\" of \"list\" has incompatible type \"floating[Any]\"; expected \"float\" [arg-type]\r\npymatgen/io/pwmat/inputs.py:366: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/io/pwmat/inputs.py:392: error: Argument \"species\" to \"Structure\" has incompatible type \"ndarray[Any, Any]\"; expected \"Sequence[Union[str, Element, Species, DummySpecies, dict[Any, Any], Composition]]\" [arg-type]\r\npymatgen/io/pwmat/inputs.py:393: error: Argument \"coords\" to \"Structure\" has incompatible type \"ndarray[Any, Any]\"; expected \"Sequence[Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/io/pwmat/outputs.py:256: error: Function \"numpy.core.multiarray.array\" is not valid as a type [valid-type]\r\npymatgen/io/pwmat/outputs.py:256: note: Perhaps you need \"Callable[...]\" or a callback protocol?\r\npymatgen/io/pwmat/outputs.py:257: error: Function \"numpy.core.multiarray.array\" is not valid as a type [valid-type]\r\npymatgen/io/pwmat/outputs.py:257: note: Perhaps you need \"Callable[...]\" or a callback protocol?\r\npymatgen/io/pwmat/outputs.py:258: error: Function \"numpy.core.multiarray.array\" is not valid as a type [valid-type]\r\npymatgen/io/pwmat/outputs.py:258: note: Perhaps you need \"Callable[...]\" or a callback protocol?\r\npymatgen/io/pwmat/outputs.py:263: error: Value of type np.array? is not indexable [index]\r\npymatgen/io/pwmat/outputs.py:264: error: Unsupported target for indexed assignment (np.array?) [index]\r\npymatgen/core/trajectory.py:171: error: Incompatible return value type (got \"Union[Structure, Trajectory]\", expected \"Structure\") [return-value]\r\npymatgen/core/trajectory.py:186: error: Incompatible return value type (got \"Union[Molecule, Trajectory]\", expected \"Molecule\") [return-value]\r\npymatgen/core/trajectory.py:293: error: Incompatible types in \"yield\" (actual type \"Union[Molecule, Structure, Trajectory]\", expected type \"Union[Structure, Molecule]\") [misc]\r\npymatgen/core/trajectory.py:326: error: Argument 1 to \"Molecule\" has incompatible type \"list[Union[str, Element, Species, DummySpecies, Composition]]\"; expected \"Sequence[Union[str, Element, Species, DummySpecies]]\" [arg-type]\r\npymatgen/core/trajectory.py:417: error: Item \"Trajectory\" of \"Union[Molecule, Structure, Trajectory]\" has no attribute \"reduced_formula\" [union-attr]\r\npymatgen/core/trajectory.py:421: error: Item \"Structure\" of \"Union[Site, Structure, Molecule]\" has no attribute \"specie\" [union-attr]\r\npymatgen/core/trajectory.py:421: error: Item \"Molecule\" of \"Union[Site, Structure, Molecule]\" has no attribute \"specie\" [union-attr]\r\npymatgen/core/trajectory.py:423: error: Item \"Structure\" of \"Union[Site, Structure, Molecule]\" has no attribute \"specie\" [union-attr]\r\npymatgen/core/trajectory.py:423: error: Item \"Molecule\" of \"Union[Site, Structure, Molecule]\" has no attribute \"specie\" [union-attr]\r\npymatgen/vis/structure_vtk.py:216: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/vis/structure_vtk.py:217: error: \"IStructure\" has no attribute \"make_supercell\" [attr-defined]\r\npymatgen/vis/structure_vtk.py:266: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/vis/structure_vtk.py:296: error: \"IStructure\" has no attribute \"center_of_mass\" [attr-defined]\r\npymatgen/vis/structure_vtk.py:299: error: \"IStructure\" has no attribute \"center_of_mass\" [attr-defined]\r\npymatgen/phonon/thermal_displacements.py:53: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/thermal_displacements.py:56: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/thermal_displacements.py:77: error: Incompatible types in assignment (expression has type \"None\", variable has type \"ndarray[Any, dtype[Any]]\") [assignment]\r\npymatgen/phonon/thermal_displacements.py:90: error: \"ndarray\" expects 2 type arguments, but 1 given [type-arg]\r\npymatgen/phonon/thermal_displacements.py:90: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/thermal_displacements.py:99: error: Argument 1 to \"len\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Sized\" [arg-type]\r\npymatgen/phonon/thermal_displacements.py:100: error: Argument 1 to \"enumerate\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/phonon/thermal_displacements.py:102: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:103: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:104: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:105: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:106: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:107: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:108: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:109: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:110: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:114: error: \"ndarray\" expects 2 type arguments, but 1 given [type-arg]\r\npymatgen/phonon/thermal_displacements.py:114: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/thermal_displacements.py:123: error: Argument 1 to \"len\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Sized\" [arg-type]\r\npymatgen/phonon/thermal_displacements.py:124: error: Argument 1 to \"enumerate\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/phonon/thermal_displacements.py:126: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:126: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:127: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:127: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:128: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:128: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:129: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:129: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:130: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:130: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:131: error: Value of type \"Union[int, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:131: error: Value of type \"Union[Any, str, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/thermal_displacements.py:415: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/dos.py:67: error: Argument 1 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:89: error: Argument 1 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:89: error: Argument 2 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:97: error: Argument 1 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:97: error: Argument 2 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:155: error: Incompatible return value type (got \"signedinteger[Any]\", expected \"int\") [return-value]\r\npymatgen/phonon/dos.py:443: error: Argument 1 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:443: error: Argument 2 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:458: error: Argument 1 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/dos.py:458: error: Argument 2 to \"PhononDos\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:128: error: Argument 1 to \"Kpoint\" has incompatible type \"Kpoint\"; expected \"ndarray[Any, Any]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:130: error: Argument 1 to \"Kpoint\" has incompatible type \"Kpoint\"; expected \"ndarray[Any, Any]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:132: error: Argument 1 to \"len\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Sized\" [arg-type]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:155: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:157: error: Incompatible return value type (got \"tuple[Kpoint, Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\", expected \"tuple[Kpoint, float]\") [return-value]\r\npymatgen/phonon/bandstructure.py:157: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:157: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[signedinteger[Any], ...]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:157: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:157: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:157: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:157: error: Invalid index type \"tuple[signedinteger[Any], ...]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:157: error: Invalid index type \"tuple[signedinteger[Any], ...]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:161: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:163: error: Incompatible return value type (got \"tuple[Kpoint, Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\", expected \"tuple[Kpoint, float]\") [return-value]\r\npymatgen/phonon/bandstructure.py:163: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:163: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[signedinteger[Any], ...]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:163: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:163: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:163: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:163: error: Invalid index type \"tuple[signedinteger[Any], ...]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:163: error: Invalid index type \"tuple[signedinteger[Any], ...]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for <= (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for <= (\"int\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:172: note: Left operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for >= (\"str\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:172: error: Unsupported operand types for >= (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:173: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"str\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"int\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"float\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"complex\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"bytes\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"max\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"str\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"int\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"float\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"complex\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"bytes\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:173: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"min\" [union-attr]\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for > (\"float\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for > (\"float\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for > (\"float\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for > (\"float\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:196: note: Left operand is of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for < (\"str\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:196: error: Unsupported operand types for < (\"bytes\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:196: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:196: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:196: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:196: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:196: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:196: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/bandstructure.py:196: error: Item \"int\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/bandstructure.py:196: error: Item \"float\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/bandstructure.py:196: error: Item \"complex\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/bandstructure.py:196: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:196: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:211: error: Argument 1 to \"len\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Sized\" [arg-type]\r\npymatgen/phonon/bandstructure.py:263: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:263: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:264: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:264: error: Invalid index type \"slice\" for \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported left operand type for - (\"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_SupportsArray[dtype[Any]]\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_SupportsArray[dtype[Any]]\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_SupportsArray[dtype[Any]]\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported left operand type for - (\"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[_SupportsArray[dtype[Any]]]\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[_SupportsArray[dtype[Any]]]\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[_SupportsArray[dtype[Any]]]\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported left operand type for - (\"str\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"str\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"str\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"str\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported left operand type for - (\"bytes\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"bytes\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"bytes\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"int\" and \"str\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"int\" and \"bytes\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"float\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"float\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"float\" and \"str\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"float\" and \"bytes\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"float\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"complex\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"complex\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"complex\" and \"str\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"complex\" and \"bytes\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"complex\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported left operand type for - (\"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" and \"int\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" and \"float\") [operator]\r\npymatgen/phonon/bandstructure.py:264: error: Unsupported operand types for - (\"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" and \"complex\") [operator]\r\npymatgen/phonon/bandstructure.py:264: note: Both left and right operands are unions\r\npymatgen/phonon/bandstructure.py:270: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:270: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[list[int], int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:270: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:270: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:270: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:270: error: Invalid index type \"tuple[list[int], int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:270: error: Invalid index type \"tuple[list[int], int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:272: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:272: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:272: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:272: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:272: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:272: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:272: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:393: error: Argument 1 to \"_reuse_init\" of \"PhononBandStructureSymmLine\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], None]\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:396: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:416: error: Argument 1 to \"append\" of \"list\" has incompatible type \"floating[Any]\"; expected \"float\" [arg-type]\r\npymatgen/phonon/bandstructure.py:443: error: Argument 1 to \"allclose\" has incompatible type \"Kpoint\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:444: error: Argument 1 to \"allclose\" has incompatible type \"Kpoint\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:447: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:447: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:447: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:447: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:447: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:447: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:447: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:449: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:449: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:449: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:449: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:449: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:449: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:449: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:450: error: Argument 1 to \"allclose\" has incompatible type \"Kpoint\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/phonon/bandstructure.py:453: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:453: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:453: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:453: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:453: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:453: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:453: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:455: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:455: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:455: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:455: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:455: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:455: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:455: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:457: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[tuple[list[float], ndarray[Any, Any]]]\") [assignment]\r\npymatgen/phonon/bandstructure.py:458: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[tuple[list[float], ndarray[Any, Any]]]\") [assignment]\r\npymatgen/phonon/bandstructure.py:573: error: Incompatible types in assignment (expression has type \"floating[Any]\", variable has type \"int\") [assignment]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:582: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:586: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"copy\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:600: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"shape\" [union-attr]\r\npymatgen/phonon/bandstructure.py:610: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:610: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:610: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:610: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:610: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:610: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:610: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:611: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:611: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:611: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:611: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:611: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:611: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:611: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:620: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:620: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:620: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:620: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:620: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:620: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:620: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:621: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:621: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, int]\" [call-overload]\r\npymatgen/phonon/bandstructure.py:621: note: Possible overload variants:\r\npymatgen/phonon/bandstructure.py:621: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/bandstructure.py:621: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/bandstructure.py:621: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/bandstructure.py:621: error: Invalid index type \"tuple[slice, int]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/bandstructure.py:622: error: Unsupported target for indexed assignment (\"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\") [index]\r\npymatgen/phonon/bandstructure.py:622: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/bandstructure.py:623: error: Unsupported target for indexed assignment (\"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\") [index]\r\npymatgen/phonon/bandstructure.py:623: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/io/zeopp.py:204: error: Item \"Site\" of \"Union[SiteCollection, Site]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/io/lobster/inputs.py:340: error: Argument 1 to \"_get_nbands\" of \"Lobsterin\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/io/lobster/inputs.py:468: error: Argument 1 to \"automatic_density_by_vol\" of \"Kpoints\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/io/lobster/inputs.py:817: error: Argument \"structure\" to \"get_basis\" of \"Lobsterin\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/io/lammps/data.py:847: error: Argument 3 to \"Structure\" has incompatible type \"ndarray[Any, Any]\"; expected \"Sequence[Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/io/lammps/data.py:1256: error: Argument 1 to \"LammpsBox\" has incompatible type \"ndarray[Any, Any]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/io/feff/inputs.py:184: error: Argument 1 to \"SpacegroupAnalyzer\" has incompatible type \"Union[Structure, Molecule]\"; expected \"Structure\" [arg-type]\r\npymatgen/io/aims/inputs.py:89: error: No overload variant of \"__setitem__\" of \"list\" matches argument types \"int\", \"ndarray[Any, Any]\" [call-overload]\r\npymatgen/io/aims/inputs.py:89: note: Possible overload variants:\r\npymatgen/io/aims/inputs.py:89: note: def __setitem__(self, SupportsIndex, list[float], /) -> None\r\npymatgen/io/aims/inputs.py:89: note: def __setitem__(self, slice, Iterable[list[float]], /) -> None\r\npymatgen/io/aims/inputs.py:99: error: Argument 3 to \"Molecule\" has incompatible type \"floating[_64Bit]\"; expected \"float\" [arg-type]\r\npymatgen/io/aims/inputs.py:101: error: Incompatible types in assignment (expression has type \"Structure\", variable has type \"Molecule\") [assignment]\r\npymatgen/io/aims/inputs.py:102: error: Argument 4 to \"Structure\" has incompatible type \"floating[_64Bit]\"; expected \"Optional[float]\" [arg-type]\r\npymatgen/io/aims/inputs.py:189: error: Incompatible types in assignment (expression has type \"Union[Structure, Molecule]\", target has type \"str\") [assignment]\r\npymatgen/io/aims/inputs.py:260: error: Argument \"default_factory\" to \"field\" has incompatible type \"Callable[[], ndarray[Any, dtype[floating[Any]]]]\"; expected \"Callable[[], Sequence[Sequence[float]]]\" [arg-type]\r\npymatgen/io/aims/inputs.py:260: error: Incompatible return value type (got \"ndarray[Any, dtype[floating[Any]]]\", expected \"Sequence[Sequence[float]]\") [return-value]\r\npymatgen/io/aims/inputs.py:614: error: Need type annotation for \"species\" [var-annotated]\r\npymatgen/io/abinit/pseudos.py:148: error: \"Pseudo\" has no attribute \"xc\" [attr-defined]\r\npymatgen/io/abinit/pseudos.py:152: error: \"Pseudo\" has no attribute \"nlcc_radius\" [attr-defined]\r\npymatgen/io/abinit/pseudos.py:169: error: \"Pseudo\" has no attribute \"path\" [attr-defined]\r\npymatgen/ext/cod.py:117: error: Dict entry 0 has incompatible type \"str\": \"IStructure\"; expected \"str\": \"Union[str, int, Structure]\" [dict-item]\r\npymatgen/entries/entry_tools.py:298: error: Argument 1 to \"update\" of \"set\" has incompatible type \"list[Union[Element, Species, DummySpecies]]\"; expected \"Iterable[Element]\" [arg-type]\r\npymatgen/electronic_structure/boltztrap.py:1596: error: Invalid index type \"Site\" for \"dict[PeriodicSite, dict[Orbital, dict[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/electronic_structure/boltztrap.py:1598: error: Invalid index type \"Site\" for \"dict[PeriodicSite, dict[Orbital, dict[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/electronic_structure/boltztrap.py:1599: error: Invalid index type \"Site\" for \"dict[PeriodicSite, dict[Orbital, dict[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/electronic_structure/boltztrap.py:1600: error: Invalid index type \"Site\" for \"dict[PeriodicSite, dict[Orbital, dict[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/electronic_structure/boltztrap.py:1602: error: Invalid index type \"Site\" for \"dict[PeriodicSite, dict[Orbital, dict[Spin, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]]]\"; expected type \"PeriodicSite\" [index]\r\npymatgen/core/tensors.py:94: error: Signature of \"__hash__\" incompatible with supertype \"ndarray\" [override]\r\npymatgen/core/tensors.py:94: note: Superclass:\r\npymatgen/core/tensors.py:94: note: None\r\npymatgen/core/tensors.py:94: note: Subclass:\r\npymatgen/core/tensors.py:94: note: def __hash__(self) -> int\r\npymatgen/core/tensors.py:96: error: \"Tensor\" has no attribute \"tostring\" [attr-defined]\r\npymatgen/apps/battery/battery_abc.py:67: error: Incompatible return value type (got \"Union[Element, Species, DummySpecies]\", expected \"Element\") [return-value]\r\npymatgen/analysis/molecule_matcher.py:1207: error: List comprehension has incompatible type List[Site]; expected List[PeriodicSite] [misc]\r\npymatgen/analysis/molecule_matcher.py:1209: error: Argument 1 to \"match\" of \"KabschMatcher\" has incompatible type \"IMolecule\"; expected \"Molecule\" [arg-type]\r\npymatgen/analysis/molecule_matcher.py:1230: error: List comprehension has incompatible type List[Site]; expected List[PeriodicSite] [misc]\r\npymatgen/analysis/molecule_matcher.py:1232: error: Argument 1 to \"match\" of \"KabschMatcher\" has incompatible type \"IMolecule\"; expected \"Molecule\" [arg-type]\r\npymatgen/analysis/interface_reactions.py:427: error: Argument 1 to \"close\" has incompatible type \"Union[Figure, SubFigure, None]\"; expected \"Union[None, int, str, Figure, Literal['all']]\" [arg-type]\r\npymatgen/analysis/interface_reactions.py:428: error: Incompatible return value type (got \"Union[Figure, SubFigure, None]\", expected \"Figure\") [return-value]\r\npymatgen/analysis/interface_reactions.py:697: error: \"PhaseDiagram\" has no attribute \"chempots\" [attr-defined]\r\npymatgen/analysis/interface_reactions.py:717: error: Unsupported operand types for - (\"float\" and \"int\") [operator]\r\npymatgen/analysis/interface_reactions.py:717: error: \"PhaseDiagram\" has no attribute \"chempots\" [attr-defined]\r\npymatgen/analysis/interface_reactions.py:722: error: Unsupported operand types for / (\"float\" and \"int\") [operator]\r\npymatgen/analysis/interface_reactions.py:722: error: Generator has incompatible item type \"float\"; expected \"bool\" [misc]\r\npymatgen/analysis/interface_reactions.py:722: error: \"PhaseDiagram\" has no attribute \"chempots\" [attr-defined]\r\npymatgen/analysis/ewald.py:447: error: Signature of \"from_dict\" incompatible with supertype \"MSONable\" [override]\r\npymatgen/analysis/ewald.py:447: note: Superclass:\r\npymatgen/analysis/ewald.py:447: note: @classmethod\r\npymatgen/analysis/ewald.py:447: note: def from_dict(cls, d: Any) -> Any\r\npymatgen/analysis/ewald.py:447: note: Subclass:\r\npymatgen/analysis/ewald.py:447: note: @classmethod\r\npymatgen/analysis/ewald.py:447: note: def from_dict(cls, dct: dict[str, Any], fmt: Optional[str] = ..., **kwargs: Any) -> EwaldSummation\r\npymatgen/analysis/chempot_diagram.py:177: error: Incompatible types in assignment (expression has type \"list[Union[Element, Species]]\", variable has type \"list[Element]\") [assignment]\r\npymatgen/analysis/chempot_diagram.py:248: error: Invalid index type \"Union[Element, Species]\" for \"dict[Element, PDEntry]\"; expected type \"Element\" [index]\r\npymatgen/analysis/chempot_diagram.py:558: error: Incompatible return value type (got \"tuple[list[PDEntry], dict[Union[Element, Species, DummySpecies], PDEntry]]\", expected \"tuple[list[PDEntry], dict[Element, PDEntry]]\") [return-value]\r\npymatgen/analysis/chempot_diagram.py:603: error: Invalid index type \"Union[Element, Species]\" for \"dict[Element, tuple[float, float]]\"; expected type \"Element\" [index]\r\npymatgen/analysis/chempot_diagram.py:609: error: Incompatible return value type (got \"dict[str, PDEntry]\", expected \"dict[str, ComputedEntry]\") [return-value]\r\npymatgen/analysis/gb/grain.py:221: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/analysis/gb/grain.py:221: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/gb/grain.py:230: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/analysis/gb/grain.py:230: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/gb/grain.py:770: error: \"IStructure\" has no attribute \"merge_sites\" [attr-defined]\r\npymatgen/analysis/gb/grain.py:772: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/analysis/gb/grain.py:772: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Union[Site, PeriodicSite]]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/ferroelectricity/polarization.py:127: error: Incompatible types in assignment (expression has type \"Union[float, floating[Any]]\", variable has type \"Optional[float]\") [assignment]\r\npymatgen/analysis/ferroelectricity/polarization.py:128: error: Argument 2 to \"get_sites_in_sphere\" of \"IStructure\" has incompatible type \"Optional[float]\"; expected \"float\" [arg-type]\r\npymatgen/analysis/diffraction/core.py:117: error: Argument \"xy\" to \"annotate\" of \"Axes\" has incompatible type \"list[Any]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/analysis/diffraction/core.py:118: error: Argument \"xytext\" to \"annotate\" of \"Axes\" has incompatible type \"list[Any]\"; expected \"Optional[tuple[float, float]]\" [arg-type]\r\npymatgen/analysis/diffraction/core.py:138: error: Argument \"xy\" to \"annotate\" of \"Axes\" has incompatible type \"list[Any]\"; expected \"tuple[float, float]\" [arg-type]\r\npymatgen/analysis/diffraction/core.py:139: error: Argument \"xytext\" to \"annotate\" of \"Axes\" has incompatible type \"list[Any]\"; expected \"Optional[tuple[float, float]]\" [arg-type]\r\npymatgen/analysis/diffraction/core.py:170: error: \"Axes\" has no attribute \"show\"; maybe \"imshow\"? [attr-defined]\r\npymatgen/alchemy/filters.py:152: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/alchemy/filters.py:154: error: \"PeriodicNeighbor\" has no attribute \"__iter__\" (not iterable) [attr-defined]\r\npymatgen/phonon/gruneisen.py:47: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:48: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for < (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for < (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for < (\"int\" and \"complex\") [operator]\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for < (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/gruneisen.py:101: note: Left operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for > (\"str\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:101: error: Unsupported operand types for > (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: error: Unsupported operand types for ** (\"_SupportsArray[dtype[Any]]\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: error: Unsupported operand types for ** (\"_NestedSequence[_SupportsArray[dtype[Any]]]\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: error: Unsupported operand types for ** (\"str\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: error: Unsupported operand types for ** (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: error: Unsupported operand types for ** (\"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:107: note: Left operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for <= (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for <= (\"int\" and \"complex\") [operator]\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/gruneisen.py:111: note: Left operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for >= (\"str\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:111: error: Unsupported operand types for >= (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:113: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/gruneisen.py:113: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, slice]\" [call-overload]\r\npymatgen/phonon/gruneisen.py:113: note: Possible overload variants:\r\npymatgen/phonon/gruneisen.py:113: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/gruneisen.py:113: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/gruneisen.py:113: error: Invalid index type \"tuple[slice, slice]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/gruneisen.py:113: error: Invalid index type \"tuple[slice, slice]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for <= (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for <= (\"int\" and \"complex\") [operator]\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/gruneisen.py:114: note: Left operand is of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for >= (\"str\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:114: error: Unsupported operand types for >= (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for <= (\"int\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for <= (\"int\" and \"complex\") [operator]\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for <= (\"int\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/phonon/gruneisen.py:116: note: Left operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for >= (\"str\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:116: error: Unsupported operand types for >= (\"bytes\" and \"int\") [operator]\r\npymatgen/phonon/gruneisen.py:122: error: No overload variant of \"__getitem__\" of \"Sequence\" matches argument type \"ndarray[Any, dtype[signedinteger[Any]]]\" [call-overload]\r\npymatgen/phonon/gruneisen.py:122: note: Possible overload variants:\r\npymatgen/phonon/gruneisen.py:122: note: def __getitem__(self, int, /) -> Any\r\npymatgen/phonon/gruneisen.py:122: note: def __getitem__(self, slice, /) -> Sequence[Any]\r\npymatgen/phonon/gruneisen.py:244: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:247: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:279: error: Argument 2 to \"__init__\" of \"PhononBandStructure\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"list[Kpoint]\" [arg-type]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:301: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:307: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"tolist\" [union-attr]\r\npymatgen/phonon/gruneisen.py:347: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:350: error: Bad number of arguments for type alias, expected: 0, given: 1 [type-arg]\r\npymatgen/phonon/gruneisen.py:392: error: Argument \"eigendisplacements\" to \"_reuse_init\" of \"PhononBandStructureSymmLine\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], None]\"; expected \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" [arg-type]\r\npymatgen/phonon/gruneisen.py:392: error: Argument \"qpoints\" to \"_reuse_init\" of \"PhononBandStructureSymmLine\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"list[Kpoint]\" [arg-type]\r\npymatgen/io/lammps/utils.py:118: error: Argument 1 to \"_add_monomer\" of \"Polymer\" has incompatible type \"IMolecule\"; expected \"Molecule\" [arg-type]\r\npymatgen/io/lammps/utils.py:140: error: Argument 1 to \"cross\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[_UnknownType]], _NestedSequence[_SupportsArray[dtype[_UnknownType]]], _UnknownType, _NestedSequence[_UnknownType]]\" [arg-type]\r\npymatgen/io/lammps/utils.py:140: error: Argument 2 to \"cross\" has incompatible type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Union[_SupportsArray[dtype[_UnknownType]], _NestedSequence[_SupportsArray[dtype[_UnknownType]]], _UnknownType, _NestedSequence[_UnknownType]]\" [arg-type]\r\npymatgen/io/lammps/utils.py:156: error: Unsupported operand types for * (\"float\" and \"_SupportsArray[dtype[Any]]\") [operator]\r\npymatgen/io/lammps/utils.py:156: error: Unsupported operand types for * (\"float\" and \"_NestedSequence[_SupportsArray[dtype[Any]]]\") [operator]\r\npymatgen/io/lammps/utils.py:156: error: Unsupported operand types for * (\"float\" and \"str\") [operator]\r\npymatgen/io/lammps/utils.py:156: error: Unsupported operand types for * (\"float\" and \"bytes\") [operator]\r\npymatgen/io/lammps/utils.py:156: error: Unsupported operand types for * (\"float\" and \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\") [operator]\r\npymatgen/io/lammps/utils.py:156: note: Right operand is of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"\r\npymatgen/io/lammps/utils.py:164: error: \"IMolecule\" has no attribute \"append\" [attr-defined]\r\npymatgen/io/lammps/utils.py:168: error: \"IMolecule\" has no attribute \"remove_sites\" [attr-defined]\r\npymatgen/io/lammps/outputs.py:68: error: Argument 1 to \"LammpsBox\" has incompatible type \"ndarray[Any, dtype[floating[_64Bit]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/io/lammps/outputs.py:68: error: Argument 2 to \"LammpsBox\" has incompatible type \"Optional[ndarray[Any, dtype[floating[_64Bit]]]]\"; expected \"Optional[Sequence[Any]]\" [arg-type]\r\npymatgen/io/feff/sets.py:245: error: Item \"Molecule\" of \"Union[Structure, Molecule]\" has no attribute \"lattice\" [union-attr]\r\npymatgen/io/cp2k/inputs.py:1972: error: Incompatible types in assignment (expression has type \"KeywordList\", target has type \"Keyword\") [assignment]\r\npymatgen/io/aims/parsers.py:259: error: Argument 3 to \"Structure\" has incompatible type \"ndarray[Any, dtype[floating[_64Bit]]]\"; expected \"Sequence[Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/io/aims/parsers.py:267: error: Argument 2 to \"Molecule\" has incompatible type \"ndarray[Any, dtype[floating[_64Bit]]]\"; expected \"Sequence[Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/io/aims/parsers.py:301: error: Unsupported target for indexed assignment (\"Optional[ndarray[Any, dtype[floating[_64Bit]]]]\") [index]\r\npymatgen/io/aims/parsers.py:492: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", target has type \"Sequence[Any]\") [assignment]\r\npymatgen/io/aims/parsers.py:624: error: Function \"numpy.core.multiarray.array\" is not valid as a type [valid-type]\r\npymatgen/io/aims/parsers.py:624: note: Perhaps you need \"Callable[...]