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https://api.github.com/repos/materialsproject/pymatgen/issues/3042 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3042/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3042/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3042/events | https://github.com/materialsproject/pymatgen/issues/3042 | 1,742,344,979 | I_kwDOACgets5n2hMT | 3,042 | Wrong typehint in `Structure.relax` | {
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"Thanks. I agree, but I am reluctant to add this because it will make ASE a core dependency for a type hint of a function that may or may not be used by most people.",
"Ah, that's a good point. We don't want to add ASE as a core dependency. @janosh, there isn't any trickery to get around the type hinting issue he... | 2023-06-05T18:36:39 | 2023-06-09T14:46:14 | 2023-06-09T14:46:14Z | MEMBER | {
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Should be type `str | Calculator` where `Calculator` is `from ase.calculators.calculator import Calculator` | {
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"That sounds great! Let me know if I can help with tests or reviewing.",
"I'll definitely be adding plenty of tests, but would love help with reviewing when I'm done! And probably fixing mypy issues...",
"Thanks. But my question is how different is it from a `AseAdaptor.get_atoms(structure).get_potential_energy... | 2023-06-05T18:40:42 | 2023-06-09T14:46:15 | 2023-06-09T14:46:15Z | MEMBER | {
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} | Currently, there is a method to do `Structure.relax` which calls an ASE calculation with the ASE Optimizer class. There should be a similar method called `Structure.run` which calls ASE to run `atoms.get_potential_energy()`. This will allow for the use of the calculator's internal optimizers if the user wishes.
I ca... | {
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"I suggest:\r\n1. We have a `run_calculation` method that replaces and extends most of the code in `relax` to be more flexible.\r\n2. We have `relax` call run_calculator with a specific set of parameters to do a relaxation.\r\n\r\n`Structure.run` as a naming sounds a bit strange to me.",
"Agreed. That'll clean th... | 2023-06-05T20:02:29 | 2023-06-09T14:47:10 | 2023-06-09T14:46:13Z | MEMBER | {
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} | Closes #3042. Closes #3043. Closes #3047.
Links:
- #3042
- #3043
- #3047
In addition to the prior issues, I also increased the range of optimizers that can be passed to `Structure.relax` so the user doesn't have to rely solely on FIRE.
For molecules, I added a `Molecule.relax()` feature that defaults to GF... | {
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"Could you try a clean re-install?\r\n\r\n```sh\r\npip uninstall -y pymatgen\r\npip cache purge\r\npip install pymatgen\r\n```\r\n\r\nIf that doesn't help, try outside a `conda` env.\r\n\r\n```sh\r\n# without a conda env active\r\npython -m venv debug\r\n. ./debug/bin/activate\r\npip install pymatgen\r\n```",
"Hi... | 2023-06-05T23:57:57 | 2023-06-15T06:33:11 | 2023-06-15T06:33:11Z | CONTRIBUTOR | {
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```
from mp_api.client import MPRester
api_key = "*****"
with MPRester(api_key) as mpr:
struct = mpr.get_structure_by_material_id("mp-2534")
```
gives the following error:
```
Traceback (most recent call last):
File "/Users/jw598/Rafael_project/code... | {
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"Naturally, installing Microsoft Visual C++ 14.0 resolves it. And I now see that's in the docs, so we're good."
