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Use convenience exports from `pymatgen/core/__init__.py` where no risk of circular imports
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Add support for parsing orbital moments from OUTCAR
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"@oashour Is this still WIP? If not, can you update the title?",
"@janosh done. The [WIP] tag was mainly because I'm a first-time contributor, and thought there might be some comments, but I have nothing to add to this unless someone spots a problem or possible improvement.",
"sorry this slipped. i forgot this is waiting on maintainer review.\r\n\r\n> However, it's a bit ugly due to the three extra boolean variables. I'm happy to rewrite that entire part to make it more compact.\r\n\r\nif you can do that in a backwards compatible manner, that'd be much apprecciated!",
"I can definitely do that, I only wrote it that way to avoid refactoring too much before talking to you folks. I'll work on this soon.",
"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe `Outcar` class in the `pymatgen` library has been enhanced to support reading and storing orbital moments for each ion in three dimensions (x, y, z). This update includes new attributes and logic for parsing these values from input files. Additionally, the testing suite has been updated to reflect these changes, ensuring that the new functionality is properly verified.\n\n## Changes\n\n| File | Summary of Changes |\n|-------------------------------|--------------------------------------------------------------------------------------------------------|\n| `.../io/vasp/outputs.py` | Updated `Outcar` class to include attributes and logic for handling orbital moments in three dimensions. |\n| `tests/io/vasp/test_outputs.py` | Expanded `test_soc` function to include additional checks for new orbital moment data. |\n\n<!-- walkthrough_end --><!-- This is an auto-generated comment: raw summary by coderabbit.ai -->\n<!--\n\n\npymatgen/io/vasp/outputs.py: ## Short Summary\n\nThe `Outcar` class in `pymatgen/io/vasp/outputs.py` has been updated to include support for reading and storing orbital moments (`orbital_moment`) on each ion as a tuple of dictionaries. Changes include the addition of attributes to store orbital moments in x, y, and z directions, along with the necessary logic to parse and populate these attributes from the input file.\n\n## Alterations to the declarations of exported or public entities\n\n- `class Outcar` in `pymatgen/io/vasp/outputs.py`:\n - Added `orbital_moment (tuple): Orbital moments on each ion as a tuple of dict` attribute.\n\n- `def __init__(self, filename) -> None` method in `class Outcar` in `pymatgen/io/vasp/outputs.py`:\n - Added `orbmom_x = []`, `orbmom_y = []`, `orbmom_z = []` variables.\n - Added `read_orbmom_x = False`, `read_orbmom_y = False`, `read_orbmom_z = False` flags.\n - Updated logic to read and populate `orbmom_x`, `orbmom_y`, `orbmom_z` based on input file content.\n - Added logic to merge x, y, and z components of orbital moments if present.\n - Updated the initialization of `self.orbital_moment` attribute with the parsed orbital moments.\n\n---\n\ntests/io/vasp/test_outputs.py: ## Summary\n\nIn the `test_soc` function of `test_outputs.py`, the `expected_orbmom` variable has been expanded to include additional dictionaries with keys `\"p\"`, `\"d\"`, and `\"tot\"`, each containing `Magmom` instances with specific values for `p`, `d`, and `tot`.\n\n-->\n<!-- end of auto-generated comment: raw summary by coderabbit.ai --><!-- This is an auto-generated comment: short summary by coderabbit.ai -->\n<!--\n\n\n### PR Objectives\n\nThe pull request (PR) number 3463, titled \"Add support for parsing orbital moments from OUTCAR,\" introduces significant enhancements to the `pymatgen` library, specifically within its VASP output parsing capabilities. The primary objective of this PR is to enable the parsing of orbital moments from the OUTCAR file generated by VASP simulations, which is crucial for studies involving magnetization properties in materials science.\n\nKey changes include:\n1. The addition of functionality to parse and store orbital moments for each ion from the OUTCAR file. This involves reading the x, y, and z components of the orbital moments and storing them appropriately.\n2. An update to the existing magnetization parsing tests to include checks for orbital moments using a specific test file (`OUTCAR.NiO_SOC.gz`).\n\nThe contributor has marked this PR as a work-in-progress (WIP) initially due to being a first-time contributor, although the technical implementation is complete. There is an openness to extending the parser to other potential sections of VASP outputs if such sections exist and there is community interest.\n\nAdditionally, the contributor acknowledges that the current implementation introduces additional boolean variables to control the parsing flow, which they admit is somewhat inelegant. They propose a potential refactoring to streamline this aspect, ensuring it remains backward compatible with existing functionalities.\n\n### Comments Summary\n\nThe discussion in the PR comments revolves around the transition of the PR from a WIP status to a ready-to-review state. Janosh, presumably a maintainer or a senior contributor, prompts the PR author, oashour, to update the PR title if it's no longer a WIP. Oashour confirms the readiness of the PR for review, mentioning that the WIP tag was more about being cautious as a new contributor rather than indicating incomplete work.\n\nJanosh acknowledges a delay in the review process and expresses interest in oashour's suggestion to refactor the implementation to reduce the use of additional boolean variables, provided it does not affect backward compatibility. Oashour responds positively, indicating a willingness to undertake this refactoring soon, initially avoiding major changes to ease the review process.\n\n### AI-Generated Summary of Generated Summaries\n\nThe `Outcar` class within `pymatgen/io/vasp/outputs.py` has been enhanced to support the parsing of orbital moments from VASP's OUTCAR files. This enhancement involves the introduction of new attributes (`orbmom_x`, `orbmom_y`, `orbmom_z`) to store the x, y, and z components of orbital moments respectively. Additionally, boolean flags (`read_orbmom_x`, `read_orbmom_y`, `read_orbmom_z`) have been implemented to control the parsing process of these components.\n\nThe parsing logic has been updated to populate these new attributes based on the content found in the OUTCAR file. Once the components are read, they are merged to form a complete representation of the orbital moments, which is then stored in the `orbital_moment` attribute of the `Outcar` class.\n\nCorrespondingly, the test suite for VASP outputs, specifically the `test_soc` function in `tests/io/vasp/test_outputs.py`, has been updated. The `expected_orbmom` variable within this function now includes additional dictionaries with keys representing different orbital contributions (`\"p\"`, `\"d\"`, `\"tot\"`), each associated with specific `Magmom` instances.\n\n### Alterations to the Declarations of Exported or Public Entities\n\n**pymatgen/io/vasp/outputs.py:**\n- **Before Changes:**\n - `class Outcar`:\n - No attributes or logic related to orbital moments.\n\n- **After Changes:**\n - `class Outcar`:\n - Added attributes: `orbital_moment (tuple): Orbital moments on each ion as a tuple of dict`.\n - `def __init__(self, filename) -> None`:\n - Added variables: `orbmom_x = []`, `orbmom_y = []`, `orbmom_z = []`.\n - Added flags: `read_orbmom_x = False`, `read_orbmom_y = False`, `read_orbmom_z = False`.\n - Updated logic to read and populate `orbmom_x`, `orbmom_y`, `orbmom_z` based on input file content.\n - Added logic to merge x, y, and z components of orbital moments if present.\n - Updated the initialization of `self.orbital_moment` attribute with the parsed orbital moments.\n\n-->\n<!-- end of auto-generated comment: short summary by coderabbit.ai -->\n\n---\n\n<details>\n\n<summary>Recent Review Details</summary>\n\n**Configuration used: .coderabbit.yaml**\n**Review profile: CHILL**\n\n<details>\n<summary>Commits</summary>\nFiles that changed from the base of the PR and between 45de1ae50e0dce96e95606bb4d0f8de3d6ced847 and c4b66a73e8cc1797df110b17db0ca5ebde5f5e75.\n</details>\n\n\n<details>\n<summary>Files selected for processing (2)</summary>\n\n* pymatgen/io/vasp/outputs.py (6 hunks)\n* tests/io/vasp/test_outputs.py (1 hunks)\n\n</details>\n\n\n\n\n\n\n\n\n\n\n<details><summary>Additional comments not posted (1)</summary><blockquote>\n<details><summary>pymatgen/io/vasp/outputs.py (1)</summary><blockquote>\n\n`1981-2013`: Check the logic for handling the reading of orbital moments. Ensure that the flags are set and reset correctly to avoid reading errors.\n\n```diff\n- elif clean == \"orbital moment (x)\":\n- orbmom_x = []\n- read_orbmom_x = True\n- read_charge, read_mag_x, read_mag_y, read_mag_z, read_orbmom_y, read_orbmom_z = (\n- False,\n- False,\n- False,\n- False,\n- False,\n- False,\n- )\n- elif clean == \"orbital moment (y)\":\n- orbmom_y = []\n- read_orbmom_y = True\n- read_charge, read_mag_x, read_mag_y, read_mag_z, read_orbmom_x, read_orbmom_z = (\n- False,\n- False,\n- False,\n- False,\n- False,\n- False,\n- )\n- elif clean == \"orbital moment (z)\":\n- orbmom_z = []\n- read_orbmom_z = True\n- read_charge, read_mag_x, read_mag_y, read_mag_z, read_orbmom_x, read_orbmom_y = (\n- False,\n- False,\n- False,\n- False,\n- False,\n- False,\n- )\n+ # Ensure the logic for setting and resetting flags is correct and robust.\n+ # This section needs careful review and potential refactoring for clarity and correctness.\n```\n\n</blockquote></details></blockquote></details>\n\n\n\n</details><!-- commit_ids_reviewed_start -->\n\n<!-- c4b66a73e8cc1797df110b17db0ca5ebde5f5e75 -->\n\n<!-- commit_ids_reviewed_end --><!-- tips_start -->\n\n---\n\nThank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. 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"i just resolved the merge conflicts. @oashour please ping us when this is ready to go",
"@janosh This should be good to go. I'm sorry it took so long--it's been hard to find the time to write the code I actually want to write.\r\n\r\nThe same approach could be used to clean up the code for the magnetization, but that should be done in another PR."
] | 2023-11-09T02:58:04
| 2024-09-22T00:15:55
|
NONE
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## Summary
Major changes:
- Add support for parsing orbital moments from OUTCAR
- Update the magnetization parsing test to check orbital moments from `OUTCAR.NiO_SOC.gz`.
## Todos
I opened this as a WIP since I have not contributed to `pymatgen` before, but it's technically complete. As far as I know, VASP does not write orbital moments anywhere besides `OUTCAR`, but if it does, I'd be happy to implement a parser if there's interest.
To minimize changes, I kept the code style consistent with the magnetization parsing in the `Outcar` class. However, it's a bit ugly due to the three extra boolean variables. I'm happy to rewrite that entire part to make it more compact.
The final thing to note is that the spin contribution to the magnetization is always with respect to `SAXIS` (there's a `#TODO` comment for that in the code), whereas orbital magnetization is always in Cartesian coordinates. Thus, the `saxis` property of the resultant `Magmom` objects for the orbital moments (the default `[0 0 1]`) is correct, but it's not generally correct for the spin contribution to the magnetic moments.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] ~Type annotations included. Check with `mypy`.~ *(none needed)*
- [x] Tests added for new features/fixes.
- [x] ~If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))~ *(not applicable)*
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PR_kwDOACgets5fD0e5
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Module-scoped imports
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"There are good reasons to not use module scope in many instances. E.g., when a function is rarely used.",
"There are 2 more conditions for it to make sense to have function-scoped imports. The import must be expensive and not already in the import tree. I'm looking out for that in these refactors but those 3 conditions almost never coincide."
] | 2023-11-09T17:26:26
| 2023-11-09T20:05:24
|
2023-11-09T18:39:40Z
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MEMBER
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Follow up to #3462.
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`ChargemolAnalysis` auto-download atomic densities if not found
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"closing as no longer on my todo list. unlikely i'll pick this up again."
] | 2023-11-09T17:37:58
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2024-09-04T14:08:55Z
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Related to https://github.com/materialsproject/atomate2/pull/587 and https://github.com/materialsproject/emmet/pull/869.
Pinging @chiang-yuan in case you want to take this over. The tests are still WIP and I didn't do any real-life robustness testing yet. E.g. do we gracefully bail if running on HPC with no network connection?
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Aims bug fixes
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[] | 2023-11-09T19:56:51
| 2023-11-09T20:19:29
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2023-11-09T20:19:29Z
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CONTRIBUTOR
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## Summary
Minor updates to the aims interface that I discovered were necessary when adapting the FHI-aims atomate2 interface to use it.
Major changes:
- feature 1: Default species directory from environment
- fix 1: Parser erroneously referred to atoms in one place
- fix 2: An error message did not use an f-string when it should have
- fix 3: Modify tests to actually test for the spotted errors
- admin 1: added headers to all source files
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets5fFoeG
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Allow Structure.interpolate to extrapolate
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[
"Yep, It's on my to-do list. I'll try to get the tests written by the end of the week.\n\nOn Nov 26, 2023, 5:16 PM, at 5:16 PM, Janosh Riebesell ***@***.***> wrote:\n>@janosh requested changes on this pull request.\n>\n>\n>\n>> @@ -2138,6 +2138,7 @@ def interpolate(\n> interpolate_lattices: bool = False,\n> pbc: bool = True,\n> autosort_tol: float = 0,\n>+ extrapolation: float = 0,\n>\n>Could you add a test for this new keyword?\n>\n>-- \n>Reply to this email directly or view it on GitHub:\n>https://github.com/materialsproject/pymatgen/pull/3467#pullrequestreview-1749446213\n>You are receiving this because you authored the thread.\n>\n>Message ID:\n>***@***.***>\n",
"Tests written",
"Looks good. I fixed that and also added some additions about cell setting & site order consistency to the docstring. If you don't think it belongs or should be in a separate PR, let me know."
] | 2023-11-10T00:28:13
| 2023-11-29T19:21:50
|
2023-11-29T19:21:50Z
|
CONTRIBUTOR
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## Summary
Major changes:
- added optional parameter to allow `Structure.interpolate()` to extrapolate beyond the `end_structure`. The parameter is the fractional amount of extrapolation beyond $q=1$ if $q$ is the normalized interpolation mode amplitude. Thus, `extrapolation=0.5` would produce structures spanning $q \in [0,1.5]$. This is helpful for capturing the outer piece of potential energy wells, e.g., when fitting a Landau model to an 2nd order structural phase transition.
## Todos
Create tests
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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PR_kwDOACgets5fMIAJ
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Hot fix: `pymatgen` package missing `potcar-summary-stats.json.bz2`
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[] | 2023-11-10T22:48:21
| 2023-11-10T23:04:53
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2023-11-10T23:04:53Z
|
MEMBER
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Fixes #3460 (probably).
Also thanks @BowenD-UCB for reporting.
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[Bug report]: pymatgen-2023.11.10 can not work properly
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[
"Seems a new release is needed. It has been fixed I guess on the git repo already.",
"Fixed in #3468 and released in [v2023.11.12](https://github.com/materialsproject/pymatgen/releases/tag/v2023.11.12)."
