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https://api.github.com/repos/materialsproject/pymatgen/issues/3882 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3882/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3882/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3882/events | https://github.com/materialsproject/pymatgen/issues/3882 | 2,355,925,685 | I_kwDOACgets6MbJK1 | 3,882 | Numpy 2.0 incompatability | {
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"Already fixed in the last commit. But there are some issues with CI on windows I am working on. ",
"Ah, very speedy! I missed that. Thanks for patching!",
"I noticed that Pymatgen is still built against the old version of NumPy.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/2b53fb1cdf08d5022894c0cb4... | 2024-06-16T18:52:54 | 2024-06-19T02:29:36 | 2024-06-16T19:44:32Z | MEMBER | {
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} | ### Python version
3.11
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu
### Current behavior
When doing `pip install pymatgen`, you get `numpy==2.0` right now. This breaks Pymatgen, so we in the short-term we need to pin `pyproject.toml` to have numpy<2 and longer term we need to fix the under... | {
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} | [Unit test from PR are now failing](https://github.com/materialsproject/pymatgen/actions/runs/9538982150/job/26288803831?pr=3880) from the new unit test added in e572d34b206f48a43fe102a1c46e0532a60ff7de. (Presumably) owing to [inaccessible MP API keys](https://stackoverflow.com/questions/73866908/github-actions-main-re... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3885 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3885/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3885/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3885/events | https://github.com/materialsproject/pymatgen/pull/3885 | 2,357,542,166 | PR_kwDOACgets5ytFTR | 3,885 | Numpy 2.0 support | {
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"> As of now, tests pass on most systems except for some binary incompatibility issues. \r\n\r\nThanks for taking us to NumPy 2! Just a gentle reminder, the actual [installed `numpy` in CI tests for Ubuntu](https://github.com/materialsproject/pymatgen/actions/runs/9933938968/job/27437503821?pr=3885) is still versio... | 2024-06-17T14:47:53 | 2024-08-22T10:54:11 | 2024-08-22T10:52:45Z | MEMBER | {
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} | This PR updates pymatgen to support np 2.0. As of now, tests pass on most systems except for some binary incompatibility issues. This PR should be merged only when all tests pass. | {
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"Thanks for catching this. However I don't think this should be removed, instead should put it after the following (I think I accidentally swapped their order in #3691 🙈, sorry): https://github.com/materialsproject/pymatgen/blob/d1fac20381f75773f23258f57b283d850a2f58c2/pymatgen/core/surface.py#L1147 \r\n\r\nAs the... | 2024-06-18T03:42:30 | 2024-07-17T04:51:09 | 2024-07-17T04:51:09Z | CONTRIBUTOR | {
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"@JaGeo Would appreciate it if you could review this. The `LobsterPy` tests passed, full test log:\r\n\r\n<details>\r\n\r\n```\r\nyang@Yang-NUC:~/test_lobsterpy$ bash run_test.sh \r\nChannels:\r\n - conda-forge\r\n - nodefaults\r\nPlatform: linux-64\r\nCollecting package metadata (repodata.json): done\r\nSolving en... | 2024-06-19T02:59:30 | 2024-08-31T03:13:24 | 2024-08-30T05:59:36Z | CONTRIBUTOR | {
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} | ## Summary
- Improve type annotations and docstring tweaks for `io.lobster.{lobsterenv/outputs}`.
- Separate unit tests for lobster inputs and outputs in acc9a1f2706b1ed9471f494d24762f308e75809d.
TODOs:
- [x] Test downstream `LobsterPy` with the script from #3873 | {
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"Parts of CrystalNN get the right information. For example:\r\n\r\n- `crystallnn.get_cn(structure, 0)` returns `8`, which is correct\r\n- `crystallnn.get_cn_dict(structure, 0)` returns `{'Co': 8}`, also correct\r\n\r\nThe StructureGraph is created in `get_bonded_structure()` which calls `from_local_env_strategy()`.... | 2024-06-21T12:10:31 | 2024-07-26T22:00:04 | 2024-07-26T22:00:04Z | NONE | {
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} | ### Python version
3.11.2
### Pymatgen version
2024.6.10
### Operating system version
macOS 14.5
### Current behavior
Take a structure with only one atom per cell, which bonds to its own images in neighboring cells. Many simple metals do that, like mp-2647057.
Apply CrystalNN to get a bonded str... | {
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"Hi @hongyi-zhao, for the time being: you can pass `{\"IVDW\" : 13}` to the `user_incar_settings` of any VASP input set and this will accomplish the same thing. The `vdW_parameters.yaml` file is more of a convenience thing than a required one\r\n\r\nBut this should be a quick add to pymatgen. The base sets file you... | 2024-06-22T14:12:54 | 2024-06-24T23:56:40 | CONTRIBUTOR | {
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VASP has implemented support for [dftd4](https://github.com/dftd4/dftd4#building-vasp-with-support-for-d4), as stated on [VASP wiki](https://www.vasp.at/wiki/index.php/DFT-D4).
On the other hand, pymatgen still doesn't support dftd4, as shown [here](https://github.com/materialsproject/pymatg... | {
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"Thanks for the PR @kavanase! It looks like we have a merge conflict before we can merge, otherwise this looks great.",
"No worries! Yep merge conflict came from some updates in the master branch since opening this, resolved now!",
"Just to bump, I think this PR is all ready to go. Fixed the merge conflict that... | 2024-06-22T20:54:07 | 2024-08-30T06:27:46 | 2024-08-30T06:27:46Z | CONTRIBUTOR | {
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} | This PR implements the `PROCAR` parsing functionality from [`easyunfold`](https://smtg-bham.github.io/easyunfold/) discussed in #3722; namely the ability to parse `PROCAR`s from spin-orbit coupling (SOC) VASP calculations (i.e. with `LSORBIT = True`), and the ability to parse multiple `PROCAR` files together (without w... | {
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"Maybe I am a bit unclear of the use case for this. What problem is this trying to solve? ",
"@shyuep \r\nFor improvement on loading and expanding YAML setting variables, see here: \r\nhttps://github.com/hongyi-zhao/pymatgen/blob/d4e85a81c0004a858155cf4e39267dcdfc0d1df0/tests/core/test_settings.py#L47-L63\r\n\r\n... | 2024-06-23T01:59:51 | 2024-06-27T15:36:49 | 2024-06-26T23:35:23Z | CONTRIBUTOR | {
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} | - Added `_expand_strings` to handle environment and user variables in YAML.
- Introduced `_load_yaml_file` for loading YAML files with variable expansion.
- Updated `_load_pmg_settings` to use `_load_yaml_file`.