\" or a callback protocol?\r\npymatgen/io/aims/parsers.py:637: error: Function \"numpy.core.multiarray.array\" is not valid as a type [valid-type]\r\npymatgen/io/aims/parsers.py:637: note: Perhaps you need \"Callable[...]\" or a callback protocol?\r\npymatgen/electronic_structure/plotter.py:2233: error: \"Dos\" has no attribute \"structure\" [attr-defined]\r\npymatgen/electronic_structure/plotter.py:2394: error: \"Dos\" has no attribute \"get_element_dos\" [attr-defined]\r\npymatgen/electronic_structure/plotter.py:2408: error: \"Dos\" has no attribute \"get_spd_dos\" [attr-defined]\r\npymatgen/electronic_structure/plotter.py:2912: error: Missing positional argument \"ticks\" in call to \"set_xticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:2913: error: Missing positional argument \"ticks\" in call to \"set_yticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:2946: error: Argument 1 to \"set_xlim\" of \"_AxesBase\" has incompatible type \"Sequence[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/electronic_structure/plotter.py:2947: error: Argument 1 to \"set_ylim\" of \"_AxesBase\" has incompatible type \"list[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/electronic_structure/plotter.py:2950: error: Missing positional argument \"ticks\" in call to \"set_xticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:2951: error: Missing positional argument \"ticks\" in call to \"set_yticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:2984: error: Argument 1 to \"set_xlim\" of \"_AxesBase\" has incompatible type \"Sequence[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/electronic_structure/plotter.py:2987: error: Missing positional argument \"ticks\" in call to \"set_xticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:2988: error: Missing positional argument \"ticks\" in call to \"set_yticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:3021: error: Argument 1 to \"set_xlim\" of \"_AxesBase\" has incompatible type \"Sequence[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/electronic_structure/plotter.py:3024: error: Missing positional argument \"ticks\" in call to \"set_xticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:3025: error: Missing positional argument \"ticks\" in call to \"set_yticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:3233: error: Missing positional argument \"ticks\" in call to \"set_xticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:3234: error: Missing positional argument \"ticks\" in call to \"set_yticks\" of \"_AxesBase\" [call-arg]\r\npymatgen/electronic_structure/plotter.py:4023: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4049: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4051: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4053: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4089: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4128: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"text\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4128: error: \"text\" of \"Axes\" gets multiple values for keyword argument \"s\" [misc]\r\npymatgen/electronic_structure/plotter.py:4199: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"scatter\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4281: error: Item \"Axes\" of \"Optional[Axes]\" has no attribute \"set_xlim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4281: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"set_xlim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4282: error: Item \"Axes\" of \"Optional[Axes]\" has no attribute \"set_ylim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4282: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"set_ylim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4283: error: Item \"Axes\" of \"Optional[Axes]\" has no attribute \"set_zlim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4283: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"set_zlim3d\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4286: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"axis\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4357: error: Item \"Axes\" of \"Optional[Axes]\" has no attribute \"plot_wireframe\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4357: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"plot_wireframe\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4365: error: Item \"Axes\" of \"Optional[Axes]\" has no attribute \"quiver3D\" [union-attr]\r\npymatgen/electronic_structure/plotter.py:4365: error: Item \"None\" of \"Optional[Axes]\" has no attribute \"quiver3D\" [union-attr]\r\npymatgen/io/lobster/outputs.py:449: error: Argument 1 to \"zopen\" has incompatible type \"Optional[str]\"; expected \"Union[str, Path]\" [arg-type]\r\npymatgen/apps/battery/insertion_battery.py:64: error: Item \"ComputedEntry\" of \"Union[ComputedEntry, ComputedStructureEntry]\" has no attribute \"structure\" [union-attr]\r\npymatgen/apps/battery/insertion_battery.py:88: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"list[Union[ComputedEntry, ComputedStructureEntry, PDEntry]]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/apps/battery/insertion_battery.py:94: error: Unsupported operand types for in (\"Entry\" and \"Iterable[Union[ComputedEntry, ComputedStructureEntry]]\") [operator]\r\npymatgen/apps/battery/insertion_battery.py:97: error: Unsupported operand types for in (\"Entry\" and \"Iterable[Union[ComputedEntry, ComputedStructureEntry]]\") [operator]\r\npymatgen/apps/battery/insertion_battery.py:111: error: Argument \"working_ion_entry\" to \"InsertionElectrode\" has incompatible type \"Union[ComputedEntry, ComputedStructureEntry, PDEntry]\"; expected \"ComputedEntry\" [arg-type]\r\npymatgen/apps/battery/insertion_battery.py:112: error: Argument \"stable_entries\" to \"InsertionElectrode\" has incompatible type \"tuple[Entry, ...]\"; expected \"Iterable[ComputedEntry]\" [arg-type]\r\npymatgen/apps/battery/insertion_battery.py:113: error: Argument \"unstable_entries\" to \"InsertionElectrode\" has incompatible type \"tuple[Entry, ...]\"; expected \"Iterable[ComputedEntry]\" [arg-type]\r\npymatgen/apps/battery/conversion_battery.py:237: error: \"AbstractVoltagePair\" has no attribute \"rxn\" [attr-defined]\r\npymatgen/analysis/structure_prediction/volume_predictor.py:199: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/structure_prediction/volume_predictor.py:204: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/phonon/plotter.py:317: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:317: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:462: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:462: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:462: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"str\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"int\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"float\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"complex\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"bytes\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:462: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:463: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:463: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"str\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"int\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"float\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"complex\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"bytes\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:463: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:468: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:468: error: No overload variant of \"__getitem__\" of \"bytes\" matches argument type \"tuple[slice, slice]\" [call-overload]\r\npymatgen/phonon/plotter.py:468: note: Possible overload variants:\r\npymatgen/phonon/plotter.py:468: note: def __getitem__(self, SupportsIndex, /) -> int\r\npymatgen/phonon/plotter.py:468: note: def __getitem__(self, slice, /) -> bytes\r\npymatgen/phonon/plotter.py:468: error: Invalid index type \"tuple[slice, slice]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"int\" [index]\r\npymatgen/phonon/plotter.py:468: error: Invalid index type \"tuple[slice, slice]\" for \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected type \"Union[SupportsIndex, slice]\" [index]\r\npymatgen/phonon/plotter.py:471: error: Argument 1 to \"LineCollection\" has incompatible type \"ndarray[Any, dtype[floating[_64Bit]]]\"; expected \"Sequence[Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]\" [arg-type]\r\npymatgen/phonon/plotter.py:474: error: Argument 1 to \"max\" has incompatible type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:474: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:474: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:474: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:474: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:474: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:475: error: Argument 1 to \"min\" has incompatible type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\"; expected \"Iterable[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:475: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:475: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:475: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:475: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:475: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/phonon/plotter.py:639: error: Incompatible return value type (got \"None\", expected \"Axes\") [return-value]\r\npymatgen/phonon/plotter.py:762: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:782: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:803: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:827: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:852: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:859: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:863: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:872: error: Argument 2 to \"_plot_thermo\" of \"ThermoPlotter\" has incompatible type \"ndarray[Any, dtype[floating[Any]]]\"; expected \"Sequence[Any]\" [arg-type]\r\npymatgen/phonon/plotter.py:914: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:914: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"_NestedSequence[_SupportsArray[dtype[Any]]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"str\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"bytes\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:915: error: Item \"_NestedSequence[Union[bool, int, float, complex, str, bytes]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"flatten\" [union-attr]\r\npymatgen/phonon/plotter.py:1000: error: Value of type \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:1000: error: Value of type \"Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" is not indexable [index]\r\npymatgen/phonon/plotter.py:1000: error: List comprehension has incompatible type List[Union[Any, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], str, int, float, complex, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]]; expected List[float] [misc]\r\npymatgen/phonon/plotter.py:1003: error: \"PhononBandStructureSymmLine\" has no attribute \"gruneisen\" [attr-defined]\r\npymatgen/io/phonopy.py:473: error: Argument \"multiplicities\" to \"GruneisenParameter\" has incompatible type \"ndarray[Any, dtype[Any]]\"; expected \"Optional[Sequence[Any]]\" [arg-type]\r\npymatgen/io/vasp/sets.py:116: error: \"VaspInputSet\" has no attribute \"user_potcar_functional\" [attr-defined]\r\npymatgen/io/vasp/sets.py:141: error: Signature of \"get_input_set\" incompatible with supertype \"InputGenerator\" [override]\r\npymatgen/io/vasp/sets.py:141: note: Superclass:\r\npymatgen/io/vasp/sets.py:141: note: def get_input_set(self) -> InputSet\r\npymatgen/io/vasp/sets.py:141: note: Subclass:\r\npymatgen/io/vasp/sets.py:141: note: def get_input_set(self, structure: Any = ...) -> VaspInput\r\npymatgen/io/vasp/sets.py:201: error: Incompatible types in assignment (expression has type \"str\", variable has type \"IO[Any]\") [assignment]\r\npymatgen/io/vasp/sets.py:203: error: No overload variant of \"join\" matches argument types \"str\", \"IO[Any]\" [call-overload]\r\npymatgen/io/vasp/sets.py:203: note: Possible overload variants:\r\npymatgen/io/vasp/sets.py:203: note: def join(str, /, *paths: str) -> str\r\npymatgen/io/vasp/sets.py:203: note: def join(Union[str, PathLike[str]], /, *paths: Union[str, PathLike[str]]) -> str\r\npymatgen/io/vasp/sets.py:203: note: def join(Union[bytes, PathLike[bytes]], /, *paths: Union[bytes, PathLike[bytes]]) -> bytes\r\npymatgen/io/vasp/sets.py:203: error: Argument \"arcname\" to \"write\" of \"ZipFile\" has incompatible type \"IO[Any]\"; expected \"Optional[Union[str, PathLike[str]]]\" [arg-type]\r\npymatgen/io/vasp/sets.py:207: error: No overload variant of \"join\" matches argument types \"str\", \"IO[Any]\" [call-overload]\r\npymatgen/io/vasp/sets.py:207: note: Possible overload variants:\r\npymatgen/io/vasp/sets.py:207: note: def join(str, /, *paths: str) -> str\r\npymatgen/io/vasp/sets.py:207: note: def join(Union[str, PathLike[str]], /, *paths: Union[str, PathLike[str]]) -> str\r\npymatgen/io/vasp/sets.py:207: note: def join(Union[bytes, PathLike[bytes]], /, *paths: Union[bytes, PathLike[bytes]]) -> bytes\r\npymatgen/io/vasp/sets.py:464: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Optional[Structure]\") [assignment]\r\npymatgen/io/vasp/sets.py:466: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Optional[Structure]\") [assignment]\r\npymatgen/io/vasp/sets.py:490: error: Signature of \"get_input_set\" incompatible with supertype \"InputGenerator\" [override]\r\npymatgen/io/vasp/sets.py:490: note: Superclass:\r\npymatgen/io/vasp/sets.py:490: note: def get_input_set(self) -> InputSet\r\npymatgen/io/vasp/sets.py:490: note: Subclass:\r\npymatgen/io/vasp/sets.py:490: note: def get_input_set(self, structure: Optional[Structure] = ..., prev_dir: Union[str, Path, None] = ..., potcar_spec: bool = ...) -> VaspInput\r\npymatgen/io/vasp/sets.py:3088: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[Sequence[Union[float, Sequence[Any]]]]\") [assignment]\r\npymatgen/io/lammps/sets.py:73: error: Dict entry 1 has incompatible type \"str\": \"Union[LammpsData, CombinedData]\"; expected \"Union[str, Path]\": \"Union[str, InputFile]\" [dict-item]\r\npymatgen/io/cp2k/sets.py:1038: error: Incompatible types in assignment (expression has type \"Section\", variable has type \"str\") [assignment]\r\npymatgen/io/aims/outputs.py:121: error: Incompatible return value type (got \"Union[Site, Molecule, Structure]\", expected \"Union[Structure, Molecule]\") [return-value]\r\npymatgen/io/aims/outputs.py:146: error: Incompatible return value type (got \"Union[Site, Molecule, Structure]\", expected \"Union[Structure, Molecule]\") [return-value]\r\npymatgen/io/aims/sets/base.py:397: error: \"ndarray\" expects 2 type arguments, but 1 given [type-arg]\r\npymatgen/io/abinit/inputs.py:755: error: Argument 2 to \"join\" has incompatible type \"Union[str, Pseudo]\"; expected \"str\" [arg-type]\r\npymatgen/analysis/elasticity/elastic.py:629: error: Incompatible types in assignment (expression has type \"list[Any]\", variable has type \"ndarray[Any, dtype[Any]]\") [assignment]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:745: error: \"_AxesBase\" has no attribute \"plot\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:747: error: \"_AxesBase\" has no attribute \"fill_between\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:756: error: \"_AxesBase\" has no attribute \"plot\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:758: error: \"_AxesBase\" has no attribute \"plot\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:778: error: Argument 1 to \"set_ylim\" of \"_AxesBase\" has incompatible type \"list[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:781: error: Argument 1 to \"set_xlim\" of \"_AxesBase\" has incompatible type \"list[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py:782: error: Argument 1 to \"set_xlim\" of \"_AxesBase\" has incompatible type \"list[float]\"; expected \"Union[float, tuple[float, float], None]\" [arg-type]\r\npymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py:1180: error: \"TargetedPenaltiedAbundanceChemenvStrategy\" has no attribute \"additional_condition\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py:1929: error: \"NbSetWeight\" has no attribute \"cn_weights\" [attr-defined]\r\npymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py:1929: error: \"NbSetWeight\" has no attribute \"initialization_options\" [attr-defined]\r\npymatgen/analysis/local_env.py:1294: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:1373: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:1625: error: \"Structure\" has no attribute \"get_covalent_bonds\" [attr-defined]\r\npymatgen/analysis/local_env.py:1773: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:1897: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/local_env.py:1913: error: Argument 1 to \"ValenceIonicRadiusEvaluator\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/analysis/local_env.py:3409: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:3481: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:3553: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:3649: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/analysis/local_env.py:4239: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/alchemy/materials.py:71: error: Unsupported right operand type for in (\"Union[AbstractTransformation, dict[str, Any]]\") [operator]\r\npymatgen/alchemy/materials.py:75: error: Value of type \"Union[AbstractTransformation, dict[str, Any]]\" is not indexable [index]\r\npymatgen/alchemy/materials.py:193: error: Too many arguments for \"VaspInputSet\" [call-arg]\r\npymatgen/alchemy/materials.py:214: error: Too many arguments for \"VaspInputSet\" [call-arg]\r\npymatgen/alchemy/materials.py:227: error: Item \"AbstractTransformation\" of \"Union[AbstractTransformation, dict[str, Any]]\" has no attribute \"pop\" [union-attr]\r\npymatgen/alchemy/materials.py:255: error: Value of type \"Union[AbstractTransformation, dict[str, Any]]\" is not indexable [index]\r\npymatgen/alchemy/materials.py:255: error: Unsupported right operand type for in (\"Union[AbstractTransformation, dict[str, Any]]\") [operator]\r\npymatgen/alchemy/materials.py:360: error: Item \"AbstractTransformation\" of \"Union[AbstractTransformation, dict[str, Any]]\" has no attribute \"pop\" [union-attr]\r\npymatgen/alchemy/materials.py:386: error: Argument \"history\" to \"TransformedStructure\" has incompatible type \"list[dict[Any, Any]]\"; expected \"Optional[list[Union[AbstractTransformation, dict[str, Any]]]]\" [arg-type]\r\npymatgen/alchemy/materials.py:386: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/alchemy/materials.py:386: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/core/surface.py:289: error: Incompatible types in assignment (expression has type \"StructureMatcher\", variable has type \"Site\") [assignment]\r\npymatgen/core/surface.py:839: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[Any]\") [assignment]\r\npymatgen/core/surface.py:849: error: Incompatible types in assignment (expression has type \"ndarray[Any, dtype[Any]]\", variable has type \"list[Any]\") [assignment]\r\npymatgen/core/surface.py:949: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/entries/compatibility.py:131: error: \"type[VaspInputSet]\" has no attribute \"CONFIG\" [attr-defined]\r\npymatgen/entries/compatibility.py:663: error: Incompatible return value type (got \"list[ConstantEnergyAdjustment]\", expected \"list[EnergyAdjustment]\") [return-value]\r\npymatgen/entries/compatibility.py:663: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/entries/compatibility.py:663: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/entries/compatibility.py:663: note: Perhaps you need a type annotation for \"adjustment_list\"? Suggestion: \"list[EnergyAdjustment]\"\r\npymatgen/entries/compatibility.py:680: error: \"EnergyAdjustment\" has no attribute \"nominal_value\" [attr-defined]\r\npymatgen/entries/compatibility.py:681: error: \"EnergyAdjustment\" has no attribute \"std_dev\" [attr-defined]\r\npymatgen/entries/compatibility.py:944: error: Incompatible return value type (got \"list[CompositionEnergyAdjustment]\", expected \"list[EnergyAdjustment]\") [return-value]\r\npymatgen/entries/compatibility.py:944: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/entries/compatibility.py:944: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/entries/compatibility.py:1082: error: Incompatible return value type (got \"list[CompositionEnergyAdjustment]\", expected \"list[EnergyAdjustment]\") [return-value]\r\npymatgen/entries/compatibility.py:1082: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/entries/compatibility.py:1082: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/entries/compatibility.py:1366: error: Argument 1 to \"append\" of \"list\" has incompatible type \"CompositionEnergyAdjustment\"; expected \"TemperatureEnergyAdjustment\" [arg-type]\r\npymatgen/entries/compatibility.py:1379: error: Incompatible return value type (got \"list[TemperatureEnergyAdjustment]\", expected \"list[EnergyAdjustment]\") [return-value]\r\npymatgen/entries/compatibility.py:1379: note: \"List\" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance\r\npymatgen/entries/compatibility.py:1379: note: Consider using \"Sequence\" instead, which is covariant\r\npymatgen/entries/compatibility.py:1379: note: Perhaps you need a type annotation for \"adjustments\"? Suggestion: \"list[EnergyAdjustment]\"\r\npymatgen/entries/compatibility.py:1383: error: Argument 1 of \"process_entries\" is incompatible with supertype \"Compatibility\"; supertype defines the argument type as \"Union[Union[ComputedEntry, ComputedStructureEntry], list[Union[ComputedEntry, ComputedStructureEntry]]]\" [override]\r\npymatgen/entries/compatibility.py:1383: note: This violates the Liskov substitution principle\r\npymatgen/entries/compatibility.py:1383: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides\r\npymatgen/analysis/surface_analysis.py:884: error: Incompatible return value type (got \"list[Line2D]\", expected \"Axes\") [return-value]\r\npymatgen/analysis/surface_analysis.py:884: error: Argument 2 to \"plot\" has incompatible type \"object\"; expected \"Union[float, Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]], str]\" [arg-type]\r\npymatgen/analysis/adsorption.py:376: error: Incompatible types in assignment (expression has type \"IMolecule\", variable has type \"Molecule\") [assignment]\r\npymatgen/analysis/adsorption.py:381: error: List comprehension has incompatible type List[Site]; expected List[PeriodicSite] [misc]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:129: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:129: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:129: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:129: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:129: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:135: error: Item \"_SupportsArray[dtype[Any]]\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:135: error: Item \"bool\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:135: error: Item \"int\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:135: error: Item \"float\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/analysis/interfaces/substrate_analyzer.py:135: error: Item \"complex\" of \"Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/transformations/site_transformations.py:362: error: Argument 1 to \"append\" of \"list\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/transformations/site_transformations.py:410: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/transformations/site_transformations.py:585: error: Argument 1 to \"get_neighbors\" of \"IStructure\" has incompatible type \"Site\"; expected \"PeriodicSite\" [arg-type]\r\npymatgen/transformations/standard_transformations.py:546: error: Incompatible types in assignment (expression has type \"IStructure\", variable has type \"Structure\") [assignment]\r\npymatgen/transformations/standard_transformations.py:546: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/transformations/standard_transformations.py:563: error: \"Structure\" has no attribute \"find_equivalent_sites\" [attr-defined]\r\npymatgen/transformations/standard_transformations.py:575: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Structure\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/transformations/standard_transformations.py:590: error: Unsupported target for indexed assignment (\"IStructure\") [index]\r\npymatgen/transformations/advanced_transformations.py:237: error: Incompatible types in assignment (expression has type \"OrderDisorderedStructureTransformation\", variable has type \"SubstitutionTransformation\") [assignment]\r\npymatgen/entries/mixing_scheme.py:158: error: Argument 1 to \"len\" has incompatible type \"Union[Union[ComputedEntry, ComputedStructureEntry], list[Union[ComputedEntry, ComputedStructureEntry]]]\"; expected \"Sized\" [arg-type]\r\npymatgen/entries/mixing_scheme.py:170: error: Item \"ComputedEntry\" of \"Union[Union[ComputedEntry, ComputedStructureEntry], list[Union[ComputedEntry, ComputedStructureEntry]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/entries/mixing_scheme.py:170: error: Item \"ComputedStructureEntry\" of \"Union[Union[ComputedEntry, ComputedStructureEntry], list[Union[ComputedEntry, ComputedStructureEntry]]]\" has no attribute \"__iter__\" (not iterable) [union-attr]\r\npymatgen/entries/mixing_scheme.py:497: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"list[ComputedStructureEntry]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/entries/mixing_scheme.py:502: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"list[ComputedStructureEntry]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/entries/mixing_scheme.py:539: error: \"Structure\" has no attribute \"entry_id\" [attr-defined]\r\npymatgen/core/interface.py:157: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/interface.py:157: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/interface.py:172: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/interface.py:172: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/interface.py:193: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"Interface\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/interface.py:194: error: \"IStructure\" has no attribute \"sort\" [attr-defined]\r\npymatgen/core/interface.py:195: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/core/interface.py:456: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/core/interface.py:458: error: Argument 1 to \"SpacegroupAnalyzer\" has incompatible type \"IStructure\"; expected \"Structure\" [arg-type]\r\npymatgen/analysis/pourbaix_diagram.py:450: error: \"PourbaixEntry\" has no attribute \"entry_list\"; maybe \"entry_id\"? [attr-defined]\r\npymatgen/analysis/pourbaix_diagram.py:490: error: Argument 1 to \"PhaseDiagram\" has incompatible type \"list[Union[ComputedEntry, PourbaixEntry]]\"; expected \"Union[Sequence[PDEntry], set[PDEntry]]\" [arg-type]\r\npymatgen/analysis/pourbaix_diagram.py:491: error: Argument 1 to \"list\" has incompatible type \"set[Entry]\"; expected \"Iterable[PourbaixEntry]\" [arg-type]\r\npymatgen/analysis/magnetism/analyzer.py:360: error: Argument 1 to \"from_sites\" of \"IStructure\" has incompatible type \"list[Site]\"; expected \"list[PeriodicSite]\" [arg-type]\r\npymatgen/analysis/magnetism/analyzer.py:365: error: Incompatible return value type (got \"IStructure\", expected \"Structure\") [return-value]\r\npymatgen/analysis/magnetism/analyzer.py:572: error: Incompatible types in assignment (expression has type \"Structure\", variable has type \"CollinearMagneticStructureAnalyzer\") [assignment]\r\npymatgen/analysis/magnetism/analyzer.py:573: error: Incompatible types in assignment (expression has type \"Structure\", variable has type \"CollinearMagneticStructureAnalyzer\") [assignment]\r\npymatgen/analysis/magnetism/analyzer.py:575: error: Argument 1 to \"matches\" of \"IStructure\" has incompatible type \"CollinearMagneticStructureAnalyzer\"; expected \"Union[IStructure, Structure]\" [arg-type]\r\npymatgen/analysis/chemenv/utils/chemenv_config.py:33: error: \"AbstractChemenvStrategy\" has no attribute \"DEFAULT_DISTANCE_CUTOFF\" [attr-defined]\r\npymatgen/analysis/chemenv/utils/chemenv_config.py:34: error: \"AbstractChemenvStrategy\" has no attribute \"DEFAULT_ANGLE_CUTOFF\" [attr-defined]\r\npymatgen/analysis/chemenv/utils/chemenv_config.py:35: error: \"AbstractChemenvStrategy\" has no attribute \"DEFAULT_ADDITIONAL_CONDITION\" [attr-defined]\r\npymatgen/analysis/chemenv/utils/chemenv_config.py:36: error: \"AbstractChemenvStrategy\" has no attribute \"DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF\" [attr-defined]\r\nFound 788 errors in 81 files (checked 279 source files)\r\n```\r\n\r\n</details>",
"types and `pymatgen` is a long story...\r\n\r\nwe're running `mypy` only locally on new commits because we've never been in the green and it would take days to fix all the legacy errors (which i've been chipping away at over the months but nowhere close to done)\r\n\r\ni realized i never bothered to check if `pyright` can be run as a commit hook. turns out there's this community-maintained repo which we might want to adopt.\r\n\r\nhttps://github.com/RobertCraigie/pyright-python\r\n\r\n[re comment](https://github.com/materialsproject/pymatgen/issues/3644#issuecomment-1959550468), pretty sure `pyright` is a higher fidelity type checker than `mypy`. just tried it out:\r\n\r\n```\r\n5314 errors, 73 warnings\r\n```\r\n",
"on a related note, the `pre-commit` version of `mypy` [injects these flags](https://github.com/pre-commit/mirrors-mypy/blob/8cd2d4056637e242709fe09f15a36f0b4b682bda/.pre-commit-hooks.yaml#L7) to avoid errors from missing packages since `mypy` is too slow as is without installing deps:\r\n\r\n```yml\r\nargs: [\"--ignore-missing-imports\", \"--scripts-are-modules\"]\r\n```",
"Could we get this in then? I don't know how quickly you'd want to make another release but this does break several other packages at the moment (even just within the MP ecosystem -- atomate2, emmet, mp_api etc). Any fixing or new linting rules could be tried out in https://github.com/materialsproject/pymatgen/pull/3646 or otherwise handled by the maintainers as they see fit going forward",
"i'll take a look at this tomorrow morning. it'll definitely be in the next release. we need one for several other issues as well",
"> thanks again @ml-evs for reporting and fixing.\r\n> \r\n> i refactored the code somewhat. i think we're in a good place now with the test added in [0245247](https://github.com/materialsproject/pymatgen/commit/0245247bf81653118ffe6e4d3db9d1e40798c85b) that will run in whatever `ase`-less we setup in #3646. i confirmed the new test passes in a venv without `ase` and is skipped otherwise\r\n\r\n~I'm afraid I don't think your refactor is advisable; the error was triggered initially for `mp_api` by emmet importing `from emmet.core.electronic_structure import BSPathType` which then hits `from pymatgen.analysis.magnetism.analyzer import ...`. The refactor (haven't tried running it) looks to me like it will now just give a clearer better error message?~\r\n\r\nScratch that, misread it! LGTM",
"> The refactor (haven't tried running it) looks to me like it will now just give a clearer better error message?\r\n\r\ni hope not. the behavior is meant to be unchanged. given this class only raises on init, i don't see how you'd get an error on import?\r\n\r\n```\r\nclass Atoms: # type: ignore[no-redef]\r\n def __init__(self, *args, **kwargs):\r\n raise no_ase_err\r\n```",
"> > The refactor (haven't tried running it) looks to me like it will now just give a clearer better error message?\r\n> \r\n> i hope not. the behavior is meant to be unchanged. given this class only raises on init, i don't see how you'd get an error on import?\r\n> \r\n> ```\r\n> class Atoms: # type: ignore[no-redef]\r\n> def __init__(self, *args, **kwargs):\r\n> raise no_ase_err\r\n> ```\r\n\r\nYou just beat my ninja edit, in the time it took me to walk to my computer to test it out - never review PRs from your phone! Thanks for updating this @janosh "
] | 2024-02-22T14:24:40
| 2024-02-23T11:27:50
|
2024-02-23T10:18:20Z
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CONTRIBUTOR
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## Summary
Hopefully closes #3644. Not sure if this is the approach you want to take.
## Todo
It would be nice to add a test or linter rule that would have caught the initial issue.
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Add a CI run that only tests non-optional deps (optimistically)
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[
"wow, that's way more possibly unbound variables than expected... π
",
"@coderabbitai ignore",
"my impression is coderabbitai is too verbose. if it has useful suggestions, they are buried in a lot of boilerplate language that you don't want to read",
"Here I come! Giving you a hand on all those `pyright` fixes. I wish you don't mind :)",
"Just to be clear I was never planning on making these fixes, I just wanted to show the issue by adding it to the CI. So feel free to close/take over/supersede this PR",
"Thanks for the input. I could help fix them and I could either push my fixes to your branch or maybe open a separate PR :) ? Which do you prefer (I'm not very experienced and would like to hear about your suggestions)?",
"Probably best to close this one and start again, the CI changes I suggested here are already out of date it seems. pyright was just being used to look for symptoms of the problem, the real change that needs to be made is running the test suite with mandatory deps only and making sure nothing fails.",
"Thanks for clarifying. I would redirect the PR directly to upstream if you don't mind (wasn't planning to pre-empt you)?",
"I won't be doing anything further on this so please go ahead!",
"Thanks!"
] | 2024-02-22T14:31:11
| 2024-04-13T10:25:56
|
2024-04-13T10:18:52Z
|
CONTRIBUTOR
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Hopefully all tests have been written in such a way that they will be skipped if the underlying required package is not found... this would hopefully catch issues like #3645 ahead of time (although better linting would do the same too and avoid the potential need to update tests to skip if packages are missing -- only the implementation code would need to include package guard).
This should be updated after #3645 is merged to see what's left: not sure if adding a whole additional test run is "worth it" for the maintainers here but it definitely shows up the issues presented and would also be robust to any weirdness with optional deps changing the values of expected tests. There might be some kind of pytest plugin that lets you re-run only the skipped tests in the previous step when considering all deps.
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broken BSPlotterProjected.get_projected_plots_dots_patom_pmorb
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[] | 2024-02-22T20:44:07
| 2024-02-23T16:45:16
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2024-02-23T16:45:16Z
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CONTRIBUTOR
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This line has been changed in #2862:
https://github.com/materialsproject/pymatgen/blame/38b9b58f16a9528cb2c8f0bc0c7889955687ae8e/pymatgen/electronic_structure/plotter.py#L1740
and the replacement of the `intersection` function with a `&` brakes the code since the second item is not a set but a list.
Solutions:
- either change it back to using the `intersection` function
- make a set of that list
I'm wondering how the tests are passing...
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Compress test vasprun.xml files
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[
"Meanwhile I noticed there are `vasprun.xml.lobster.spin` and `vasprun.xml.lobster.nonspin` in `pymatgen/tests/files`. I did a global search and didn't see them being used anywhere. Do you have any idea? @JaGeo Thanks!",
"> Meanwhile I noticed there are `vasprun.xml.lobster.spin` and `vasprun.xml.lobster.nonspin` in `pymatgen/tests/files`. I did a global search and didn't see them being used anywhere. Do you have any idea? @JaGeo Thanks!\r\n\r\nRemove them if they are not used anymore ",
"> I would go ahead to clean up (notice all VASP test files seem to be placed flat inside the files dir, they might deserve their own vasp dir) [...] Would open a separate PR for that.\r\n\r\nplease do! that would be nice",
"> excellent work @DanielYang59! this has been on my todo list for a very long time. π\r\n> \r\n> in retrospect, i should have proceeded in smaller chunks like this PR rather trying to do everything at once in #3132.\r\n\r\nNo problem at all @janosh. This cannot have been done so easily without the foundation laid in #3132.\r\n\r\nYes I guess chopping up tasks into small pieces make everything much easier (easier to work on, easier to review and easier to track and revert in case anything goes wrong).\r\n\r\nI just notice that `compress-test-files` branch but that seems quite out of date. Can you please update that branch and I would push future clean-ups there. Thanks! π ",
"> Can you please update that branch and I would push future clean-ups there.\r\n\r\nno need, please keep making PRs to `master`. we can just delete `compress-test-files`"
] | 2024-02-23T03:48:19
| 2024-02-23T09:01:31
|
2024-02-23T08:15:56Z
|
CONTRIBUTOR
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Compressed (`gzip`) test vasprun.xml files.