] | 2023-11-12T06:36:43
| 2023-11-13T03:07:38
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2023-11-13T03:07:12Z
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NONE
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### Problem
I recently update pymatgen using pip and then everything seems to be broken. The main reason is that there is a file missing under pymatgen.io.vasp
```
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/pymatgen/io/vasp/__init__.py", line 10, in <module>
from .inputs import Incar, Kpoints, Poscar, Potcar, PotcarSingle, VaspInput
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/pymatgen/io/vasp/inputs.py", line 1602, in <module>
class PotcarSingle:
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/pymatgen/io/vasp/inputs.py", line 1694, in PotcarSingle
potcar_summary_stats = loadfn(POTCAR_STATS_PATH)
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/monty/serialization.py", line 63, in loadfn
with zopen(fn, "rt") as fp:
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/monty/io.py", line 40, in zopen
return bz2.open(filename, *args, **kwargs)
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/bz2.py", line 319, in open
binary_file = BZ2File(filename, bz_mode, compresslevel=compresslevel)
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/bz2.py", line 85, in __init__
self._fp = _builtin_open(filename, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/pymatgen/io/vasp/potcar_summary_stats.json.bz2
```
Do I need to install anything to make things work?
### Proposed Solution
N/A
### Alternatives
_No response_
|
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PR_kwDOACgets5fPVHK
| 3,470
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Define `PBE64Base.yaml` for new VASP PBE_64 POTCARs
|
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[
"See attached mostly-complete POTCAR benchmark from PBE (2011 - 2022 Materials Project) to PBE_54 to PBE_64 (proposed).\r\n[POTCAR_analysis.xlsx](https://github.com/materialsproject/pymatgen/files/13369140/POTCAR_analysis.xlsx)\r\n\r\n",
"See https://github.com/materialsproject/pymatgen/discussions/3488 for ongoing discussion of potential PBE 6.4 PSP changes."
] | 2023-11-12T18:16:39
| 2023-11-30T15:50:23
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2023-11-15T20:02:36Z
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MEMBER
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Related to #3342.
The only input set affected by this PR is `MatPESStaticSet` (#3254) which now inherits from `PBE64Base`.
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PR_kwDOACgets5fP8HL
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Add `Composition.charge` and `charge_balanced` properties
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[] | 2023-11-13T01:07:58
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2023-11-13T01:23:07Z
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c47cf6d6c breaking: add `Substitutor.charge_balanced_tol: float = 1e-9` used in `_is_charge_balanced()`, prev had to be strictly 0
5945e95d5 refactor
723a56209 `Composition` add properties `charge` and `charge_balanced`
c5f8c7b71 Add `TestComposition.test_is_charge_balanced`
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PR_kwDOACgets5fbB_k
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Fix weak `__str__` tests across pymatgen
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Replace tests 'str(x) is not None' with actual expected value
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[] | 2023-11-15T00:33:44
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2023-11-15T04:26:24Z
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CONTRIBUTOR
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this will close #3465
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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[
"@janosh I use monkeypatch to mock the class method directly (rather than through module namespace) and add `fake_path` to `atomic_densities_path` to force the mock download function to be called. I think this work minimally already. Let me know what you think.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/65eb4fe1a59a23bbbbc2ccfe931c75ef29f64905/tests/command_line/test_chargemol_caller.py#L140",
"@chiang-yuan I would like to merge this, but no tests are being run for some reason. Only pre-commit was run. Pls make sure the test suite is run properly. Thanks.",
"@shyuep sorry this is a bit old and I am not sure why we need to test fake download as that does not really test if we download the file but mocks it offline. I could take care of autodownloads with #3778 together and the test there will really download chargmol during CI workflow",
"i'll close this for the same reason as #3465 (i.e. stalled). feel free to re-open if you want to resolve merge conflicts @chiang-yuan."
] | 2023-11-15T04:59:35
| 2024-09-04T14:11:04
|
2024-09-04T14:11:03Z
|
CONTRIBUTOR
|
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|
Try to close #3465
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] ~~If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))~~
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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PR_kwDOACgets5ffwjV
| 3,475
|
Aims stress voigt to 3x3
|
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[
"Closing to remove irrelevant changes"
] | 2023-11-15T09:06:11
| 2023-11-15T09:06:49
|
2023-11-15T09:06:49Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- fix 1: FHI-aims stress properties are now 3x3 matrices
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets5ffxmI
| 3,476
|
Convert all FHI-aims stresses to be 3x3 instead of Voigt notation
|
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[] | 2023-11-15T09:09:09
| 2023-11-21T16:42:54
|
2023-11-21T16:42:53Z
|
CONTRIBUTOR
|
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Previously used voigt
## Summary
Major changes:
- fix 1: all stresses are 3x3 now
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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PR_kwDOACgets5ftjXR
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Improve doc strings substitution_probability.py
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[] | 2023-11-17T06:45:13
| 2023-11-17T14:54:10
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2023-11-17T14:54:10Z
|
MEMBER
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## Summary
Just saw this inconsistency by chance. The doc string claims the input are structures but then `get_el_sp` is used on the object.
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PR_kwDOACgets5fyoBQ
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`(Structure|Molecule).alphabetical_formula`
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fc7d8dba2 fix AssertionError assert structure # for mypy
cbb44a235 fix PhononDosPlotter.get_plot only ax.set_ylim if relevant_y is non-empty
77191b672 PhononDosPlotter.get_plot add legend keyword to customize legend
1cee2f5e4 Add alphabetical_formula property to SiteCollection class
5f2d7bf55 add TestIStructure.test_alphabetical_formula
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Improvements to `PhononDosPlotter` and `PhononBSPlotter`
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6bb14f9e4 PhononDosPlotter.get_plot add legend keyword to customize legend
df68ddccc improve UX by preventing common user mistake in PhononDosPlotter passing DOS as 1st arg
42459489d Remove debug logging statements in PhononBSPlotter._make_ticks
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8f72e6566 fix phonon/test_dos.py test class names
c4ebf6037 better variable names
16d236a87 add PhononDos.__repr__ method and test it
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Bond Valence equation error
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[
"The bond valence values are coupled to statistics related to the oxidation states. Even if the value might not be correct, we would need to keep it consistent with the model for the oxidation states. Thus, a potential solution would be much more complex.",
"In any case, thank you for pointing this out.",
"@shyuep Do you maybe have more insight into the development of this method and potential reasons for the difference between paper and implementation? (The scale factor alone does not make up for the deviation but I haven't checked all of the ionic radii and potential scaling there)",
"To be honest, this is so long ago that I don't really remember. If I don't recall wrongly, the actual implementation was based on the work of Stefan Adams (on using BV to calculate diffusion pathways) and my hazy memory suggests that one of Stefan's work provided the value of 0.37 and I confirmed it verbally with him. But feel free to check his work. It is also possible this was an implementation error. But I don't really think the values make that huge a difference in qualitative analyses, and BV is ultimately a highly empirical method.",
"We could add a note that this discrepancy of 0.31 and 0.37 exists or make it adjustable, but as the oxidation state estimator depends on this method, we cannot really change the default without causing a major mess. 0.31 that is implemented here, is the constant suggested by Pauling but not the one that shows up in later work (0.37).\r\n\r\n@shyuep opinions?",
"However, I am also still not getting the bond valance parameters in the file. According to the paper, there should also be an oxidation state dependency. Maybe, it is indeed an adapted model. I don't really have time to investigate in more detail.",
"I could get a couple of words in edgewise. As far as I understand the 0.37<>0.31 substitution is just a mistake because of the explanation in the text written not enough clearly and coincidental mentioning of the very old work of Pauling where he used b=0.31 in the next sentence. When skimming through the text, one can easily perceive 0.31 as the b parameter of the equation used in the cited work.\r\n\r\nThe dependence on the oxidation state indeed exists, but it is really small and only for some bonds it is significant, like those mentioned in the article: \"_Omitted were data for the following bonds: O-F, O-O, F-F, Cu-O, Cu-F Ag-O, and Ag-F. R for the first three are much longer (by about 0.2 A) than predicted; R for the last four are known to depend strongly on the oxidation state of the metal and they are also significantly longer than predicted_\".\r\n\r\nThe whole method presented in the paper is devoted to finding R BV parameter (in the form R =ri + rj - f(ci,cj,ri,rj)) for bonds to electronegative elements. The b parameter though is fixed at 0.37, since many empirical R values for bonds are derived with the same b=0.37 BV parameter. Quote from the article: \"_We used 600 values of R determined from crystal and molecular structures for bonds to as many as 16 different “electronegative\" elements and found the best values of c and r that minimized the squared deviation of the calculated and observed values of R for 75 elements._\" Again, no oxidation state dependence is envisaged, which makes this approach universal.",
"Thanks for clarifying! (Sorry for just skimming through the paper)\r\n\r\nWe still have the issue that the subsequent oxidation state model is based on old parameters. ",
"@trioxane Are the parameters listed here agreeing with the publication from 1991? \r\n\r\n[`pymatgen/analysis/bvparam_1991.yaml`](https://github.com/materialsproject/pymatgen/blob/ec750ca15d02cdd51b0c0a7a4408af8e0d259223/pymatgen/analysis/bvparam_1991.yaml)",
"Yes, these are the _r_ and _c_ parameters from the Table 1 in the cited article used for calculating R values for different bonds to electronegative elements.",
"I also went back to the implementation and especially the documentation of the oxidation state predictor. \r\n\r\nAs far as I understand, the oxidation states are estimated by a Naive Bayes estimator. The p(bv/ox_state) is estimated by a 1d normal distribution and p(ox_state) is simply the relative frequency of the ox_state. Then, one uses the bond valence sum to get the probabilities. I assume that the gaussian normal distribution for each oxstate has been computed by getting the mean bond valence sum and also the standard deviation (but this isn't exactly clear). Thus, a naive Bayes classifier.\r\n\r\nThe documentation calls it a \"maximum a posteriori estimation method\". I would like to replace this with \"Naive Bayes classifier\".\r\nhttps://github.com/materialsproject/pymatgen/blob/ac8a7e9cd93ba9f7afeaced45dc28af6d4e151d4/pymatgen/analysis/bond_valence.py#L104\r\n\r\nThe documentation seems to mix up posterior and prior here: https://github.com/materialsproject/pymatgen/blob/ac8a7e9cd93ba9f7afeaced45dc28af6d4e151d4/pymatgen/analysis/bond_valence.py#L113\r\n\r\n@shyuep do you maybe remember more details? If you agree, I would at least like to update the documentation and maybe also add a warning about the 0.31 somewhere in the documentation of the code.",
"I haven’t caught up with this issue yet, but wanted to raise awareness that there are much newer datafiles of bond valence parameters available from the IUCr:\r\n\r\nhttps://www.iucr.org/resources/data/datasets/bond-valence-parameters",
"Similar to the mentioned issue above (wrong b value), this would mean recomputing the classifier again (or using the model with different parameters?). I have also no real feeling if these changes will affect the classifier much.",
"I know this is not really an urgent matter, but as this oxidation state predictor is an important part of many subsequent codes, the MP website, it might be good to adapt the documentation. Happy to do it. I just want to know that I didn't misunderstood the method."
] | 2023-11-19T16:39:11
| 2024-02-03T12:39:23
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NONE
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### Problem
In the `pymatgen/pymatgen/analysis/bond_valence.py` module in the two functions `calculate_bv_sum `and `calculate_bv_sum_unordered` there is an error in the value of `b` parameter of the BV equation. In the two functions the BV for a given bond is calculated as `vij = exp((R - nn.nn_distance * scale_factor) / 0.31)` with `b` parameter written as 0.31, though the original [paper](https://pubs.acs.org/doi/pdf/10.1021/ja00009a002) reads "Here b is commonly taken to be a “universal” constant equal to 0.37 Á; we use this equation with this value of b throughout."
### Proposed Solution
Just substitute 0.31 with 0.37 in the equation
### Alternatives
_No response_
|
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Q-Chem: `QCInput` could handle `JOBTYPE` better in various ways
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[] | 2023-11-21T07:55:18
| 2023-11-21T08:32:18
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## Problem
### Part 1
https://github.com/materialsproject/pymatgen/blob/c8154cd5c1591734795232b1c7be581417f270b5/pymatgen/io/qchem/inputs.py#L178-L188
The list of valid job types in `QCInput` does not include all the valid ones that Q-Chem takes. I must admit, I don't really know why Pymatgen is bothering with checking the validity of the input flags (seems out of scope), but regardless, there are several missing.
### Part 2
Also, `QCInput` will [raise a `ValueError`](https://github.com/materialsproject/pymatgen/blob/c8154cd5c1591734795232b1c7be581417f270b5/pymatgen/io/qchem/inputs.py#L194-L195) if no job type is specified, but the default value in Q-Chem is "SP". So, `QCInput` should still be able to write an input file if no job type is explicitly specified by the user.
### Part 3
EDIT: I guess this is more just me being pedantic. Let's ignore this one.
The appropriate name for the job type according to the Q-Chem manual is `JOBTYPE` (case-insensitive). However, `QCInput` internally uses `job_type` (with the underscore). To make sure `QCInput` handles things appropriately, it will automatically convert `jobtype` to `job_type`. This is, in principle, fine. However, one would expect that the written input file would revert back to what the Q-Chem manual states, which is `jobtype` without the underscore. `QCInput` does not do this.
Yes, this is minor, but I found this incredibly confusing as a new user of `QCInput` but existing user of Q-Chem itself. Presumably, Q-Chem ignores the underscores, although I was not aware of this since it doesn't seem to be documented anywhere.
## Proposed Solution
### Part 1
Add support for additional job types listed in the above table. While `QCInput` might not actually support all the various features, there are several job types that are valid and missing, e.g. "SINGLE_POINT" as a synonym to "SP". If some are not explicitly supported by `QCInput`, a different error should be raised specifically for those.
### Part 2
Allow for no job type at all (i.e. effectively a single point).
### Part 3
In the `__str__` method of `QCInput`, switch back to using `jobtype` to be in alignment with the Q-Chem manual.
### Alternatives
_No response_
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Aims input sets
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[
"Is there something I have to do in my personal fork to prevent the VASP errors when running the CI tests?",
"@tpurcell90 This error is genuinely yours:\r\n\r\n```py\r\n properties = (\"energy\", \"free_energy\", \"forces\")\r\n \r\n in_set = AimsInputSet(parameters, Si, properties)\r\n assert check_file(geometry_in_str, in_set.geometry_in.get_str())\r\n assert check_file(control_in_str, in_set.control_in.get_str())\r\n> assert parameters_json_str == in_set.parameters_json\r\nE assert '{\\n \"xc\": \"... 2\\n ]\\n}' == '{\\n \"xc\": \"... 2\\n ]\\n}'\r\nE {\r\nE \"xc\": \"pbe\",\r\nE - \"species_dir\": \"D:\\\\a\\\\pymatgen\\\\pymatgen\\\\tests\\\\io\\\\aims\\\\species_directory\\\\light\",\r\nE ? - - - - - - - -\r\nE + \"species_dir\": \"D:\\a\\pymatgen\\pymatgen\\tests\\io\\aims\\species_directory\\light\",\r\nE \"k_grid\": [\r\nE 2,\r\nE 2,\r\nE 2\r\nE ]\r\nE }\r\n\r\ntests\\io\\aims\\test_input_set.py:278: AssertionError\r\n```\r\n\r\nThe others are also on the `master` branch and something I need to find time to fix. Nothing to worry about.",
"I moved in all of the input generator stuff from atomate2 into here.\r\n\r\nShould I make a separate conftest file for aims?",
"I just saw the windows error If this does not pass I will try to compile everything on windows and see what I need to do to solve it. ",
"everything should now be ready for review",
"Ready to merge?",
"Do I need to make any changes to the code?",
"@tpurcell90 Thanks for this contribution and sorry for the slow reply. I haven't had time to review this lately. I hope I'll get to it this week. Feel free to ping.",
"No worries, I know this time of year can be busy",
"> do we actually need this many new test files? are they all needed to test separate functionality?\r\n> \r\n> left a few comments in the code\r\n\r\nThe tests are for all possible InputSet combinations to make sure none of the corner cases break\r\n\r\nEdit: Made the corrections to the code",
"Ready to merge?",
"while i really appreciate the thorough test coverage, i'm a bit reluctant to merge so many new test files. most of them are small which makes them unproblematic but several like `tests/io/aims/aims_input_generator_ref/relax-default-sd-si/aims.out.gz` are ~50KB. still not a huge deal but you sure there's no redundancy among them?",
"> while i really appreciate the thorough test coverage, i'm a bit reluctant to merge so many new test files. most of them are small which makes them unproblematic but several like `tests/io/aims/aims_input_generator_ref/relax-default-sd-si/aims.out.gz` are ~50KB. still not a huge deal but you sure there's no redundancy among them?\r\n\r\nI have condensed down the test files as much as possible without harming the coverage. ",
"Huge thank you from a frequent pymatgen user for this large amount of work, @tpurcell90 !"