] | 2023-06-06T07:04:48 | 2023-06-06T07:06:45 | 2023-06-06T07:06:44Z | MEMBER | {
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```python
Building wheels for collected packages: pymatgen
Building editable for pymatgen (pyproject.toml) ... error
error: subprocess-exited-with-error
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"Could you share how this differs from `EnumerateStructureTransformation` backed by `enumlib`?",
"Also, thank you for the clearly described and illustrated issue.",
"Hi @mkhorton, thank you very much for your comment! I just found out about `EnumerateStructureTransformation`. Upon checking the documentation, it... | 2023-06-06T09:02:56 | 2023-07-18T21:08:37 | CONTRIBUTOR | {
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} | #### Problem
For molecular dynamics simulation and machine learning data generation of random structures, one might desire to have a routine that transforms a given disordered structure $S$ to a set of randomly ordered structures $\\{S'_i\\}$, where each randomly ordered structure $S'_i$ has the same overall composi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3050 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3050/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3050/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3050/events | https://github.com/materialsproject/pymatgen/pull/3050 | 1,743,746,491 | PR_kwDOACgets5STKzd | 3,050 | Extend lobsterenv for coop/cobi | {
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"Hi @JaGeo , if you have any more suggestions / changes let me know ",
"@naik-aakash , very nice! I have added my tiny suggestion on the documentation and naming (which was initially, of couse, my fault ;))! ",
"Ready to be merged from my side! @naik-aakash \r\n\r\n@janosh , this is ready to be reviewed! :)",
... | 2023-06-06T12:18:25 | 2024-01-10T12:23:31 | 2023-07-24T14:43:22Z | CONTRIBUTOR | {
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- Extended lobsterenv.py module to work for ICOBILIST/ICOOPLIST
- Added test cases
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"This is done (I hope)."
] | 2023-06-06T17:34:30 | 2023-06-09T20:02:55 | 2023-06-09T20:02:55Z | MEMBER | {
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} | This is just a tracker to keep tabs on it. It is my understanding that `matgl` is the new standard repo to use if you want a pre-trained m3gnet model.
~Note: From looking at the `matgl` `setup.py` file, there might be a file path or two that might cause issues on Windows. Also, the pinned versions in the `setup.py` ... | {
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"CI failure caused by legacy `MPRester`, unrelated to PR."
] | 2023-06-07T03:51:14 | 2023-06-07T06:46:57 | 2023-06-07T06:46:23Z | MEMBER | {
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"This is great, thanks @montoyjh! 👍 "
] | 2023-06-08T18:18:13 | 2023-06-09T05:48:15 | 2023-06-09T05:48:12Z | CONTRIBUTOR | {
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The Pourbaix diagram was generating multi-entries with the wrong composition because of Reaction coefficient handling. This fixes the issue by using the explicit list of reaction coefficients, rather than the hash retrieval, and adds a regression test that fails previously but passes now.
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"@shyuep We could in principle remove the `TWINE_USERNAME` and `TWINE_PASSWORD` secrets from this repo after this is merged. But prob better to keep, esp. until the next release to make sure this actually works.\r\n"
] | 2023-06-09T05:42:03 | 2023-06-09T08:27:43 | 2023-06-09T08:27:42Z | MEMBER | {
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"Thanks @exenGT, I added a question to the associated issue.",
"@janosh All your suggestions have been addressed in my latest commits.",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3057?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm... | 2023-06-10T00:22:39 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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"Hi @HegemonyTao, the symmetry finding algorithms come via a third-party library called \"spglib\". The best way to understand this library is to read their paper:\n\nhttps://arxiv.org/pdf/1808.01590.pdf\n\nI hope this helps!",
"> Hi @HegemonyTao, the symmetry finding algorithms come via a third-party library cal... | 2023-06-12T02:43:25 | 2023-06-12T04:05:41 | NONE | {
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Hi developers, I am very curious about the method of analyzing the space group of the given crystal structure you have achieved. But when I tried to read the source code, I found that you had already encapsulated it into a pyd file, which made it difficult for me to understand how the method was imple... | {
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"Based on [`git blame` from 7 years ago](https://github.com/materialsproject/pymatgen/commit/48c9b1f5676241d02235bebe82aaab5cb2fd17f7), @montoyjh might know more.\r\n\r\n@matthewkuner Could you specify what the error is and post the output of `structure.to('material_id.json')` in HTML `<details>` (just start typing... | 2023-06-12T17:22:58 | 2023-06-13T21:57:49 | CONTRIBUTOR | {
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For the structure below, an error occurs when attempting to create the IEEE rotation matrix. I believe it is due to this structure, which is identified as monoclinic by the SpaceGroupAnalyzer, hav... | {
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"@janosh: I can confirm after running tests locally that everything works fine with `Molecule.calculate()` when `matgl` is not installed, but when you install `matgl` in the same environment as `tblite[ase]`, the GFN2-xTB calculations that `tblite` runs yield convergence errors and therefore fails the test suite.\r... | 2023-06-12T19:30:30 | 2023-06-13T14:30:33 | 2023-06-13T14:30:33Z | MEMBER | {
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"@arosen93 Pls fix....",
"@shyuep: Will fix it ASAP right after this meeting. There's no need for it to be required. Something must have been missed.",
"Thanks, @janosh "
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I installed pymatgen today and tried to use `pymatgen.io.structure.Structure`. It failed because of this import https://github.com/materialsproject/pymatgen/blob/82f108a3cba5f12b88b95fecb4e3b775ca9de6c6/pymatgen/core/structure.py#L27
`ase` is currently an optional requirement. After installing `a... | {
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"Thanks! ",
"No problem. Please let me know if this issue still arises anywhere else!",
"Just a heads up that this PR was merged empty and so #3061 isn't actually fixed yet. I'll re-open that issue and re-apply the fix."
