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https://api.github.com/repos/materialsproject/pymatgen/issues/3780 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3780/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3780/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3780/events | https://github.com/materialsproject/pymatgen/issues/3780 | 2,257,829,642 | I_kwDOACgets6Gk78K | 3,780 | Incompatibility Issue with ALGO Parameter in Incar and Vasprun Classes | {
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} | ### Python version
Python 3.9
### Pymatgen version
Version: 2024.4.13
### Operating system version
Ubuntu 20.04 LTS
### Current behavior
There appears to be an inconsistency in handling the `ALGO` parameter between the `Incar` and `Vasprun` classes. Specifically, when setting the `ALGO` parameter to "GW0" using ... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe modification involves updating the type of exception thrown in a specific function within the test suite for VASP sets. Previously, an `OSError` was raised, but now it has been changed to a `... | 2024-04-23T13:26:42 | 2024-04-24T02:09:22 | 2024-04-24T02:09:21Z | CONTRIBUTOR | {
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Fix wrong error type in tests for `io.vasp.sets` in #3771, should be `RuntimeError` instead of `OSError` | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **New Features**
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates to the pymatgen library focus on refining the handling of VASP output files. Enhancements include improved logic for ionic convergence checks, streamlined class initializations... | 2024-04-23T19:22:13 | 2024-04-23T22:57:10 | 2024-04-23T22:57:10Z | CONTRIBUTOR | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe changes involve enhancing parameter descriptions, improving code readability, and updating file paths for better organization and accessibility within the codebase across multiple files in di... | 2024-04-25T17:43:49 | 2024-04-26T01:48:16 | 2024-04-25T18:35:41Z | CONTRIBUTOR | {
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I've been testing using `Zeo++` with pymatgen using `io/zeopp` and found that some of the tests were failing. I've determined that the tests were failing due to incorrect file paths to the tests files.
Major changes: Fixed incorrect file path in zeopp test file
- fix 1: `f"{TEST_FILES_DIR}/cssr/EDI.css... | {
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FURB192: https://docs.astral.sh/ruff/rules/sorted-min-max | {
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"do we want to merge this as partially complete and leave some of the todos for later?",
"Thanks for asking. I was facing some resistance while trying to install them (maybe that's the reason they're not installed in CI). And what make things worse is that I never use any of these.\r\nSome help would be appreciat... | 2024-04-26T02:42:19 | 2024-08-24T13:43:28 | 2024-08-06T14:57:48Z | CONTRIBUTOR | {
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- Install some optional dependencies in CI, to fix #3684.
- Fix patch for `bader_caller` (setting `PATH` to empty is easier than changing the `patch` location, and serves the same result where `bader` cannot be found in `PATH`)
### Partially installed on Ubuntu
- `boltztrap2`: only with `pip` (`uv`... | {
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"Using the following revision, expected interpolation results have been obtained. \r\n\r\n self.xpoints = np.linspace(0.0, (self.dim[0]-1)/self.dim[0], num=self.dim[0])\r\n self.ypoints = np.linspace(0.0, (self.dim[1]-1)/self.dim[1], num=self.dim[1])\r\n self.zpoints = np.linspace(0.0, (self.di... | 2024-04-28T02:18:08 | 2024-04-28T06:08:48 | NONE | {
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} | ### Python version
Python 3.11.4
### Pymatgen version
pymatgen 2024.3.1
### Operating system version
Windows 10
### Current behavior
When I use the interpolation method implemented in pymatgen.io.common.VolumetricData, it is found that the results for valence charge density are slightly different compared to tho... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe changes involve streamlining configurations, updating URLs, and enhancing error messages across the project files. These adjustments aim to improve setup clarity, documentation accuracy, and us... | 2024-04-28T10:11:06 | 2024-05-15T01:14:34 | 2024-04-28T22:17:04Z | CONTRIBUTOR | {
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} | ## Exclude `gulp` from package data
- See discussion in #3788, the binaries and libs of super outdated `gulp` (11 yrs old) should not be included in the package data. And it's taking up half of the package size:
```bash
pymatgen-2024.4.13 % du -sh * | sort -hr
15M pymatgen
10M cmd_line ... | {
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"@janosh : this broke some code in pymatgen-analysis-diffusion and thus also in emmet, particularly the change from `symmop` to `symm_op` in `Structure.apply_operation`. Can we announce breaking changes or avoid them if they're made for code style?",
"@janosh Seriously, stop breaking stuff with this kind of cosme... | 2024-04-28T22:20:08 | 2024-05-10T19:41:08 | 2024-04-28T22:41:26Z | MEMBER | {
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"It seems I cannot re-open this for some reason. This was closed by the accidentally included `to fix` keyword but was not fixed.\r\n> 7fac0b466bbb18372334b87c990c46a1096b6415 need to fix #3791",
"Thanks for the fix @janosh, the Windows tests failing in CI is due to a matplotlib issue https://github.com/materials... | 2024-04-29T03:17:59 | 2024-08-04T14:06:08 | 2024-08-04T11:16:08Z | CONTRIBUTOR | {
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} | ## `datetime.datetime.utcnow()` deprecated
See discussion in https://github.com/materialsproject/pymatgen/pull/3705#discussion_r1537225117, `datetime.datetime.utcnow()` is marked as deprecated and might be [removed after Python 3.12](https://discuss.python.org/t/deprecating-utcnow-and-utcfromtimestamp/26221/15).
... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates across various modules in the `pymatgen` package primarily involve semantic adjustments in docstrings for clarity and consistency, and a notable shift from using `np.average` t... | 2024-04-30T01:00:31 | 2024-04-30T17:07:08 | 2024-04-30T11:46:12Z | MEMBER | {
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"this is probably import overhead from loading `pandas` and maybe other big packages. if you start an interactive python session first, wait for it to load and then run `poscar = Structure.from_file(\"./POSCAR\")` on its own, i expect it will be faster\r\n",
"Thanks for the input! I'm not quite sure as I didn't h... | 2024-04-30T11:43:52 | 2024-11-13T17:49:47 | 2024-11-13T17:49:47Z | CONTRIBUTOR | {
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} | ### Summary
- `from monty.json import xxx` significantly slowly down core modules, as `torch` is eagerly imported
- [ ] Might need to look into other commonly used modules
For example:
```bash
python -X importtime -c "from pymatgen.core.structure import Structure" 2> pmg.log && tuna pmg.log
```
With `torc... | {
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"@fxcoudert thanks for reporting! will be fixed by #3797"
] | 2024-04-30T22:17:52 | 2024-05-01T17:18:13 | 2024-05-01T17:18:13Z | NONE | {
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} | ### Python version
3.11.5
### Pymatgen version
2024.4.13
### Operating system version
_No response_
### Current behavior
When `get_points_in_sphere()` is called with `zip_results=False`, it returns a tuple of numpy arrays:
```
return frac_coords, distances, indices, images
```
However, if it ... | {
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| Time to close | 3 days, 15:49:52 | 1 day, 4:59:30 | 9 days, 14:23:36 |
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"This is a feature not a bug. We have stated explicitly that StructureMatcher is based on coordinate mapping. Unless the coordinates are highly precise and the same tolerances are used, two matched structures do not need to have the same space group. ",
"This report is supposed to be regarded as a warning to the ... | 2024-05-01T03:15:28 | 2024-05-02T09:36:54 | 2024-05-01T10:11:22Z | NONE | {
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} | ### Python version
Python 3.9 (issue not related to this)
### Pymatgen version
2024.3.1
### Operating system version
Mac Os Sonoma 14.3. (issue not related to this)
### Current behavior
StructureMatcher has been frequently used recently to evaluate crystal structure generators such as CDVAE and crystal structur... | {
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**before**
**after**
there were multiple issues in `BSPlo... | {
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"> Wondering what is the best way to push commit to another person's PR without being a maintainer?\r\n\r\nthe way you did is exactly right, i.e. open a PR to the WIP branch",
"@janosh Can you review this please? I also fixed the unit tests.\r\n\r\nHowever I'm not sure if we should set \"orbital\" as subscript, f... | 2024-05-02T12:12:11 | 2024-05-15T01:11:16 | 2024-05-02T14:17:17Z | CONTRIBUTOR | {
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Give a hand on #3798.
- Set orbital in subplot title as subscript, and increase the title font size.
- Allow user to set marker size.
- Docstring tweaks.
- Fixed a typo in `io.adf` for repeated `start` as keyword and position args.
- Minor type fixes.
Wondering what is the best way to push commi... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe update involves adjusting the index range for parsing dipole information in `chargemol_caller.py` of `pymatgen` and adding a new test assertion in `test_chargemol_caller.py` to validate the p... | 2024-05-02T15:24:01 | 2024-05-02T16:09:34 | 2024-05-02T16:06:52Z | CONTRIBUTOR | {
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Major changes:
- fix 1: _get_dipole_info was previously getting the y and z component and the magnitude instead of x,y and z. The only test case was 0,0,0 so it was never noticed.
Previously the dipole was only checked for the spin unpolarized structure with no dipoles (I added some extra spaces to ma... | {
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"Notifying @munrojm too, since this would affect MP database builds.",
"To remind ourselves of the anions including in the experimental data used to fit the corrections, I re-generated this list using the same `oxi_state_guess` logic used within the correction scheme:\r\n\r\n| Element | Oxidation State | Co... | 2024-05-03T06:37:47 | 2024-06-09T02:58:48 | 2024-06-09T02:58:47Z | MEMBER | {
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} | ## Issue
This PR relates to the `MaterialsProject2020Compatibility` scheme, and cases in which structures might be heavily over-stabilized in error, leading to unrealistic structures potentially being placed on the convex hull.
In brief,
* Anion corrections are applied in cases where an element may not be an a... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates to the `pymatgen` library enhance its chemical composition and periodic table functionalities by incorporating the concept of radioactivity. These changes introduce a new `radi... | 2024-05-03T15:10:51 | 2024-05-03T16:29:31 | 2024-05-03T16:29:31Z | CONTRIBUTOR | {
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Major changes:
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`.\n\nIf you change your mind, j... | 2024-05-03T22:07:47 | 2024-05-04T10:47:03 | 2024-05-04T10:47:01Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/tqdm/tqdm/releases">tqdm's releases</a>.</em></p>
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<h2>tqdm v4.66.3 stable</h2>
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} | ### Python version
3.12
### Pymatgen version
2024.5.1
### Operating system version
Ubuntu 20
### Current behavior
Parsing CP2K output files gets stuck in an infinite loop during the function `parse_initial_structure` on line 319 in `pymatgen/io/cp2k/outputs.py`. I believe this is due to the string on line 334 no... | {
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Adds a `.from_ase_atoms()` method to `Structure` to complement the pre-existing `.to_ase_atoms()`. In reality, this is just a shorthand for the adapter, but it felt awkward to have one direction but not the other.
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} | ## Bug in `core.composition` comparison
Open this in case it got forgotten.
As found out by @janosh in https://github.com/materialsproject/pymatgen/pull/3792#discussion_r1584003750, there is an obvious bug with `Composition` comparison where `True` is returned too early:
https://github.com/materialsproject/pyma... | {
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"I'm not a maintainer, but if you could provide the cif file and code snippet to reproduce this issue, that would be very helpful :)",
"Here is a **minimally reproducible example** with the structure (Crystal.cif) attached, highlighting that the argument `check_occu` cannot turn off the occupancy check. In this ... | 2024-05-09T05:14:42 | 2024-05-30T19:34:44 | 2024-05-30T19:34:44Z | NONE | {
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} | ### Python version
3.11.8
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
Hi all,
I was trying to deal with a crystal structure (in .cif format) that had warnings on having occupancy issues:
```
"UserWarning: Some occupancies ([1.0, ... (x876)]) sum to > 1! If the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3817 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3817/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3817/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3817/events | https://github.com/materialsproject/pymatgen/pull/3817 | 2,287,553,541 | PR_kwDOACgets5u-8rl | 3,817 | [Deprecation] Replace `Element` property `is_rare_earth_metal` with `is_rare_earth` to include Y and Sc | {
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"@janosh. Can you please review this one? Thanks!",
"Just want to mention here that I expect lot's of code to be broken. \r\nIs there a way to notify users of this change or have a deprecation period?",
"Thanks for commenting!\r\n\r\nI'm not sure quite to properly notify users in this case (except for insert a ... | 2024-05-09T12:07:36 | 2024-05-31T19:11:51 | 2024-05-30T19:55:41Z | CONTRIBUTOR | {
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} | ## Summary
- [**Deprecation**] Replace `Element` property `is_rare_earth_metal` with `is_rare_earth` to include Y and Sc, remove `is_rare_earth_metal` after `2025-01-01`.