] | 2023-11-21T17:38:34
| 2024-01-29T17:12:51
|
2024-01-29T16:50:57Z
|
CONTRIBUTOR
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## Summary
Adds the `aims_input_set` from atomate2 into pymatgen
Major changes:
- feature 1: AimsInputSet is now here
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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Add gradient, Hessian, and orbital coeffs scratch file parsers to `pymatgen.io.qchem.outputs`
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"@janosh: This should be ready for review. As I mentioned above, this code was largely written by @samblau --- I added some simple tests and cleaned up the linting errors. Longer term, it would probably make sense to create a new `QCScratch(MSONable)` class that parses scratch files in a directory. However, I have not implemented that here (unless you feel it necessary).",
"@janosh: Thanks! I gzip'd the files. Should be good to go from my end at least :)",
"@janosh: All good now!"
] | 2023-11-26T06:16:40
| 2023-12-19T01:05:15
|
2023-12-02T21:57:42Z
|
MEMBER
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## Summary
This PR adds function to `pymatgen.io.qchem.outputs` to parse (scratch) gradient, Hessian, and previous orbital coefficient files made by Q-Chem.
**Note**: 99% of the credit for this goes to @samblau. I am simply moving it into pymatgen where it belongs.
## Todos
I need to add tests. There are also some things that are definitely better done with numpy vectorization, but it's not a huge issue.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Standardise and update VASP input sets
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[
"Thanks, this is great stuff (as usual)!🥇 \r\n\r\n> Previously, respecting `user_incar_settings` was left down to specific input set implementations and there were a number of examples where this was not respected\r\n\r\nDo you think this needs better test coverage? In general, just having looked at the whole code and knowing `atomate2`, any parts that stand out as having particularly poor test coverage? Happy to help write more tests.",
"Just wanted to say thank you for this! Both from pymatgen and atomate2 perspective!",
"Just to note that the remaining failing tests are also failing on the master branch currently, and not to do with this PR (seems like it is missing PBE64 potcars).",
"Thank you for this! \r\nI do have a question tho---do you think the existing tests are sufficient to ensure that these changes truly do not break anyone's code/expectations? Or should more testing be added?",
"> do you think the existing tests are sufficient to ensure that these changes truly do not break anyone's code/expectations? \r\n\r\nThat is a good question. It is almost impossible to catch all edge cases. That said, we could probably develop a quick testing suite that generates input files using the old input sets for a range of structures and options and then compares them to the new input sets.\r\n\r\nI would very much appreciate help with this if possible.",
"> Just to note that the remaining failing tests are also failing on the master branch currently, and not to do with this PR (seems like it is missing PBE64 potcars).\r\n\r\nJust pushed a fix (816cd3af75be0040defa631de0733b91663882ac) for the failing test on `master`. (CC @esoteric-ephemera)\r\n\r\n> I would very much appreciate help with this if possible.\r\n\r\nIs this otherwise ready to go from your side? I.e. is now the time to add tests?",
"> Is this otherwise ready to go from your side? I.e. is now the time to add tests?\r\n\r\nYes, from my point of view this should be ready for more testing. I just added some commits that aim to minimise the diff.",
"Hello everyone,\r\n\r\nThanks for this @utf, I think it's very good work and a very good way forward to merge the two input sets implementations lying respectively in pymatgen and atomate2 and I definitely agree with the need to **not** have two different implementations of the input generators/sets.\r\n\r\nI have a couple of questions and/or comments though, no idea if any of this can be addressed in any way.\r\n\r\n1. Are all the input generators in atomate2 gonna be in pymatgen ultimately ? In this PR, the ones already existing in pymatgen have been modified so that, as you mention a/ they are backward-compatible in pymatgen, b/ they can be used in atomate1 and c/ they can be used in atomate2. I did not test that but I trust you on this ;)\r\n2. The current input generators (and input sets) in atomate2 follow the abstract interface defined in pymatgen/io/core (not only vasp, also CP2K, abinit/ongoing PR, aims/ongoing PR, Qchem/ongoing PR). Here the vasp input sets will work due to some part being duck typed wrt the pymatgen.io.core generator/set interface (e.g. the VaspInput returned by get_input_set, is not an InputSet as defined in the InputGenerator interface, hence it works \"only\" because VaspInput also has a write_input method). I would think that it is good to have an overall standard as much as possible there, which is even more important with all the ongoing work being done in atomate2 for having common workflows (elastic workflow, phonons, ... which can be done using \"any\" code following the \"contract). Would it be possible to have VaspInput be a subclass of InputSet ?\r\n3. The naming (and probably this is to keep full backward compatibility in pymatgen, no idea if something can be done there) can be confusing for the user in atomate2: a job maker in atomate2 requires an input_set_generator as an argument and will be passed an object called a \"VaspInputSet\". (Side note on this: pymatgen vasp input sets have always been of great use to many people, but I always found the name weird, a set of inputs, to me is a set of inputs, and it could be generated manually or automatically, through a generator or a factory or else...). Note that my main point here is on the VaspInputSet name, not the VaspInput. If something were to be made possible here, I would prefer having VaspInputSet being a VaspInputGenerator, and the VaspInput stay as VaspInput (this last one is, I think, not confusing for the user). Anyway again, no idea if this is open to discussion/possible (or e.g. if an alias could be done, so that \"former\" pymatgen users don't need to change their code, and atomate2 users can use the \"new\" name, is it good/bad ? I don't have a strong opinion on that, and it's not up to me anyway :) )\r\n4. Corollary of points 1., 2. and 3., if some specific vasp input generators stay in atomate2 for some reason, and others (more general) are in pymatgen, and both are kind of different (the general ones being \"VaspInputSet\", the specific ones being \"VaspInputGenerator\", I would guess it would add more confusion to the atomate2.\r\n\r\nI understand there has already been many discussions on this topic but maybe some of these questions could be addressed somehow ? (VaspInput becoming a subclass of InputSet and VaspInputSet having \"VaspInputGenerator\" alias ? other ideas ?)\r\n",
"I always assumed the `Set` in `VaspInputSet` came from generating a _set_ of input files (INCAR, POSCAR, ...) but maybe that's wrong.\r\n\r\nI'm open to adding an alias `VaspInputSet` -> `VaspInputGenerator` and deprecating `VaspInputSet`. But I'll let others weigh in as well.",
"Thanks for your thoughts @davidwaroquiers.\r\n\r\n> Are all the input generators in atomate2 gonna be in pymatgen ultimately? \r\n\r\nThat is the goal. If there are some very specialised input sets needed for an atomate2 workflow then potentially they don't have to go in pymatgen. But by and large, the input sets will live in pymatgen and the workflow code will live in atomate2.\r\n\r\n> Would it be possible to have VaspInput be a subclass of InputSet?\r\n\r\nI'm in favour of this, since we have the abstract interface defined and there are a growing number of codes that support it. The downsides to doing this are small as far as I can see and won't require breaking any existing pymatgen code.\r\n\r\n> I would prefer having VaspInputSet being a VaspInputGenerator, and the VaspInput stay as VaspInput\r\n\r\nI understand the logic here but I'm personally against renaming VaspInputSet. I think this will add additional confusion to existing pymatgen users. If necessary we could rename any remaining input sets in atomate2 to match the pymatgen naming, and also optionlly update the `input_set_generator` field on the atomate2 makers (although this last point will be more disruptive).\r\n\r\n> I'm open to adding an alias VaspInputSet -> VaspInputGenerator and deprecating VaspInputSet.\r\n\r\nOn the point of `VaspInputSet`, I think there is a strong case for merging `DictSet` and `VaspInputSet`. Currently, the `VaspInputSet` object is not useable by itself and is only functional when used as a superclass for `DictSet`. This is because the `potcar` property uses the `potcar_symbols` property, which in turn tries to access `self._config_dict` which is only present in `DictSet` subclasses. E.g., see here: https://github.com/materialsproject/pymatgen/blob/a48d541f8f3611b9c1924bf17ae45e0c625796ed/pymatgen/io/vasp/sets.py#L98 \r\n\r\nMy suggestion would be: \r\n- Merge `VaspInputSet` properties and functions into `DictSet`.\r\n- Deprecate `VaspInputSet`.\r\n- Leave `VaspInput` as it is (but make it a subclass of `InputSet`.\r\n\r\nI think this leaves the overall picture cleaner since now there is no confusion between `VaspInput` and `VaspInputSet`.\r\n\r\nOn a separate note, I've found the `pymatgen/io/vasp/sets.py` file to be getting quite enormous (currently 3337 lines). Can we turn sets into a package and have a number of modules (e.g., `base`, `mp`, `mit`, `atomate2`, `mvl`). We can import all the input sets in `sets/__init__.py` so that nobody's code is broken. I'm happy to do that in this PR if others agree.\r\n",
"Go right ahead with the file split! I've been considering merging DictSet and VispInputSet as well so no convincing needed here but was planning to deprecate DictSet. Why keep that?",
"My thought process is that most (if not all) people who have made a custom input set will have subclassed `DictSet` rather than `VaspInputSet` (for the reasons listed above). So keeping `DictSet` will mean their code won't break. E.g., a quick GitHub search brings up:\r\n- https://github.com/SMTG-Bham/doped/blob/1aa49ddb3e3715dc1e07a005d05d8620d3d67975/doped/vasp.py#L102\r\n- https://github.com/henniggroup/MPInterfaces/blob/030f9adcfd4989db6208feaec526561dbc58a670/mpinterfaces/instrument.py#L46\r\n- https://github.com/cmdlab/Hetero2d/blob/bd3371aa098d31bb8d2173febaa56c411ce3f0d3/hetero2d/io/VaspInterfaceSet.py#L36\r\n\r\nI'll just note that the features in this PR will not break these other implementations!",
"I think this is a really important point! ",
"We can have a long deprecation period or even keep `DictSet` around as a permanent alias (though I'm against that) but `DictSet` is a misnomer imo. `VaspInputSet` is clearly a more self-explanatory name.",
"Thanks for the feedback @utf and indeed I agree with trying to be backward compatible with existing code using pymatgen.\r\n\r\nI understand the push towards keeping VaspInputSet (or DictSet for the matter). Still, it confuses me: the VaspInputSet (or the DictSet, if VIS properties and methods are merged into it) has a get_input_set method, which should return a (subclass of) InputSet (i.e. the VaspInput object, currently not a subclass of InputSet). If a change from VaspInputSet (DictSet) to VaspInputGenerator (?) is not on the table, I think it could even be considered to change the pymatgen/io/core interface:\r\n\r\ne.g. InputSet becoming an object called e.g. \"Input\", and InputGenerator becoming an InputSet. That way the InputSet is a \"factory\"/\"generator\" object that returns an Input object. This means modifying all atomate2 generators and sets but I think it decreases confusion (my preference still being on generators being VaspInputGenerators and InputSets being InputSets, although again, I acknowledge the problems for existing users/codes of pymatgen).\r\n\r\nOn a general level, while I agree that backward incompatible changes should be avoided as much as possible, in some cases, it can be beneficial (either from a developer or from a user's perspective). In this case, I would think that having a long deprecation period for VaspInputSet to change it to VaspInputGenerator would have been ok and would be beneficial for both the user (a vasp input generator generates a set of inputs, i.e. a vasp input set/ or just vasp input) and the developer (clear api defined in pymatgen/io/core).\r\n\r\nIn any case, I will of course adhere to the decisions made.",
"Hi @davidwaroquiers, agreed that the naming is confusing. I'll defer to others as to the exact direction taken if deprecations/renaming is to happen.",
"My decision is that I have no problems with having an alias called VaspInputGenerator. But VASPInputSet will not be deprecated. Let's be pragmatic - there are many things we probably want to rename. But deprecation of classes/methods creates headaches and unless there is an actual practical benefit, i.e., a large change in functionality or the API, these should not be done.",
"> My decision is that I have no problems with having an alias called VaspInputGenerator. But VASPInputSet will not be deprecated. Let's be pragmatic - there are many things we probably want to rename. But deprecation of classes/methods creates headaches and unless there is an actual practical benefit, i.e., a large change in functionality or the API, these should not be done.\r\n\r\nHi @shyuep,\r\n\r\n\r\nThanks for providing your input and decision on this. I think an alias would definitely be perfect as it will allow both former users and codes to continue working without changing their implementations/scripts and atomate2 users (or new pymatgen users/codes if they prefer the *Generator naming).\r\n\r\n\r\nBest,",
"We discussed at the atomate2 meeting, I think the plan is for @Zhuoying to add more tests and then propose merging this\r\n",
"@Zhuoying When are the tests going to be done? Surely it does not take several months to write a few tests?",
"In the interest of getting this unstuck I suggest we merge this PR _as is_ (thanks again @utf!) and add tests later _if_ we discover any problems.",
"I - cautious by nature - would like to point out that this is a core functionality of pymatgen. Thus, in my opinion, we should merge it only if we are sure that such bugs are very unlikely. (Decision is up to you all as maintainers, of course!)",
"> Thus, in my opinion, we should merge it only if we are sure that such bugs are very unlikely \r\n\r\nExisting tests are passing which is meaningful since test coverage on VASP IO is decent. IMO we shouldn't hold this PR to higher standards than PMG in general and frankly, bugs are not _that_ unlikely in PMG.",
"> and frankly, bugs are not that unlikely in PMG\r\n\r\ncase in point 386b969 and 882452e",
"(Thanks. I know that there are bugs in pymatgen and that they are not unlikely. Also in my code. 😉 I don't see why this is supporting fewer tests though 😅)\r\n\r\nAs I said, maintainers have to decide. And I even gave a 👍 for the point that existing tests are passing. ",
"> I don't see why this is supporting fewer tests though\r\n\r\nmore test coverage is always good but it seems like no one has time to actually write the tests right now",
"I can support the effort of writing more tests - where do we feel like current test coverage is lacking?\r\n\r\nAlso, does this PR cover the recent atomate2 [PR](https://github.com/materialsproject/atomate2/pull/648) that corrected how dict-like `user_incar_settings` objects are handled?",
"@esoteric-ephemera yes it does!",
"@utf Thanks for the nice PR and @janosh @shyuep Thanks for approving and merging it.\r\nI have submitted another PR #3576 to add tests. We can discuss any controversial default settings under that PR.\r\n\r\n@esoteric-ephemera Thanks for offering the efforts. Any tests on Magmomldau are welcome (currently coverage not very high). Also we are roaming between atomate2 and pymatgen to accommodate the recent changes.\r\n\r\n",
"@esoteric-ephemera @Zhuoying have a look at the output of\r\n\r\n```sh\r\npip install pytest pytest-coverage\r\n# cd into pmg repo\r\npytest tests/io/vasp --cov pymatgen/io/vasp\r\n```\r\n\r\nfor where new tests are most needed:\r\n\r\n```\r\n---------- coverage: platform darwin, python 3.11.7-final-0 ----------\r\nName Stmts Miss Cover\r\n--------------------------------------------------\r\npymatgen/io/vasp/__init__.py 3 0 100%\r\npymatgen/io/vasp/help.py 35 35 0%\r\npymatgen/io/vasp/inputs.py 1074 112 90%\r\npymatgen/io/vasp/optics.py 186 18 90%\r\npymatgen/io/vasp/outputs.py 2351 210 91%\r\npymatgen/io/vasp/sets.py 1204 79 93%\r\n--------------------------------------------------\r\nTOTAL 4853 454 91%\r\n```\r\n\r\nuse `--cov-report html` for an interactive line-by-line browser report"
] | 2023-11-26T22:54:21
| 2024-01-26T12:41:03
|
2024-01-20T07:12:39Z
|
MEMBER
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## Summary
This PR refactors the VASP input sets to make them compatible with atomate2 and fixes some of the issues that have been raised previously.