### Summary:
Total vasprun.xml file size reduced by 78.67% (361 MB -> 77 MB), with test runtime largely unaffected (increased by 1.05% but could be random error)
### Before compression:
Total vasprun.xml file size:
```bash
> find . -type f -name 'vasprun*' -exec du -ch {} + | awk 'END {print}'
361M total
```
Test runtime:
```bash
........................................................................... [ 25%]
........................................................................... [ 51%]
........................................................................... [ 77%]
................................................................. [100%]
============================== slowest 30 durations ===============================
7.53s call tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
6.71s call tests/io/vasp/test_optics.py::TestVasprun::test_optics
4.45s call tests/io/vasp/test_outputs.py::TestOutcar::test_stopped
4.44s call tests/io/vasp/test_outputs.py::TestOutcar::test_stopped_old
4.41s call tests/io/vasp/test_sets.py::TestMPStaticSet::test_grid_size_from_struct
2.93s call tests/io/vasp/test_outputs.py::TestAeccars::test_read_write_file
2.59s call tests/io/vasp/test_outputs.py::TestVasprun::test_standard
2.38s call tests/io/vasp/test_outputs.py::TestOutcar::test_avg_core_poten
2.35s call tests/io/vasp/test_outputs.py::TestVasprun::test_projected_magnetisation
2.24s call tests/io/vasp/test_outputs.py::TestVasprun::test_dfpt_ionic
2.14s call tests/io/vasp/test_outputs.py::TestOutcar::test_read_piezo_tensor
1.75s call tests/io/vasp/test_outputs.py::TestOutcar::test_init
1.53s call tests/io/vasp/test_outputs.py::TestVasprun::test_kpointset_electronvelocities
1.53s call tests/io/vasp/test_outputs.py::TestVasprun::test_update_potcar
1.35s call tests/io/vasp/test_outputs.py::TestVasprun::test_nonlmn
1.26s call tests/io/vasp/test_outputs.py::TestVasprun::test_eigenvalue_band_properties_separate_spins
1.25s call tests/io/vasp/test_outputs.py::TestChgcar::test_init
0.97s call tests/io/vasp/test_outputs.py::TestVasprun::test_smart_efermi
0.88s call tests/io/vasp/test_outputs.py::TestOutcar::test_nplwvs
0.86s call tests/io/vasp/test_outputs.py::TestOutcar::test_drift
0.85s call tests/io/vasp/test_outputs.py::TestVasprun::test_energies
0.83s call tests/io/vasp/test_outputs.py::TestChgcar::test_soc_chgcar
0.66s call tests/io/vasp/test_sets.py::TestMPAbsorptionSet::test_rpa
0.62s call tests/io/vasp/test_outputs.py::TestVasprun::test_as_dict
0.58s call tests/io/vasp/test_outputs.py::TestVasprun::test_get_band_structure
0.56s call tests/io/vasp/test_outputs.py::TestOutcar::test_read_table_pattern
0.55s call tests/io/vasp/test_outputs.py::TestOutcar::test_electrostatic_potential
0.51s call tests/io/vasp/test_outputs.py::TestVasprun::test_search_for_potcar
0.50s setup tests/io/vasp/test_outputs.py::TestChgcar::test_add
0.44s call tests/io/vasp/test_outputs.py::TestVasprun::test_float_overflow
290 passed in 77.92s (0:01:17)
```
### After compression:
Total vasprun.xml file size:
```bash
> find . -type f -name 'vasprun*' -exec du -ch {} + | awk 'END {print}'
77M total
```
Test runtime:
```bash
........................................................................... [ 25%]
........................................................................... [ 51%]
........................................................................... [ 77%]
................................................................. [100%]
============================== slowest 30 durations ===============================
8.01s call tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
6.54s call tests/io/vasp/test_optics.py::TestVasprun::test_optics
4.70s call tests/io/vasp/test_outputs.py::TestOutcar::test_stopped
4.61s call tests/io/vasp/test_outputs.py::TestOutcar::test_stopped_old
4.24s call tests/io/vasp/test_sets.py::TestMPStaticSet::test_grid_size_from_struct
2.73s call tests/io/vasp/test_outputs.py::TestAeccars::test_read_write_file
2.68s call tests/io/vasp/test_outputs.py::TestVasprun::test_standard
2.44s call tests/io/vasp/test_outputs.py::TestVasprun::test_dfpt_ionic
2.38s call tests/io/vasp/test_outputs.py::TestVasprun::test_projected_magnetisation
2.35s call tests/io/vasp/test_outputs.py::TestOutcar::test_avg_core_poten
2.14s call tests/io/vasp/test_outputs.py::TestOutcar::test_read_piezo_tensor
1.72s call tests/io/vasp/test_outputs.py::TestOutcar::test_init
1.57s call tests/io/vasp/test_outputs.py::TestVasprun::test_update_potcar
1.52s call tests/io/vasp/test_outputs.py::TestVasprun::test_kpointset_electronvelocities
1.32s call tests/io/vasp/test_outputs.py::TestVasprun::test_eigenvalue_band_properties_separate_spins
1.30s call tests/io/vasp/test_outputs.py::TestVasprun::test_nonlmn
1.17s call tests/io/vasp/test_outputs.py::TestChgcar::test_init
1.01s call tests/io/vasp/test_outputs.py::TestVasprun::test_smart_efermi
0.94s call tests/io/vasp/test_outputs.py::TestOutcar::test_nplwvs
0.88s call tests/io/vasp/test_outputs.py::TestOutcar::test_drift
0.86s call tests/io/vasp/test_outputs.py::TestChgcar::test_soc_chgcar
0.85s call tests/io/vasp/test_outputs.py::TestVasprun::test_energies
0.64s call tests/io/vasp/test_sets.py::TestMPAbsorptionSet::test_rpa
0.64s call tests/io/vasp/test_outputs.py::TestVasprun::test_as_dict
0.55s call tests/io/vasp/test_outputs.py::TestOutcar::test_read_table_pattern
0.54s call tests/io/vasp/test_outputs.py::TestVasprun::test_search_for_potcar
0.52s call tests/io/vasp/test_outputs.py::TestOutcar::test_electrostatic_potential
0.51s setup tests/io/vasp/test_outputs.py::TestChgcar::test_add
0.47s call tests/io/vasp/test_outputs.py::TestVasprun::test_get_band_structure
0.43s call tests/io/vasp/test_outputs.py::TestVasprun::test_float_overflow
290 passed in 78.74s (0:01:18)
```
### Project-wise `pytest` run
<details>
<summary>Expand </summary>
Apparently I have many missing dependencies...
```bash
........................................................................... [ 2%]
........................................................................... [ 5%]
.....................................s.............................sss..... [ 7%]
..........................................sssss.....s..s..................s [ 10%]
.............................................ss.......................s.... [ 13%]
.ssssssss.................................................................. [ 15%]
........................................................................... [ 18%]
........................................................................... [ 21%]
........................................................................... [ 23%]
...........................................sssss..ss..sssssssssssssssssssss [ 26%]
ssssssssssssssssss......................................................... [ 29%]
........................................................................... [ 31%]
........................................................................... [ 34%]
................................s...................................ss..... [ 37%]
................ssss..........................................s.......s.... [ 39%]
...........................s............................................... [ 42%]
.................................................ssssssssssssssssssssssssss [ 45%]
sss........................................................................ [ 47%]
..........sssssssssssssssssss.............................................. [ 50%]
........................................................................... [ 53%]
............................ss.sssssssssssssssssssssssssssssssssssssssss.ss [ 55%]
........................................................................... [ 58%]
........................................................................... [ 61%]
........................................................................... [ 63%]
........................................................................... [ 66%]
........................................................................... [ 69%]
..................................s..................s..................... [ 71%]
........................................................................... [ 74%]
........................................................................... [ 77%]
..............................................................ssssssssss... [ 79%]
........................................................................... [ 82%]
........................................................................... [ 85%]
........................................................................... [ 87%]
........................................................................... [ 90%]
........................................................................... [ 93%]
................................................................s..sssss..s [ 95%]
sssssss...ssssss...s...........s..................ssss..................... [ 98%]
..............ss.............................. [100%]
============================== slowest 30 durations ===============================
22.38s call tests/electronic_structure/test_plotter.py::TestBSPlotterProjected::test_methods
15.93s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_plot
14.38s call tests/symmetry/test_kpath_lm.py::TestKPathLatimerMunro::test_kpath_generation
13.20s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_average_gruneisen
12.85s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_acoustic_debye_temp
12.61s call tests/analysis/test_structure_analyzer.py::TestMiscFunction::test_average_coordination_number
12.60s call tests/io/test_phonopy.py::TestGruneisen::test_gruneisen_parameter
12.59s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_thermal_conductivity_slack
12.45s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_tdos
12.42s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_as_from_dict
12.37s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_debye_temp_phonopy
12.34s call tests/analysis/elasticity/test_elastic.py::TestDiffFit::test_fit
12.34s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_frequencies
12.20s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_multi
11.88s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_phdos
11.83s call tests/phonon/test_gruneisen.py::TestGruneisenParameter::test_gruneisen
9.52s call tests/io/vasp/test_outputs.py::TestVasprun::test_runtype
8.58s call tests/analysis/test_prototypes.py::TestAflowPrototypeMatcher::test_prototype_matching
8.16s call tests/analysis/elasticity/test_elastic.py::TestElasticTensorExpansion::test_get_yield_stress
7.85s call tests/io/vasp/test_optics.py::TestVasprun::test_optics
7.30s call tests/core/test_surface.py::MillerIndexFinderTests::test_generate_all_slabs
6.84s call tests/core/test_surface.py::TestSlab::test_symmetrization
6.03s setup tests/io/lammps/test_data.py::TestCombinedData::test_as_lammpsdata
5.99s call tests/core/test_surface.py::TestSlabGenerator::test_nonstoichiometric_symmetrized_slab
5.53s call tests/symmetry/test_kpath_sc.py::TestBandStructureSC::test_kpath_generation
5.37s call tests/core/test_trajectory.py::TestTrajectory::test_extend
5.36s call tests/io/lobster/test_lobsterenv.py::TestLobsterNeighbors::test_get_info_cohps_to_neighbors
5.14s call tests/test_cli.py::test_pmg_structure
5.09s call tests/core/test_trajectory.py::TestTrajectory::test_xdatcar_write
4.97s call tests/io/vasp/test_sets.py::TestMPStaticSet::test_grid_size_from_struct
============================= short test summary info =============================
SKIPPED [1] tests/analysis/test_functional_groups.py:15: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/io/test_babel.py:16: could not import 'openbabel.pybel': No module named 'openbabel'
SKIPPED [1] tests/io/test_packmol.py:20: packmol executable not present
SKIPPED [1] tests/analysis/magnetism/test_analyzer.py:247: enumlib not present
SKIPPED [3] tests/analysis/test_bond_dissociation.py:16: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:80: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:66: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:71: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:113: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:108: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_fragmenter.py:156: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_graphs.py:344: graphviz executables not present
SKIPPED [1] tests/analysis/test_graphs.py:572: could not import 'openbabel': No module named 'openbabel'
SKIPPED [2] tests/analysis/test_local_env.py:289: could not import 'openbabel': No module named 'openbabel'
SKIPPED [1] tests/analysis/test_local_env.py:1339: critic2 executable not present
SKIPPED [1] tests/analysis/test_molecule_matcher.py:258: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:152: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:156: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:162: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:240: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:246: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:252: OBAlign is missing, Skipping
SKIPPED [1] tests/analysis/test_molecule_matcher.py:173: OBAlign is missing, Skipping
SKIPPED [1] tests/command_line/test_bader_caller.py:118: bader executable not present
SKIPPED [1] tests/command_line/test_bader_caller.py:86: bader executable not present
SKIPPED [1] tests/command_line/test_bader_caller.py:67: bader executable not present
SKIPPED [1] tests/command_line/test_bader_caller.py:23: bader executable not present
SKIPPED [1] tests/command_line/test_bader_caller.py:133: bader executable not present
SKIPPED [1] tests/command_line/test_critic2_caller.py:22: critic2 executable not present
SKIPPED [1] tests/command_line/test_critic2_caller.py:58: critic2 executable not present
SKIPPED [1] tests/command_line/test_enumlib_caller.py:23: enum_lib not present.
SKIPPED [1] tests/command_line/test_enumlib_caller.py:91: enum_lib not present.
SKIPPED [1] tests/command_line/test_enumlib_caller.py:79: enum_lib not present.
SKIPPED [1] tests/command_line/test_enumlib_caller.py:121: enum_lib not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:64: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:37: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:165: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:138: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:208: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:244: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:104: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:129: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:134: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:125: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:110: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:120: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:116: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:255: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:190: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:286: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:298: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:281: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:322: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:311: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:318: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:329: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:325: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:349: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:339: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:345: gulp not present.
SKIPPED [1] tests/command_line/test_gulp_caller.py:352: gulp not present.
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:64: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:98: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:29: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:48: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:56: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:74: mcsqs executable not present
SKIPPED [1] tests/command_line/test_mcsqs_caller.py:86: mcsqs executable not present
SKIPPED [1] tests/command_line/test_vampire_caller.py:35: vampire executable not present
SKIPPED [1] tests/core/test_structure.py:91: enumlib or mcsqs executable not present
SKIPPED [1] tests/core/test_structure.py:1627: could not import 'chgnet': No module named 'chgnet'
SKIPPED [1] tests/core/test_structure.py:1693: could not import 'matgl': No module named 'matgl'
SKIPPED [1] tests/core/test_structure.py:1604: could not import 'chgnet': No module named 'chgnet'
SKIPPED [1] tests/core/test_structure.py:1704: could not import 'matgl': No module named 'matgl'
SKIPPED [1] tests/core/test_structure.py:1714: could not import 'matgl': No module named 'matgl'
SKIPPED [1] tests/core/test_structure.py:1722: could not import 'matgl': No module named 'matgl'
SKIPPED [1] tests/core/test_structure.py:2315: Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] tests/core/test_structure.py:2325: Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] tests/core/test_surface.py:668: This test relies on neighbor orders and is hard coded. Disable temporarily
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:262: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:249: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:184: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:212: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:240: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:102: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:128: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:216: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:141: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:118: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:86: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:220: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:153: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:170: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap.py:43: No x_trans.
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:78: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:59: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:97: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:92: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:126: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:123: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:118: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:165: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:150: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:180: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:192: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:284: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:253: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_boltztrap2.py:310: No boltztrap2, skipping tests...
SKIPPED [1] tests/electronic_structure/test_plotter.py:289: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:296: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:303: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:310: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:317: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:324: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:331: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:338: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:345: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:352: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:359: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:366: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:373: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:380: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:387: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:394: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:401: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:408: No x_trans executable found
SKIPPED [1] tests/electronic_structure/test_plotter.py:415: No x_trans executable found
SKIPPED [1] tests/ext/test_cod.py:18: No mysql.
SKIPPED [1] tests/ext/test_cod.py:23: No mysql.
SKIPPED [1] tests/ext/test_matproj.py:503: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:471: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:410: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:121: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:46: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:198: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:367: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:59: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:194: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:217: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:130: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:163: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:297: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:188: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:371: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:393: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:113: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:116: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:205: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:272: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:339: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:314: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:147: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:213: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:343: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:348: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:363: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:52: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:456: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:423: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:483: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:487: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:171: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:180: Legacy PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:521: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:539: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:621: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:645: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:649: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:691: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_matproj.py:872: PMG_MAPI_KEY environment variable not set or MP API is down.
SKIPPED [1] tests/ext/test_optimade.py:37: PMG_MAPI_KEY env var not set or MP is down.
SKIPPED [1] tests/ext/test_optimade.py:19: PMG_MAPI_KEY env var not set or MP is down.
SKIPPED [1] tests/io/qchem/test_outputs.py:299: OpenBabel not installed.
SKIPPED [1] tests/io/qchem/test_outputs.py:336: OpenBabel not installed.
SKIPPED [1] tests/io/test_zeopp.py:68: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:37: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:112: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:81: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:143: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:132: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:164: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:187: file free_sph.cif not present
SKIPPED [1] tests/io/test_zeopp.py:210: zeo not present.
SKIPPED [1] tests/io/test_zeopp.py:231: zeo not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:101: enum_lib not present.
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SKIPPED [1] tests/transformations/test_advanced_transformations.py:245: enum_lib not present.
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SKIPPED [1] tests/transformations/test_advanced_transformations.py:360: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:300: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:338: enum_lib not present.
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SKIPPED [1] tests/transformations/test_advanced_transformations.py:348: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:488: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:536: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:545: enum_lib not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:603: mcsqs not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:613: mcsqs not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:634: mcsqs not present.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:666: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:652: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:677: icet not installed.
SKIPPED [1] tests/transformations/test_advanced_transformations.py:784: hiphive not present. Skipping...
SKIPPED [1] tests/transformations/test_site_transformations.py:213: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:223: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:237: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:254: enum_lib not present.
SKIPPED [1] tests/transformations/test_standard_transformations.py:248: enum_lib not present.
SKIPPED [1] tests/util/test_graph_hashing.py:44: could not import 'emmet.core.graph_hashing': No module named 'emmet.core'
SKIPPED [1] tests/util/test_graph_hashing.py:61: could not import 'emmet.core.graph_hashing': No module named 'emmet.core'
2609 passed, 215 skipped in 690.26s (0:11:30)
```
</details>
### Follow-up work
I would go ahead to clean up (notice all VASP test files seem to be placed flat inside the `files` dir, they might deserve their own `vasp` dir) and compress some other VASP test files (CHGCAR*, OUTCAR*) later. Would open a separate PR for that.