- Added tests for variable expansion, including $HOME, user-defined variables, and tilde (~) expansion. | {
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"Thanks for saying that and reviewing.\r\n\r\nCan I get a quick comment on https://github.com/materialsproject/pymatgen/pull/3892#discussion_r1649879457 please? I don't expect a unit test to pass only on some certain random seed :)"
] | 2024-06-23T02:12:20 | 2024-08-09T00:12:29 | 2024-08-07T20:06:26Z | CONTRIBUTOR | {
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} | ## Summary
Follow up #3871:
- Enable [Ruff rule family "N"](https://docs.astral.sh/ruff/rules/#pep8-naming-n), fix violation of [NPY002](https://docs.astral.sh/ruff/rules/numpy-legacy-random/) (the use of legacy `np.random`)
> NumPy recommends using a dedicated Generator instance rather than the random variate... | {
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"We are a team of 2-3 people working on this. It is simply not yet implemented. \r\n\r\nThe code has been built for PBE POTCARs, 54. This is also the default in the LOBSTER input sets.",
"We could add a note that it has only been implemented for PBE_54 if there isn't already.",
"> We could add a note that it ha... | 2024-06-25T04:20:41 | 2024-06-25T05:03:46 | CONTRIBUTOR | {
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} | I tried to create the input files using [this example](https://github.com/JaGeo/LobsterPy/tree/main/examples/Create_inputs_example) for vasp and lobster via lobsterpy as follows, but failed:
```python
$ cat create_and_test_potcar.py
from pymatgen.io.vasp.inputs import Potcar, PotcarSingle
import os
# Specify ... | {
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"Unluckily, there are still several errors. Some are related to the upstream chgnet and scipy and cannot be fixed here.",
"@njzjz sorry for the lack of reply here! looks like this is almost finished. thanks for the effort! feel free to skip the failing chgnet tests for now. re `scipy`, we'll have to pin to `<1.14... | 2024-06-25T20:31:21 | 2024-10-23T02:21:46 | 2024-08-08T23:03:18Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- fix 1: Build against NPY2 instead of NPY1. This will support both NPY1 and NPY2. See https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice.
- fix 2: Replace `np.int_t` (missing in NPY2) with `np.int64_t` and `np.float_` with `np.float64`.
- fix 3: Replace `l... | {
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"Can I have your advice on defining the comparability here please? Thanks a lot in advance. @shyuep @mkhorton @janosh ",
"There is no meaning to comparing compositions.",
"Thanks for your quick response. I assume you mean we don't define comparison to be chemically meaningful, but just for sorting purpose (as p... | 2024-06-26T03:17:44 | 2024-06-26T11:16:11 | 2024-06-26T05:20:07Z | CONTRIBUTOR | {
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} | ## Summary
- Fix #3815.
### Unchanged behavior
```python
# Single element
print(Composition({"O": 2}) > Composition({"O": 1})) # True
# Multiple shared elements
print(Composition({"Fe": 3, "O": 4}) > Composition({"Fe": 2, "O": 3})) # True
# Superset
print(Composition({"C":1, "O": 2}) > Composition(... | {
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"Is there anything that should be done here? (besides removing `src/pymatgen/analysis/aflow_prototypes.json` file from codespell :))",
"MErged. Thanks."
] | 2024-06-26T11:40:14 | 2024-07-08T12:37:12 | 2024-07-03T18:34:05Z | CONTRIBUTOR | {
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} | ## Summary
This PR adds a Molecular Dynamics input set generator for FHI-aims, making it possible to build input files for the internal implementation of MD in aims.
Major changes:
- An `MDSetGenerator` class is added for FHI-aims, with API resembling that of Vasp MD input set
## Todos
None
## Checkli... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3897 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3897/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3897/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3897/events | https://github.com/materialsproject/pymatgen/pull/3897 | 2,375,958,828 | PR_kwDOACgets5zqw6j | 3,897 | Bug fix for ComputedEntry from_dict | {
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"Thanks for the fix."
] | 2024-06-26T18:01:40 | 2024-09-25T17:54:09 | 2024-06-26T18:58:56Z | CONTRIBUTOR | {
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} | In `pymatgen.entries.computed_entries`, `ComputedEntry` takes three optional fields: `energy_adjustments`, `parameters`, `data`, which are not correctly read in by its `from_dict` method. This is because, for example:
```
parameters = {k: MontyDecoder().process_decoded(v) for k, v in (dct.get("parameters", {})}
```
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https://api.github.com/repos/materialsproject/pymatgen/issues/3898 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3898/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3898/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3898/events | https://github.com/materialsproject/pymatgen/issues/3898 | 2,376,168,487 | I_kwDOACgets6NoXQn | 3,898 | @cached_class decorator prevents class methods of Compatibility objects from being used in multiprocessing as they can't be pickled | {
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"This seems to be the motivation for the decorator: https://github.com/materialsproject/pymatgen/pull/2450 suggesting it may be necessary, pinging @munrojm for input on whether this is likely still potential issue given changes to the api/rester",
"Talked to @janosh and he thinks we can probably resolve this with... | 2024-06-26T20:03:50 | 2024-07-19T17:47:08 | 2024-07-19T17:47:08Z | CONTRIBUTOR | {
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} | The use of this decorator leads to the error message:
```python
self = <joblib.parallel.BatchCompletionCallBack object at 0x3376ec590>
def _return_or_raise(self):
try:
if self.status == TASK_ERROR:
> raise self._result
E AttributeError: Can't pickle local obj... | {
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"This PR is fine but there are failing tests.",
"@shyuep these failing tests seem to be \"tests\" that make sure the input sets stay the same. Some hashes are out of date. \r\n\r\nThey say one should notify all input set owners: \r\n@mkhorton @janosh and you as well @shyuep \r\n\r\n",
"Thanks for the PR @hongy... | 2024-06-26T23:44:50 | 2024-07-23T10:43:14 | 2024-07-23T10:43:14Z | CONTRIBUTOR | {
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} | Add VASP setting for the dftd4 vdW functional, as discussed in https://github.com/materialsproject/pymatgen/issues/3889.
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"Thanks @CompRhys!\r\n\r\nI think some comment strings need to be updated: for example, there is a claim that `PatchedPhaseDiagram` uses the same `as_dict()` as `PhaseDiagram` but this is not the case (`computed_data`, i.e. including the qhull entries, are not stored). Otherwise this looks great."
] | 2024-06-28T16:12:30 | 2024-07-17T14:59:37 | 2024-07-17T14:59:37Z | CONTRIBUTOR | {
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} | ## Summary
- modularize the keep redundant spaces code, and fix the algorithm which previously didn't get rid of all the redundant spaces.
## 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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https://api.github.com/repos/materialsproject/pymatgen/issues/3901 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3901/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3901/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3901/events | https://github.com/materialsproject/pymatgen/pull/3901 | 2,382,656,718 | PR_kwDOACgets50AdnT | 3,901 | prettify periodic_table.json for readability | {
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"Pls test the loading speeds on the pretty vs non pretty version. This is something that is loaded often. So every millisecond counts. I would not prioritize being able to read the JSON directly since people seldom do it and it can always be pretty printed if needed. ",
"@shyuep good point; the impact does not ap... | 2024-07-01T02:25:03 | 2024-10-10T01:54:23 | 2024-07-02T12:49:12Z | CONTRIBUTOR | {
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} | Prettify `periodic_table.json` to improve its readability. (using the Prettify JSON VS Code extension)
I considered the alternative of converting to YAML so that comments could be inserted (see #3851 ), but I found the following way back in the git log from 2011:
```
--
Date: Mon Nov 14 13:19:54 2011 -0500
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https://api.github.com/repos/materialsproject/pymatgen/issues/3902 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3902/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3902/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3902/events | https://github.com/materialsproject/pymatgen/pull/3902 | 2,384,018,791 | PR_kwDOACgets50FJME | 3,902 | Add electronic structure methods for Species | {
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"@shyuep can I have your thoughts on this implementation? I think all that remains to finish the PR is entering data for the rest of the common oxidation states, but before I spend time on that I want to make sure this looks workable to you. Thanks!",
"> @shyuep can I have your thoughts on this implementation? I ... | 2024-07-01T14:32:44 | 2024-07-16T20:27:36 | 2024-07-16T20:27:36Z | CONTRIBUTOR | {
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} | ## Summary
Replacing #3851 , this PR implements `electronic_structure`, `full_electronic_structure`, and `valence` methods for `Species`.