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"Thank you! 👍 I remember wanting to clarify this myself at some point and then forgot. 😅 "
] | 2023-06-13T11:59:05 | 2023-06-13T12:12:54 | 2023-06-13T12:12:40Z | CONTRIBUTOR | {
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"Be aware that disordered magnetic materials are possible. I've never been entirely satisfied with the distinction between Species.spin and the magmom site property, but the former does allow a disordered magnetic material to be defined, while the latter does not.",
"I would distinguish spin as an theoretical con... | 2023-06-13T23:06:07 | 2023-06-16T06:15:10 | NONE | {
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Writing to cif is fixed when the structure is modified such that spins are not defined, but replaced by de... | {
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```py
for idx, specie in enumerate(species):
sites.append(Site(specie, coords[idx], properties=prop))
```
where `species` is `dict`, not list so to get value, must be `species[idx]`, not `specie`.
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a18903217 remove many no longer needed `monty.tempfile.ScratchDir(".")`
@shyuep It's a bit more magical since people who don't look at `PymatgenTest` won't know that their test... | {
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"Just to confirm, the problem is `\"End of Dataset\"` not being on a new line?",
"Yes, exactly",
"Thanks for reporting this!\nI think the last fix on parsing fixed one white space problem and created another. I'm currently on family leave until the end of next week I can fix it when I come back.",
"I think th... | 2023-06-14T12:40:40 | 2023-08-15T16:26:38 | 2023-08-15T16:26:38Z | CONTRIBUTOR | {
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} | #### Description
Reading and writing POTCAR file with the Potcar class from pymatgen.io.vasp seems broken.
#### Repro
To reproduce the problem, I start with a file:
POTCAR
```
PAW Sb 04Feb1998
5.00000000000000
[...]
0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
End of Dataset
PA... | {
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"This PR has been open for a while and fixed some of the previous magnetic moment problems. I apologize for not adding tests yet to get it merged.\r\n\r\nHowever, with the recent changes in `Species` properties (related to spin), the`MagOrderingTransformation` code is again broken. I don't really understand what ha... | 2023-06-15T22:56:00 | 2023-07-14T17:25:44 | 2023-07-14T13:54:23Z | MEMBER | {
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} | This PR addresses the bugs described in #3006. To summarize: changes to default magnetic moments introduced in #2727 now mean that structures with only partially defined magnetic moments (e.g., on half the sites) cannot be successfully analyzed by `SpaceGroupAnalyzer`. This was encountered when performing magnetic orde... | {
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"@kamronald does this still handle species with oxidation state correctly?",
"@mkhorton good point, I just checked and it does not handle them properly, I'll fix that",
"@mkhorton oxidation states are now properly saved",
"Thanks @kamronald! 👍 \r\n\r\nIIUC @mkhorton in https://github.com/materialsproject/pym... | 2023-06-15T23:25:21 | 2024-08-03T19:01:57 | NONE | {
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} | Change the "atom site type symbol", such that the element symbol is saved instead of the full species string (which includes site properties). This fixes Issue #3065, allowing for accurate writing of structures containing species properties to CIF and MCIF files.