https://github.com/materialsproject/pymatgen/blob/6c696cdb327621d5d16c675478f4ed0e024feea1/pymatgen/core/periodic_table.py#L689-L692
- Update de... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3818 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3818/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3818/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3818/events | https://github.com/materialsproject/pymatgen/issues/3818 | 2,288,195,400 | I_kwDOACgets6IYxdI | 3,818 | Check inputs provided to MPRester functions | {
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} | ### Feature Requested
Implement sanity checks for inputs to the MPRester functions in pymatgen
### Proposed Solution
MP is getting non-sensical requests such as `/materials/summary/?_fields=material_id&formula=Emission+Factor&_limit=1000` from user agent `pymatgen/2023.7.17 (Python/3.8.12 Windows/10)`. The formula c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3819 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3819/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3819/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3819/events | https://github.com/materialsproject/pymatgen/pull/3819 | 2,290,724,849 | PR_kwDOACgets5vJrlf | 3,819 | Improve unphysical (greater than 1) occupancy handling in `CifParser` and add missing site label `if not check_occu` | {
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"@janosh. Can you please review (and comment) on this? Thanks."
] | 2024-05-11T06:48:35 | 2024-05-31T19:11:18 | 2024-05-30T19:34:43Z | CONTRIBUTOR | {
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} | ## Summary
To fix #3816.
- Raise `ValueError` if occupancy exceeds `occupancy_tolerance` and if `check_occu`, with a more descriptive error message.
- [**Need Confirmation**] Allow any occupancy (ignore `occupancy_tolerance`) in cif when `not check_occu` in 7cf5ba93ed57b1167171aee7ab35043c74da3037, a warning wo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3820 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3820/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3820/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3820/events | https://github.com/materialsproject/pymatgen/pull/3820 | 2,290,794,849 | PR_kwDOACgets5vJ6c4 | 3,820 | Improve type annotations and comments for `io.cif` | {
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"@janosh. Could you please review this as well? Thanks!",
"Thanks for reviewing!"
] | 2024-05-11T08:59:29 | 2024-05-31T19:09:33 | 2024-05-15T16:34:21Z | CONTRIBUTOR | {
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} | ## Summary
- Add type annotations and tweak comments for `io.cif`
- Minor code format tweak
- Simplify "check to see if" to "check if" in comments
- Remove `if __name__ == "__main__"` from `core.libxcfunc` (legacy from another PR)
### Potentially Breaking Changes (very unlikely)
1. Make `parse_oxi_states` a... | {
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} | ### Python version
3.11
### Pymatgen version
2024.5.1
### Operating system version
_No response_
### Current behavior
When calling `VaspInputSet.get_input_set()`, the returned `VaspInput` has a broken `.as_dict()` method. That is reported below. The returned `VaspInput` is already a `dict`, so that... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3822 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3822/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3822/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3822/events | https://github.com/materialsproject/pymatgen/pull/3822 | 2,291,261,729 | PR_kwDOACgets5vLVFO | 3,822 | Add types annotations for `core.interface` | {
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"Not working on this for now, would reopen it later.",
"@janosh Would appreciate it if you could review this at your convenience, thanks!",
"@janosh Just ping you again in case it got forgotten :) No rush",
"Thanks for reviewing! Appreciate that"
] | 2024-05-12T10:00:07 | 2024-06-06T11:17:33 | 2024-06-06T11:16:25Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
- Add types annotations for `core.interface`
- Use more specific types for `ClassVar`
### New custom type aliases
```
Tuple3Ints = tuple[int, int, int]
Tuple3Floats = tuple[float, float, float]
```
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} | ## Summary
Major changes:
- Adapt to the latest version of PWmat output files, while also being compatible with older versions of output files。
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixe... | {
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"## Outdated\r\n\r\n### Investigating failure of unit test `test_get_slabs`\r\nhttps://github.com/materialsproject/pymatgen/blob/40b0165c7e841df6971b6d2960623a127c20e81c/tests/core/test_surface.py#L439-L455\r\n\r\n`z_ranges`:\r\n```\r\n> old_implementation:\r\n[(0, 0.09444), (0, 0.04316999999999993), (0.09444, 0.16... | 2024-05-13T04:49:06 | 2024-05-31T19:10:30 | 2024-05-30T19:33:50Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Follow up #3748.
- Use `isclose` over `==` for overlap check in `SlabGenerator.get_slabs`
- Add a new `ztol` arg to control the behavior of `get_slabs`, default to `0` to keep consistency with previous behavior
### Use `isclose` over `==` for overlap check in `SlabGenerator.get_slabs`
Previously... | {
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"Looks like we still have the issue where `uv` cannot install `torch` randomly. I would report this to `uv` soon.\r\n\r\nTo fix this, we might need to install `torch` and explicitly skip `torch` for `uv`. \r\n\r\nBefore this PR, even after `torch` is already successfully installed by `pip`, calling `uv pip install ... | 2024-05-13T08:17:21 | 2024-11-21T03:25:38 | 2024-11-21T03:24:37Z | CONTRIBUTOR | {
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### Revert to install `torch` with `uv`
Also link to #4063, **`pip install torch` is taking up 70% of the total dep install time**
Revert to `pytorch` installation with `uv` in CI,
- [x] It appears https://github.com/astral-sh/uv/issues/1921 has been resolved.