Major changes:
- Electronic configurations of ions is added to `periodic_table.json`. Instead of a single string, the `["Electronic structure"]` key for each element is now ... | {
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updates:
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- [github.com/adamchainz/blacken-docs: 1.16.0 → 1.18.0](https://github.com/adamchainz/blacken-docs/compare/1.16.0...1.18.0)
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https://api.github.com/repos/materialsproject/pymatgen/issues/3906 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3906/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3906/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3906/events | https://github.com/materialsproject/pymatgen/issues/3906 | 2,386,484,762 | I_kwDOACgets6OPt4a | 3,906 | Build up customized pourbaix entries | {
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"I realize the relevant entries are available in mp_api repo. However, is there a way to let user to customize the ion entries? Especially when new ion data is found?"
] | 2024-07-02T14:54:33 | 2024-07-02T15:24:37 | NONE | {
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} | ### Feature Requested
I am not sure if such feature is already existing. Can someone create a new entry for ions for building pourbaix diagram? According to https://journals.aps.org/prb/pdf/10.1103/PhysRevB.85.235438, one just need to define the correction of E(exp-DFT). However, I did not find any function in pymatge... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3907 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3907/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3907/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3907/events | https://github.com/materialsproject/pymatgen/issues/3907 | 2,387,732,993 | I_kwDOACgets6OUeoB | 3,907 | VASP Convergence Testing | {
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} | ### Feature Requested
So far, there is no systematic method for doing VASP Convergence Testing. So, it would be nice to add this feature to pymatgen.
### Proposed Solution
Maybe something adapted from the following implementatoin:
https://github.com/kavanase/vaspup2.0
### Relevant Information
See https... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3908 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3908/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3908/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3908/events | https://github.com/materialsproject/pymatgen/pull/3908 | 2,388,491,035 | PR_kwDOACgets50Ub1X | 3,908 | add option to color phonon bands as per gruneisen parameter value | {
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"Hi @shyuep, @janosh, @mkhorton and @JaGeo, I have added this new functionality to the Grüneisen parameter BS plotter. Happy to address review comments if there are any, or else it can be merged 😄 ",
"Great thanks. "
] | 2024-07-03T12:21:44 | 2024-07-03T13:27:30 | 2024-07-03T13:27:20Z | CONTRIBUTOR | {
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This new functionality was initially implemented as part of ongoing workflow development for computing the Grüneisen parameter in atomate2, see https://github.com/materialsproject/atomate2/pull/752
As it mainly relies on the pymatgen code with minor additions, I think it would be appropriate if the code re... | {
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"Unittests need to be added for the new parameters.",
"Noting this is a partial duplicate of #3899, let's merge #3899. Thanks @hongyi-zhao "
] | 2024-07-06T02:29:00 | 2024-07-23T10:43:15 | 2024-07-23T10:43:15Z | CONTRIBUTOR | {
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- Added `PBE_64` to the list of valid POTCARs.
- Updated documentation to include `PBE_64`.
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<li><a href="https://github.com/certifi/python-certifi/commit/bd8153872e9c6fc98f4023df9c2deaffea2fa463"><code>bd81538</code></a> 2024.07.04 (<a href="https://redirect.github.com/certifi/python... | {
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"This PR may not be a good way. Another way I can think of is to modify [vdw_parameters.yaml](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/vdW_parameters.yaml) as follows:\r\n\r\n```yaml\r\ndiff --git a/src/pymatgen/io/vasp/vdW_parameters.yaml b/src/pymatgen/io/vasp/vdW_parameters.y... | 2024-07-07T06:50:34 | 2024-07-27T04:01:04 | 2024-07-23T10:43:15Z | CONTRIBUTOR | {
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} | Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. For the related discussion and information, see below:
https://www.vasp.at/forum/viewtopic.php?t=19551
https://github.com/dftd3/simple-dftd3/blob/3a50cbdf8566b3caa8760499ae21746ec9a5e535/assets/parameters.toml#L80-L82 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3915 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3915/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3915/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3915/events | https://github.com/materialsproject/pymatgen/pull/3915 | 2,400,027,382 | PR_kwDOACgets507Zkj | 3,915 | Fix chemical system method for different oxidation states | {
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"Thanks for reporting and fixing @danielzuegner, this seems like a clear bug. We should get this merged :) "
] | 2024-07-10T07:54:29 | 2024-08-09T00:07:27 | 2024-07-26T15:07:07Z | CONTRIBUTOR | {
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} | ## Summary
Currently, when the same element occurs in multiple oxidation states in a structure (e.g., `Composition({"Na+": 1, "Na2+": 1, "Cl-": 1})`), `structure.composition.chemical_system` yields that element repeated, e.g., `Composition({"Na+": 1, "Na2+": 1, "Cl-": 1})`), `structure.composition.chemical_system ==... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3916 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3916/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3916/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3916/events | https://github.com/materialsproject/pymatgen/pull/3916 | 2,401,246,003 | PR_kwDOACgets50_pCY | 3,916 | Add new MP input sets / concurrently update MatPES POTCARs | {
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"@esoteric-ephemera is this PR ready for merging?",
"@matthewkuner debugging some potential issues with the Ba pseudo (updated to the GW one) - hope to have an update soon",
"Copying a suggestion here:\r\n\r\n> @esoteric-ephemera a late suggestion, but can we set GGA_COMPAT to False? See [here](https://www.vas... | 2024-07-10T16:53:13 | 2025-02-23T17:45:06 | 2025-01-09T16:37:48Z | CONTRIBUTOR | {
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} | This PR adds new MP input sets that resulted from a benchmarking effort over the past year. For the benchmarks, refer to:
- https://github.com/materialsproject/foundation/pull/26
- [Reference living document](https://drive.google.com/file/d/1fUUx0wrrtMRcSss5yv3NiQuC7J5IiEKL/view)
Critical updates include:
- POTCA... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3917 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3917/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3917/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3917/events | https://github.com/materialsproject/pymatgen/pull/3917 | 2,401,376,462 | PR_kwDOACgets51AF8P | 3,917 | added cp2k_output cube to pymatgen volume parser | {
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"@DanielYang59 any chance you can help me with this ",
"Sorry I have never used CP2K... But I could probably answer some general questions. So is there anything I could help with?\r\n\r\n@JaGeo Any chance you know who is maintaining the CP2K module? Thanks! @nwinner maybe (from the `__author__`)?\r\n\r\n",
"@D... | 2024-07-10T18:11:38 | 2024-07-19T12:00:05 | 2024-07-19T12:00:05Z | NONE | {
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} | ## Summary
added a function parse_cube() in pymatgen.io.cp2k.output
slight change in parse_initial_structure() ... cp2k output different ...i used cp2k/cp2k-git-feb-2022 to generate outputs....