## Summary
Major updates:
Change the "atom site... | {
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"Openbabel seems to be missing. Not sure why. Should be unrelated to this change. \r\n\r\nMany unrelated failing tests 🙈",
"Yeah I think that's caused by a the latest `mp-api` release. Thank for the cleanup!",
"Thanks!\r\n\r\n Maybe @munrojm could also shortly check if it should be an \"and\" rather than an \"... | 2023-06-17T06:41:24 | 2023-06-17T08:35:44 | 2023-06-17T07:09:09Z | MEMBER | {
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} | HI @janosh ,
I removed and simplified the tests. I am still not sure why there is an "or" for the other tests. In my opinion, the result should be always the same for one structure.
It's also redundant to test if g has a certain k-point and then later on tests if point g has the same kpoint or point xyz has a cer... | {
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697dec8eb more precise error message testing
0f1256ca8 breaking: change Composition bad key error type from TypeError to KeyError | {
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"Ready to go, @janosh! "
] | 2023-06-18T15:49:52 | 2023-06-18T18:29:25 | 2023-06-18T18:10:45Z | MEMBER | {
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"Thank you!! 🙏",
"If the user doesn't have ASE installed though, the test still skips right? On mobile so can't see what `ase_loaded` does. ",
"No, running _all_ tests now requires `ase` to be installed. I think that's fine. Running tests locally usually involves specifying a path to a test module so you only ... | 2023-06-18T16:54:04 | 2023-07-14T14:07:51 | 2023-06-18T17:27:29Z | MEMBER | {
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} | Tests were set to skip if `ase` not importable (now removed so we catch this in the future).
@arosen93 `sys.path.insert(0, getsitepackages()[0])` is admittedly an ugly hack but, like you said, preferable over a breaking module rename. | {
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"I'm having trouble installing `openbabel` on Mac so can't run this test myself. Is this value correct?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/47af172ac90ff5e23ce76bbaa5cb8b695d165a82/pymatgen/analysis/tests/test_fragmenter.py#L120\r\n\r\n I'm concerned these tests are apparently being skipped in ... | 2023-06-18T17:16:16 | 2023-06-22T23:02:58 | 2023-06-22T23:02:58Z | CONTRIBUTOR | {
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} | #### Description
Testing pymatgen 2023.05.31 on debian unstable, all tests pass except
test_babel_PC_with_RO_depth_0_vs_depth_10 from analysis/tests/test_fragmenter.py
#### Repro
Steps to reproduce the behavior:
1. Build from source, including pymatgen test-files
2. `pytest-3 -vv pymatgen/analysis/tests/... | {
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"@janosh, I tried to add more type hinting but mypy was raising very weird errors. ",
"Where functions are returning a large tuple containing various types and lengths of data, it might be helpful to wrap them up as a NamedTuple. This would be backward-compatible as you still _can_ access the elements by index, b... | 2023-06-19T06:34:11 | 2023-06-19T15:45:11 | 2023-06-19T15:45:09Z | MEMBER | {
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@janosh : happy to hear additional thoughts from you. | {
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"> One thing to keep in mind is that returned objects are not necessarily unique anymore, they could be returned again through the cache.\r\n\r\nThis sounds like a foot gun we should stay away from. Could you describe your motivation for this change? Maybe there's a safer way to go about this.",
"Closing this as ... | 2023-06-19T11:55:45 | 2023-06-27T20:18:51 | 2023-06-27T20:01:11Z | CONTRIBUTOR | {
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- One thing to keep in mind is that returned objects are not necessarily unique anymore, they could be returned again through the cache.