**This PR does not introduce any breaking changes. The API for the input sets has not changed and pymatgen users can continue to use their existing code.**
The input sets are compatible with pymatgen, atomate1, and atomate2. The most drastic change is that now all input sets are dataclasses. This made addressing the following issues easier and also should make it easier to create new input sets in the future. Note, I did not copy the atomate2 input sets to pymatgen, instead I refactored the pymatgen input sets specifically to avoid any breaking changes.
### Issues addressed
Closes #3492.
In addition to updating the `get_vasp_input` function to allow starting from a previous directory, this PR addresses the following points:
- Clarity: Previously, input set logic was scattered over the `__init__`, `.incar`, `override_from_prev_calc` functions. Some input sets inherited from `DictSet`, some from `MPRelaxSet`, some from `MPStaticSet`. This made it difficult to pin down why a particular setting was getting set. Now, all logic specific to an input set is provided in the `incar_updates` and `kpoints_updates` property functions that define any changes to the base input set config. This function is also used when starting from a previous calculation, so all the logic is in one place.
- Consistency: Previously, respecting `user_incar_settings` was left down to specific input set implementations and there were a number of examples where this was not respected (e.g., see EDIFF setting in `MPStaticSet` or `MPNonSCFSet` where it is not possible to specify MAGMOM through user_incar_settings). Now, `user_incar_settings` is always applied in a standard way and will always take precedence.
- Shared functionality: I noticed that there were a number of features that are shared across multiple input sets but had been re-implemented multiple times. For example, line mode k-point generation for PBE and HSE. I also found that some features, such as automated KSPACING in the Scan input sets might be desired features in other input sets (e.g., static calculations). I've therefore tried to put logic in the base input set where possible to share these common/broadly useful functionalities. Now, If one wants to make a MPScanBS input set, one doesn't need to duplicate the line mode generation logic a third time.
- A minor point, but I found that some similar input sets, like `MPNonSCFSet` and `MPHSEBSSet` did not have feature parity. E.g., `MPNonSCFSet` had optics modes which also make sense for `MPHSEBSSet`. I tried to add feature parity between similar input sets where possible.
- I also found that the `override_from_prev` and `from_prev_calc` were defined repeatedly in most input sets. I therefore moved these functions to the base `DictSet`. I also added an option `inherit_incar` to dict set which can be `True`, `False`, or a list of keys to inherit (as copied from `MatPESSet`). If a class has `inherit_incar` enabled and but uses the `from_prev` function to initialise their input set, the only thing that will get used is the `Structure` from the previous directory and the bandgap information.
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I_kwDOACgets53-rUY
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circular import when importing SpaceGroup
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[] | 2023-11-27T19:07:46
| 2023-11-27T21:34:25
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2023-11-27T21:34:25Z
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CONTRIBUTOR
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@janosh It looks like the issue from #2470 was reintroduced into pymatgen v2023.11.12
To Reproduce:
``` python
from pymatgen.symmetry.groups import SpaceGroup
```
The traceback:
``` python
Traceback (most recent call last):
Cell In[1], line 1
from pymatgen.symmetry.groups import SpaceGroup
File ~\AppData\Local\anaconda3\envs\simmate_dev\Lib\site-packages\pymatgen\symmetry\groups.py:21
from pymatgen.core.operations import SymmOp
File ~\AppData\Local\anaconda3\envs\simmate_dev\Lib\site-packages\pymatgen\core\__init__.py:23
from pymatgen.core.structure import IMolecule as IMolecule
File ~\AppData\Local\anaconda3\envs\simmate_dev\Lib\site-packages\pymatgen\core\structure.py:47
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
File ~\AppData\Local\anaconda3\envs\simmate_dev\Lib\site-packages\pymatgen\symmetry\maggroups.py:17
from pymatgen.symmetry.groups import SymmetryGroup, in_array_list
ImportError: cannot import name 'SymmetryGroup' from partially initialized module 'pymatgen.symmetry.groups' (most likely due to a circular import) (C:\Users\nxj625\AppData\Local\anaconda3\envs\simmate_dev\Lib\site-packages\pymatgen\symmetry\groups.py)
```
As an extra, this code actually works fine in case someone needs a quick-fix:
``` python
from pymatgen.symmetry import groups # dummy import that makes others behave normally
from pymatgen.symmetry.groups import SpaceGroup
```
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PR_kwDOACgets5gegA6
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Revert `pymatgen/symmetry/groups.py` module-scoped `SymmOp` import causing circular import
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[] | 2023-11-27T19:48:47
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2023-11-27T21:34:23Z
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Closes #3485.
Apologies! I broke this in https://github.com/materialsproject/pymatgen/pull/3464.
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`PhononDosPlotter.plot_dos()` add support for existing `plt.Axes`
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Updates for Vasprun with MD simulations
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[] | 2023-12-01T10:12:15
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2023-12-01T21:56:42Z
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CONTRIBUTOR
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## Summary
I propose a few minor changes in the `Vasprun` object when parsing MD simulations and especially those produced with the ML option.
* the `converged_ionic` property was False for an MD simulation. But the check did not seems reasonable for an MD
* the number of steps for a simulation that involves ML MD is not given by the length of `ionic_steps`
* in case of NPT simulation the parsing of stresses for ML MD simulations was missing
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PR_kwDOACgets5hGe9t
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Add multipole parsing for Q-Chem IO
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[
"How does this look, @janosh?",
"I think your most recent proposed changes (particularly the use of str.split() to form the key lists) save a small number of characters at the expense of increasing cognitive load.\r\n\r\nAs long as this gets merged, I don't really care, but at some point I'd love to chat with you about coding style in PMG. Ultimately code needs to be read by human beings; as such, I strongly believe that efficiency (in terms of LOC or characters or whatever) should not be the ultimate goal.\r\n\r\n(For clarity, this critique isn't aimed at your previous requested changes. Using the key lists and enumerate() probably also somewhat increase cognitive load, but in that case I'd say the cleanup was well worth it.)",
"@espottesmith Fair enough reverted in 93078ff. I know @shyuep will definitely agree with you there. I like `str.split` if it avoids multiple line breaks. Personally don't find it hard to read/reason about and the more code fits on one screen height, usually the easier to debug in my experience..."
] | 2023-12-04T21:01:05
| 2023-12-19T01:05:31
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2023-12-05T17:06:58Z
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CONTRIBUTOR
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Minor PR. Just adding electric multipole (up through hexadecapole) parsing for Q-Chem.
Tests for relevant classes pass locally, black and ruff seem happy enough for the files I changes. Didn't check mypy, so here's praying.
|
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Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests
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2024-01-17T08:43:31Z
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CONTRIBUTOR
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- In `io.vasp.outputs`, rewrote the `Vasprun.get_potcars` function to not fail in cases where multiple files named `POTCAR*` are found in the cwd, but only one is actually a POTCAR
- Added fake POTCAR libraries to replace real POTCAR libraries in `tests/files` to stop infringing VASP copyright. Also added a PBE_64 fake POTCAR library to support [PR #3484](https://github.com/materialsproject/pymatgen/pull/3484)
- To resolve #3556 , make `potcar_summary_stats` a private attr of `pymatgen.io.vasp.inputs.PotcarSingle` (rename to `_potcar_summary_stats`)
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I_kwDOACgets54soMg
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`reciprocal_density` not working in `MPHSEBSSet`
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[
"@fraricci Thanks for pointing this out. Your fix needs to be accompanied by a new test so PRs welcome!\r\n\r\n@utf Good example for https://github.com/materialsproject/pymatgen/pull/3484#issuecomment-1826933582",
"Just to note that this was also fixed in #3484 \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/40337f3881b612679f5730b21675e61372d300c4/pymatgen/io/vasp/sets.py#L1587",
"With a test?",
"Nope, definitely need to add a test."
] | 2023-12-04T23:14:19
| 2023-12-06T03:00:52
|
2023-12-06T03:00:52Z
|
CONTRIBUTOR
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```py
In [24]: MPHSEBSSet(structure,mode="Uniform",reciprocal_density=100).reciprocal_density
Out[24]: 50
In [25]: MPHSEBSSet(structure,mode="Uniform",user_kpoints_settings={"reciprocal_density":100}).reciprocal_density
Out[25]: 50
# the only way to get it right
In [26]: MPHSEBSSet(structure,mode="Uniform",user_kpoints_settings={"reciprocal_density":100},reciprocal_density=100).reciprocal_density
Out[26]: 100
```
I think this is due to this flawed implementation in io.vasp.sets
```py
if not reciprocal_density or "reciprocal_density" not in self.user_kpoints_settings:
self.reciprocal_density = 50
else:
self.reciprocal_density = reciprocal_density or self.user_kpoints_settings["reciprocal_density"]
```
here how it should be:
```py
if reciprocal_density or "reciprocal_density" in user_kpoints_settings:
self.reciprocal_density = reciprocal_density or self.user_kpoints_settings["reciprocal_density"]
else:
self.reciprocal_density = 50
```
@janosh do you mind including this fix into one of your next pushes?
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PR_kwDOACgets5hIObC
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Fix pdplotter.show with matplotlib backend
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[
"> Thanks @lbluque! 👍 \n> \n> Can we change this method to return the `ax` (`fig` for plotly)? Don't see a reason not to return. And add a test for the return type?\n\nThat looks like the `get_plot` method already does. This is for the `show` method to display the plot, in which the current implementation only works with the plotly backend. ",
"> That looks like the `get_plot` method already does.\r\n\r\nI know but does it hurt to return anyway? I guess it could actually. I think in Jupyter if some code calls `plt.show()` and you don't assign the returned figure to a variable the cell will render the returned figure and so it would be shown twice? If that's the case then you're right and we shouldn't return.",
"Awesome thanks for adding the tests! lgtm"
] | 2023-12-05T04:44:01
| 2023-12-07T04:31:02
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2023-12-06T22:31:36Z
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CONTRIBUTOR
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## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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[
"Just a general point, there are several approaches to adding interstitial atoms in the [pymatgen-analysis-defects](https://github.com/materialsproject/pymatgen-analysis-defects/) package, including\r\n\r\n- [Voronoi](https://github.com/materialsproject/pymatgen-analysis-defects/blob/aaa68e29ffa84599f306984b0f95eaa212081e8f/pymatgen/analysis/defects/generators.py#L307) and\r\n- [charge based methods](https://github.com/materialsproject/pymatgen-analysis-defects/blob/aaa68e29ffa84599f306984b0f95eaa212081e8f/pymatgen/analysis/defects/generators.py#L397)\r\n\r\n@jmmshn can comment more, but perhaps pymatgen-analysis-defects is a better place for this code?\r\n",
"👍 to all the great suggestions from @Andrew-S-Rosen and @utf.",
"@sheriftawfikabbas there are a couple of helper functions here \r\n\r\nhttps://github.com/materialsproject/pymatgen-analysis-defects/blob/main/pymatgen/analysis/defects/utils.py\r\n\r\nThat might do similar things. Also, I noticed that there is a choice of a 3x3x3 supercell implicit in the code. I think that is something we should avoid doing.\r\nAnd example of how that is handled is here:\r\nhttps://github.com/materialsproject/pymatgen-analysis-defects/blob/main/pymatgen/analysis/defects/supercells.py\r\n",
"I'll go ahead and close this for now.",
"Thanks everyone for the great comments, will apply and resubmit the PR.\r\n",
"@sheriftawfikabbas If the helper functions @jmmshn mentioned don't do the trick, consider submitting the PR to https://github.com/materialsproject/pymatgen-analysis-defects instead.",
"So in my experience, Voronoi doesn't work great but charge density requires additional data. So if this works and is roughly symmetry-aware like the charge density is I think it could be really useful.\r\n\r\nSince this is a density field you can probably just subclass the ChargeInterstitialGenerator. I am curious about whether the minima you find this way will be meaningful but I guess we will wait and see.\r\n\r\nAlso, I agree that this should go into the defects package since the infrastructure for dealing with interstitials is already there.",
"Awesome, will move the code to the defects package and try your suggestion.\r\n",
"Interesting, just found that the [3x3x3] supercell trick was also used in\r\nthe QModel class to overcome the PBC issue\r\n\r\nQuoting\r\nhttps://github.com/materialsproject/pymatgen-analysis-defects/blob/main/pymatgen/analysis/defects/utils.py\r\nlines 286,287:\r\n # Make 3x3x3 supercell\r\n # This is a trick to resolve the periodical boundary issue.\r\n\r\nWill try to find an alternative strategy for that.\r\n\r\nSherif\r\n\r\n\r\nOn Wed, Dec 6, 2023 at 9:42 AM Sherif Abbas <\r\n***@***.***> wrote:\r\n\r\n> Awesome, will move the code to the defects package and try your suggestion.\r\n>\r\n> Sherif\r\n>\r\n> On Wed, Dec 6, 2023 at 9:41 AM Jimmy Shen ***@***.***>\r\n> wrote:\r\n>\r\n>> So in my experience, Voronoi doesn't work great but charge density\r\n>> requires additional data. So if this works and is roughly symmetry-aware\r\n>> like the charge density is I think it could be really useful.\r\n>>\r\n>> Since this is a density field you can probably just subclass the\r\n>> ChargeInterstitialGenerator. I am curious about whether the minima you find\r\n>> this way will be meaningful but I guess we will wait and see.\r\n>>\r\n>> Also, I agree that this should go into the defects package since the\r\n>> infrastructure for dealing with interstitials is already there.\r\n>>\r\n>> —\r\n>> Reply to this email directly, view it on GitHub\r\n>> <https://github.com/materialsproject/pymatgen/pull/3494#issuecomment-1841745681>,\r\n>> or unsubscribe\r\n>> <https://github.com/notifications/unsubscribe-auth/AMWNHORPSQDTRBTZ2YX7O3LYH6PILAVCNFSM6AAAAABAHC7ZDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBRG42DKNRYGE>\r\n>> .\r\n>> You are receiving this because you were mentioned.Message ID:\r\n>> ***@***.***>\r\n>>\r\n>\r\n",
"Oh yeah, I didn't read the initial PR carefully enough. I thought the 3x3x3 was enforced on an output or something. I didn't realized it was to help with finding point at the boundary. Either way it looks like subclassing `ChargeInterstitialGenerator` is what you want.\r\n"
] | 2023-12-05T05:31:55
| 2023-12-05T23:21:24
|
2023-12-05T22:30:07Z
|
NONE
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## Summary
Major changes:
- feature 1: add_interstitial() method
## Todos
Optimisation of the loops for larger structures.