I have benchmarked the planar average using pymatgen against cubecruncher(https://www.cp2k.org/tools:cubecruncher)...
The... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3918 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3918/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3918/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3918/events | https://github.com/materialsproject/pymatgen/issues/3918 | 2,404,972,411 | I_kwDOACgets6PWPd7 | 3,918 | Cannot get element projected data | {
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} | ### Python version
Python.3.12.4
### Pymatgen version
2024.6.10
### Operating system version
_No response_
### Current behavior
banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements', vb_energy_range=2, cb_energy_range=2, font='Times New Roman', axis_fontsize=20)
Results: UserWarning: Ca... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3919 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3919/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3919/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3919/events | https://github.com/materialsproject/pymatgen/issues/3919 | 2,406,419,166 | I_kwDOACgets6Pbwre | 3,919 | More robust parsing of (electronic) piezoelectric tensor from OUTCAR | {
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} | ### Feature Requested
Using VASP v6.3.2:
1. Running a calculation with LEPSILON=.TRUE. and LRPA=.FALSE. produces the following OUTCAR line: `PIEZOELECTRIC TENSOR (including local field effects) for field in x, y, z (C/m^2)`. This line does not match the search string in `pymatgen > io > vasp > outputs.py` ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3920 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3920/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3920/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3920/events | https://github.com/materialsproject/pymatgen/pull/3920 | 2,406,827,366 | PR_kwDOACgets51SZxf | 3,920 | Format aflow_prototypes.json and exclude it from codespell check in pre-commit | {
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} | ### Summary
- Similar to #3901, format `aflow_prototypes.json`
- Ignore this file from codespell check in pre-commit, otherwise it would always fail | {
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} | I was trying to enable `boltztrap` in CI test, and found the URL is not valid anymore it appears: https://github.com/materialsproject/pymatgen/blob/35b1f448c5842b9b13c0ace0f3fe811bbcb5ffd1/src/pymatgen/electronic_structure/boltztrap.py#L1-L17
Also the same one in the `requires` decorator: https://github.com/material... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3922 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3922/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3922/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3922/events | https://github.com/materialsproject/pymatgen/issues/3922 | 2,410,512,744 | I_kwDOACgets6PrYFo | 3,922 | Adapt pymatgen.symmetry.analyzer to new spglib (>=2.5.0) output data format | {
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"I'm happy to implement this change :)",
"Thanks @DanielYang59 !! 😀"
] | 2024-07-16T08:13:34 | 2024-07-16T13:33:06 | 2024-07-16T13:33:06Z | CONTRIBUTOR | {
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} | ### Feature Requested
The recent spglib release v2.5.0 changed the output data types from dict to new classes like SpglibDataset.
https://spglib.readthedocs.io/en/stable/releases.html#v2-5-0-9-jul-2024
The dict-like interface is planned to be removed, so it will be necessary to adapt the pymatgen interface in the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3923 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3923/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3923/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3923/events | https://github.com/materialsproject/pymatgen/pull/3923 | 2,410,569,737 | PR_kwDOACgets51e9S1 | 3,923 | Migrate `spglib` to new `SpglibDataset` format with version 2.5.0 | {
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"@kaueltzen Is everything looking good to you?",
"Thanks for reviewing. @janosh For some reason [all tests in windows are failing](https://github.com/materialsproject/pymatgen/actions/runs/9957894146/job/27510952746)? Doesn't looks like owing to this PR and still need to find out why I guess "
] | 2024-07-16T08:42:28 | 2024-07-16T13:42:41 | 2024-07-16T13:33:05Z | CONTRIBUTOR | {
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} | ### Summary
- Migrate `spglib` to new data format as pointed out by @kaueltzen, to fix #3922
- Add types for `SpacegroupAnalyzer` and `PointGroupAnalyzer`
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https://api.github.com/repos/materialsproject/pymatgen/issues/3926 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3926/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3926/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3926/events | https://github.com/materialsproject/pymatgen/pull/3926 | 2,411,329,928 | PR_kwDOACgets51hiaI | 3,926 | Add multiwfn QTAIM parsing capabilities | {
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"Hey @shyuep @janosh @mkhorton, can I get someone's eyes on this? Everything is working as expected, and I don't anticipate adding more major features at this point.",
"Yo, pinging this again @shyuep @janosh @mkhorton. Can anyone take a look and help me get this merged?",
"Thanks for this PR @espottesmith, apol... | 2024-07-16T14:34:01 | 2024-08-09T00:08:01 | 2024-07-30T19:51:33Z | CONTRIBUTOR | {
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} | ## Summary
This PR adds parsing capabilities for Mulitwfn. Currently, the functionality is limited to parsing quantum theory of atoms in molecules (QTAIM) information.
Shout-out to @santi921. A lot of this code is his, and I've mostly cleaned it up, simplified it, and added tests.
## Checklist
- [X] Google ... | {
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"@DanielYang59 Sorry, it seems that my changes have conflicts with the recent updates, I remake another pull request using the recent version",
"I understand merge conflicts could be confusing but don't worry. Merge conflicts are common things that would happen when you and another person try to make changes to t... | 2024-07-17T05:25:54 | 2024-09-12T08:54:03 | 2024-09-11T12:52:48Z | CONTRIBUTOR | {
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1. fixing problem for the lll_reduce process when making slabs, doing mapping before updating the structure
2. allow to set ftol of the termination distances for hierarchical cluster so that some non-identical terminations close ... | {
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"I'm guessing you might have a `pymatgen.py` file shadowing the real `pymatgen` package, let me know if it's not the case :)",
"Same issue here. Python 3.12, Pymatgen version 2024.6.10, CentOS Linux 7. Trying to run\r\n\r\n```\r\nfrom pymatgen.io.pwscf import PWInput\r\n```\r\n\r\nafter installing my forked pymat... | 2024-07-17T06:53:33 | 2024-07-23T12:39:27 | 2024-07-23T12:39:27Z | CONTRIBUTOR | {
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3.11
### Pymatgen version
2024.06.10
### Operating system version
Mac
### Current behavior
I am tr... | {
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"@janosh Would appreciate it if you could review this as well, thanks!",
"Thanks for reviewing!"