- Arguments to `get_el_sp` must be `Hashable`, luckily this seems to be... | {
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} | #### Description
When selective dynamics is activated during a run but not all atomic sites are allowed to move (for instance, when calculating finite difference phonons at only a few sites with `IBRION = 5`), `Vasprun` in `pymatgen.io.vasp.outputs` erroneously sets the rank of the force constant matrix to be `(3 x ... | {
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Fix is to change to immutable types like `tuple` or [`frozendict`](https://git... | {
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This PR fixes an error in the **hill_formula** property of the Composition object, which occurs in cases where C, H, and other element/s with symbol ordering alphabetically before H are present at the same time. In such a case, H should be placed directly after C, but this is not implemented nor tested in... | {
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} | #### Description
test_plotting in electron_structures uses `==` equality to test floating point numbers. This inevitably fails, e.g. on i386 https://ci.debian.net/data/autopkgtest/testing/i386/p/pymatgen/34643142/log.gz
#### Repro
Steps to reproduce the behavior:
1. Go to 'pymatgen/electronic_structure/tes... | {
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"> I wonder if this wouldn't be a good convenience method for molecule.\r\n\r\nGood idea! Would you like to submit a PR that moves this method to the `Molecule` class and also adds a unit test for it?\r\n",
"Moving the method, yes. Just wondering if this is the best representation as you can use site number, elem... | 2023-06-22T04:53:48 | 2023-06-24T05:56:18 | 2023-06-23T13:31:45Z | MEMBER | {
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Thanks @esoteric-ephemera for pointing out the fix. 👍 | {
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Todo: Check why test failure was not caught in our CI. `openbabel` not installed correctly? | {
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"@janosh I don't understand why this test would be failing. Hints are appreciated.",
"Ah, they have been failing already before. Okay. I was just confused that it was related to molecules."
] | 2023-06-23T06:53:14 | 2023-06-23T13:31:44 | 2023-06-23T13:31:43Z | MEMBER | {
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I really just moved the method. It's not sophisticated yet but maybe someone can build on this implementation. I therefore left a todo. | {
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"> I am not sure the issue is pymatgen related or emmet-related.\r\n\r\nNeither I think. I assume bandstructures should not be saved using `numpy` types, so just an issue with our db.\r\n\r\n@munrojm Would a re-parse fix this?\r\n\r\n@JaGeo Here's a temporary workaround:\r\n\r\n```py\r\njson.dump(band.as_dict(), f,... | 2023-06-23T07:40:05 | 2023-06-23T13:29:06 | MEMBER | {
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I am not sure the issue is pymatgen related or emmet-related.
The following code fails as the BandstructureSymmline cannot be converted to a serializable json....
```Python
from mp_api.client import MPRester
import json
with MPRester("YOURKEY") as a:
band=a.get_bandstructure_by_material_id... | {
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"@janosh: A small note. If you do \r\n```python\r\nfrom chgnet.model.dynamics import CHGNetCalculator\r\n```\r\n\r\nthen you have imported an ASE calculator. You can provide the calculator as a kwarg via `Structure.relax(calculator=CHGNetCalculator)` just like any other calculator. I'm not sure if this would reduce... | 2023-06-24T01:34:49 | 2023-06-25T22:56:43 | 2023-06-25T22:56:42Z | MEMBER | {
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} | Following hot (or not?) on the heels of #3044, this PR adds `calculator="chgnet"` as a recognized option to `Structure.relax()` and `Structure.calculate()` for running [CHGNet](https://github.com/CederGroupHub/chgnet)-powered structure relaxations and static calculations.
@BowenD-UCB This is a 1st draft. Will requir... | {
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} | ## Summary
Minor misspell fix in error message
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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"I think it's ok to keep Quacc since it's likely of interest to some members of the `pymatgen` user base but I'm fine either way. Let me know if you want to merge as is.",
"Let's remove it for now :) Feel free to merge as-is."
] | 2023-06-26T15:39:11 | 2023-06-26T20:48:39 | 2023-06-26T20:48:39Z | MEMBER | {
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} | Closes #3102.
Changes:
- I added [Atomate2](https://github.com/materialsproject/atomate2), which seemed like a clear one to have included.