- [ ] [The following intermittent e... | {
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"@janosh. Please review this, thanks.\r\n\r\nWondering if we could automate this checking?",
"> Wondering if we could automate this checking?\r\n\r\n`ruff` has an open issue about implementing this rule which you could upvote and/or leave a comment\r\n\r\nhttps://github.com/astral-sh/ruff/issues/2302",
"this is... | 2024-05-13T14:53:28 | 2024-05-14T14:59:37 | 2024-05-14T14:54:21Z | CONTRIBUTOR | {
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} | ## Summary
- Guard `TYPE_CHECKING` only imports
- Format docstring to Google style in `io.aims.sets`
### Can we automate this check (and fix)?
`flake8` provides [`TYP001` rule](https://github.com/asottile/flake8-typing-imports) to check this, but doesn't seem able to correct it automatically. Have to run `fl... | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/releases">nokogiri's releases</a>.</em></p>
<blockquote>
<h2>v1.16.5 / 2024-05-13</h2>
<h3>Security</h3>
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"For some reason, replacing the magic `__hash__` method of `SymmOp` in bf2a953acfdd3f48a4c379b7030b3c897e43c8bf breaks a unit test of `core.structure` (`test_from_prototype`):\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/51180fc2ef7ae4208ac244d820f05ce17d57f9c2/pymatgen/core/operations.py#L92-L93\r\n\r\... | 2024-05-14T03:27:52 | 2024-05-14T13:41:08 | 2024-05-14T13:20:20Z | CONTRIBUTOR | {
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} | ## Summary
- Add/improve types for `core`
- Replace hard-coded class call with `type(self)`
- Replace all `[0:x]` with `[:x]`
### Add types for remaining part of `core`, follow up of #3814.
- [x] `core.molecular_orbitals`
- [x] `core.operations`
- [x] `core.sites`
- [x] `core.spectrum`
- [x] `core.tensor`
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https://api.github.com/repos/materialsproject/pymatgen/issues/3830 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3830/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3830/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3830/events | https://github.com/materialsproject/pymatgen/issues/3830 | 2,295,757,954 | I_kwDOACgets6I1nyC | 3,830 | A minor document error in `POTCAR Setup`. | {
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} | The document [here](https://pymatgen.org/installation.html#potcar-setup) says:
> In practice, this entire process might look something like the following:
>
> ```
> pmg config -p /path/to/pseudos/potcar_PBE.54/ /path/to/pseudos/pmg_potcars/
> pmg config -p /path/to/pseudos/potcar_LDA.54/ /path/to/pseudos/pmg_po... | {
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"Thanks for reviewing.\r\n\r\nMeanwhile I would say `uv install torch` seems to have a higher and higher failure rate for some reason. We have always been seeing it to fail. Should we consider revert to slower but more reliable `pip`? ",
"we're already installing it with `pip`. maybe there's a flag in `uv pip in... | 2024-05-15T10:02:15 | 2024-05-15T12:18:41 | 2024-05-15T11:51:39Z | CONTRIBUTOR | {
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- Move test structures out of `util` directory
We might need a better name for the directory? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3832 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3832/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3832/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3832/events | https://github.com/materialsproject/pymatgen/pull/3832 | 2,300,282,259 | PR_kwDOACgets5vqQ2V | 3,832 | Improve type annotations for `core.(trajectory/units)` | {
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"Can I have this one reviewed please? @janosh ",
"Thanks for reviewing! Appreciate that."
] | 2024-05-16T12:32:54 | 2024-05-17T14:26:36 | 2024-05-17T13:23:54Z | CONTRIBUTOR | {
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} | ### Summary
- Improve type annotations for `core.trajectory` and `core.units`
- Nest `_get_si_unit` and `_check_mappings` inside the only methods that call them in `Unit`
### Extend the following to support argument "unit" as both `str` and `Unit`
- `__init/new__` of `FloatWithUnit` and `ArrayWithUnit`
- `get_... | {
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} | It appears the case for [multiple-byte units](https://en.wikipedia.org/wiki/Byte) for memory is incorrect. And we should be aware that `b/B` refer to `bit/byte` respectively.
https://github.com/materialsproject/pymatgen/blob/bb68c780834fea588f35420e1835ed3b21894a44/pymatgen/core/units.py#L77-L87 | {
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"I think these paths look correct to me, perhaps I'm wrong.\r\n\r\nThe `potcar_PBE/LDA.54/` in the first two paths refers to the directory where the POTCARs are stored.\r\n\r\nThe last path looks a bit confusing, perhaps:\r\n```diff\r\n- pmg config --add PMG_VASP_PSP_DIR /path/to/pseudos/pmg_potcars/pmg_potcars\r\n... | 2024-05-16T14:47:09 | 2024-05-18T01:22:46 | 2024-05-17T13:19:02Z | CONTRIBUTOR | {
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"All makes sense to me! ",
"@janosh, I will try to review soon. ",
"@janosh As I told you before, pls consult before making this kind of cosmetic stuff. Otherwise, you are going to be doing a lot of redundant work. Given that most people just jump to the relevant class in the IDE, why would this split be needed... | 2024-05-16T20:43:47 | 2024-06-04T20:41:29 | 2024-05-23T14:39:05Z | CONTRIBUTOR | {
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} | This PR continues #3484 by updating the `pymatgen.io.vasp.DictSet` class to include features from the former atomate2 `VaspInputGenerator` class.
This allows transitioning `atomate2` to exclusively use `pymatgen` input sets in https://github.com/materialsproject/atomate2/pull/854.
These added features (such as `aut... | {
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} | Bumps [rexml](https://github.com/ruby/rexml) from 3.2.5 to 3.2.8.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/releases">rexml's releases</a>.</em></p>
<blockquote>
<h2>REXML 3.2.8 - 2024-05-16</h2>
<h3>Fixes</h3>
<ul>
<li>Suppressed a warning</li>
</ul>
<h2>REXM... | {
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"@janosh Can you please review this? Thanks.",
"Thanks for reviewing and the tweaks!",
"Hello,\r\nToday I ran into an issue while using pymatgen 2024.5.31, that I think might be related to this contribution. I am using a fresh conda environment, python 3.11, with pymatgen installed via `pip install pymatgen`. I... | 2024-05-17T14:16:56 | 2024-06-04T12:32:32 | 2024-05-25T07:54:32Z | CONTRIBUTOR | {
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- Improve type annotations for `core.structure`
- Fix some `type: ignore[reportPossiblyUnboundVariable]`
#### A question from me:
What is the difference between `np.ndarray`, `ArrayLike` and `NDArray` for typing?