] | 2024-07-17T08:28:08 | 2024-07-24T11:21:33 | 2024-07-24T11:09:04Z | CONTRIBUTOR | {
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- Replace expired BoltzTraP link, to close #3921
- Some nitpicking docstring tweaks
- Remove unused `.gitignore` items | {
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} | ### Python version
3.12.4
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
1. Some namelist options (e.g., `calculation`, `pseudo_dir`, `ecutwfc`) are not parsed in correctly when their values end with a trailing comma. This becomes an issue when we try to read ... | {
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Fix wrong parsing in `io.pwscf.PWInput.from_str()` of
- Namelist options ending with comma (`,`), and
- `ATOMIC_SPECIES` and `ATOMIC_POSITIONS` cards for structures with oxidation states,
to close https://github.com/materialsproject/pymatgen/issues/3930 | {
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"Any updates on if this can get merged in?",
"Test added via static-no-kgrid-si test. \r\n\r\nUnit test can also be added if you prefer that too"
] | 2024-07-17T19:30:27 | 2024-08-06T15:53:23 | 2024-08-06T15:53:23Z | CONTRIBUTOR | {
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} | Need to use the transpose of the inverse matrix for recipmatrix
## Summary
Major changes:
- fix 1: FHI-aims k-grid sizes from a density
## 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 @CompRhys for the PR. Wondering if we should add `n_workers` to the pymatgen config yaml? If pymatgen is doing processing in parallel in different aspects of the code, might be good to be able to set the correct parallelization centrally",
"Regarding default for n_workers i'm not opposed but I would alway... | 2024-07-17T20:02:03 | 2024-08-09T00:11:35 | 2024-08-02T22:34:59Z | CONTRIBUTOR | {
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Adds the option to use joblib to apply corrections in parallel, this depended on https://github.com/materialsvirtuallab/monty/pull/691 which was linked to https://github.com/materialsproject/pymatgen/issues/3898. Opening this PR incase maintainers think it's a useful addition to the code.
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"@shyuep @janosh @mkhorton Can you please review this hot fix? Thanks!"
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- A hot fix for #3928, where the `setuptools` in not configured to include the complete `pymatgen` package (all subpackages are missing) after moving to the src layout.
- (description is incorrect, see #4018) ~~Turn off `include-package-data`, which [is `true` by default](https://setuptools.pypa.io/en/l... | {
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- Raise `DeprecationWarning` as errors, which might help us [adapt earlier for deprecation](https://numpy.org/devdocs/dev/depending_on_numpy.html#runtime-dependency-version-ranges)
> Furthermore, we recommend to raise errors on warnings in CI for this job, either all warnings or otherwise at least Depr... | {
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"This is ready to be reviewed. I don't know why ruff is failing, I did not make changes in io.vasp, io.aims and analysis. ",
"Hi @janosh, @shyuep, @mkhorton, whenever you have some time, this is ready to be reviewed. It would be great for us if these changes could be included in the next release, to facilitate de... | 2024-07-18T09:19:24 | 2024-07-26T15:10:26 | 2024-07-26T15:07:21Z | CONTRIBUTOR | {
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In recent developments in Abinit, the variables `intgden` and `ratsph` have been added in the netCDF output files. These correspond to the computed integrated density around atoms and the integration radii. The former can be interpreted as the local magnetic moment on each atom. Since this is a useful qua... | {
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3.10
### Pymatgen version
master
### Operating system version
_No response_
### Current behavior
Hey, two remarks regarding the `is_subgroup` method of `SpaceGroup`:
First, the current implementation does not allow isomorphic group-subgroup relationships (same space group type... | {
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"The failing linting does not stem from our changes.\r\n",
"Once the other tests pass, this is ready for review ",
"@shyuep @mkhorton @janosh this pull request is ready for review. The linting issues show up in different parts of the code.",
"There are many mysteries in the world of linters, including why the... | 2024-07-19T11:30:05 | 2024-08-09T00:06:25 | 2024-07-23T21:25:07Z | MEMBER | {
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Added code to also allow to search for orthorhombic supercells. Here, I also introduce the option to check for a `maximum_length` of the cells
@QuantumChemist will now take over and write the tests for this class and fix the linting etc. :) | {
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} | ### Feature Requested
When saving the `PhaseDiagram` it could reduce the memory footprint if to keep track of the ids of entries rather than just save multiple copies of entries in the separate lists.
### Proposed Solution
Refactor the PhaseDiagram class to use `@property` to return the different lists of ent... | {
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"Hey @shyuep @mkhorton @janosh this is ready to be reviewed."
] | 2024-07-19T14:44:27 | 2024-11-13T17:53:19 | 2024-11-13T17:53:19Z | CONTRIBUTOR | {
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} | ## Summary
Resolves #3937 .
### SpaceGroup
- enabled isomorphic group subgroup relationships, added test
- Constrained https://github.com/materialsproject/pymatgen/blob/02341828b94a001b4f3cbdae6b24eaeeb0df7d7d/src/pymatgen/symmetry/groups.py#L528 to non-klassengleiche group subgroup relationships so cases like `a... | {
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"I don't understand why the `lint` action is looking at files that didn't change in this PR. Please advise if I need to take action somehow to fix.\r\n\r\n```\r\n src/pymatgen/analysis/local_env.py:3051:32: PLR1714 Consider merging multiple comparisons: `m not in (j, k)`. Use a `set` if the elements are hashable.\r... | 2024-07-20T13:37:55 | 2024-07-31T15:56:22 | 2024-07-31T15:56:21Z | CONTRIBUTOR | {
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Major changes:
1. Fixes a serious bug in `Ion.get_reduced_formula_and_factor` introduced by [this commit](https://github.com/materialsproject/pymatgen/commit/b4a70eef7666743459a6e242a0efc18762ff3b49). The bug could cause certain formulas to be parsed incorrectly, resulting in a different stoichiometry... | {
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"Hi @Jeff-oakley, this is implemented in `pymatgen.entries.mixing_scheme` as `MaterialsProjectDFTMixingScheme`"
] | 2024-07-21T03:42:18 | 2024-07-23T17:20:07 | NONE | {
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} | ### Feature Requested
It seems that mix GGA/GGAU/R2SCAN is not available as a compatibility option? I did not see that class in pymatgen.entries.compatibility. However in the paper below, it has been indicated that this workflow is already implemented.
https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMa... | {
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This is a follow up to #3902 to address an inconsistent behavior I encountered. The major change in this PR is that `full_electronic_structure` is now always returned as a sorted list according to the Madelung rule, so that the final element is always the valence shell. Prior to this PR, this was sometime... | {
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"@janosh Please review this at your convenience, thanks!",
"Thanks for reviewing!"
] | 2024-07-22T07:11:58 | 2024-07-24T11:23:11 | 2024-07-24T11:16:29Z | CONTRIBUTOR | {
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} | ### Summary
- Correct method `get_projection_on_elements` docstring of `Procar` class, where the band index and kpoint index is reversed.
https://github.com/materialsproject/pymatgen/blob/27d90b777cedc80593d93b6e8b66dee04c167460/src/pymatgen/io/vasp/outputs.py#L3915-L3916
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"Hi @shyuep , @janosh , @mkhorton and @JaGeo , this PR is ready for review.",
"Thanks @janosh for the feedback. I will try to address the comments next week :smile: ",
"Hi @JaGeo and @janosh , I have now addressed review comments now and could be merged if there are no further comments.\r\n\r\nPS: Regarding ... | 2024-07-22T15:10:11 | 2024-08-16T09:20:24 | 2024-08-16T09:20:01Z | CONTRIBUTOR | {
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} | # Summary
1. Add possibility to compare phonon dos , implementation is similar to electronic dos as implemented in https://github.com/materialsproject/pymatgen/pull/2772
2. Add `Wasserstein `distance as metric besides existing Tanimoto index
# Todo's
- [x] Add methods to compute fingerprints and compare phon... | {
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- The atomic concentrations of each material in the ternary graph are added to the 2D and 3D ternary graphs for readability.