- I removed [`m3gnet`](https://github.com/materialsvirtuallab/m3gnet) in place of [`matgl`](https://github.com/materialsvirtuallab/matgl) since the former is archived and to be... | {
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"@drew-parsons Thanks for pointing this out! Note that this is not the only reason `MoleculeMatcherTest` isn't being run in CI. We're also not installing `openbabel`. IIRC we had serious installation issues in the past causing us to drop it. Just tried again on macOS and couldn't install. But happy to give it a try... | 2023-06-26T16:17:50 | 2023-06-27T02:27:15 | 2023-06-27T02:27:15Z | CONTRIBUTOR | {
"total": 0,
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} | #### Description
[pymatgen/analysis/tests/test_molecule_matcher.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/tests/test_molecule_matcher.py) conditionally uses OBAlign from openbabel. openbabel is accessed by
```
import openbabel
```
and availability of OBAlign registered with... | {
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"Good catch! Thanks for reporting! Fix incoming."
] | 2023-06-26T18:19:51 | 2023-06-27T02:30:06 | 2023-06-27T02:30:05Z | CONTRIBUTOR | {
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} | #### Description
The recent PR#3901 added pytest exception context to tests. In the case of test_construction in analysis/tests/test_graphs.py it [gave](https://github.com/materialsproject/pymatgen/blob/6871dae21f245db8dafdf3767182ec7dc64f094a/pymatgen/analysis/tests/test_graphs.py#L615)
```
with pytest.... | {
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"Yep, this looks perfect -- thanks @janosh.",
"Yay, took a bit longer than expected but I think I added `duecredit` decorators for all DOIs in doc strings. Have to admit my focus was wavering towards the end so might have missed a few. But we can always add more later.",
"Don't worry! Well done finding so many!... | 2023-06-26T20:28:18 | 2023-06-27T19:29:29 | 2023-06-27T15:25:38Z | MEMBER | {
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} | Following this morning's MP Foundation meeting where I took this over from @mkhorton, this is a draft PR that adds `duecredit` class decorators and module citations to a dozen files to gather feedback before doing the rest.
@mkhorton Let me know if this is what you had in mind and I'll do the rest. | {
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"Quick qn: what is the purpose of this? Speed up?",
"Having the arrays contiguous makes it faster., which I had already added in the previous PR #3015.\r\n\r\nHowever, we noticed that when called internally by a structure where the lattice matrix or frac_coords had been changed in such a way (such as applying str... | 2023-06-26T23:20:09 | 2023-06-26T23:47:28 | 2023-06-26T23:47:24Z | CONTRIBUTOR | {
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} | ## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
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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"@drew-parsons I fixed the `openbabel` import but I'm leaving out the openbabel install in CI which is also needed to get this test running again. Would you like to submit a PR for that?",
"I'm not sure how to patch the github CI. I'm working with the debian CI testing at https://ci.debian.net/packages/p/pymatgen... | 2023-06-27T01:50:13 | 2023-06-27T21:34:09 | 2023-06-27T02:27:13Z | MEMBER | {
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"Thanks @xjf729, I believe this change was the result of an API change in networkx, good catch!"
] | 2023-06-27T06:57:59 | 2023-06-27T14:03:43 | 2023-06-27T14:03:43Z | CONTRIBUTOR | {
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} | In line 2602 and 2603, `g` is `MultiDiGraph` and has no attribute `node`.
## Summary
Major changes:
- fix 1: change g.node to g.nodes
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
T... | {
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"This test runs successfully in our Ubuntu, macOS and Windows CIs. Not sure how the huge differences in your logs might come about\r\n\r\n```logs\r\nMax absolute difference: 6.20711553e+09\r\nMax relative difference: 1.72207694e+23\r\n```\r\n\r\nThe last meaningful change to this test I could find is 72bd76c9d573f6... | 2023-06-28T11:01:05 | 2023-10-01T20:40:16 | 2023-10-01T19:39:43Z | CONTRIBUTOR | {
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The NthOrderElasticTensorTest.test_from_diff_fit in test_elastic.py fails on mips64el fails during build-time tests on the mips64el architecture.