```python
ArrayLike: type[Buffer] | type[_SupportsArray[dtype[Any]]] | type[_Nested... | {
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"@shyuep Can I have your advice on this please? This should be very similar to the change to `Element`, and I scheduled the same grace period until `2025-01-01`",
"@shyuep Can you please review this? It should be very similar to #3817.\r\n\r\nThe rationale for this change is that something like `KB` (kilobyte) a... | 2024-05-18T03:46:18 | 2024-06-18T12:10:56 | 2024-06-17T15:25:37Z | CONTRIBUTOR | {
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} | ## Summary
- Correct cases for memory units in `core.units` to fix #3833
- Fix `FloatWithUnit.from_str` to correctly detect `unit_type` from string with space between the value and the unit
### Correct cases for memory units in `core.units`
I assume this is another breaking fix, so I marked the incorrect uni... | {
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} | ### Python version
3.10.8
### Pymatgen version
2023.7.20
### Operating system version
MacOS Sonoma 14.4.1
### Current behavior
In the attached Gaussian .log file, there are lines such as following:
> Excited State 1: 2.316-A 0.7744 eV 1601.13 nm f=0.0084 <S**2>=1.091
where the spin multiplicity in ... | {
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"I think only [the incremental set](https://github.com/JaGeo/LobsterPy/issues/306#issuecomment-2191633777) needs to be generated and provided.",
"If you want to do it, you are surely invited to do so. I am happy to check.",
"I need to study the logic behind [your script](https://github.com/JaGeo/LobsterPy/issue... | 2024-05-20T18:30:55 | 2024-06-26T23:11:52 | MEMBER | {
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} | ### Feature Requested
Make the LobsterSets available to the latest Potcars
### Proposed Solution
Adapt the Lobstersets and create a new yaml file for optimal bas functions.
### Relevant Information
None | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/psf/requests/releases">requests's releases</a>.</em></p>
<blockquote>
<h2>v2.32.0</h2>
<h2>2.32.0 (2024-05-20)</h2>
<h2>🐍 PYCON US 2024 EDITION 🐍</h2>
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"Thanks for suggesting this, I'm currently working on this.\r\n"
] | 2024-05-21T15:38:02 | 2024-12-11T02:01:56 | 2024-12-11T02:01:56Z | MEMBER | {
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} | ### Feature Requested
In VASP, the NBANDS parameter describes the number of bands. It can be modified on-the-fly by VASP, potentially even overriding the setting chosen by the user. This is done based on the number of cores requested for the calculation. Therefore, knowing the NBANDS VASP actually uses is quite useful... | {
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"I tried following your procedure and could not convert the file using ASE 3.23\r\n\r\n```\r\n File \"/home/wladerer/.local/lib/python3.10/site-packages/ase/spacegroup/spacegroup.py\", line 876, in spacegroup_from_data\r\n spg = Spacegroup(symbol, None, datafile)\r\n File \"/home/wladerer/.local/lib/python3.10... | 2024-05-23T11:44:24 | 2024-08-04T23:29:42 | NONE | {
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} | ### Python version
3.11.4
### Pymatgen version
2023.12.18
### Operating system version
Rocky Linux 9.2
### Current behavior
The cif file of the crystal YUTYOC is recognized as the P/6mmm space group category when it is parsed, but the P6mm space group category is marked in the cif file.My code is following.
#... | {
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"It affects the Materials Project website as well. ",
"Before @kaueltzen starts to correct it, we would like to ask for feedback on this as this will be a breaking change with potentially major effects. The symbol is clearly wrong. Nevertheless, people work with the wrong symbol. \r\n\r\n@shyuep @janosh, thoughts... | 2024-05-24T17:27:03 | 2025-03-02T15:00:55 | 2024-07-14T19:30:29Z | CONTRIBUTOR | {
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3.10
### Pymatgen version
2024.5.1 or master
### Operating system version
_No response_
### Current behavior
output of minimal example:
```
48 Pnnn1
50 Pban1
59 Pmmn1
68 Ccce1
70 Fddd1
85 P4/n1
125 P4/nbm1
126 P4/nnc1
129 P4/nmm1
130 P4/ncc1
201 Pn-31
203 Fd-31
222 Pn-3n1
224 Pn... | {
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} | ## Summary
Major changes:
- fix 1: Replace deprecated `delim_whitespace=True` with `sep="\s+"` (see https://pandas.pydata.org/docs/reference/api/pandas.read_csv.html)
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests adde... | {
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"No objection from me. Does anyone know if the VASP developers have included this information in the vasprun.xml now as well?"
] | 2024-05-28T18:34:36 | 2024-05-29T17:35:15 | CONTRIBUTOR | {
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OUTCARs (typically) print out the magnetic moments for each atom at the end of _each_ ionic step. Wouldn't that information be useful to store for every ionic step? | {
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"@JaGeo Can you please review this? And let me know if there is any concern, thanks :)",
"Maybe next week. Sorry!",
"> Maybe next week. Sorry!\r\n\r\nAll good. No worries at all, whenever you have time :)",
"> @JaGeo Can you please review this? And let me know if there is any concern, thanks :)\r\n\r\nI could... | 2024-05-30T08:18:24 | 2024-06-09T01:55:02 | 2024-06-08T15:39:40Z | CONTRIBUTOR | {
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} | ## Simplify case handling in `lobster.inputs`
- [**Potentially breaking**] Rename class variable `LISTKEYWORDS` to `LIST_KEYWORDS` for consistency.