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"Thanks for this PR @JoshuaNgXY! Since it deals with plotting can you add some screenshots?",
"Sure, here are the before and after for the ternary and quaternary plots.\r\n\r\n## Ternary Plot Update:\r\n### Old\r\n\r\n\r\n###... | 2024-07-22T21:19:51 | 2024-08-09T13:22:17 | 2024-08-09T13:22:17Z | CONTRIBUTOR | {
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} | ## Summary
The atomic concentrations of each material in the ternary graph are added to the 2D and 3D ternary graphs for readability. A toggle is added to the quaternary graph hull surfaces.
Extra labels added to hovertext of the Voltage graph for readability.
## Adding atomic concentrations:
- Atomic concen... | {
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"Many thanks for this contribution. "
] | 2024-07-26T07:23:19 | 2024-08-09T00:07:02 | 2024-07-26T09:05:21Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
* Add functions to get phonon properties (phonon band structures and phonon DOS) to `_MPResterBasic`, so that a non-power user can retrieve this properties without using `mp-api` making `_MPResterBasic` closer in line with `_MPResterLegacy` in terms of the properties that can be retrieve... | {
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"I think this is intended: https://github.com/materialsproject/pymatgen/blob/5256fce19f7366d33fd5b062bd41cc5cb713505f/src/pymatgen/io/vasp/inputs.py#L1776-L1788\r\n\r\n**Probably** because POTCAR itself doesn't carry a one-to-one mapping to VASP version (but compatible functionals) itself with its `LEXCH` tag. I co... | 2024-07-26T15:12:07 | 2024-07-31T02:48:43 | NONE | {
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} | ### Python version
3.12.4
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu-22.04
### Current behavior
I have a POTCAR file written with PBE_54. When I read it into a Potcar object, potcar.functional will equal PBE instead of PBE_54.
### Expected Behavior
I would expect it to be PBE_54 to refl... | {
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"This doesn't look like an issue related to `pymatgen`:\r\n> ERROR: Could not install packages due to an OSError: Missing dependencies for SOCKS support.\r\n\r\nLooks like your SOCKS support is missing, maybe try `pip install pysocks` before `pre-commit`?",
"I've installed `pysocks` before creating this issue, bu... | 2024-07-26T15:27:22 | 2024-07-28T02:03:34 | 2024-07-27T08:35:15Z | CONTRIBUTOR | {
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} | I want to reimplement https://github.com/materialsproject/pymatgen/pull/3914, but the `pre-commit` command suggested [here](https://pymatgen.org/contributing.html#coding-guidelines) failed as stated below:
The revised file:
```
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git d... | {
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"The issue here seems to be that the build specifies,\r\nhttps://github.com/materialsproject/pymatgen/blob/98c57888cc4f17ef4d8692d777ad0d1806ee7ae9/pyproject.toml#L5\r\n\r\nWhich wont work with numpy>=2.0. \r\n\r\nTo fix quickly, downgrade numpy.\r\n\r\nTo actually support numpy>=2.0, looks like the build system ha... | 2024-07-26T17:48:30 | 2024-09-02T17:22:35 | 2024-09-02T17:22:35Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.10.12
### Pymatgen version
pymatgen-2024.7.18
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
```
>>> from pymatgen.core import Lattice
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/felixtherrien/envs/ocpe... | {
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"Ah, so there was a dual bug, an error in the test too? Thanks for fixing.",
"> Ah, so there was a dual bug, an error in the test too? Thanks for fixing.\r\n\r\nYeah, I'm 99% sure the test is wrong."
] | 2024-07-26T17:56:56 | 2024-07-26T22:00:01 | 2024-07-26T21:48:49Z | CONTRIBUTOR | {
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} | # `StructureGraph.get_coordination_of_site` gives wrong number for small unit cells
Refer to #3888
The `StructureGraph` object assumes that periodic images of the edges will added twice in the graph so the coordination number algorithm assumes that all self-connections are double-counted.
However, we have upd... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3955 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3955/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3955/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3955/events | https://github.com/materialsproject/pymatgen/pull/3955 | 2,433,237,196 | PR_kwDOACgets52oji2 | 3,955 | Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. | {
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"Thanks."
] | 2024-07-27T04:40:22 | 2024-09-10T13:16:38 | 2024-08-21T18:55:37Z | CONTRIBUTOR | {
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} | This is the reimplementation of https://github.com/materialsproject/pymatgen/pull/3914, and the test has been added.
For the related discussion and information, see below:
https://www.vasp.at/forum/viewtopic.php?t=19551
https://www.vasp.at/forum/viewtopic.php?t=19658
https://github.com/dftd3/simple-dftd3/blob/3a5... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3956 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3956/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3956/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3956/events | https://github.com/materialsproject/pymatgen/issues/3956 | 2,437,524,364 | I_kwDOACgets6RSauM | 3,956 | Adding PBE_64 support: Clarification on hash types used in POTCAR hash files. | {
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"Hi @hongyi-zhao, the hash-based identification is deprecated right now, those files (vasp_potcar_pymatgen_hashes.json and vasp_potcar_file_hashes.json) are maintained for backwards compatibility. Only the summary stats should be updated moving forward. \r\n\r\nSupport for `PBE_64` pseudopotentials was added to pym... | 2024-07-30T10:48:56 | 2024-09-18T01:09:07 | CONTRIBUTOR | {
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I'm working on adding support for PBE_64 potentials in pymatgen. This requires updating two JSON files containing POTCAR hash information:
1. [vasp_potcar_pymatgen_hashes.json](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json)
2. [vasp_potca... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3957 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3957/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3957/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3957/events | https://github.com/materialsproject/pymatgen/issues/3957 | 2,438,557,359 | I_kwDOACgets6RWW6v | 3,957 | Vasp Incar check_params() can't handle Union types | {
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"Ah ok I see why this was not caught. In tests.io.vasp.inputs, the only test for Incar.check_params() is\r\n\r\n```python \r\n def test_check_params(self):\r\n # Triggers warnings when running into invalid parameters\r\n with pytest.warns(BadIncarWarning) as record:\r\n incar = Incar(\r\... | 2024-07-30T19:45:19 | 2024-08-02T21:59:54 | 2024-08-02T21:59:54Z | CONTRIBUTOR | {
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} | ### Python version
3.11.9
### Pymatgen version
2024.6.10
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
Error Message:
```
Traceback (most recent call last):
File "/home/wladerer/github/abvio/tests/test_incar.py", line 356, in test_valid_model
incar.check_params()
File "/home... | {
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"This might be a silly question, but is changing the \"type\" parameter in the json file possible? The following evaluates to typing.Union\r\n \r\n```python\r\ntype(eval('bool | str'))\r\n```\r\nExample:\r\n\r\n```\r\n>>> isinstance(True, eval('bool | str'))\r\nTrue\r\n>>> isinstance(\"string thing\", eval('bool | ... | 2024-07-31T03:08:32 | 2024-08-09T00:11:03 | 2024-08-02T21:59:53Z | CONTRIBUTOR | {
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- Fix Incar `check_params` for `Union` type, to fix #3957, changed `incar_parameters.json` of Union type to use `isinstance` syntax directly. Otherwise Python 3.9 Windows don't support type checking with `isinstance(data, Union[str, float])`.