The error log reports
```
=================================== FAILURES ===================================
_________________ NthOrderElasticTensorTe... | {
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"I can't repro this. Tried about 7 times. I get 638 entries every time.\r\n\r\n> which actually contains no energy adjustment related to the GGA/GGA+U/R2SCAN scheme\r\n\r\nI'm not very familiar with our r2SCAN/GGA mixing scheme but I think what might be happening here is that we place r2SCAN energies onto the GGA(+... | 2023-06-28T13:52:50 | 2025-01-28T18:13:51 | CONTRIBUTOR | {
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} | I found that the entry `mp-1181334-GGA+U` for `Cu-Fe-Li-O-Te` chemical system can disappear and reappear in the processed entries result occasionally, when the GGA/GGA+U/R2SCAN scheme correction was conducted multiple times. The inconsistency issue happened about every third run in my test -- although the codes below b... | {
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"@janosh And another fix that adds more flexibility to the DOSCAR reading of Lobster files.",
"Linting is failing because IStructure and Structure do not agree with each other. Not sure how to fix it."
] | 2023-06-29T08:42:18 | 2023-06-29T15:39:58 | 2023-06-29T15:39:57Z | MEMBER | {
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"your code does not even work because there is no arg called spacegroup in the from_spacegroup method. There is also no arg called symbols. While I definitely know how to fix this myself, I think it is generally a good practice to provide actual working code to minimize the load on developers when you are asking fo... | 2023-06-29T16:01:09 | 2023-06-30T23:13:07 | NONE | {
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I'm trying to reproduce the structure of [LLZO on materials project](https://next-gen.materialsproject.org/materials/mp-942733?chemsys=La-Li-O-Zr) using `pymatgen.core.Structure.from_spacegroup()` and it looks like the La wychoff coordinates give the incorrect multiplicity. I'm getting a structure w... | {
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"<details><summary>Per-file size reduction</summary>\r\n\r\n| File | Original Size (B) | Compressed Size (B) | Reduction (%) |\r\n|:------------------------------------------------------|--------------------:|----------------------:|----------------:|\r\n| Sn_d... | 2023-07-05T00:11:43 | 2024-08-03T19:01:57 | MEMBER | {
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Here's a 1st swing at compressing all test files. Takes the total size of the `test_files` from ~900 MB to 243 MB (73 % reduction) using simple Gzip compression as implemented in the Python standard library.
<details><summary>Migration script <code>compress_test_files.py</code></summary>
```py
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"There's a [newer release out now that's sound](https://pypi.org/project/pymatgen/2023.7.11/#files). I guess we could delete the old partial release but not sure if that creates more problems than it solves. Usually you deprecate a broken release rather than delete but looks like PyPI doesn't have a deprecation fea... | 2023-07-06T02:27:12 | 2023-07-12T03:36:12 | 2023-07-11T15:21:37Z | NONE | {
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There is only one wheel file available for v2023.6.28 on PyPI (`pymatgen-2023.6.28-cp39-cp39-macosx_11_0_arm64.whl`). All other versions are missing: the wheels for Linux, macOS, and Windows (Python 3.8-3.11) at https://pypi.org/project/pymatgen/2023.6.28/#files:
![image](https://github.com/mater... | {
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} | #### Problem
I'm interested in having access to the site labels in a cif file when reading a structure ("_atom_site_label"). I need this to classify different groups of sites with the same symbol.
#### Proposed Solution
I think these data can be made available via `Structure.site_properties`.
In [`pymatgen... | {
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"Thanks @stefsmeets! 👍 ",
"Sorry, was a bit trigger happy on the merge. Tests didn't run on account of this change [1975b921f](https://github.com/materialsproject/pymatgen/commit/1975b921f038dbc523a8800c2c3ad4598a6f73d5#diff-faff1af3d8ff408964a57b2e475f69a6b7c7b71c9978cccc8f471798caac2c88R26) I just reverted. Co... | 2023-07-06T10:20:26 | 2023-07-07T19:22:42 | 2023-07-06T18:26:04Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- feature 1: Read site labels from cif file and store these under `Structure.site_properties`.
Closes #3135
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [... | {
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"Thanks for the feedback! I added a bunch of tests for the new code. Let me know if there is anything else."
] | 2023-07-10T12:37:00 | 2023-07-14T07:28:45 | 2023-07-13T23:13:09Z | CONTRIBUTOR | {
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} | ## Summary
This PR follows up from #3136 which was reverted because of CI test failures, see https://github.com/materialsproject/pymatgen/pull/3136#issuecomment-1624198814 . This PR addresses these issues.