#### Use `{lowercase: camalCase}` to simplify key case handling, for the following methods:
Now lower-case keys are used internally, and Camel case keys are reserv... | {
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"I would add a NotImplemented for Specie unitl someone wants to take a crack at implementing this for Species. It is non-trivial since there are some special rules for removing electrons, especially things related to d10 configs.",
"Thanks for the quick action @shyuep . I'll see about following up on this. It app... | 2024-05-30T17:06:03 | 2024-05-30T18:27:32 | CONTRIBUTOR | {
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} | ### Python version
Python 3.10.6
### Pymatgen version
2024.5.1
### Operating system version
Ubuntu (Windows WSL2)
### Current behavior
`Species.full_electronic_structure` and `electronic_structure` do not properly account for the number of electrons when an oxidation state other than zero is assigned, for exampl... | {
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"See also #3849 , which is related",
"Upon further research, both NIST and the CRC handbook list electronic structures _without_ reference to energy ordering (e.g., '[Kr].4d10.5s2'), so the existing behavior in `pymatgen` should probably be left as-is.\r\n\r\nA future PR will improve the documentation of this poi... | 2024-05-30T17:10:46 | 2024-06-14T21:15:15 | 2024-06-14T21:14:35Z | CONTRIBUTOR | {
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Python 3.10.6
### Pymatgen version
2024.5.1
### Operating system version
Ubuntu (Windows WSL2)
### Current behavior
the `full_electronic_structure` and `electronic_structure` properties of `Element` and `Species` do not correctly order energy levels. For example, the 4s orbital h... | {
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"Note: due to 'prettifying' the .json file, the full diff is not very useful. I suggest viewing the changes associated only with the 2nd commit and/or using https://jsondiff.com/ to see exactly which values I changed.",
"~~This change seems to have caused some problems with `get_crystal_field_spin`, causing a few... | 2024-05-30T18:53:38 | 2024-06-14T21:13:12 | 2024-06-14T21:13:12Z | CONTRIBUTOR | {
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} | ## Summary
- Rearranges electronic structures according to the correct energy levels. Checked against
- implements `full_electronic_structure`, `electronic_structure`, and `valence` for `Species`
- "prettify" `periodic_table.json` to make it more readable as a standalone file
https://ptable.com/#Electrons/Expan... | {
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"@shyuep Sorry for the trouble caused surrounding import of `Self`. As it seems to be causing trouble in the v2024.5.31, can I ask for yanking this release and issue a new one? Apologize again for this oversight"
] | 2024-05-31T21:16:52 | 2024-07-04T13:42:26 | 2024-06-03T16:09:27Z | MEMBER | {
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} | this ensures pymatgen is compatible with both the oldest and newest dependency versions it allows in `setup.py`.
future CI runs will discover version clashes like the one for `monty` reported in https://github.com/materialsproject/pymatgen/pull/3752#issuecomment-2142967807 before releasing to pypi
also fix `typing_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3853 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3853/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3853/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3853/events | https://github.com/materialsproject/pymatgen/pull/3853 | 2,329,186,236 | PR_kwDOACgets5xMslS | 3,853 | Fix filter condition for warn msg of unphysical site occupancy in `io.cif` | {
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"@janosh I pushed this hot fix to address the error message issue"
] | 2024-06-01T14:57:20 | 2024-06-04T00:41:09 | 2024-06-03T16:22:16Z | CONTRIBUTOR | {
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- Fix a mistake in #3819, where the `filter` condition is incorrect, and also cast `filter` to `list`.
- Add unit test for this error message
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} | ### Python version
python 3.10.8
### Pymatgen version
2024.5.1
### Operating system version
_No response_
### Current behavior
https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/interfaces/coherent_interfaces.py
line 142-147: the dictionary assumes all different terminations has differen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3855 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3855/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3855/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3855/events | https://github.com/materialsproject/pymatgen/issues/3855 | 2,330,942,933 | I_kwDOACgets6K713V | 3,855 | TypeError: deprecated() got an unexpected keyword argument 'deadline' | {
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"Yes we already noticed this https://github.com/materialsproject/pymatgen/pull/3752#issuecomment-2142967807, please try to update `monty` version to latest with `pip install -U monty`",
"@DanielYang59 Yes. Your tip does the trick.\r\n\r\nBut, should the `deadline=(2025, 1, 1)` in the following line be removed or ... | 2024-06-03T11:51:29 | 2024-06-03T15:26:03 | 2024-06-03T15:26:03Z | CONTRIBUTOR | {
"total": 0,
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} | ### Python version
Python 3.11.1
### Pymatgen version
2024.5.31
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
Description: When trying to import MPRester from mp_api.client, I encountered a TypeError related to the deprecated decorator in the pymatgen library. The error messa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3856 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3856/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3856/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3856/events | https://github.com/materialsproject/pymatgen/issues/3856 | 2,331,048,301 | I_kwDOACgets6K8Plt | 3,856 | [CI] All unit tests failing perhaps related to lastest `chgnet` 0.3.7 release | {
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"closing as it seems to be related to upstream https://github.com/CederGroupHub/chgnet/issues/160, nothing to do with `pymatgen`"
] | 2024-06-03T12:37:53 | 2024-06-03T14:12:16 | 2024-06-03T14:12:15Z | CONTRIBUTOR | {
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```
error: Failed to download distributions
Caused by: Failed to fetch wheel: chgnet==0.3.7
Caused... | {
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"pinging @esoteric-ephemera since i can't request a review from you but would be great to get your thoughts if any",
"Seems reasonable to me. I am not familiar with the `W_HASH` variants.",
"This looks good to me! This can also benefit those who are newer to VASP and only care about more recent generations of p... | 2024-06-04T00:29:01 | 2024-06-04T16:19:47 | 2024-06-04T16:19:46Z | MEMBER | {
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} | the current `PotcarSingle.functional_dir` hard-codes the subfolder structure of `PMG_VASP_PSP_DIR`. e.g. the subfolder containing the `PBE_64` POTCARs _must_ be named `POT_PAW_PBE_64`. this causes problems e.g. in cases where the POTCARs are shared across an HPC cluster and users don't have permissions to rename shared... | {
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"Many thanks for this @kaueltzen!\r\n\r\nIn case it is helpful in future, adding a note that the `maggroups` module in pymatgen uses a different dataset (from ISO-MAG, used with permission). It may or may not be helpful to cross-check information, since it's a superset of the crystallographic groups.\r\n\r\n**Impor... | 2024-06-04T12:13:07 | 2024-07-15T12:02:51 | 2024-07-14T19:30:29Z | CONTRIBUTOR | {
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} | ## Summary
Fixes #3845 , #3861 and #3862 .