**Would appreciate it if anyone has smarted way to reso... | {
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"Thank you for reporting this. I am personally not an expert for this module. \r\n\r\n@shyuep, do you by chance have some insights here? This comment has been added more than 8 years ago. "
] | 2024-07-31T11:28:38 | 2024-07-31T11:34:26 | NONE | {
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} | I've just been going through the NMR analysis module and noticed the comment about the sign inconsistency across the two papers referenced. I'm not sure there _is_ a sign inconsistency between the papers, and the sign chosen in the code appears to be incorrect (I may be wrong, so double-check!)
In equation 20 from ... | {
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"excellent catch!\r\n\r\n> Therefore, it may not make a lot of sense to give site properties here at all or at least a warning\r\n\r\nthanks for pointing that out. i'm leaning towards not trying to translate site properties from `Structure` to `SymmetrizedStructure` at all in order to not mislead users. a warning m... | 2024-08-01T09:01:07 | 2024-08-01T11:04:06 | CONTRIBUTOR | {
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} | ### Python version
3.10
### Pymatgen version
master or 2024.7.18
### Operating system version
Debian GNU/Linux 11
### Current behavior
The current implementation of `__str__` of `SymmetrizedStructure` appends site properties as per the index of `self.equivalent_sites`, not of the actual site index.
https://gith... | {
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"No idea why the test are failing...",
"likely caused by the recent [`torch==2.4.0`](https://pypi.org/project/torch/2.4.0/) release\r\n\r\nunrelated issue but just noticed [`matgl` is not setting a minimum `torch` version](https://github.com/materialsvirtuallab/matgl/blob/main/pyproject.toml#L56) @kenko911"
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Major changes:
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"Just to aid in diagnosing this, the relevant output is the following\r\n```\r\n/home/wladerer/.venv/base/lib/python3.10/site-packages/pymatgen/io/cif.py:1285: UserWarning: Issues encountered while parsing CIF: 3 fractional coordinates rounded to ideal values to avoid issues with finite precision.\r\nSkipping relat... | 2024-08-01T17:01:45 | 2024-08-08T01:48:14 | NONE | {
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} | ### Python version
python 3.12.4
### Pymatgen version
2024.7.18
### Operating system version
Linux Mint 21.3
### Current behavior
the wrong number of Oxygen and Silicon atoms is generated from the Cif file.
### Expected Behavior
The correct number of Oxygen and Silicon atoms. 72 Oxygen atoms and 36 silicon ato... | {
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} | an attr access interface change was missed in Tensor when spglib was upgraded to >=2.5.0 (#3923)
spglib throws the following deprecation warning currently:
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/releases">rexml's releases</a>.</em></p>
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<h2>REXML 3.3.3 - 2024-08-01</h2>
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} | ### Feature Requested
This is either a bug or feature request, I am unsure which.
I was wondering which version of critic2 is compatible with the Critic2Analysis class? I see that it is looking for some properties that are formatted differently than in my cpreport json file.
For reference, this is the input ... | {
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"I've installed the dev and optional dependencies per the guidance [here](https://pymatgen.org/contributing.html). There were no problems with my local pre-commit and pytest checks. So, I don't know why the PR failed to pass some of the tests.",
"And, @hongyi-zhao , thank you!",
"There seems to be some conflict... | 2024-08-02T03:11:34 | 2024-08-24T08:18:49 | 2024-08-24T08:18:48Z | CONTRIBUTOR | {
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} | This is an enhancement and re-implementation of https://github.com/materialsproject/pymatgen/pull/3899 and the PRs suggested to include in it.
Add VASP setting for the dftd4 vdW functional and extend `PBE_64` support:
- Add `IVDW: 13` for dftd4 in `vdW_parameters.yaml`
- Support `PBE_64` functional in `MPScanRel... | {
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} | fix the import sorting issue [affecting many PRs](https://github.com/materialsproject/pymatgen/pull/3876#issuecomment-2248527074) after 9100860d7d didn't ensure [`pymatgen` is recognized as a first-party package](https://docs.astral.sh/ruff/settings/#lint_isort_known-first-party) | {
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"Thanks for reporting this. I might help fix this, but more importantly I should push #3786 a bit :)",
"I think it might need to be replaced with\r\n```\r\npdfs = {path.split(\"/\")[-1] for path in glob(f\"{self.tmp_path}/*.pdf\")}\r\n```\r\ncontrolling handling of the split output",
"Please open a PR if you wo... | 2024-08-02T22:29:45 | 2024-08-05T11:18:45 | 2024-08-05T11:18:45Z | CONTRIBUTOR | {
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} | There is an error in python3.12 in the analysis test_graph at
https://github.com/materialsproject/pymatgen/blob/940eb60cbc2848530b2560f75d56298a3c3f714c/tests/analysis/test_graphs.py#L376C9-L376C76
Output running tests is
```py
_________________________ TestStructureGraph.test_draw _________________________
se... | {
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"All good! Can you leave this to me? :) https://github.com/materialsproject/pymatgen/blob/380a81bada34f3e38636f5edf9cdc19154633e99/pyproject.toml#L218",
"And no pressure of course, just a gentle reminder that there are still a few typing PRs (starting from #3873, the others are branched from this) that is waiting... | 2024-08-03T11:08:11 | 2024-08-03T13:47:24 | 2024-08-03T11:19:36Z | MEMBER | {
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"Not so much a bug as providing misinformation or unnecessary warning. Sorry about the mislabeling.",
"@cajfisher Thank you for reporting this. Could you check a newer version of pymatgen and see if this problem still persists? (We had this pull request recently: https://github.com/materialsproject/pymatgen/pull/... | 2024-08-04T05:41:18 | 2024-08-05T13:04:51 | 2024-08-05T13:04:51Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.11.5
### Pymatgen version
2024.2.8
### Operating system version
Windows 11
### Current behavior
The cif file below produces a "non-stoichiometric" error:
io/cif.py:1134: UserWarning: Incorrect stoichiometry:
CIF={'O': 5.0, 'Si': 2.0}
PMG={'Si': 12.0, 'O': 24.0}
... | {
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"Thanks for the fix. I'm still looking into the issue, as I just installed `pygraphviz` in CI and I was having a different error for that particular test for some reason (both in CI and locally) https://github.com/materialsproject/pymatgen/actions/runs/10246364887/job/28343300325?pr=3786.\r\n\r\n**Update**: Issued ... | 2024-08-05T08:10:14 | 2024-08-05T11:18:44 | 2024-08-05T11:18:44Z | CONTRIBUTOR | {
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} | The pdfs list must be constructed from filenames only without other path components, i.e. use last entry from split()
## Summary
Major changes:
- fix: fix list of pdf files in test_draw (test_graph)
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. C... | {
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"thanks @nisse3000 for the detailed issue and for your PR! 👍 not my area of expertise but i'll review the code and wait for @mkhorton to weigh on the discrepancy between quadrant and semicircle functions",
"Hi all,\r\n\r\nThanks for your work in this PR. Do we have a sense for whether the new function (which is ... | 2024-08-05T08:44:53 | 2024-09-10T19:55:01 | CONTRIBUTOR | {
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Python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
Thanks to Dr. Wagner from MPI for Chemical Physics of Solids in Dresden I became aware of the issue that the function _semicircle_integral in class CrystalNN does not correctly calculat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3974 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3974/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3974/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3974/events | https://github.com/materialsproject/pymatgen/pull/3974 | 2,447,974,843 | PR_kwDOACgets53alLW | 3,974 | Added _quadrant_integral function in CrystalNN | {
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"This is not how you use NearestNeighbor. You are supposed to use one of the other analysis tools to get a NearestNeighbor object. This is not a bug. Please refer to the documentation and python tutorial on how such classes work."