## Checklist
- [x ] Google format doc strings added. Check with `ruff`.
- [x ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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PR_kwDOACgets5hKNhJ
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fix TypeError when attr force_field not exists
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[
"> Can you please add a test for this?\r\n\r\nSure, I have added a test for CombinedData."
] | 2023-12-05T10:24:12
| 2023-12-07T01:53:29
|
2023-12-06T17:28:41Z
|
CONTRIBUTOR
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## Summary
Major changes:
- feature 1: ...
- fix 1: Fix bug "TypeError: argument of type 'NoneType' is not iterable". Not all LammpsData in CombinedData should have attribute force_field, replace this `NoneType` attribute with `[]` to skip unexisting force_field.
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Avoid redirects in `MPRester` requests
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[
"Thanks @janosh! Probably not worth adding tests for it. I'd suggest to either keep it in mind for any new `MPRester.request()` calls or to ensure that `MPRester.request()` always adds a trailing-slash."
] | 2023-12-05T22:21:53
| 2023-12-05T23:05:46
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2023-12-05T23:02:50Z
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MEMBER
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add trailing slash to all MPRester requests to avoid unnecessary redirects
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Test improvements
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MEMBER
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5fe1c8e86f update ruff-pre-commit to v0.1.7
aa89d614e1 fic doc str indent
571f33e5c7 improve test_get_neighbor_list
0ffd0c9743 improve test_ebands_input
fd23063b88 improve asserts in test_get_feff_pot
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PR_kwDOACgets5hPuYy
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fix reciprocal_density in MPHSEBSSet and tests
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This implements the fix proposed in and closes #3492.
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Enforce zval to be an integer to avoid improper syntax in .cri file
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"@janosh is it really always an integer in VASP?",
"VASP manual states it is a REAL value: https://www.vasp.at/wiki/index.php/ZVAL",
"IIUC the issue here is about writing critic2 input files, not parsing of `ZVAL` from VASP files",
"Thanks. Yes, I have seen it now as well. "
] | 2023-12-06T05:44:41
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2024-01-08T10:10:35Z
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CONTRIBUTOR
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| ERROR: type should be string, got "https://github.com/materialsproject/pymatgen/blob/ebd776900edfc45bd3b9f045e1e04db1e2d2752b/pymatgen/command_line/critic2_caller.py#L198C1-L198C17\r\n\r\nMain issue:\r\n**formatting for zval is incorrect, causes failure when running .cri file**\r\n\r\nDefault behavior of the pmg Potcar object that is initialized by the Critic2Caller.from_path() method returns zval as a float rather than an int:\r\n\r\nSource from line 1640 in pymatgen.io.vasp\r\n```python\r\n parse_functions = dict(\r\n LULTRA=_parse_bool,\r\n LUNSCR=_parse_bool,\r\n LCOR=_parse_bool,\r\n LPAW=_parse_bool,\r\n EATOM=_parse_float,\r\n RPACOR=_parse_float,\r\n POMASS=_parse_float,\r\n ZVAL=_parse_float,\r\n```\r\n\r\nWhich causes an error because the float is not converted to int\r\n\r\n```python\r\n if not zpsp:\r\n potcar_path = get_filepath(\r\n \"POTCAR\",\r\n \"Could not find POTCAR, will not be able to calculate charge transfer.\",\r\n path,\r\n suffix,\r\n )\r\n\r\n if potcar_path:\r\n potcar = Potcar.from_file(potcar_path)\r\n zpsp = {p.element: p.zval for p in potcar}\r\n```\r\n\r\nFor anyone with the same issue, remove POTCAR from the directory and pass zpsp as an argument. \r\n\r\nOtherwise you will get a similar error in the output:\r\n\r\n```\r\n%% load int.CHGCAR id chg_int zpsp H 1.0 Au 11.0 C 4.0 S 6.0\r\n\r\nERROR : load int.CHGCAR id chg_int zpsp H 1.0 Au 11.0 C 4.0 S 6.0\r\nERROR (load): wrong syntax in ZPSP\r\n```\r\n\r\n\r\n"
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Enforce `zval` to be an integer to avoid improper syntax in `.cri` file
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[
"Thanks a lot! We need a test for this fix."
] | 2023-12-06T05:53:38
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2024-01-08T10:10:34Z
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Closes #3501.
Formatting for `zval` in Critic2Caller.from_path() method wrote `zval` as a `float` rather than an `int`, causing failure when running `.cri` file.
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Error with Locpot.from_file/Species.from_str
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[
"<b> Update </b>\r\nI noticed I had the same issue when trying to instantiate a Structure from a CONTCAR file... It seems that my compilation of VASP produces a CONTCAR file that features a slash after each element on the 6th line such as ```X/ Y/ Z/``` instead of the usual ```X Y Z```. It works as it should when I remove these slashes.\r\n\r\nI think it would be nice to be able to treat this situation directly in pymatgen."
] | 2023-12-06T10:10:43
| 2023-12-08T15:25:49
|
NONE
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<b> Problem </b>
When I try to instantiate a ```pymatgen.io.vasp.outputs.Locpot``` object from the file, I get an ```IndexError``` from the ```Species.from_str``` call. I am using pymatgen v2023.11.12.
<b> Example </b>
```
Python 3.11.6 | packaged by conda-forge | (main, Oct 3 2023, 10:40:35) [GCC 12.3.0] on linux
>>> from pymatgen.io.vasp import Locpot
>>> Locpot.from_file("LOCPOT")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 3438, in from_file
(poscar, data, data_aug) = VolumetricData.parse_file(filename)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/io/vasp/outputs.py", line 3281, in parse_file
poscar = Poscar.from_str("\n".join(poscar_string))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py", line 432, in from_str
struct = Structure(
^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/core/structure.py", line 3670, in __init__
super().__init__(
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/core/structure.py", line 929, in __init__
site = PeriodicSite(
^^^^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/core/sites.py", line 334, in __init__
species = Composition({get_el_sp(species): 1}) # type: ignore
^^^^^^^^^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/core/periodic_table.py", line 1414, in get_el_sp
return Species.from_str(obj) # type: ignore
^^^^^^^^^^^^^^^^^^^^^
File "/home/vtrinquet/anaconda3/envs/test_pmg/lib/python3.11/site-packages/pymatgen/core/periodic_table.py", line 1051, in from_str
properties = {tokens[0]: ast.literal_eval(tokens[1])}
~~~~~~^^^
IndexError: list index out of range
```
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I_kwDOACgets548QXm
| 3,504
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Order matters for checking equality of structure
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[
"Oh dear, loss of symmetry in `__eq__` is pretty serious, esp. in the core `Structure` class.\r\n@bpuchala Thanks for reporting and thanks for finding the root cause! 🙏 \r\n\r\nI'm in favor of making `Structure.__eq__` more discriminative by promoting `Elements` to `Species` with oxi state 0 so that\r\n\r\n```py\r\nelement_structure == species_structure\r\n>>> False\r\n# and\r\nspecies_structure == element_structure\r\n>>> False\r\n```\r\n\r\n but I'm interested to hear @shyuep and @mkhorton's opinions.\r\n\r\n@bpuchala Would you be able to submit a fix for this that implements the type promotion so we can see if there are any unintended downstream implications?",
"> @bpuchala Would you be able to submit a fix for this that implements the type promotion so we can see if there are any unintended downstream implications?\r\n\r\nSorry, I'm just a user here :)",
"I would just fix Element such that it only equates equal to Element and not Specie. I dislike the ElementBase implementation. I think it overcomplicates matters relative to just a straight Enum.",
"> I would just fix Element such that it only equates equal to Element and not Specie.\r\n\r\nThat's already the case.\r\n\r\n```py\r\nfrom pymatgen.core import Element, Species\r\n\r\nElement('O') == Species('O')\r\n>>> False\r\n```\r\n> I dislike the `ElementBase` implementation. I think it overcomplicates matters relative to just a straight Enum.\r\n\r\nI've said the same thing in the past. IIRC @mkhorton had some reservations about that.",
"@janosh No, that wasn't the case. Species(\"Fe\", 0) == Element(\"Fe\") but Element(\"Fe\") != Species(\"Fe\", 0). That was the whole crux of the issue reported. I already pushed a fix."
] | 2023-12-06T17:31:47
| 2023-12-08T18:51:16
|
2023-12-08T18:46:19Z
|
NONE
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It can matter what is on the left hand side or right hand side of `Structure.__eq__`. For example, the following asserts pass:
```py
from pymatgen.core import IStructure
lattice_vectors = [[5.692, 0.0, 0.0], [0.0, 5.692, 0.0], [0.0, 0.0, 5.692]]
coords_frac = [
[0.0, 0.0, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0],
[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5],
]
element_structure = IStructure(
lattice=lattice_vectors,
species=["Na"] * 4 + ["Cl"] * 4,
coords=coords_frac,
coords_are_cartesian=False,
)
species_structure = IStructure(
lattice=lattice_vectors,
species=["Na+"] * 4 + ["Cl-"] * 4,
coords=coords_frac,
coords_are_cartesian=False,
)
assert element_structure != species_structure
assert species_structure == element_structure
```
This seems to come down to the implementations of `Species.__eq__` vs `ElementBase.__eq__` and how inheritance is handled. `ElementBase.__eq__` uses ``isinstance(other, Element)``, which allows the lhs to be an `Element` and the rhs to be a `Species` with any oxidation state and still return True. I expected that `==` would either in effect convert the Element to a Species with oxidation state 0 before comparison or always return False if the types were not the same, but I'm not sure what the developers intend.
|
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PR_kwDOACgets5heCWa
| 3,505
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`CifParser` only warn about `primitive` default value change to `False` if not passed to `parse_structures` explicitly
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[] | 2023-12-07T22:22:59
| 2023-12-07T22:37:27
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2023-12-07T22:37:26Z
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MEMBER
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This gets rid of unnecessary warnings where the user or `pymatgen` internal code is passing in `primitive=True` or `False` to `CifParser.parse_structures` explicitly and so doesn't need to be warned about a change in default value.
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I_kwDOACgets55GvQP
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|
Vasprun return invalid run type PBE
|
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[] | null |
[
"It appears to me that the `get_correction` method under `pymatgen.entries.compatibility` explicitly requires the `run_type` to be in `{\"GGA\", \"GGA+U\"}`, which in this case the `run_type` is `PBE`. However:https://github.com/materialsproject/pymatgen/blob/1dd74a8479ee700552accea770c3ceda85ef89c9/pymatgen/io/vasp/outputs.py#L612-L630\r\n\r\n I'm not quite familiar with the definations in Pymatgen but it seems `PBE` should be a subset of `GGA`? Is this a compatibility issue?",
"Also noticed the handling of non-GGA `run_type` is inconsistent. In the `get_correction` method of `pymatgen.entries.compatibility` module there is a duplicate check of `run_type`:\r\nhttps://github.com/materialsproject/pymatgen/blob/1dd74a8479ee700552accea770c3ceda85ef89c9/pymatgen/entries/compatibility.py#L468-L482",
"Thanks for raising @DanielYang59, this can be improved and I will reply about proposed changes in #3534 . However, I want to make a note here for posterity. Typically a user should call `process_entries` rather than `get_adjustments` to apply corrections, e.g.:\r\n\r\n```py\r\nfrom pymatgen.io.vasp import Vasprun\r\nfrom pymatgen.entries.compatibility import MaterialsProjectCompatibility\r\nvasprun1 = Vasprun(\"data/mp_1595_vasprun.xml\")\r\nentry1 = vasprun1.get_computed_entry(inc_structure=True)\r\ncompatibility = MaterialsProjectCompatibility()\r\ncompatibility.process_entries(entry1)\r\n```\r\n\r\nThis allows the compatibility class to decide what to do with the entry in the event of a `CompatibilityError` (which can be set via a kwarg to `process_entries`\r\n\r\n```py\r\ndef process_entries(\r\n self,\r\n entries: AnyComputedEntry | list[AnyComputedEntry],\r\n clean: bool = True,\r\n verbose: bool = False,\r\n inplace: bool = True,\r\n on_error: Literal[\"ignore\", \"warn\", \"raise\"] = \"ignore\",\r\n) -> list[AnyComputedEntry]:\r\n \"\"\"Process a sequence of entries with the chosen Compatibility scheme.\r\n\r\n Warning: This method changes entries in place! All changes can be undone and original entries\r\n restored by setting entry.energy_adjustments = [].\r\n\r\n Args:\r\n entries (AnyComputedEntry | list[AnyComputedEntry]): A sequence of\r\n Computed(Structure)Entry objects.\r\n clean (bool): Whether to remove any previously-applied energy adjustments.\r\n If True, all EnergyAdjustment are removed prior to processing the Entry.\r\n Defaults to True.\r\n verbose (bool): Whether to display progress bar for processing multiple entries.\r\n Defaults to False.\r\n inplace (bool): Whether to adjust input entries in place. Defaults to True.\r\n on_error ('ignore' | 'warn' | 'raise'): What to do when get_adjustments(entry)\r\n raises CompatibilityError. Defaults to 'ignore'.\r\n\r\n Returns:\r\n list[AnyComputedEntry]: Adjusted entries. Entries in the original list incompatible with\r\n chosen correction scheme are excluded from the returned list.\r\n \"\"\"\r\n```"
] | 2023-12-08T02:04:59
| 2024-01-08T16:06:42
|
2024-01-08T16:06:42Z
|
NONE
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Hi, I would like to apply the legacy corrections with MaterialsProjectCompatibility. However, an invalid run-type was returned by Vasprun.
```
from pymatgen.io.vasp import Vasprun
from pymatgen.entries.compatibility import MaterialsProjectCompatibility, AnionCorrection
vasprun1 = Vasprun("data/mp_1595_vasprun.xml")
entry1 = vasprun1.get_computed_entry(inc_structure=True)
compatibility = MaterialsProjectCompatibility()
entry_ = compatibility.get_adjustments(entry1)
```
Error
```
CompatibilityError: Entry vasprun-2023-12-08 10:44:39.983016 has invalid run type PBE. Discarding.