Includes the following changes in the symmetry module:
- The SpaceGroup symbol attribute now refers to its Hermann-Mauguin symbol with underscore notation of screw axes.
- The setting of the 7 rhombohedral space group types is now stored in an additional hexagonal bool... | {
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"thanks for reporting! pretty sure this was not intentional but @esoteric-ephemera would know best.\r\n\r\nalways good to learn where we need to add more tests :)",
"It seems [here](https://github.com/materialsproject/pymatgen/pull/3835/files#diff-2b61e131c3f0a2a133effdfb20a2b8b6c84690d55bcd81b6d01ea4ecebdb9b0dR2... | 2024-06-04T17:47:51 | 2024-06-06T12:39:44 | 2024-06-06T12:39:44Z | MEMBER | {
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} | ### Python version
3.11
### Pymatgen version
2024.5.31
### Operating system version
_No response_
### Current behavior
It seems there was a recent breaking change to the `VaspInput` class that I didn't see communicated. I wanted to report it here to make sure it wasn't a bug. Feel free to close if ... | {
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} | ### Feature Requested
References PR #3859 , specifically https://github.com/materialsproject/pymatgen/pull/3859#discussion_r1626142699
A class method `from_space_group()` will be added to the PointGroup class to instantiate point groups that belong to the 32 crystal classes from a SpaceGroup symbol. This will also ... | {
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"wow, love your detailed issue reports with discovery context and repro steps. keep that up! 👍 \r\n\r\nregarding the issue, your proposed fix sounds good to me. i hope others with more experience weigh in though\r\n\r\n> fix would be to not remove whitespaces in the Hermann-Mauguin symbol when loading SYMM_OPS",
... | 2024-06-05T11:04:56 | 2024-07-15T07:56:12 | 2024-07-15T07:56:12Z | CONTRIBUTOR | {
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} | ### Python version
3.10
### Pymatgen version
2024.5.1 or master
### Operating system version
_No response_
### Current behavior
This issue was noticed when working on #3859 and #3861 .
In `SpaceGroup.SYMM_OPS` the translational information in screw axes is appended without an underscore, e.g. "Pmc21" while in... | {
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"@janosh Ready for review now, thanks for your time :)",
"Thanks for reviewing, and I really appreciate your merging this before splitting `vasp.sets` :)"
] | 2024-06-05T12:45:12 | 2024-06-07T13:03:47 | 2024-06-07T13:02:55Z | CONTRIBUTOR | {
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- Improve types for `io.vasp.sets` and comment tweaks
- Replace hard coded class names
- Use `deadline` in `deprecated` decorator for easier tracking of deprecated functions
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"Ah there would be a million merge conflicts for #3863 😭 \r\n\r\nI don't have any objection for this PR, but could we \"possibly\" split from #3863? As I think splitting would be easier (cut and paste) than reapplying all changes?",
"In favor, thanks @janosh! The `sets.py` file was getting far too unwieldly.",
... | 2024-06-05T22:51:49 | 2024-08-09T16:40:30 | 2024-08-07T18:54:46Z | MEMBER | {
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no breaking changes expecte... | {
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"Thanks @yanghan234, I will merge this."
] | 2024-06-06T05:52:40 | 2024-09-07T04:25:31 | 2024-06-09T03:11:08Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- This PR solved the issue in #3780
`pymatgen` automatically converts the input `ALGO` to the leading capitalized format, e.g. `GW0` will be converted to `Gw0` and written to `vasprun.xml`. In such case, `Vasprun` would fail to parse the results. In this PR, I fixed this bug.
Tag... | {
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} | ### Python version
Python 3.9
### Pymatgen version
2024.6.4
### Operating system version
_No response_
### Current behavior
The documentation of the argument `all_oxidation_state` is inconsistent with what the code really does.
**According to doc, `common_oxidation_states` and `icsd_oxidation_states` are used... | {
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} | Simple bug fix for when elements have non-integer oxidation states assigned to them. Pymatgen can assign non-integer charges to sites, but when trying to initialize `Species` with non-integer oxidation state:
```
from pymatgen.core import Species
Species("C0.25+")._oxi_state
```
this raises an `AttributeError`.
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"Will re-open if needed.",
"how come it's no longer needed? seems like a sensible change",
"Feel free to merge. I was indifferent. ",
"i guess i'm still missing something. if it avoids an error that occurred in practice for @samblau, it's a keeper, no?",
"I only encountered this error because I was dealing ... | 2024-06-08T02:50:49 | 2024-06-09T01:29:45 | 2024-06-09T01:22:05Z | MEMBER | {
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} | Broader context: This PR basically impacts nobody and is just a marginally safer way to index the `MSONAtoms` info key when parsing the dictionary representation.
Technical details: As noted by @samblau, if for some reason your `MSONAtoms.as_dict()` representation no longer has an `atoms_info` key, then doing `MSONA... | {
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"@DanielYang59 could you trigger the atomate2 tests?",
"@JaGeo Thanks for commenting. Can you let me how to achieve that? It should only be possible when pushing to `master` I guess?https://github.com/materialsproject/pymatgen/blob/624e6eb5cfefbf5736fe31b8910dd19c1042e94e/.github/workflows/test.yml#L94\r\n\r\nThi... | 2024-06-09T03:12:40 | 2024-06-22T00:39:49 | 2024-06-21T15:11:33Z | CONTRIBUTOR | {
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- Enable more `ruff` rules
- Revert an accidental change in tests for `io.lobster.inputs` in https://github.com/materialsproject/pymatgen/pull/3848#discussion_r1632144875
- Other format tweaks
### Enable more [`ruff` rules](https://docs.astral.sh/ruff/rules/)
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`spglib` will not raise if symmetry cannot be determined, but will instead return `None`. This is not currently handled in `SpacegroupAnalyzer`.