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PR_kwDOACgets5nwftB
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LOBSTER IO improvements
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[] | 2024-02-23T13:44:10
| 2024-03-13T18:01:55
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2024-02-24T08:34:29Z
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CONTRIBUTOR
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# Changes
1. Make Lobsterout class MSONABLE
2. Add test
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PR_kwDOACgets5nwoLR
| 3,650
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`Kpoint.__eq__` and `PhononBandStructureSymmLine.__eq__` methods + tests
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2024-02-23T14:20:24Z
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MEMBER
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2231ec528c plotter.py and phonon band structure: improve doc strings + refactor
7c47053e32 Add Kpoint.__eq__ method
50efc02308 Add test for Kpoint equality
8b63b10640 Add PhononBandStructureSymmLine.__eq__ method
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Fix `BSPlotterProjected.get_projected_plots_dots_patom_pmorb` fix set & list intersect
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[] | 2024-02-23T16:18:32
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Closes #3647.
slightly improve `BSPlotterProjected` test coverage
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[Dev] Tests for `Bader` not running properly
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[
"thanks for reporting! the whole `bader` is very brittle atm. i was hoping we could transition to [`pybader`](https://github.com/adam-kerrigan/pybader/issues/1) at some point in the future to have less install and subprocess shenanigans but development there seems to have stalled.\r\n\r\nif you could fix the current implementation, that would be great! π ",
"> thanks for reporting! the whole `bader` is very brittle atm. i was hoping we could transition to [`pybader`](https://github.com/adam-kerrigan/pybader/issues/1) at some point in the future to have less install and subprocess shenanigans but development there seems to have stalled.\r\n\r\nYes it seems `pybader` is stalled for some reason...\r\n\r\n> if you could fix the current implementation, that would be great! \r\n\r\nWell I have made too many promises (in `pymatviz` and `pymatgen`, and my own codebase) but having too limited time π. I would certain give this a try when I have time but I cannot promise that at this moment sorry. \r\n\r\n",
"> Well I have made too many promises (in pymatviz and pymatgen, and my own codebase) but having too limited time π.\r\n\r\ni know the problem π \r\n\r\ndon't worry, nobody's going to hold you to those promises. any help is appreciated and none is expected",
"I just had a look at why test for `Bader_caller` is failing. \r\n\r\nIt looks like `BaderAnalysis` sliced a central part from the complete charge density:\r\nhttps://github.com/materialsproject/pymatgen/blob/dc60d35a21fd7b55d82c65bb078afc4a2c0e9bbf/pymatgen/command_line/bader_caller.py#L194-L224\r\n\r\nAs the \"encompassing volume\" is determined on the fly:\r\nhttps://github.com/materialsproject/pymatgen/blob/dc60d35a21fd7b55d82c65bb078afc4a2c0e9bbf/pymatgen/command_line/bader_caller.py#L209-L216\r\n\r\nThe shapes for charge density array of different atoms differ, and therefore the error in test from trying to calculating the sum of arrays in different shapes:\r\nhttps://github.com/materialsproject/pymatgen/blob/dc60d35a21fd7b55d82c65bb078afc4a2c0e9bbf/tests/command_line/test_bader_caller.py#L129-L131\r\n\r\nSo the fix should be pretty straightforward (zero-pad charge density arrays to consistent shape).\r\n\r\nBut I'm not sure about the underlying reasoning behind this @janosh @shyuep , as this seems to be a breaking change so I guess should avoid this (if I pad the charge array inplace in `BaderAnalysis`), or should I keep this behaviour and just pad the arrays in tests? \r\n\r\nThanks a lot for any suggestion π .\r\n",
"> So the fix should be pretty straightforward (zero-pad charge density arrays to consistent shape).\r\n>\r\n> But I'm not sure about the underlying reasoning behind this @janosh @shyuep , \r\n\r\nthis is actually news to me. i hadn't looked closely at the implementation before. if the tests produce arrays of different shapes then i don't understand how they could have passed in the past? maybe @Andrew-S-Rosen knows more?\r\n\r\npotential for breakage from zero padding seems small but i'm still leaning towards just padding the arrays in tests to fix CI rather than changing the implementation",
"Thanks for the quick response and for sharing your thoughts.\r\n\r\n> if the tests produce arrays of different shapes then i don't understand how they could have passed in the past? \r\n\r\nNot sure... I just checked an early (on Dec 6, 2023, expired after 90 days) [workflow logs](https://github.com/materialsproject/pymatgen/actions/runs/7107688676/job/19349608425) and it seems at least back then the tests passed just fine (`pytest split 3`) π :\r\n```bash\r\n6.70s call tests/command_line/test_bader_caller.py::TestBaderAnalysis::test_atom_parsing\r\n```\r\n\r\nMaybe I didn't understand the implementation correctly?\r\n\r\n> potential for breakage from zero padding seems small but i'm still leaning towards just padding the arrays in tests to fix CI rather than changing the implementation\r\n\r\nIf we change the implementation to zero-pad the `atomic_densities`, then the behaviour of this function would change to produce consistent shapes for `atomic_densities` (which would break downstream process). So I guess it's better not to change this for now. Or we could make zero-pad optional during `__init__` if necessary.\r\n",
"I have never used `parse_atomic_densities = True` so can't help much here (the default is `False`). I must be honest --- I'm not entirely sure of the purpose of this task anyway. The bader analysis is already breaking down the charge density on a per-atom basis. Why would I want pymatgen to \"Enable atomic partition of the charge density\" separately from this in a more rudimentary way?",
"that's funny, i was wondering the same thing but figured i'm missing something obvious.\r\n\r\nSo maybe the right path forward is to put a deprecation warning on this functionality with a removal date and see if anyone objects before then?",
"> So maybe the right path forward is to put a deprecation warning on this functionality with a removal date and see if anyone objects before then?\r\n\r\nI would lean towards yes (with a somewhat generation deprecation period), unless it's used in the MP builders for some reason. CC @munrojm",
"sure, let's do 1 year deprecation. `emmet` only uses [`bader_analysis_from_path(dir_name, suffix=suffix)`](https://github.com/materialsproject/emmet/blob/47cecca5fe1d0720b9848fe1da3439c76e647484/emmet-core/emmet/core/vasp/calculation.py#L748) (i.e. `parse_atomic_densities=False`).\r\n\r\n@DanielYang59 would you like to submit a PR to close this issue?",
"> Why would I want pymatgen to \"Enable atomic partition of the charge density\" separately from this in a more rudimentary way?\r\n\r\nI was wondering too (thought there is some reasoning I didn't know about...), thanks a lot for pointing out.\r\n\r\n\r\n\r\n> sure, let's do 1 year deprecation. `emmet` only uses [`bader_analysis_from_path(dir_name, suffix=suffix)`](https://github.com/materialsproject/emmet/blob/47cecca5fe1d0720b9848fe1da3439c76e647484/emmet-core/emmet/core/vasp/calculation.py#L748) (i.e. `parse_atomic_densities=False`).\r\n> \r\n> @DanielYang59 would you like to submit a PR to close this issue?\r\n\r\nGlad to help, thanks for the helpful discussion.",
"Fixed in #3656"
] | 2024-02-24T02:54:23
| 2024-03-15T03:47:51
|
2024-02-26T08:50:42Z
|
CONTRIBUTOR
|
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### Summary
Noticed two `Bader` related issues:
- GitHub test workflow doesn't download Bader properly
- Tests for Bader fails
### Test workflow not running properly
While trying to clean up test files for VASP, I noticed tests for `Bader` in (tests/command_line/test_bader_caller.py) (apparently depends on VASP output files) in the GitHub workflow doesn't seem to run properly (though the tests seem to pass, until one checks the details):
```bash
Run wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
--2024-02-23 16:46:06-- http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
Resolving theory.cm.utexas.edu (theory.cm.utexas.edu)... 146.6.145.114
Connecting to theory.cm.utexas.edu (theory.cm.utexas.edu)|146.6.145.114|:80... connected.
HTTP request sent, awaiting response... 403 Forbidden
2024-02-23 16:46:06 ERROR 403: Forbidden.
Error: Process completed with exit code 8.
```
Seen the screenshot:
### Test for `Bader` fails
If running on a local machine with Bader properly installed, I then get:
```python
__________________ TestBaderAnalysis.test_atom_parsing ___________________
self = <tests.command_line.test_bader_caller.TestBaderAnalysis testMethod=test_atom_parsing>
def test_atom_parsing(self):
# test with reference file
analysis = BaderAnalysis(
chgcar_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4",
potcar_filename=f"{TEST_FILES_DIR}/POTCAR.Fe3O4",
chgref_filename=f"{TEST_FILES_DIR}/CHGCAR.Fe3O4_ref",
parse_atomic_densities=True,
)
assert len(analysis.atomic_densities) == len(analysis.chgcar.structure)
> assert np.sum(analysis.chgcar.data["total"]) == approx(
np.sum([dct["data"] for dct in analysis.atomic_densities])
)
/home/yang/Developer/pymatgen/tests/command_line/test_bader_caller.py:129:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/home/yang/Developer/pymatgen/venv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:2313: in sum
return _wrapreduction(a, np.add, 'sum', axis, dtype, out, keepdims=keepdims,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
obj = [array([[[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
... [0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]]), ...]
ufunc = <ufunc 'add'>, method = 'sum', axis = None, dtype = None
out = None
kwargs = {'initial': <no value>, 'keepdims': <no value>, 'where': <no value>}
passkwargs = {}
def _wrapreduction(obj, ufunc, method, axis, dtype, out, **kwargs):
passkwargs = {k: v for k, v in kwargs.items()
if v is not np._NoValue}
if type(obj) is not mu.ndarray:
try:
reduction = getattr(obj, method)
except AttributeError:
pass
else:
# This branch is needed for reductions like any which don't
# support a dtype.
if dtype is not None:
return reduction(axis=axis, dtype=dtype, out=out, **passkwargs)
else:
return reduction(axis=axis, out=out, **passkwargs)
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (14,) + inhomogeneous part.
/home/yang/Developer/pymatgen/venv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:88: ValueError
```
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Clean up test files: VASP outputs
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[
"Do you have any comments so far before I proceed? @janosh \r\n\r\n### Test file naming\r\n\r\nRegarding the test file naming conventions, I would like to hear about your suggestions. Taking `vasprun.xml` for example, I'm thinking of:\r\n- Keep `vasprun` as the header so that they could be listed and grouped properly. For example `bad_vasprun.xml` should not be used.\r\n- Use `xml.gz` as the tail to respect the file extension.\r\n\r\nIn this case, maybe either `vasprun_something.xml.gz` or `vasprun.something.xml.gz`? Which one would you suggest? Or don't change them at this moment? I would then leave a README there after this too.\r\n\r\n### Tests for `borg` broken\r\n\r\nMeanwhile my relocations seem to break tests for `borg`, as the outputs and inputs for VASP are now not inside the same dir:\r\nhttps://github.com/materialsproject/pymatgen/blob/c05931c44ddf5558a6aab964e6edc52c7edb8362/tests/apps/borg/test_hive.py#L28-L30\r\n\r\nWhich seems to pack `os.listdir()`:\r\nhttps://github.com/materialsproject/pymatgen/blob/c05931c44ddf5558a6aab964e6edc52c7edb8362/pymatgen/apps/borg/hive.py#L104-L113\r\n\r\nBut I'm not familiar with `borg` so 28c784cc9c02f964b0a3c3d610d8f461be12f759 may not be a rational fix. Can you help me double check this?\r\n\r\nThanks a lot π !",
"Guess I would need to improve the in-place decompression behaviour of `bader_caller` in this PR, otherwise tests would never pass (test file `CHGCAR.Fe3O4.gz` would be decompressed and following tests dependending on it would fail with `FileNotFoundError`), as discussed in:\r\nhttps://github.com/materialsproject/pymatgen/pull/3656#issuecomment-1963538547\r\n\r\nIt could be bypassed though by altering the test order but doesn't resolve this problem. So better just fix it.",
"> Do you have any comments so far before I proceed? @janosh\r\n\r\nsorry, i must have missed this!\r\n\r\n> In this case, maybe either vasprun_something.xml.gz or vasprun.something.xml.gz? Which one would you suggest? \r\n\r\ni prefer `vasprun_something.xml.gz`\r\n\r\n> Meanwhile my relocations seem to break tests for borg, as the outputs and inputs for VASP are now not inside the same dir:\r\n\r\ni think the way to go about this is copy all input files to `self.tmp_path` first and then pass that tmp dir to `borg`. let me know if that doesn't work",
"> sorry, i must have missed this!\r\n\r\nNo worries at all and no rush.\r\n\r\n> > In this case, maybe either vasprun_something.xml.gz or vasprun.something.xml.gz? Which one would you suggest?\r\n> \r\n> i prefer `vasprun_something.xml.gz`\r\n\r\nGood to hear! As I'm leaning towards the same and have already made the changes in c4d7e6af84385b2fb5bdddc6caa751daa9aeb731, 0fa962d58324dcd847877d1d83a5f42d41236e2e, f2e0526e169a97029a714f9606d511b6bb16262e hours before π \r\n\r\n\r\n> i think the way to go about this is copy all input files to `self.tmp_path` first and then pass that tmp dir to `borg`. let me know if that doesn't work\r\n\r\nThat makes sense (with some file IO overhead).\r\n\r\n",
"> That makes sense (with some file IO overhead).\r\n\r\nmight be enough actually to just symlink the files instead of making actual copies if the decompression leaves the original file in place",
"Some off-topic stuff just for note here.\r\n\r\nIt seems test workflows run much slower on Windows than Ubuntu for some reason (I'm working on WSL2-Ubuntu and run test is pretty painful even with `pytest-xdist`). For example for [job](https://github.com/materialsproject/pymatgen/actions/runs/8076321542/job/22064596206):\r\n| Split | Windows | Ubuntu |\r\n| ----- | -------- | ------ |\r\n| 1 | 9m 41s | 6m 57s |\r\n| 2 | Β 14m 40s | 7m 47s |\r\n| 3 | 13m 34s | 9m 3s |\r\n| 4 | 9m 47s | 7m 25s |\r\n| 5 | Β 14m 20s | 4m 25s |\r\n| 6 | 16m 6s | 6m 50s |\r\n| 7 | 14m 26s | 5m 38s |\r\n| 8 | 11m 45s | 6m 10s |\r\n| 9 | 18m 47s | 7m 2s |\r\n| 10 | Β 11m 18s | 6m 48s |",
"i noticed that as well. not sure why but also haven't investigated this at all yet. my suspicion was the windows runner just use slower hardware but maybe that's wrong and it's something in our test setup.\r\n\r\neither way it makes sense to occasionally update the `.pytest-durations.json` file that determines how the workload is optimally split across concurrent test runners so they all take roughly equally long. and as the code changes, that file needs to be updated once in a while",
"> my suspicion was the windows runner just use slower hardware but maybe that's wrong and it's something in our test setup.\r\n\r\nNot sure (don't have much knowledge about Github Actions...). But I guess it has something to do with the runners themselves, as I notice there're others reporting [this](https://github.com/actions/runner-images/issues/7320) as well. \r\n\r\n> either way it makes sense to occasionally update the `.pytest-durations.json` file that determines how the workload is optimally split across concurrent test runners so they all take roughly equally long. \r\n\r\nWell I don't think this would help much though... As currently Windows runners seem consistently slower than Ubuntu, so even we balance the runtime of both sides, the final run time would still be determined (and slowed) by Windows πΏ \r\n",
"Leave a quick note for myself:\r\n\r\nI'm working on fixing the tests for `borg` but find the situation is quite tricky... \r\n\r\nI never use `borg` before nor read the docs. But there seems to be some hard-coded parts for example:\r\nhttps://github.com/materialsproject/pymatgen/blob/442d740eb7794d360cb35f187e271b3debb7f047/pymatgen/apps/borg/hive.py#L104-L125\r\n\r\nWhich seems to be explained in https://github.com/materialsproject/pymatgen/blob/442d740eb7794d360cb35f187e271b3debb7f047/pymatgen/apps/borg/hive.py#L70-L75\r\n\r\nI guess I would need to symlink a dedicated test dir for it, because I noticed changing the file names may very likely to change which dir it would `assimilate` and yield the test quite fragile.\r\n\r\nAlso in the test itself the target dir for `assimilate` is a bit implicit (doesn't say where the data is collected from): https://github.com/materialsproject/pymatgen/blob/442d740eb7794d360cb35f187e271b3debb7f047/tests/apps/borg/test_hive.py#L27-L38\r\n\r\nBut I would find out the target later.\r\n",
"Please review @janosh.\r\n\r\nI have to keep the test file name for `borg` as `vasprun.xml.xe.gz` instead of the expected `vasprun.xe.xml.gz` because it is hardcoded to collect info from vasprun files of pattern `vasprun.xml*`:\r\nhttps://github.com/materialsproject/pymatgen/blob/b96d9e147e21489b377166f8839de8fab47e3e69/pymatgen/apps/borg/hive.py#L104-L133\r\n\r\nI wouldn't touch the source code because I don't have proper knowledge of `borg`.\r\n\r\nNoticed some tests are failing because `pydantic` and `matgl` are missing. Not sure about the reason though.",
"> Well I don't think this would help much though... As currently Windows runners seem consistently slower than Ubuntu, so even we balance the runtime of both sides, the final run time would still be determined (and slowed) by Windows πΏ\r\n\r\nthat's certainly true\r\n\r\n> I have to keep the test file name for `borg` as `vasprun.xml.xe.gz` instead of the expected `vasprun.xe.xml.gz` because it is hardcoded to collect info from vasprun files of pattern `vasprun.xml*`:\r\n\r\nsure, makes sense\r\n\r\n> Noticed some tests are failing because `pydantic` and `matgl` are missing. Not sure about the reason though.\r\n\r\nnot sure either `pydantic` should not be needed at all and `matgl` should be installed in CI. i can try to debug tomorrow\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/b96d9e147e21489b377166f8839de8fab47e3e69/setup.py#L81",
"> not sure either `pydantic` should not be needed at all and `matgl` should be installed in CI. i can try to debug tomorrow\r\n> \r\n> https://github.com/materialsproject/pymatgen/blob/b96d9e147e21489b377166f8839de8fab47e3e69/setup.py#L81\r\n\r\nThat would be much appreciated. Also noticed tests only failed for Ubuntu not Windows. \r\n\r\nIt seems `matgl` is installed successfully during CI run stage `Install dependencies`:\r\n```bash\r\nSuccessfully installed ....... matgl-1.0.0 ......\r\n```\r\n\r\nAnd import error is triggered for importing from the submodule not the `matgl` lib itself:\r\n```\r\n if calculator.lower() == \"m3gnet\":\r\n try:\r\n import matgl\r\n> from matgl.ext.ase import M3GNetCalculator\r\n```\r\n",
"> I have to keep the test file name for `borg` as `vasprun.xml.xe.gz` instead of the expected `vasprun.xe.xml.gz` because it is hardcoded to collect info from vasprun files of pattern `vasprun.xml*`:\r\n\r\nWell I came up with a solution in bd87dea6d6bb4a156cc40cdd327b7aab41089644: create a symlink with `ScratchDir`, now all files follow the same pattern π .\r\n",
"Thanks for reviewing @janosh! (I was about to redefine a `VASP_OUT_DIR` after cleaning up all vasp files, but glad you helped me out, thanks a ton π). I would proceed to other clean up once I have time and glad I could help."