```
[mp_1595_vasprun.xml.zip](https://github.com/materialsproject/pymatgen/files/13608078/mp_1595_vasprun.xml.zip)
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PR_kwDOACgets5hnhwA
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`PhononBSPlotter.plot_compare()` add legend labels
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[] | 2023-12-10T17:25:21
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MEMBER
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90a26c5bfd bump actions/setup-python to v5
4d739850b4 add **kwargs to get_plot_gs() to customize ax.plot()
6e56052f00 rename single-letter vars
4e08e01165 add label kwarg PhononBSPlotter and to plot_compare method to show in legend
fe3973805b fix PhononDosPlotter.get_plot dropping default font size when passing **kwargs
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Reduce the lower-bound pin on numpy
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[
"@janosh: I was looking to see if I could lower the numpy bound (i.e. see if the suite still passes)",
"The errors here are not from your `numpy` version change but would have also happened on `master`.\r\n\r\nI just fixed them in https://github.com/materialsproject/pymatgen/pull/3507.",
"@janosh: Yup, just noticed that. Either way, my test was a failure anyway because I was still installing the new numpy version. I could try again and re-open this when I get a minute."
] | 2023-12-10T17:42:37
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2023-12-10T18:55:28Z
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MEMBER
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This is a test to see if the >=1.25.0 is actually needed.
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Add capability for Vasprun to read KPOINTS_OPT data
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[
"> i'm a bit concerned here that the tests pass even if you remove all attributes from\r\n> \r\n> ```python\r\n> @dataclass\r\n> class KpointOptProps:\r\n> \"\"\"Simple container class to store KPOINTS_OPT data in a separate namespace. Used by Vasprun.\"\"\"\r\n> \r\n> tdos: Dos | None = None\r\n> idos: Dos | None = None\r\n> pdos: list | None = None\r\n> efermi: float | None = None\r\n> eigenvalues: dict | None = None\r\n> projected_eigenvalues: dict | None = None\r\n> projected_magnetisation: np.ndarray | None = None\r\n> kpoints: Kpoints | None = None\r\n> actual_kpoints: list | None = None\r\n> actual_kpoints_weights: list | None = None\r\n> dos_has_errors: bool | None = None\r\n> ```\r\n> \r\n> i.e.\r\n> \r\n> ```python\r\n> @dataclass\r\n> class KpointOptProps:\r\n> \"\"\"Simple container class to store KPOINTS_OPT data in a separate namespace. Used by Vasprun.\"\"\"\r\n> ```\r\n> \r\n> works fine too. the attributes help with IDE auto-complete and type checking of course but maybe @bfield1 can think about more stringent tests for this?\r\n> \r\n> either way, merging because of the very long wait time. sorry about that.\r\n\r\nMy rationale was that some vasprun.xml files would not have all that data in them (e.g. if your calculation doesn't have magnetism, it wouldn't have a `projected_magnetisation` field, I don't think. Or if your calculation didn't use `LORBIT`, it won't have any `projected_*` fields). I felt it was safer for the end user if the blank fields returned `None` rather than throwing an `AttributeError`.\r\n\r\nBut I can indeed consider some way to test this behaviour and ensure it acts as expected. I'll open another pull request once I get around to it.\r\n\r\nAnyway, thanks for working with me on this."
] | 2023-12-10T23:04:22
| 2024-02-23T18:55:07
|
2024-02-23T11:23:19Z
|
CONTRIBUTOR
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## Summary
This pull request resolves Issue #3455 , implementing parsing functionality for band structures generated using KPOINTS_OPT.
KPOINTS_OPT is a new VASP feature which provides an alternative method for specifying k-points for hybrid band structures.
The KPOINTS_OPT-related data is now read in by the Vasprun class, and `Vasprun.get_band_structure` defaults to reading the KPOINTS_OPT-based eigenvalues if present.
## Unfinished tasks
- Implement KPOINTS_OPT functionality for density of states. As the DOS is accessed using a property rather than a function, it is unclear what the best interface would be. The current pull request reads and saves the data from `vasprun.xml`, but it doesn't have a convenient getter. Regardless, the other features of this pull request stand without this feature.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
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Fix legend label order in `PhononBSPlotter.plot_compare()`
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2023-12-12T19:24:09Z
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Thanks @JaGeo for noticing! 👍 Added better testing to make sure this won't regress in the future and clearer doc string to avoid confusion.
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Define arithmetic ops `__add__` `__sub__` `__mul__` `__neg__` `__eq__` for `PhononDos` with tests
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b98e12f21a `PhononBSPlotter.plot_compare()` add keyword `on_incompatible: Literal["raise", "warn", "ignore"] = "raise"`
314512682c add return type to `PhononDos` method doc strings
6072af8b2a define arithmetic dunder methods for `PhononDos` `__add__` `__sub__` `__mul__` `__neg__` `__eq__`
47addacb70 test `PhononDos` arithmetic ops and equality in
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Add `pymatgen.io.pwmat` module
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[
"Thanks a lot! This is much appreciated! 👍 \n\nWe also need extensive tests for these three new features.",
"Hi, Janosh. I have made the modifications according to your feedback and further added comments. It is my first PR in github, I'm not familiar with this😂\r\n\r\nPlease check if there are any unreasonable things, i will continue to modify it. \r\n\r\nThanks!🤝",
"Thank you for your guidance and assistance. You are really nice😄. @janosh "
] | 2023-12-13T05:22:45
| 2024-01-18T11:21:42
|
2024-01-18T11:21:42Z
|
CONTRIBUTOR
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## Summary
PWmat is a GPU-accelerated first-principles calculation software developed under the leadership of Professor Lin-wang Wang. I am currently utilizing it for my research project, and in the course of this work, I have written some scripts. I hope to submit them to pymatgen to assist more people in conveniently handling data in the PWmat format. This submission includes only structure file and trajectory file, and I plan to continue developing code for other input and output files in subsequent submissions.
Major changes:
- feature 1: Add `pymatgen.io.pwmat.inputs.AtomConfig` which is input/output structure file, work as POCAR in vasp.
- feature 2: Add `pymatgen.io.pwmat.outputs.Movement` which is trajectory file generated when running MD.
- feature 3: Add pwmat fmt within Structure.from_file() and Structure.from_str().
- feature 4: Add object for output files of PWmat: OUT.FERMI, REPORT, DOS.totalspin and so on.
## Todos
In the future, I will contribute code processing other input and output files for PWmat.
|
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I_kwDOACgets55jwS2
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Zeo++ installation
|
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[
"Unfortunately this is very old code that few people uses. You will need to contact the Zeo++ developers on this as we do not support Zeo++ directly.",
"However, the related description of `Zeo++` still appears in the current [document](https://pymatgen.org/installation.html):\r\n\r\n> Zeo++: For defect structure generation. This is required in addition to installing the zeo Python package.\r\n> [...]\r\n\r\n> Zeo++\r\n> \r\n> If you use the defects analysis package, you will need to install Zeo++.\r\n> \r\n> The download and installation instructions for Zeo++ can be found here: http://www.zeoplusplus.org/"
] | 2023-12-13T10:33:56
| 2024-02-03T06:07:55
|
2023-12-13T16:49:40Z
|
NONE
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Hello,
I would like to use Zeo++ but I had some problems with the installation. The installation instruction seems to be missing from the documentation but is available from previous discussions (https://github.com/materialsproject/pymatgen/issues/290).
I had problems with this download command: svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk # password is 'anonsvn'. The error is the following:
`svn: E170013: Unable to connect to a repository at URL 'https://code.lbl.gov/svn/voro/trunk'
svn: E175013: Access to '/svn/voro/trunk' forbidden
`
I also tried to download Zeo++ from this page directly (https://www.zeoplusplus.org/) but I am not sure how to link it to pymatgen. When I have cython, how do I find cython_wrapper and create the binding?
Can you please provide some instructions on this? Thanks a lot in advance.
Best regards,
Xiliang
|
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Equalize `Phonon(Dos|BS)Plotter` colors, allow custom plot settings per-DOS
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[] | 2023-12-13T23:10:53
| 2023-12-14T01:54:18
|
2023-12-14T01:54:17Z
|
MEMBER
|
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669568ba48 make temp optional to allow falling back to t if temp not passed
cb7f2bc4d7 allow passing arbitrary kwargs into PhononDosPlotter.add_dos for use in e.g. color customization
64cd6ced61 change default line colors of PhononDosPlotter and PhononBSPlotter to tab:10
6deff781bd fix overlapping an non-symbol band struct x-labels
|
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I_kwDOACgets55txt8
| 3,515
|
conda-forge version is incompatible with python 3.12
|
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[] | 2023-12-14T16:27:15
| 2023-12-14T16:27:15
|
CONTRIBUTOR
|
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The `conda-forge` version of `pymatgen` is currently not compatible with `python` 3.12, even though this version is supported by pymatgen in general.
Is it possible to update the conda build to track the latest github / `pip` releases?
```
Could not solve for environment specs
The following packages are incompatible
├─ pymatgen is installable with the potential options
│ ├─ pymatgen [2019.10.16|2019.10.3|...|2020.3.2] would require
│ │ └─ python >=3.6,<3.7.0a0 , which can be installed;
│ ├─ pymatgen [2019.10.16|2019.10.3|...|2020.3.2] would require
│ │ └─ python >=3.7,<3.8.0a0 , which can be installed;
│ ├─ pymatgen [2019.11.11|2019.12.22|...|2020.3.2] would require
│ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
│ ├─ pymatgen [2020.10.20|2020.10.9|...|2021.2.8.1] would require
│ │ ├─ python >=3.6,<3.7.0a0 , which can be installed;
│ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ ├─ pymatgen [2020.10.20|2020.10.9|...|2022.1.7] would require
│ │ ├─ python >=3.7,<3.8.0a0 , which can be installed;
│ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ ├─ pymatgen [2020.10.20|2020.10.9|...|2023.8.10] would require
│ │ ├─ python >=3.8,<3.9.0a0 , which can be installed;
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ ├─ pymatgen [2020.10.20|2020.11.11|...|2023.9.25] would require
│ │ ├─ python >=3.9,<3.10.0a0 , which can be installed;
│ │ └─ python_abi 3.9.* *_cp39, which can be installed;
│ ├─ pymatgen [2022.0.16|2022.0.17|...|2023.9.25] would require
│ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
│ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ └─ pymatgen [2022.11.7|2023.05.31|...|2023.9.25] would require
│ ├─ python >=3.11,<3.12.0a0 , which can be installed;
│ └─ python_abi 3.11.* *_cp311, which can be installed;
└─ python 3.12** is uninstallable because there are no viable options
├─ python 3.12.0 conflicts with any installable versions previously reported;
├─ python 3.12.0 would require
│ └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported;
└─ python 3.12.0rc3 would require
└─ _python_rc , which does not exist (perhaps a missing channel).
````
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| 2,042,691,415
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PR_kwDOACgets5iDj7H
| 3,516
|
Add bold flag to `latexify`
|
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[] | 2023-12-15T00:19:11
| 2023-12-15T02:45:50
|
2023-12-15T02:45:49Z
|
MEMBER
|
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LaTeX ignores bold surrounding text for subscripts in math mode so need to specify `\mathbf` explicitly to get bold subscripts.
**Before**
**After (with `bold=True`)**
f91c0195c7 better var names
97cb2efc9b add bold flag to latexify to support bold subscripts
8952c923ab simplify tick generation in PhononBSPlotter._make_ticks
44233e327b add n_bands property to PhononBSPlotter
|
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PR_kwDOACgets5iD9LK
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|
`Composition` raise `ValueError` if `formula` string is only numbers and spaces
|
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[
"Doesn't catch the \"NaN\" -> float(\"NaN\") edge case\r\n\r\n```py\r\n>>> Composition(float(\"NaN\"))\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"pymatgen/pymatgen/core/composition.py\", line 127, in __init__\r\n elem_map = dict(*args, **kwargs) # type: ignore\r\nTypeError: 'float' object is not iterable\r\n>>> float(\"NaN\")\r\nnan\r\n```\r\n\r\nI was going to add another check:\r\n\r\n```python\r\nfrom math import isnan\r\n...\r\n if len(args) == 1 and isinstance(args[0], Composition):\r\n elem_map = args[0]\r\n elif len(args) == 1 and isinstance(args[0], str):\r\n elem_map = self._parse_formula(args[0]) # type: ignore\r\n elif len(args) == 1 and isnan(args[0]):\r\n raise ValueError(\"float('NaN') is not a valid Composition, did you mean str('NaN')?\")\r\n else:\r\n elem_map = dict(*args, **kwargs) # type: ignore\r\n```"
] | 2023-12-15T03:08:07
| 2023-12-15T18:00:27
|
2023-12-15T03:29:14Z
|
MEMBER
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Controlled by new `strict: bool = True` parameter to `_parse_formula`.
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| 2,044,153,587
|
I_kwDOACgets55107z
| 3,518
|
Raise `Composition` `ValueError` when passing `float("NaN")`
|
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[] | 2023-12-15T18:02:13
| 2023-12-15T19:40:28
|
2023-12-15T19:40:28Z
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MEMBER
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#3517 doesn't catch the `"NaN" -> float("NaN")` edge case
```py
>>> Composition(float("NaN"))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pymatgen/pymatgen/core/composition.py", line 127, in __init__
elem_map = dict(*args, **kwargs) # type: ignore
TypeError: 'float' object is not iterable
>>> float("NaN")
nan
```
I was going to add another check:
```python
from math import isnan
...
if len(args) == 1 and isinstance(args[0], Composition):
elem_map = args[0]
elif len(args) == 1 and isinstance(args[0], str):
elem_map = self._parse_formula(args[0]) # type: ignore
elif len(args) == 1 and isnan(args[0]):
raise ValueError("float('NaN') is not a valid Composition, did you mean str('NaN')?")
else:
elem_map = dict(*args, **kwargs) # type: ignore
```
_Originally posted by @CompRhys in https://github.com/materialsproject/pymatgen/issues/3517#issuecomment-1857265305_
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PR_kwDOACgets5iInXe
| 3,519
|
Raise `ValueError` for `float('NaN')` in `Composition`
|
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[] | 2023-12-15T18:17:18
| 2023-12-15T19:40:28
|
2023-12-15T19:40:27Z
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MEMBER
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Closes #3518
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| 2,044,901,533
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PR_kwDOACgets5iLCTk
| 3,520
|
Add `PhononDos.mae()` and `PhononBandStructure.has_imaginary_gamma_freq()` methods
|
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[
"Have you checked the tolerance in detail? I think it might be very tight. Similar for the overall tolerance",
"I just copied the `tol=1e-5` from the existing `has_imaginary_freq` method but use `tol=1e-3` in my own analysis. Should we increase to `tol=1e-3` by default?",
"> I just copied the `tol=1e-5` from the existing `has_imaginary_freq` method but use `tol=1e-3` in my own analysis. Should we increase to `tol=1e-3` by default?\r\n\r\nYes, this would be great! \r\n\r\nI haven't spotted anything else when reading the pull-request. However, I haven't tested it in detail."
] | 2023-12-16T18:49:24
| 2023-12-16T19:58:30
|
2023-12-16T19:58:29Z
|
MEMBER
|
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@JaGeo Would be great to get your review on this, esp. the new `PhononDos.mae()` and `PhononBandStructure.has_imaginary_gamma_freq()` methods.
|
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I_kwDOACgets554-Sd
| 3,521
|
can't install pymatgen==2023.2.28 on Apple Silicon.
|
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[
"Any reason you need to install `2023.2.28`, an outdated version?",
"> Any reason you need to install `2023.2.28`, an outdated version?\n\nThe latest version of \"nomad-lab\" requires it.",
"@KatiGithub https://github.com/nomad-coe/nomad/pull/91 may solve that issue. Feel free to report back here if that's not the case."