Major changes:
- feature 1: Read site labels from cif file and store these under `Structure.site_properti... | {
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"I don't think this was a design choice per se. The general idea was to return an object that would allow `show` to be called and for some basic testing of the plot generation code. I have no problems with changing it to returning a Figure object.\r\n\r\nThe plotly backend came much later and so is a bit more coher... | 2023-07-10T17:35:21 | 2023-09-15T10:09:06 | 2023-08-17T22:35:34Z | CONTRIBUTOR | {
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This may be more a clarification than a bug necessarily.
I have noticed that many of the plotting methods using the `matplotlib` backend return the `matplotlib.pyplot` module.
For example in the [phase diagram plotter](https://github.com/materialsproject/pymatgen/blob/9f0c7c28fee6681058dadbaafd2... | {
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if key in dict:
val = dict[key]
del dict[key]
```
to
```py
val = dict.pop(key, None)
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3140 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3140/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3140/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3140/events | https://github.com/materialsproject/pymatgen/pull/3140 | 1,797,367,662 | PR_kwDOACgets5VHjyk | 3,140 | Breaking: Rename `[SomeCode]ParserError` to `[SomeCode]ParseError` and inherit from `SyntaxError` | {
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```py
class SyntaxError(Exception):
msg: str
lineno: int | None
offset: int | None
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} | ## Explicit test for POTCAR writing
Added basic test to make sure that the written POTCAR file is readable by VASP.
in response to Issue #3068 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3142 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3142/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3142/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3142/events | https://github.com/materialsproject/pymatgen/issues/3142 | 1,797,944,663 | I_kwDOACgets5rKnVX | 3,142 | `MaterialsProjectDFTMixingScheme.process_entries()` should have a kwarg to avoid POTCAR checks | {
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"I would go one step further - why not have a global setting that disables all POTCAR checks? This can be in the pmgrc. ",
"I would personally appreciate an option to avoid all POTCAR-related checks because then I don't have to do extra work just to have Pymatgen tell me I know what I'm doing. Although, finding w... | 2023-07-11T02:15:43 | 2023-07-11T04:10:08 | 2023-07-11T03:27:40Z | MEMBER | {
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} | When using `MaterialsProjectDFTMixingScheme.process_entries()`, if the user does not provide `ComputedStructureEntry` objects with POTCAR symbols in `.parameters`, the mixing scheme will crash. While it's understandable to do a validity check by default, there should be a kwarg to disable this.
If a user is trying t... | {
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"You are the hero we don't deserve.",
"Closes #2952 as well?",
"Pls do not merge this. I have a different fix.",
"@arosen93 Re #2952 not 100% sure since there was talk of a `ComputedEntry.from_settings` method in that issue. Not sure if anyone still wants that if you can set `MaterialsProject2020Compatibility... | 2023-07-11T04:18:06 | 2023-07-12T23:48:39 | 2023-07-12T23:03:15Z | MEMBER | {
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} | Closes #2499, closes #2952 (and #3142).
07f9730c2 add check_potcar: bool = True to PotcarCorrection
c0087761e add check_potcar: bool = True to MaterialsProject2020Compatibility
19f88c07e add check_potcar: bool = True to MaterialsProjectDFTMixingScheme
0209a5ab1 fix broken test due to modified error msg
| {
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"This can be closed. The strategy going forward is to add new `Site` properties directly as 1st-level instance attributes rather than as keys in the `Site.properties` dict. See #3137 for an example which added `Site.label`."
] | 2023-07-11T14:39:07 | 2023-07-14T02:42:33 | 2023-07-14T02:42:33Z | MEMBER | {
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} | `site_properties` not being typed causes downstream problems (see e.g. #3137).
Imagine we had explicit types for possible site properties: `ScalarProperty`, `PolarVectorProperty`, `AxialVectorProperty`, etc, `Categorical`, `Comment`. Something physical like `Magmom` could be handled under this system, and also somet... | {
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} | ## Summary
Major changes:
Fixes tests in `pymatgen/entries` after compressing and renaming files.
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