] | 2024-08-05T23:20:54 | 2024-08-05T23:27:51 | 2024-08-05T23:27:51Z | NONE | {
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3.11.2
### Pymatgen version
2024.4.13
### Operating system version
MacOS Ventura 13.5.1 (22G90)
### Current behavior
When using the NearNeighbors class functions like get_nn_info(), get_all_nn_info(), and get_nn_shell_info(), the function is unable to read all the input parameters.
For exa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3976 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3976/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3976/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3976/events | https://github.com/materialsproject/pymatgen/issues/3976 | 2,455,466,151 | I_kwDOACgets6SW3Cn | 3,976 | Some type annotations errors when trying to merge master into my local development branch. | {
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"I could probably give a hand on this, but it's really hard for me to say anything useful just from those code pieces. Can you perhaps provide the link to the branch in question?",
"i see the same errors by running `pre-commit run --all-files` on the `master` branch. you might have to set `entry: env MYPYPATH=src... | 2024-08-08T10:40:08 | 2024-08-10T01:16:29 | 2024-08-09T00:07:55Z | CONTRIBUTOR | {
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```shell
(datasci) werner@x13dai-t:~/Public/repo/github.com/materialsproject/pymatgen.git$ git commit -am 'merge master'
[INFO] Checking merge-conflict files only.
ruff............................ | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3977 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3977/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3977/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3977/events | https://github.com/materialsproject/pymatgen/pull/3977 | 2,455,614,855 | PR_kwDOACgets53094Q | 3,977 | Fix `mypy` errors on master branch | {
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"Thanks for reviewing. There was one type error for `io.cp2k` I haven't got to fix, isn't it failing on your side?"
] | 2024-08-08T11:59:11 | 2024-08-09T21:11:29 | 2024-08-09T00:07:54Z | CONTRIBUTOR | {
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- Fix `mypy` errors on master branch, to fix #3976
- Docstring tweaks | {
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} | ## Summary
Checks the inputs to Trajectory following an issue encountered where `get_positions()` method can return more positions than sites depending on filters.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for... | {
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When indexing a trajectory the site properties would be assigned to the structure/molecule but the frame properties would not be propagated down to the structure/molecule in question.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with ... | {
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During calculations on a ZnCu structure from the Materials Project (mp-987), I noticed that I cannot reproduce the energies provided on their website, despite using parameters from MPRelaxSet in pymatgen. The energies obtained from VASP relaxations lie approx. 500 meV (i.e. ~250 meV/atom) above the reporte... | {
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"closing as even more breaking auto-\"fixes\" than expected 😅 "
] | 2024-08-08T23:21:00 | 2024-09-08T21:17:48 | 2024-08-08T23:30:30Z | MEMBER | {
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} | ### Python version
Python 3.10.6
### Pymatgen version
2024.8.8
### Operating system version
Windows
### Current behavior
```
rxn: 12 LiCuS -> Cu + Cu7S4 + 4 Li3CuS2
rxn_e: 0.003
reactants: ['H2O', 'LiCuS']
products: ['H2S', 'Cu', 'Cu7S4', 'Li3CuS2']
--------------after normalization to H2O---------------
r... | {
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- Fix mypy errors for `io.cp2k`
- `mypy` now ignore `override` error globally, rationale: it's common practice and intended to write methods that have different signatures with parent class | {
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"Looks like `fdint` is needed by unit test as well: https://github.com/materialsproject/pymatgen/blob/9703a1c3a364f87d43692172d30010813f2a9159/tests/electronic_structure/test_boltztrap.py#L22\r\n\r\nNever mind, just found https://github.com/materialsproject/pymatgen/pull/2714",
"@janosh Please review this at your... | 2024-08-09T05:07:52 | 2024-09-06T13:04:49 | 2024-09-06T12:53:04Z | CONTRIBUTOR | {
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} | ### Summary
- Install more optional dependencies in CI, follow up #3786 (originally #3684)
### Installed
- [x] `x_trans`: https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap
- [x] `vampire`: https://vampire.york.ac.uk/download/ Ubuntu test split 3
- [x] `OBAlign`: Use the [`openbabel-whee... | {
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"@shyuep @mkhorton @janosh could you have a look at this PR please? Thank you! 😄 ",
" I will merge this as this is a very minor change in a method that I recently implemented and all tests are passing (everything is backward compatible anyway)",
"> I will merge this as this is a very minor change in a method ... | 2024-08-09T10:15:57 | 2024-08-09T12:04:43 | 2024-08-09T10:41:15Z | CONTRIBUTOR | {
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I would like to set the step_size more coarse for the "cubic" supercells without the force_90_degree constraints as the previous step_size has led ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3987 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3987/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3987/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3987/events | https://github.com/materialsproject/pymatgen/pull/3987 | 2,457,674,283 | PR_kwDOACgets5374qS | 3,987 | Revert "Minor change for step_size in CubicSupercellTransformation.apply_transformation " | {
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"Cannot revert at the moment, as the connection to COD is failing. Will do this, as soon as possible."
] | 2024-08-09T11:03:39 | 2024-08-09T13:18:43 | 2024-08-09T13:18:42Z | MEMBER | {
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"This has been fixed with the 2024.8.9 emergency release.",
"Thank you!",
"@shyuep please unrevert my #3865 PR. just add back the \r\n`get_vasprun_outcar` function that was accidentally dropped during merge conflict resolution which I might add was unnecessarily confusing because you moved everything to a `src`... | 2024-08-09T16:20:27 | 2024-08-12T04:24:31 | 2024-08-09T17:25:00Z | MEMBER | {
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3.11
### Pymatgen version
pymatgen 2024.8.8
### Operating system version
_No response_
### Current behavior
```python
from pymatgen.io.vasp.sets import get_vasprun_outcar
```
The above used to work on pymatgen < 2024.8.8 but does not exist any longer in pymatgen >= 2024.8.8.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3989 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3989/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3989/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3989/events | https://github.com/materialsproject/pymatgen/pull/3989 | 2,458,280,210 | PR_kwDOACgets53958A | 3,989 | Revert "Split VASP input sets into submodules" | {
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1. I did not agree to this.
2. It clearly broke something. See #3988 | {
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"merged_at... |
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