] | 2023-12-16T22:20:39
| 2023-12-20T18:25:41
|
2023-12-20T18:25:40Z
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NONE
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Because of a project, I require specifically pymatgen version 2023.2.28.
Specs:
Apple M1 Pro
Python v3.10
The installation process keeps failing at the "building wheel" stage with this error output.
```py
Error compiling Cython file:
------------------------------------------------------------
...
#ensure correct shape
fcoords1, fcoords2 = np.atleast_2d(fcoords1, fcoords2)
pbc = lattice.pbc
cdef int n_pbc = sum(pbc)
cdef int n_pbc_im = 3 ** n_pbc
^
------------------------------------------------------------
pymatgen/util/coord_cython.pyx:93:26: Cannot assign type 'double' to 'int'
Compiling pymatgen/util/coord_cython.pyx because it changed.
[1/1] Cythonizing pymatgen/util/coord_cython.pyx
Traceback (most recent call last):
File "/Volumes/dev/apps.bin/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Volumes/DATA/dev/apps.bin/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Volumes/DATA/dev/apps.bin/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 404, in build_wheel
return self._build_with_temp_dir(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 389, in _build_with_temp_dir
self.run_setup()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 26, in <module>
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/normal/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 368, in run
self.run_command("build")
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 88, in run
_build_ext.run(self)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 249, in build_extension
_build_ext.build_extension(self, ext)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension
new_ext = cythonize(
^^^^^^^^^^
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/private/var/folders/hg/286ym9wj2s1cydsd33_yct7w0000gn/T/pip-build-env-asx1ygx4/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: pymatgen/util/coord_cython.pyx
[end of output]
```
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PR_kwDOACgets5iMIuj
| 3,522
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QCInput: add docstrings for svp and pcm_nonels
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[
"Thanks @rkingsbury! 👍 "
] | 2023-12-17T15:08:43
| 2024-10-10T01:55:03
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2023-12-17T15:47:55Z
|
CONTRIBUTOR
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## Summary
Documents the `svp` and `pcm_nonels` kwargs of `QCInput`. Closes #3432
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I_kwDOACgets55_P9O
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NEB label error units
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[] | null |
[
"Could you @Asif-Iqbal-Bhatti please include a minimal code snippet so that I could identify the issue more easily? Which module was used to produce this plot (is it `NEBAnalysis` under `pymatgen.analysis.transition_state`)? Thanks.\r\n\r\nI just looked into the [following code](https://github.com/materialsproject/pymatgen/blob/c67739a902785b6539af297bc237db07055e4c2e/pymatgen/analysis/transition_state.py#L186C1-L195C14) and didn't notice anything suspicious (the code permlink wouldn't render for some reason)\r\n```\r\nif label_barrier:\r\n data = zip(x * scale, y)\r\n barrier = max(data, key=lambda d: d[1])\r\n ax.plot([0, barrier[0]], [barrier[1], barrier[1]], \"k--\")\r\n ax.annotate(\r\n f\"{np.max(y) - np.min(y):.0f} meV\",\r\n xy=(barrier[0] / 2, barrier[1] * 1.02),\r\n xytext=(barrier[0] / 2, barrier[1] * 1.02),\r\n horizontalalignment=\"center\",\r\n )\r\n```\r\n\r\nMeanwhile could you please also let me know your pymatgen version as well (use `pip show pymatgen | grep Version`)?\r\n\r\n",
"i just tested `NEBAnalysis.get_plot()` locally and get the correct value in the barrier label.\r\n\r\n@Asif-Iqbal-Bhatti does your plot involve post-processing? can you post a code snippet to repro your plot?"
] | 2023-12-18T13:03:42
| 2024-01-22T19:49:32
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2024-01-22T19:49:32Z
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NONE
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Hello,
I want to report that using the NEB analysis object to get the diffusion barrier, there is a label value error on the barrier height. I have attached one of the NEB plots. If you see the y-axis scale and barrier value, it does not make sense. It should be 20.4 meV, not 204 meV.
Asif
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PR_kwDOACgets5iSyE9
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`PhononDos.get_smeared_densities` return unchanged for `sigma=0`
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[] | 2023-12-18T18:34:15
| 2023-12-18T19:01:32
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2023-12-18T18:48:37Z
|
MEMBER
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47fc96b6fd PhononDos.get_smeared_densities add special case for 0 Gaussian smearing
7079c6134c remove unnecessary assignment in test_dos.py
c3681eafa1 test sigma=0 in TestPhononDos.test_get_smeared_densities
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PR_kwDOACgets5iUhui
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Add `PhononDos.get_last_peak()`
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[] | 2023-12-19T00:40:52
| 2023-12-19T00:58:33
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2023-12-19T00:58:32Z
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MEMBER
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New method to find the last peak in the phonon DOS defined as the highest frequency with a DOS value at least `threshold` * height of the overall highest DOS peak. In case no peaks are high enough to match, the threshold is reset to half the height of the second-highest peak.
A peak is any local maximum of the DOS as a function of frequency. Use `dos.get_interpolated_value(peak_freq)` to get density at `peak_freq`.
8f6315dbc9 add PhononDos.get_last_peak()
e3b47947f1 add TestPhononDos.test_get_last_peak
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I_kwDOACgets56Dwpr
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[Feature Request]: Temperature effects in Pourbaix analysis?
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[
"This is a great idea that I'd love to see implemented.\r\nOn Mon, Dec 18, 2023, 6:34 PM Richard Tran ***@***.***> wrote:\r\n\r\n> Problem\r\n>\r\n> At the moment, all analysis in pourbaix_diagram.py assumes that we are\r\n> operating under room temperature. As a result, we assume all free energies\r\n> will have a prefactor of 0.0591 for the pH variable i.e. pH * k_B * T *\r\n> ln(10) (in eV) where T= 298K (RT) and k_B * T * ln(10) = 0.0591.\r\n>\r\n> *Is there a (chemical or implementation) reason why we do not make this\r\n> more generalized by adding a temperature variable in the Pourbaix diagrams?*\r\n>\r\n> Maybe we can set it to a default of T = 298K so the behavior doesn't\r\n> change, but still allow users to modify if they want to analyze aqueous\r\n> electrochemical systems under different temperature conditions? If this is\r\n> reasonable, I can submit a small pull request later to implement\r\n> Proposed Solution\r\n>\r\n> Add a temperature variable that changes the pH prefactor to any method or\r\n> function that uses \"PREFAC\". Default all temperature variables to 298K so\r\n> that the PREFAC value stays at 0.0591 unless the user manually changes\r\n> temperature.\r\n> Alternatives\r\n>\r\n> *No response*\r\n>\r\n> —\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/materialsproject/pymatgen/issues/3526>, or unsubscribe\r\n> <https://github.com/notifications/unsubscribe-auth/ABRRSNHQAZAZZTRFR6OKK4DYKD4KRAVCNFSM6AAAAABA2OSIPWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2DOOBQGYYDKOI>\r\n> .\r\n> You are receiving this because you are subscribed to this thread.Message\r\n> ID: ***@***.***>\r\n>\r\n",
"> This is a great idea that I'd love to see implemented.\r\n> […](#)\r\n> On Mon, Dec 18, 2023, 6:34 PM Richard Tran ***@***.***> wrote: Problem At the moment, all analysis in pourbaix_diagram.py assumes that we are operating under room temperature. As a result, we assume all free energies will have a prefactor of 0.0591 for the pH variable i.e. pH * k_B * T * ln(10) (in eV) where T= 298K (RT) and k_B * T * ln(10) = 0.0591. *Is there a (chemical or implementation) reason why we do not make this more generalized by adding a temperature variable in the Pourbaix diagrams?* Maybe we can set it to a default of T = 298K so the behavior doesn't change, but still allow users to modify if they want to analyze aqueous electrochemical systems under different temperature conditions? If this is reasonable, I can submit a small pull request later to implement Proposed Solution Add a temperature variable that changes the pH prefactor to any method or function that uses \"PREFAC\". Default all temperature variables to 298K so that the PREFAC value stays at 0.0591 unless the user manually changes temperature. Alternatives *No response* — Reply to this email directly, view it on GitHub <#3526>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABRRSNHQAZAZZTRFR6OKK4DYKD4KRAVCNFSM6AAAAABA2OSIPWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2DOOBQGYYDKOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>\r\n\r\nSounds good, I was curious what your thoughts on this was going to be. I'll try to make some time this week to push it through. It shouldn't be too much trouble I think"
] | 2023-12-19T02:34:00
| 2023-12-19T04:36:40
|
CONTRIBUTOR
|
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### Problem
At the moment, all analysis in pourbaix_diagram.py assumes that we are operating under room temperature. As a result, we assume all free energies will have a prefactor of 0.0591 for the pH variable i.e. pH * k_B * T * ln(10) (in eV) where T= 298K (RT) and k_B * T * ln(10) = 0.0591.
**Is there a (chemical or implementation) reason why we do not make this more generalized by adding a temperature variable in the Pourbaix diagrams? e.g. maybe Pourbaix diagrams are for room temperature analysis only and doesn't make sense beyond that temperature?**
Maybe we can set it to a default of T = 298K so the behavior doesn't change, but still allow users to modify if they want to analyze aqueous electrochemical systems under different temperature conditions? If this is reasonable, I can submit a small pull request later to implement
### Proposed Solution
Add a temperature variable that changes the pH prefactor to any method or function that uses "PREFAC". Default all temperature variables to 298K so that the PREFAC value stays at 0.0591 unless the user manually changes temperature.
### Alternatives
_No response_
|
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PR_kwDOACgets5iV6t_
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Fix label propagation in `Symmetry.from_spacegroup`
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[] | 2023-12-19T08:17:59
| 2023-12-19T16:21:17
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2023-12-19T15:56:29Z
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CONTRIBUTOR
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Hi all, another small PR that makes sure labels are passed when a `Symmetry.from_spacegroup` is used. This follows-up on an earlier PR: https://github.com/materialsproject/pymatgen/pull/3183
## Summary
Major changes:
- fix 1: Fix label propagation in `Symmetry.from_spacegroup`
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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Add GitHub Issue Templates
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[
"Changes made accordingly. Thanks for your explainations here.",
"@janosh Thanks for reviewing and the comments. Actually my first time PR, just started to working in the community and would try to keep working with you guys.",
"That sounds great! The more, the merry! 😄 "
] | 2023-12-20T03:20:17
| 2023-12-28T03:03:27
|
2023-12-20T03:48:37Z
|
CONTRIBUTOR
|
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# Summary
This pull request addresses suggestions to solve #3449 by adding two new issue templates.
Major changes:
- Added a new issue template for "Bug Report."
- Included an issue template for "Feature Request," aligning it with the original issue template format.
Please feel free to provide any suggestions or feedback.
|
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https://github.com/materialsproject/pymatgen/pull/3529
| 2,049,764,382
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PR_kwDOACgets5ibdbW
| 3,529
|
Bug fix: SpectrumPlotter.add_spectra
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[
"Hi @janosh, I have added a test in pymatgen.tests.vis.test_plotters\r\n\r\nAlso, I added a line to check the given object has attributes x and y in SpectrumPlotter.add_spectrum. This can directly point out the problem that the given object has no x and y.\r\n\r\n```\r\nassert hasattr(spectrum, \"x\") and hasattr(\r\n spectrum, \"y\"\r\n ), f\"{type(spectrum)} has no attribute x and y, please check!\"\r\n```\r\n\r\nPlease let me know if anything is needed."
] | 2023-12-20T03:22:30
| 2023-12-20T17:43:30
|
2023-12-20T17:43:30Z
|
CONTRIBUTOR
|
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**Original `SpectrumPlotter` in `pymatgen.vis.plotters`**
```python
def add_spectra(self, spectra_dict, key_sort_func=None):
"""
Add a dictionary of doses, with an optional sorting function for the
keys.
Args:
dos_dict: dict of {label: Dos}
key_sort_func: function used to sort the dos_dict keys.
"""
keys = sorted(spectra_dict, key=key_sort_func) if key_sort_func else list(spectra_dict)
for label in keys:
self.add_spectra(label, spectra_dict[label])
```
**Issue 1:**
The original docstring suggests using the Dos object, but attributes x and y were already overridden to energies and densities in Dos, which caused the error:
```
AttributeError: 'Dos' object has no attribute 'x'
```
Although the `DosPlotter` is available to plot DOS, I think this function shouldn't be deprecated because it can still parse `Spectrum`.
**Suggestion 1:**
Update the docstring to reflect Spectrum support.
**Issue 2:**
When I passed in `Spectrum`, it resulted in the error:
```
in add_spectra
keys = sorted(spectra_dict, key=key_sort_func) if key_sort_func else list(spectra_dict)
TypeError: 'XAS' object is not callable
```
**Reason:** Recursive call within the function.
**Suggestion 2:**
Modify:
```python
self.add_spectra(label, spectra_dict[label])
```
to:
```python
self.add_spectrum(label, spectra_dict[label])
```
**Note:**
1. I used similar codes with `pymatgen.tests.vis.test_plotters.py` to test.
```python
from __future__ import annotations
import json
import os
import matplotlib.pyplot as plt
import numpy as np
from monty.json import MontyDecoder
from pymatgen.analysis.xas.spectrum import XAS
from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
from pymatgen.vis.plotters import SpectrumPlotter
from pymatgen.electronic_structure.dos import DOS
test_dir = f"{TEST_FILES_DIR}/spectrum_test"
with open(f"{test_dir}/LiCoO2_k_xanes.json") as fp:
spect_data_dict = json.load(fp, cls=MontyDecoder)
xanes = XAS.from_dict(spect_data_dict)
plotter = SpectrumPlotter(yshift=0.2)
xanes_dict = dict()
xanes_dict["LiCoO2"] = xanes
xanes = xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
xanes_dict["LiCoO2 + noise"] = xanes
xanes_dict["LiCoO2 - replot"] = xanes
plotter.add_spectra(xanes_dict)
ax = plotter.get_plot()
plotter.save_plot('test3.png', img_format='png')
```
2. This is my first time submitting a pull request at Pymatgen. Please let me know if anything is incorrectly formatted or needs improvement. Thank you :)
|
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| 2,051,168,055
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PR_kwDOACgets5igSQu
| 3,530
|
Improve `PhononBandStructure.has_imaginary_gamma_freq()` by checking for negative freqs at all q-points close to Gamma
|
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[] | 2023-12-20T19:47:06
| 2023-12-20T20:17:46
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2023-12-20T20:17:45Z
|
MEMBER
|
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6087d5d90 PhononDos.get_last_peak reduce threshold value from 10% to 5%
8649e793a PhononBandStructure add max_freq() equivalent to min_freq() method
0dd35274e i->idx
d92f0e748 test_bandstructure.py add new test cases for (min|max)_freq
f77779c25 refactor symbol mapping in ExcitingInput and PhononBandStructure
dddd81e8b add get_gamma_point() method to PhononBandStructure
d16e6efa2 add test_get_gamma_point
878ef99b9 big improvement to has_imaginary_gamma_freq: check for negative frequencies at all q-points close to the gamma point, not just the gamma point itself
141679141 fix test_has_imaginary_freq in test_bandstructure.py
ac38d6572 PhononBandStructure add width() method
2b70e03d4 add test_width for PhononBandStructure
|
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PR_kwDOACgets5ihqsQ
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Add default issue template labels
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[
"Good idea, thanks @DanielYang59!",
"Cheers! @janosh "
] | 2023-12-21T02:12:02
| 2023-12-21T02:25:21
|
2023-12-21T02:15:42Z
|
CONTRIBUTOR
|
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# Summary
Add default issue template labels, as I notice most recent issues are not assigned a label by the raiser, and also the prefix was removed as suggested by @janosh in #3528.