] | 2024-02-24T06:04:00
| 2024-03-07T07:39:31
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2024-03-07T07:34:28Z
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CONTRIBUTOR
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## Clean up test files: VASP outputs
This is the first step of cleaning up test files: VASP outputs, relocate VASP output files to a dedicated dir (`vasp/outputs`) under `tests` dir to tidy up the `files` dir.
With the aim to clean up test files so that future developers could easily find and reuse existing test files whenever possible.
## TODOs
- [x] Relocate `vasprun.xml` c68d5c3d15791d148b4e6e6f2e09b6900c5249b7 and 2c8eba79da95f040ec2baa6c915a4ad7987e7f07
- [x] Relocate `OUTCAR` ee6df808d69a0bcd9694c45535c268eb0bed5511
- [x] Relocate `CHGCAR` 37868cedcfddc8491ff117c669722d3decbbe126
- [x] Relocate `DOSCAR` 649152a9cd2f24fe834dc321a4f5825a69e68f4b
- [x] Relocate `EIGENVAL` 1bba1bf3cfe5abdfbff7f9370b3de2b0a90630db
- [x] Relocate `PROCAR` 099c2058257c4d42746a7a73f3ae92f24414a07d
- [x] Relocate `WAVECAR` 428c326bc515cbbab4d8279e016048f1dd2d72a3
- [x] Relocate `XDATCAR` 0044e4984a71e0b3f1408d83ee2fef803a277327 and bd07afd6a4b26f6918bdd0c515864a45a0369e0f
- [x] Relocate `LOCPOT` 897fa39ee37ae596fc865e374275ef97527b335d
- [x] Relocate `CONTCAR` cb9fd86985140b7dd1039d9fe1c97f881ebe181e
- [x] Relocate other VASP output files (`DYNMAT` 8c691924455d042f0684d7496226ef2814b32123, `ELFCAR` 71964ad5eb4f436b51dd53135a9fcf6b9e1cd728, `IBZKPT` eb33d4082305fd76c0d56202d2b0ebdcef22826d, `WAVEDER` 002225f9ab4f584e77dc6b51591a7d5e780aa26b, `OSZICAR` b2d9040289f3eaf070d13c7c646e1b9d615b7766).
- [x] Remove duplicates a7301ba0df2cb3b364de0cdd5050eb0dfff83666, 82c37296eb8ce00b429634b4cc62f5e8131d28ac
- [x] Unify test file namings a1c25f7e35abc23aa5dd5a0b0b7c13a84a5c6dc0, c4d7e6af84385b2fb5bdddc6caa751daa9aeb731, 0fa962d58324dcd847877d1d83a5f42d41236e2e, f2e0526e169a97029a714f9606d511b6bb16262e
## Future follow up PRs
- Clean up VASP input files
- Group and clean up dedicated VASP dirs, for example `tests/files/relaxation`, `tests/files/kpoints_opt` and more.
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Lobsterout update doc-string to match renamed class variable
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[
"Hi @JaGeo,@janosh this change in doc-string got leftout with small changes done before merging. So would be great if this could be merged as well π ",
"@janosh I merged it as it was a tiny doc change. "
] | 2024-02-24T10:02:32
| 2024-03-01T14:20:58
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2024-02-24T10:17:30Z
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CONTRIBUTOR
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Deprecate `_parse_atomic_densities` in `BaderAnalysis` and fix `Bader` test setup
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[
"Meanwhile this PR only fixes the second half of #3652.\r\n\r\nFirst half of the GitHub workflow run still needs to be fixed (`wget` failed with `403 Forbidden` error) @janosh .",
"Test setup for `Bader` seems to have been fixed using `https` instead of `http`. Then every test workflow would get the following error:\r\n```python\r\n_____________________ TestBaderAnalysis.test_atom_parsing ______________________\r\n\r\nself = <tests.command_line.test_bader_caller.TestBaderAnalysis testMethod=test_atom_parsing>\r\n\r\n def test_atom_parsing(self):\r\n # test with reference file\r\n analysis = BaderAnalysis(\r\n chgcar_filename=f\"{TEST_FILES_DIR}/CHGCAR.Fe3O4\",\r\n potcar_filename=f\"{TEST_FILES_DIR}/POTCAR.Fe3O4\",\r\n chgref_filename=f\"{TEST_FILES_DIR}/CHGCAR.Fe3O4_ref\",\r\n parse_atomic_densities=True,\r\n )\r\n \r\n assert len(analysis.atomic_densities) == len(analysis.chgcar.structure)\r\n \r\n> assert np.sum(analysis.chgcar.data[\"total\"]) == approx(\r\n np.sum([dct[\"data\"] for dct in analysis.atomic_densities])\r\n )\r\n```\r\n\r\nMaybe I still should zero-pad them in the test (hopefully fix the issue)? @janosh (Or just remove/supress this test if no one is using it anyway?)",
"> Maybe I still should zero-pad them in the test\r\n\r\nyes, we should fix the test instead of removing it while the functionality is still available",
"Should be good for now, please review @janosh .\r\n\r\nThough everything _seems to be working_, there is still a minor issue here: As `Bader` itself cannot work directly on compressed files like `.gz`, `BaderAnalysis` would need to `decompress` corresponding files during runtime:\r\nhttps://github.com/materialsproject/pymatgen/blob/dc60d35a21fd7b55d82c65bb078afc4a2c0e9bbf/pymatgen/command_line/bader_caller.py#L99-L131\r\n\r\nThis leads to some issues:\r\n- `file.gz` would be converted to `file` after `BaderAnalysis` initialization.\r\n- Run unit test with `test_bader_caller` would decompress test files too (As we're working towards compressing test files).\r\n\r\nMeanwhile I think it might be better not to alter files in place, both during runtime and test time. As such I think it might make sense to alter the behaviour of `BaderAnalysis` a bit to decompress the test file in to a duplicate (and remove it afterwards). I would pin myself here to do this after cleaning up test files.\r\n",
"> decompress the test file in to a duplicate (and remove it afterwards). I would pin myself here to do this after cleaning up test files.\r\n\r\nthat sounds good! by \"after cleaning up test files\" do you mean in or after #3653?",
"> by \"after cleaning up test files\" do you mean in or after #3653?\r\n\r\nI think after #3653, still to make each PR on a dedicated topic π ",
"Thanks for reviewing and those helpful suggestions @janosh "
] | 2024-02-26T02:37:17
| 2024-03-15T02:29:34
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2024-02-26T08:48:23Z
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CONTRIBUTOR
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### Summary
- Clean up `__init__` of `BaderAnalysis`
- Mark `parse_atomic_densities` in `BaderAnalysis` as deprecated, to be removed on 26 Feb 2025, as discussed in #3652.
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PR_kwDOACgets5n47vt
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Fix `get_niggli_reduced_lattice` if entering A1 case
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[] | 2024-02-26T09:34:03
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2024-02-26T12:36:12Z
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CONTRIBUTOR
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## Summary
Major changes:
- fix 1: I found a bug at `pymatgen/core/lattice.py::Lattice::get_niggli_reduced_lattice`.
- After updating lattice parameters at A1, variables `A, B, ...` also need to be updated.
- Otherwise, condition checking would be wrong at A2 or later.
- Therefore, I added a line for updating `A, B, C, E, N, Y`.
- This is not minimal, but the simplest I think.
- Also, added a test that fails before the fix and succeeds after the fix.
- Correct values were calculated by spglib.
## Todos
If this is work in progress, what else needs to be done?
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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I_kwDOACgets6AY9Aw
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`Structure.replace_species` leaves label intact resulting in confusing/misleading label
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[
"Proposed solution in https://github.com/materialsproject/pymatgen/pull/3183#issuecomment-1959355057: update the label to `Composition({\"Au\": 0.5, \"Cu\": 0.5}).formula`"
] | 2024-02-26T12:09:19
| 2024-03-05T19:12:24
|
2024-03-05T19:12:24Z
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CONTRIBUTOR
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> I noticed that performing a `Structure.replace_species` operation leaves the label intact, leading to a misleading label or a confusing end-user experience (for example, replacing `Au` with `{"Au": 0.5, "Cu": 0.5}` will leave the label as `Au`). Do you have any thoughts on this @stefsmeets?
_Originally posted by @mkhorton in https://github.com/materialsproject/pymatgen/issues/3183#issuecomment-1955173223_
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PR_kwDOACgets5n6SbU
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Use `np.eye(3)` instead of `[[1, 0, 0], [0, 1, 0], [0, 0, 1]]` for identies
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[] | 2024-02-26T12:41:10
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2024-02-26T13:05:49Z
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MEMBER
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just code cleanup
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PR_kwDOACgets5oH6eX
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Avoid `bader_caller` from altering compressed file in place
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[
"Please review @janosh. Thanks.\r\n\r\nMaybe relocate the utility function to a more general accessible location (as I notice there are other tests seem to alter compressed file in place as well, cannot remember which one at the moment, would tag them in the future once I find any)?\r\n\r\nTests for `test_cod` seems to fail but this should not be related to this PR, `ERROR 2003 (HY000): Can't connect to MySQL server on 'www.crystallography.net:3306' (10060)`",
"Thanks for viewing @janosh . Glad I could help."
] | 2024-02-28T04:13:20
| 2024-03-04T02:14:22
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2024-03-01T14:17:44Z
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CONTRIBUTOR
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### Summary: Avoid bader_caller from altering compressed file in place
- Prevent `bader_caller` from altering compressed test in place, see https://github.com/materialsproject/pymatgen/pull/3656#issuecomment-1963538547
- Removed `bader_exe_path` to encourage users to add `Bader` executable to PATH for simplicity
- Other format clean ups
### Details
Added a utility function `temp_decompress` to copy compressed file and decompress the copied file in `ScratchDir`. If the file is not compressed, would just pass to avoid unnecessary file OPs.
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PR_kwDOACgets5oOogO
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Fix installation.md formatting
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[] | 2024-02-28T22:59:29
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2024-02-29T12:00:54Z
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MEMBER
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## Summary
There was a missing ```, making the public docs look awful. I was the culprit. Oops. All patched!
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PR_kwDOACgets5oVOe2
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Remove BadPoscarWarning when POSCAR elements set by POTCAR
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[
"Just came across this PR randomly... I guess I added this warning in #3539. I just had another look and I think this PR is right and I misunderstood the implementation. This https://github.com/materialsproject/pymatgen/blob/d07164fd27b955010ad411033d262ef3d935d09c/pymatgen/io/vasp/inputs.py#L259-L267\r\nis nested under `check_for_potcar`. (I thought ~`from_file` is falling to element check from `POTCAR` because `POSCAR` is badly formatted~, which seems not true). I'm sorry for this oversight and thanks for fixing this @esoteric-ephemera .",
"> I'm sorry for this oversight\r\n\r\nno worries. we live and learn :)"
] | 2024-02-29T19:27:11
| 2024-03-08T20:29:09
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2024-02-29T19:49:22Z
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CONTRIBUTOR
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A `BadPoscarWarning` was recently added to `pymatgen.io.vasp.inputs.Poscar` when the elements in the POSCAR are identified by the order of elements in the POTCAR file. Reading in the element names from POTCAR is valid VASP input, and it's [even permitted to omit the species names in POSCAR](https://www.vasp.at/wiki/index.php/POSCAR) because VASP reads them from POTCAR:
```This line lists the species of the present ions. The given order should match the order of species appearing in the POTCAR file. This line is optional, if omitted the species names are taken from the POTCAR file.```
This PR just removes the warning.
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I_kwDOACgets6A3vkc
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My kernel keeps dying when importing CifParser
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[
"could this be related to https://github.com/materialsproject/pymatgen/pull/3664?\r\n\r\nwhat do you get for `os.getenv(\"CI\")`?",
"Thanks for the response. I'm unaware what CI is though. After importing `os`, `os.getenv(\"CI\")` returns `None`, both before and after importing pymatgen",
"Good. Just wanted to confirm. Then I don't think it can't be the issue we just fixed.\nAs to what's causing it instead, perhaps you can try in a new python environment or on a different machine to see if the issue persists",
"Thanks for the response. I think I narrowed it down to the `spglib` library. That seems to kill my kernel when importing. I'll contact them to see what the problem is.",
"ah, in that case you might be hitting https://github.com/spglib/spglib/issues/197. what's your version?",
"I have version 2.3.1\r\nI could be wrong, but I suspect the issue is that I'm using an apple M2 chip. The C bindings need to be compiled for the osx-arm64 architecture and it seems like it's not tested yet for that yet.",
"should work. i was using it fine on an M2 Max chip last year",
"closing this as an upstream issue for now"
] | 2024-02-29T21:00:03
| 2024-03-01T19:43:27
|
2024-03-01T19:43:27Z
|
NONE
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### Python version
3.9.18
### Pymatgen version
2024.2.23
### Operating system version
MacOS 14.2.1 (M2 chip)
### Current behavior
I'm new to pymatgen, but my python kernel keeps dying when I import CifParser using the following command:
`from pymatgen.io.cif import CifParser`
It happens when both in the terminal and in jupyter notebook and I tried updating all of my package managers (conda, pip, brew). I never experienced this before working with python. Any advice would be welcome.