As a result, a common issue encountered is calling `Structure.get_space_group_info` for a structure where symmetry cannot be determined leading to an opaque ... | {
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"One more thing: i feel we again need to install LobsterPy with these changes. If you have time for this, @DanielYang59 , this would be highly appreciated. (Atomate2 will now be done automtically at least)",
"> i feel we again need to install LobsterPy with these changes. \r\n\r\nI assume you mean \"test\" `Lob... | 2024-06-10T03:02:09 | 2024-08-09T00:11:48 | 2024-08-03T13:46:46Z | CONTRIBUTOR | {
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- Improve type annotations and docstring for `electronic_structure`
- [x] `bandstructure`
- [x] `cohp`
- Replace unnecessary single-item list extend with `append` in 8e252388e718415140142a69605896342a5e16c3 [for performance](https://stackoverflow.com/questions/725782/in-python-what-is-the-differenc... | {
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"please stop calling other people's contributions irrelevant (i assume you're referring to https://github.com/materialsproject/pymatgen/pull/3831).\r\n\r\n> PymatgenTest is used not just within Pymatgen but a lot of downstream packages\r\n\r\nin my opinion, having a publicly exported `PymatgenTest` class was an ant... | 2024-06-10T15:17:04 | 2024-06-18T11:15:51 | 2024-06-11T02:52:49Z | MEMBER | {
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} | ### Python version
any
### Pymatgen version
2024.6.4
### Operating system version
_No response_
### Current behavior
PymatgenTest.get_structure fail if `tests` is not are not present, e.g., if it is installed from pip.
@DanielYang59 @janosh You cannot do this kind of thing. PymatgenTest is used not just with... | {
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"I would put this in pymatgen.ext rather than pymatgen.io. The ext are external interfaces to things like API resources. E.g., matproj is in pymatgen.ext. Thanks.",
"Given this is purely for conversion to/from the OPTIMADE schema, `io` is appropriate (but yes, any API-calling code lives in `ext`).\r\n\r\nThanks f... | 2024-06-11T14:10:57 | 2024-08-07T17:52:59 | 2024-08-07T17:52:59Z | CONTRIBUTOR | {
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} | ## Summary
This PR adds a converter between the `pymatgen.core.Structure` object and an OPTIMADE structure resource, migrated primarily out of https://github.com/Materials-Consortia/optimade-python-tools/blob/master/optimade/adapters/structures/pymatgen.py with the aim to remove it from our library.
## Todos
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"Would it be possible to reintroduce the default `species_dir` behavior? For some people using only one set of defaults is relatively okay",
"otherwise this looks good from an fhi-aims perspective. This will break atomate2 tests but we can fix that once it is merged",
"> Would it be possible to reintroduce the ... | 2024-06-12T12:58:18 | 2024-07-08T13:18:34 | 2024-06-20T14:37:20Z | CONTRIBUTOR | {
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This PR adds new SpeciesDefaults object to account for files with the default definitions of species-related keywords (integration grids, basis sets...) in FHI-aims, named _species' defaults_. This is done to abstract away the work with species' defaults from the `AimsControlIn` object, to bring the API m... | {
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"ready for review",
"Thanks for the PR @tpurcell90, can you expand on:\r\n\r\n> How it deals with spins is not through magmoms, but FHI-aims uses magmoms exclusively\r\n\r\nI'm not sure I understand, apologies.",
"> Thanks for the PR @tpurcell90, can you expand on:\r\n> \r\n> > How it deals with spins is not th... | 2024-06-12T17:06:58 | 2024-09-08T04:16:12 | 2024-09-07T20:41:52Z | CONTRIBUTOR | {
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} | How it deals with spins is not through magmoms, but FHI-aims uses magmoms exclusively
## Summary
Modifying FHI-aims inputs to work with the magnetism workflows in atomate2
## Todos
If this is work in progress, what else needs to be done?
## Checklist
- [x] Google format doc strings added. Check with `... | {
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"Thanks @kavanase, happy to merge this once the tests are updated. Really appreciate the detailed issue description.",
"If I understand correctly, this does not fix the issue of the inaccurate CBM itself however?",
"Hi @mkhorton, yes this doesn't fix the issue of the inaccurate CBM, but just makes the calculati... | 2024-06-15T20:07:53 | 2024-09-10T13:18:01 | 2024-08-31T05:45:47Z | CONTRIBUTOR | {
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} | `FermiDos.get_doping` performs an integral over the density of states with the Fermi Dirac occupations to determine the carrier concentrations. However, it starts the conduction band integral (`cb_integral`) from `self.idx_cbm` and vice versa with `self.idx_vbm` for the valence band integral.
But, these attributes ... | {
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"@janosh Apologize for trying to mess up your weekend, just ping you to get this tracked as well and no rush at all. Thanks!",
"Thanks! Have a nice weekend ahead!"
] | 2024-06-16T02:40:13 | 2024-08-09T00:11:56 | 2024-08-03T15:53:36Z | CONTRIBUTOR | {
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} | ## Summary
- Improve types and docstring cleanups for (follow up of #3873):
- `electronic_structure.core`
- `electronic_structure.dos`
- Nest private `classmethod` (which should not be `classmethod` but `staticmethod`) `get_transformation_matrix` inside `get_moment` method 2843854ea848a5a21898593a26acd8d... | {
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"See https://numpy.org/devdocs/numpy_2_0_migration_guide.html#numpy-2-migration-guide for summary of possibly required changes"
] | 2024-06-16T14:27:21 | 2024-06-16T15:18:59 | 2024-06-16T15:18:59Z | CONTRIBUTOR | {
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} | ### Python version
python 3.11.9
### Pymatgen version
2024.06.10
### Operating system version
Ubuntu (Windows WSL2)
### Current behavior
import `Element` from pymatgen raises an `ImportError`
### Expected Behavior
The import should work.
### Minimal example
```Python
from pymatgen.core import Element
../../... | {
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