### Expected Behavior
I expected no problems importing
### Minimal example
```Python
from pymatgen.io.cif import CifParser
```
### Relevant files to reproduce this bug
_No response_
|
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PR_kwDOACgets5oYr56
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Fix RuntimeError triggered in CI of downstream packages
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[
"Has this issue been fixed? It looks like I am still seeing this error in my CI test.\r\n\r\nhttps://github.com/qzhu2017/PyXtal/actions/runs/8304091691/job/22729255439",
"this was released 2 weeks ago in [v2024.3.1](https://github.com/materialsproject/pymatgen/releases/tag/v2024.3.1). your errors should disappear once you update"
] | 2024-03-01T09:20:59
| 2024-03-16T06:15:44
|
2024-03-01T10:04:43Z
|
MEMBER
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we have a major problem with how deprecation removal reminders are currently setup for CI causing other package CI runs to fail. [in this case with](https://github.com/CederGroupHub/chgnet/actions/runs/8105153971/job/22153023416)
```py
E RuntimeError: remove the change of default primitive=True to False made on 2023-10-24
```
this will affect any package using `pymatgen` in CI.
this PR solves the issue in two places `CifParser.parse_structures()` and `BaderAnalysis._parse_atomic_densities()`.
i'll make a hot-fix release right after this is merged. thanks @BowenD-UCB for reporting!
this poorly written code was added by me in https://github.com/materialsproject/pymatgen/commit/9e27ca89b01de23c0088b3d631f85f489a4a5fb7 and released in [v2023.11.10](https://github.com/materialsproject/pymatgen/releases/tag/v2023.11.10). given this affects all intermediate releases, it's probably too much to yank them all from PyPI:
- [v2023.11.12](https://github.com/materialsproject/pymatgen/releases/tag/v2023.11.12)
- [v2023.12.18](https://github.com/materialsproject/pymatgen/releases/tag/v2023.12.18)
- [v2024.1.26](https://github.com/materialsproject/pymatgen/releases/tag/v2024.1.26)
- [v2024.1.27](https://github.com/materialsproject/pymatgen/releases/tag/v2024.1.27)
- [v2024.2.1](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.1)
- [v2024.2.20](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.20)
- [v2024.2.23](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.23)
- [v2024.2.8](https://github.com/materialsproject/pymatgen/releases/tag/v2024.2.8)
luckily, the error will only show up in CI runs, not in user-facing code.
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I_kwDOACgets6BCoib
| 3,666
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Robustness of `Poscar` parser should be further improved
|
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[
"It seems you started with an empty first line, which should be the comment line. And therefore the `Lu3` line is treated as the `scaling factor` line thus the error.\r\n\r\nThis should work:\r\n```python\r\nfrom pymatgen.io.vasp.inputs import Poscar\r\n\r\nposcar_text = \"\"\"Lu3\r\n1.0\r\n8.212068 -1.711729 -0.004637\r\n8.212068 1.711729 -0.004637\r\n7.856937 -0.000000 2.938818\r\nLu\r\n3\r\ndirect\r\n0.000000 0.000000 -0.000000 Lu\r\n0.221900 0.221900 0.221900 Lu\r\n0.778100 0.778100 0.778100 Lu\r\n\"\"\"\r\n\r\nPoscar.from_str(poscar_text)\r\n```",
"Thank you, @DanielYang59. Apologies about the false report here! I was trying to track down a `BadPoscarWarning`, and it seems like this was a false flag. I'll close this issue until I can find the actual source of the problem. In hindsight, I think the source of my issue was likely some file ending issue when transferring files between Windows/Linux.",
"No worries at all. Not sure if you mean #3662 (to which I confessed...). I tried to run your code on my MacOS machine and didn't notice any `BadPoscarWarning`.\r\n\r\nMaybe you can try `git config --global core.autocrlf input` to automatically handle file ending as described [here](https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration)? Not sure if this would be helpful though.\r\n> This setup should leave you with CRLF endings in Windows checkouts, but LF endings on macOS and Linux systems and in the repository.\r\n\r\n",
"Nah, what I mean is I transferred a POSCAR from my Linux machine to Windows (or vice versa) and imagine that this probably was potentially the root cause of my problem. In any case, it's all good! "
] | 2024-03-02T19:59:22
| 2024-03-05T02:40:24
|
2024-03-04T16:50:20Z
|
MEMBER
|
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|
### Python version
3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
When using the various Pymatgen input parsing utilities on the POSCAR below, a `BadPoscarWarning` is raised even though it is seemingly valid. I've drilled down to the root cause below.
### Expected Behavior
A valid parse.
### Minimal example
```Python
from pymatgen.io.vasp.inputs import Poscar
poscar_text = """
Lu3
1.0
8.212068 -1.711729 -0.004637
8.212068 1.711729 -0.004637
7.856937 -0.000000 2.938818
Lu
3
direct
0.000000 0.000000 -0.000000 Lu
0.221900 0.221900 0.221900 Lu
0.778100 0.778100 0.778100 Lu
"""
Poscar.from_str(poscar_text)
```
Reports:
```python
ValueError: could not convert string to float: 'Lu3'
```
### Relevant files to reproduce this bug
_No response_
|
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I_kwDOACgets6BCrV2
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Improper parsing of `METAGGA` flag in `Vasprun` parser
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[
"I just had a quick look (quite busy this week sorry) and found this seems not specific to `METAGGA`, \r\nfor example `print(vr.parameters[\"ALGO\"])` would also trigger `KeyError: 'ALGO'`. Not sure about the reason though.\r\n\r\nMeanwhile `Vasprun` indeed got these tags as `.incar` but not into `.parameters` (haven't got time to look into):\r\n```python\r\nprint(vr.incar)\r\n\r\nALGO = All\r\nEDIFF = 1e-05\r\nEDIFFG = -0.02\r\nENAUG = 1360.0\r\nENCUT = 680.0\r\nIBRION = 2\r\nICHARG = 1\r\nISIF = 3\r\nISMEAR = 2\r\nISPIN = 2\r\nKPAR = 4\r\nKSPACING = 0.22\r\nLAECHG = True\r\nLASPH = True\r\nLCHARG = True\r\nLELF = False\r\nLMAXMIX = 6\r\nLMIXTAU = True\r\nLREAL = Auto\r\nLVTOT = True\r\nLWAVE = False\r\nMAGMOM = 3*0.6\r\nMETAGGA = R2scan\r\nNELM = 200\r\nNPAR = 4\r\nNSW = 99\r\nPREC = Accurate\r\nSIGMA = 0.14\r\n```\r\n\r\n\r\nA side note, docstring for the internal `_parse` method is completely missing (I could help add one if no one else volunteer):https://github.com/materialsproject/pymatgen/blob/442d740eb7794d360cb35f187e271b3debb7f047/pymatgen/io/vasp/outputs.py#L326-L337",
"@DanielYang59 it looks like `ALGO` is also missing from the `<parameters>` section of the `vasprun.xml` file, hence why it too was not showing up. \r\n\r\nTo summarize, it seems the there are several parameters that are strangely omitted from the `<parameters>` section of the `vasprun.xml` even though they are valid in the `<incar>` (and other) sections. This then causes the `KeyError`.\r\n\r\nI'm not exactly sure the best way to handle this one because `vr.parameters` is indeed reporting accurate information, and populating it with flags from other fields seems perhaps unwise. My concern is mostly with codes that use this information to get the `run_type`, like to generate the MP compatibility data. But I guess that should be handled in those packages directly.\r\n\r\nSo, perhaps this should be closed and handled elsewhere where needed? Hopefully this was an issue resolved in newer versions of VASP.",
"Closing this as a VASP bug, not a pymatgen bug. "
] | 2024-03-02T20:22:48
| 2024-03-05T02:40:56
|
2024-03-05T02:40:55Z
|
MEMBER
|
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|
### Python version
3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
The `Vasprun` parser is not properly parsing the METAGGA flag, which can introduce some painful downstream effects related to MP (see my original report in emmet https://github.com/materialsproject/emmet/issues/960).
```python
from pymatgen.io.vasp import Vasprun
vr = Vasprun("vasprun.xml.gz")
print(vr.parameters["METAGGA"]) # raises a KeyError
```
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/14470682/vasprun.xml.gz)
My guess is because that even though
```
<i type="string" name="METAGGA"> R2scan</i>
```
is in the `<incar>` section, it's not elsewhere in the file. I can confirm the meta-GGA is applied in the `OUTCAR`.
If I recall correctly, this omission in the `vasprun.xml` was present in certain older versions of VASP, but perhaps it was fixed more recently? It'd be good to confirm this with VASP 6.4.
Maybe the solution here is to get a dictionary of parameters form the incar field and then merge the two dictionaries, with that from the incar field having lower priority.
|
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`MSONAtoms` may not serialize appropriately if the `.info` flag is populated
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[
"I don't actually know that this one is readily solvable since people can dump whatever they want into `.info`, and the logic for the (de)serialization is in `monty`.\r\n\r\nI'll close this as a result but wanted to report it anyway. "
] | 2024-03-03T19:04:47
| 2024-03-04T21:31:43
|
2024-03-04T21:31:43Z
|
MEMBER
|
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### Python version
3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
The recently introduced `MSONAtoms` class in https://github.com/materialsproject/pymatgen/pull/3619 gives Pymatgen additional flexibility in making ASE `Atoms` objects `MSONable`, helping with lossless (de)serialization. This method generally works well, but JSON serialization can fail if the `.info` attribute of the `Atoms` object contains an `MSONable` entry.
### Expected Behavior
The `MSONAtoms` should be JSON serializable via the various `monty` utilities (for instance).
### Minimal example
```Python
from pymatgen.core import Structure
from monty.serialization import dumpfn
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
mson_atoms = structure.to_ase_atoms()
mson_atoms.info["test"] = structure
dumpfn(mson_atoms, "test.json")
```
or...
```python
from ase.build import bulk
from pymatgen.io.ase import AseAtomsAdaptor
from monty.serialization import dumpfn
atoms = bulk("Cu")
atoms.info["test"] = AseAtomsAdaptor().get_structure(atoms)
structure = AseAtomsAdaptor.get_structure(atoms)
mson_atoms = structure.to_ase_atoms()
dumpfn(mson_atoms, "test.json")
```
In both cases, you get
```
TypeError: Cannot convert object of type <class 'pymatgen.core.structure.Structure'> to dictionary for JSON
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3668/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3668/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3669
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3669/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3669/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3669/events
|
https://github.com/materialsproject/pymatgen/issues/3669
| 2,165,927,751
|
I_kwDOACgets6BGW9H
| 3,669
|
POTCAR setting problem
|
{
"login": "lihaojie87",
"id": 50283726,
"node_id": "MDQ6VXNlcjUwMjgzNzI2",
"avatar_url": "https://avatars.githubusercontent.com/u/50283726?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/lihaojie87",
"html_url": "https://github.com/lihaojie87",
"followers_url": "https://api.github.com/users/lihaojie87/followers",
"following_url": "https://api.github.com/users/lihaojie87/following{/other_user}",
"gists_url": "https://api.github.com/users/lihaojie87/gists{/gist_id}",
"starred_url": "https://api.github.com/users/lihaojie87/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/lihaojie87/subscriptions",
"organizations_url": "https://api.github.com/users/lihaojie87/orgs",
"repos_url": "https://api.github.com/users/lihaojie87/repos",
"events_url": "https://api.github.com/users/lihaojie87/events{/privacy}",
"received_events_url": "https://api.github.com/users/lihaojie87/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
}
] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hey @lihaojie87, it looks like VASP is now distributing these (from the portal) as \"PAW POTCAR files: LDA & PW91 & PBE (outdated)\" with the description:\r\n> The LDA, PW91 and PBE PAW datasets (snapshot: 05-05-2010, 19-09-2006 and 06-05-2010, respectively). These files are outdated, not supported and only distributed as is.\r\n\r\nWe're actively updating the POTCARs used at MP so this won't be an issue moving forwards"
] | 2024-03-04T04:52:41
| 2024-03-11T17:17:48
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
### Python version
Python 3.12.0
### Pymatgen version
2024.3.1
### Operating system version
Windows
### Current behavior
I have already downloaded the POTCAR into D:\DFT\POTCAR\origin and the folder contents is
```
> ls
Directory: D:\DFT\POTCAR\origin
Mode LastWriteTime Length Name
---- ------------- ------ ----
d---- 2024/3/1 21:40 ο potpaw_LDA.52
d---- 2024/3/1 21:09 ο potpaw_LDA.54
d---- 2024/3/1 21:09 ο potpaw_LDA.64
d---- 2024/3/1 21:40 ο potpaw_PBE.52
d---- 2024/3/1 21:09 ο potpaw_PBE.54
d---- 2024/3/1 19:02 ο potpaw_PBE.64
```
when I use the command to generate my_psp
`pmg config -p D:\DFT\POTCAR\origin D:\DFT\POTCAR\MY_PSP`
there is no problem and the folder contents of D:\DFT\POTCAR\MY_PSP is
```
> ls
Directory: D:\DFT\POTCAR\MY_PSP
Mode LastWriteTime Length Name
---- ------------- ------ ----
d---- 2024/3/4 12:29 ο POT_GGA_PAW_PBE_52
d---- 2024/3/4 12:29 ο POT_GGA_PAW_PBE_54
d---- 2024/3/4 12:28 ο POT_LDA_PAW_52
d---- 2024/3/4 12:28 ο POT_LDA_PAW_54
d---- 2024/3/4 12:29 ο potpaw_PBE.64
```
As you can see, there is 6 origin POTCAR but only generate 5 new POTCAR dir.
When I use `job = GenerateVaspInputJob(input_set="pymatgen.io.vasp.sets.MPRelaxSet", contcar_only=False)
` to generate vasp input file there will give an error :
```
OSError: You do not have the right POTCAR with functional='PBE' and label Ni_pv in your VASP_PSP_DIR. Paths tried: ['D:\\DFT\\POTCAR\\MY_PSP\\POT_GGA_PAW_PBE\\POTCAR.Ni_pv', 'D:\\DFT\\POTCAR\\MY_PSP\\POT_GGA_PAW_PBE\\Ni_pv\\POTCAR']
```
I check the source code which shows `"potpaw_PBE": "POT_GGA_PAW_PBE"`. Which version of POTCAR is potpaw_PBE?
```
name_mappings = {
"potpaw_PBE": "POT_GGA_PAW_PBE",
"potpaw_PBE_52": "POT_GGA_PAW_PBE_52",
"potpaw_PBE_54": "POT_GGA_PAW_PBE_54",
"potpaw_PBE.52": "POT_GGA_PAW_PBE_52",
"potpaw_PBE.54": "POT_GGA_PAW_PBE_54",
"potpaw_LDA": "POT_LDA_PAW",
"potpaw_LDA.52": "POT_LDA_PAW_52",
"potpaw_LDA.54": "POT_LDA_PAW_54",
"potpaw_LDA_52": "POT_LDA_PAW_52",
"potpaw_LDA_54": "POT_LDA_PAW_54",
"potUSPP_LDA": "POT_LDA_US",
"potpaw_GGA": "POT_GGA_PAW_PW91",
"potUSPP_GGA": "POT_GGA_US_PW91",
}
```
### Expected Behavior
Correctly generate vasp input files
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No response_
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3669/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3669/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
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