- Add default label "bug" for `Report a Bug`.
- Add default label "enhancement" for `Feature Request`.
|
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PR_kwDOACgets5izRzB
| 3,534
|
Fix vasp run type handling for GGA+U scheme
|
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"@janosh Yes sure. I would try to get my hands on that ASAP. \r\n\r\nI adjusted the imports to alphabet order while I was fixing the run type issue, but that commit seems to have been reversed by workflow or something?",
"Imports are auto-sorted by `ruff`. No need to worry about that.",
"Thanks for clarifying @janosh . However I just realize insteading of diving in and removing `raise error` altogether, I would need to figure out **why `PBE` is not considered `GGA` in the first place**. Do you have any idea? Could this be some consistency issue (for example the original code is intended for generate GGA, and then more specific GGA functional names for example PBE are introduced.)\r\n\r\nAs from my understanding, PBE is a specific GGA exchange-correlation functional as defined in:https://github.com/materialsproject/pymatgen/blob/1dd74a8479ee700552accea770c3ceda85ef89c9/pymatgen/io/vasp/outputs.py#L612-L630\r\n\r\nMeanwhile, the Hubbard+U method should work for PBE functional [here](https://www.vasp.at/wiki/index.php/NiO_GGA%2BU) for example, and thus there is no good reason to rule out PBE from GGA+U scheme?",
"> I would need to figure out why PBE is not considered GGA in the first place. Do you have any idea?\r\n\r\n@rkingsbury Might know what the thought process behind this was? Might have something to do with the MP correction scheme only being designed to be applied to MP compatible VASP runs using e.g. `MPRelaxSet`. If we get clarity on this, would be good to leave a code comment to address future questions.",
"Hi @DanielYang59 , thanks for raising this; it should be addressed. However it is important not to change the error into a warning. It's intended that a user calls `process_entries` to apply corrections rather than `get_adjustments`. If called that way, there is a kwarg that defines the behavior when `get_adjustments` raises an error (by default the error is ignored). \r\n\r\nI believe this default causes the entry to be passed through to the returned list, albeit without any energy corrections being applied. See docstring:\r\n\r\n```py\r\ndef process_entries(\r\n self,\r\n entries: AnyComputedEntry | list[AnyComputedEntry],\r\n clean: bool = True,\r\n verbose: bool = False,\r\n inplace: bool = True,\r\n on_error: Literal[\"ignore\", \"warn\", \"raise\"] = \"ignore\",\r\n) -> list[AnyComputedEntry]:\r\n \"\"\"Process a sequence of entries with the chosen Compatibility scheme.\r\n\r\n Warning: This method changes entries in place! All changes can be undone and original entries\r\n restored by setting entry.energy_adjustments = [].\r\n\r\n Args:\r\n entries (AnyComputedEntry | list[AnyComputedEntry]): A sequence of\r\n Computed(Structure)Entry objects.\r\n clean (bool): Whether to remove any previously-applied energy adjustments.\r\n If True, all EnergyAdjustment are removed prior to processing the Entry.\r\n Defaults to True.\r\n verbose (bool): Whether to display progress bar for processing multiple entries.\r\n Defaults to False.\r\n inplace (bool): Whether to adjust input entries in place. Defaults to True.\r\n on_error ('ignore' | 'warn' | 'raise'): What to do when get_adjustments(entry)\r\n raises CompatibilityError. Defaults to 'ignore'.\r\n\r\n Returns:\r\n list[AnyComputedEntry]: Adjusted entries. Entries in the original list incompatible with\r\n chosen correction scheme are excluded from the returned list.\r\n \"\"\"\r\n```\r\n\r\nAs to the core of your question - you are correct that PBE is one type of GGA functional, but within the MP Compatibility classes we often refer to PBE as \"GGA\" and \"PBE+U\" as \"GGA+U\". I suspect this is because we have to return something if there is no explicitly set functional in the INCAR, and VASP defaults to PBE.\r\n\r\nSee my code review comments for my suggested fix (which will need to be confirmed by passing unit tests). I think this is the cleanest way forward.\r\n\r\n",
"Hi @rkingsbury thanks so much for the valuable inputs and suggestions, I will have a look and try to think of a proper improvement for this (as I'm pretty much a beginner). ",
"Thanks @rkingsbury for the explanation! Your fix looks much cleaner than mine (also no need to change the tests). I might close this PR here. Good work!",
"> Thanks @rkingsbury for the explanation! Your fix looks much cleaner than mine (also no need to change the tests). I might close this PR here. Good work!\r\n\r\nThanks @DanielYang59 , I didn't mean to pre-empt you (that's why I didn't open a PR against the upstream repo, just my own fork). I just thought that was the easiest way to explain what I was talking about. If you're up for it, please copy what I have there into your solution, because you were the one that identified this issue, and I like the changes you made to the docstrings!\r\n\r\nWe also need to make sure the tests pass on the upstream CI, which I have not done (I only tested locally).",
"Hi @rkingsbury thanks a lot for that. That's totally alright, you fixed it nice and clean, so the honor should go to you (Janosh revised the type hint for the docstring). There is no reason for me to copy your fix as mine. Also I have already committed the minor changes to the other PR #3539 (would also appreciate it if you could review and put some comments there if possible).\r\n\r\nThe most important thing for me now is that I learned a lot from you and everyone here. Please go ahead to merge the fix. Thanks!"
] | 2023-12-27T02:20:04
| 2024-01-09T01:48:53
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2024-01-04T01:45:20Z
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CONTRIBUTOR
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## Summary
- Fixed inconsistent non-GGA run type handling, to fix #3506.
## Need suggestions from maintainer
As discussed in #3506, the run type of "PBE" is not treated as "GGA" which seems to be inconsistent with the defination in the following part: https://github.com/materialsproject/pymatgen/blob/1dd74a8479ee700552accea770c3ceda85ef89c9/pymatgen/io/vasp/outputs.py#L612-L630
Is this intended, or is it a compatibility issue? I maybe able to help fix it but would need input from maintainers on what is expected.
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Add `PhononDos.r2_score` method
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4ee30c175 add PhononDos.r2_score method
50d7c2e63 add TestPhononDos.test_r2_score
547cb669e better get_linear_interpolated_value err msg
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"also, could you rebase your branch onto pymatgen `master`?",
"I'm really sorry @janosh. I must have been messing with commits trying to rebase and combine my commit history. Should I close this PR and reopen a new one? "
] | 2023-12-31T13:34:01
| 2024-01-01T01:51:00
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2024-01-01T01:51:00Z
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CONTRIBUTOR
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Tasks finished to resolve #2753:
- Added a codespace container configuration file.
- Added a brief guide to use codespace container for issue reproduction.
- Added link in issue template to encourage users to try this new workspace.
However I still need advice on handling user feedbacks, as I failed to identify any way to create a link or share a snapshot to an existing codespace, as @janosh suggested.
> We'd link this codespace in our issue template and invite people to launch it, copy-paste their code into it and then paste the link to the codespace into their issue.
The closest I could find currently is the [Live Share](https://docs.github.com/en/codespaces/developing-in-a-codespace/working-collaboratively-in-a-codespace), which allows multiple users to work on a single codespace in real-time. But I don't think this is what we're looking for though. This would require the user to publicly share a link to a codespace and might have security risks.
So far the best solution to me still remains to run the code in the codespace, and **paste the output back to the issue** manually (until a feature such as sharing a snapshot is out). In doing so, we could help pre-configure the reproduction environment and information collection mechanisms, also avoiding all sorts of non-pymatgen issues (python not installed properly, outdated pymatgen or dependency, and so on).
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"Also to answer your @janosh question in #3536 that:\r\n\r\n> Shouldn't this markdown be part of the issue template?\r\n\r\nMy idea is to keep the issue template clean (and it is not a tutorial at the end of the day), and make codespace optional (instead of \"pushing\" codespace to users). \r\n\r\nHowever it occurs to me that it might be better to move the guidance **figure** into the issue template, and put the introductory stuff into the repro template (if the use follows the figure and open up the codespace, the repro template would be presented)? In doing this we could avoid an extra readme file. What do you think?\r\n\r\nAgain I'm really sorry for messing around with the commit history. But after one hour's experiment I'm now much more confident with git workflow (Just realize could rewrite commit history so reopen a PR is not necessary). Thanks.\r\n",
"> In doing this we could avoid an extra readme file. What do you think?\r\n\r\nyes exactly, i think avoiding an extra readme file which many people might miss would be nice. could you make that change?",
"Done @janosh. I merged the separate guide README.md into the issue template (folded by default to minimize disturbance to the template overall). Let me know if you would like to see more changes.",
"@janosh Look good to me. Good work @janosh. 1 core should suffice.",
"@janosh It seems you might have left the outputs inside the repro template ipynb?\r\n\r\n> date: 2024-01-08\r\n> Python version: 3.11.6\r\n> pymatgen version: 2023.11.12\r\n> pymatgen version: 2023.11.12\r\n\r\nAlso the `Now share the code and outputs in a [new GitHub issue]` seems to point to an empty issue template. Can you please replace the url with `https://github.com/materialsproject/pymatgen/issues/new?assignees=&labels=bug&projects=&template=bug_report.yaml`?\r\n\r\nI wouldn't create a PR just for this on my side. Thanks!",
"Thanks @DanielYang59, good catch! 👍 "
] | 2024-01-01T03:05:36
| 2024-01-26T12:40:31
|
2024-01-08T08:55:23Z
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CONTRIBUTOR
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Tasks finished to resolve #2753 (#3536 is messed up):
- Added a codespace container configuration file.
- Added a brief guide to use codespace container for issue reproduction.
- Added link in issue template to encourage users to try this new workspace.
However I still need advice on handling user feedbacks, as I failed to identify any way to create a link or share a snapshot to an existing codespace, as @janosh suggested.
> We'd link this codespace in our issue template and invite people to launch it, copy-paste their code into it and then paste the link to the codespace into their issue.
The closest I could find currently is the [Live Share](https://docs.github.com/en/codespaces/developing-in-a-codespace/working-collaboratively-in-a-codespace), which allows multiple users to work on a single codespace in real-time. But I don't think this is what we're looking for though. This would require the user to publicly share a link to a codespace and might have security risks.
So far the best solution to me still remains to run the code in the codespace, and **paste the output back to the issue** manually (until a feature such as sharing a codespace snapshot is out). In doing so, we could help pre-configure the reproduction environment and information collection mechanisms, also avoiding all sorts of non-pymatgen issues (python not installed properly, outdated pymatgen or dependency, and so on).
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Unable to parse `LOCPOT` with VASP 6.4.2
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[
"An easy workaround for this issue is to use VASP version 6.4.0.\r\nIf using the newer VASP version 6.4.2, need to update INCAR with `LVTOT = \"False\"` (to not parse from LOCPOT file). This can be done by using `update_user_incar_settings` command.",
"So if I understand correctly, VASP 6.4.2 adds the extra `/` to the LOCPOT, but earlier versions do not? I wonder if this is intended behavior or a bug in VASP 6.4.2. \r\n\r\nUltimately, to fix this we'll need to figure out whether it's an issue with VASP, something to be updated in `TaskDocument`, or something to updated in `pymatgen`. Interested to hear if @janosh or @utf have noticed anything like this.",
"Correct, VASP 6.4.2 adds the extra / to the LOCPOT. It might be because the newer version is intended to work with the newer hash pseudopotentials.",
"@abhardwaj73 Thanks for bringing this up! Just to add some context from @sudarshanv01 (VASP dev) who confirmed the added slash in 6.4.2 as expected behavior:\r\n\r\n> - The slash is part of the LOCPOT header formats, most possible other files that have the same header. They are supposed to be there for labeling the PAW with the SHA number of the potential\r\n> - A potential fix is to change pymatgen parsing to make sure that the atomic species are parsed even if they have the /\r\n\r\n@esoteric-ephemera added\r\n\r\n> we should fix this on the PMG side - it's going to affect CHG*, AECCAR*, and LOCPOT. Anything with charge density parsing will break ",
"Hey @abhardwaj73 , this was hopefully fixed in a pymatgen [PR](https://github.com/materialsproject/pymatgen/pull/3542). Would you be able to install pymatgen from git (`pip install git+https://github.com/materialsproject/pymatgen.git`) and let us know if this is working now?",
"closing as fixed in https://github.com/materialsproject/pymatgen/pull/3542 after migrating issue from `atomate2` to `pymatgen`. new `pymatgen` release coming later this week.",
"Hello @esoteric-ephemera and @janosh, Thanks for your help in resolving these atomate2 issues. I used the `pip install git+https://github.com/materialsproject/pymatgen.git` version to run the `MPMetaGGADoubleRelaxMaker` atomate2 workflow, and got the following error for a FCC Silicon system:\r\n\r\n```\r\n2024-01-25 16:50:31,434 INFO MP pre-relax 1 failed with exception:\r\nTraceback (most recent call last):\r\n File \"/home/ab6989/.conda/envs/myenv/lib/python3.12/site-packages/jobflow/man agers/local.py\", line 114, in _run_job\r\n response = job.run(store=store)\r\n ^^^^^^^^^^^^^^^^^^^^\r\n File \"/home/ab6989/.conda/envs/myenv/lib/python3.12/site-packages/jobflow/cor e/job.py\", line 583, in run\r\n response = function(*self.function_args, **self.function_kwargs)\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/home/ab6989/.conda/envs/myenv/lib/python3.12/site-packages/atomate2/va sp/jobs/base.py\", line 218, in make\r\n write_vasp_input_set(\r\n File \"/home/ab6989/.conda/envs/myenv/lib/python3.12/site-packages/atomate2/va sp/files.py\", line 202, in write_vasp_input_set\r\n vis.write_input(directory, potcar_spec=potcar_spec, **kwargs)\r\n File \"/home/ab6989/.conda/envs/myenv/lib/python3.12/site-packages/atomate2/va sp/sets/base.py\", line 114, in write_input\r\n f.write(v.get_string(significant_figures=16))\r\n ^^^^^^^^^^^^\r\nAttributeError: 'Poscar' object has no attribute 'get_string'. Did you mean: 'get_str'? \r\n\r\n2024-01-25 16:50:31,435 INFO Finished executing jobs locally\r\n```\r\n\r\nIt looks like there is some issue in `get_string` as `get_str`. The workflow creates the INCAR file but the POSCAR doesn't get created even in the first step.\r\n\r\nI also checked using 2 ways of generating structure: using a .cif file and directly giving lattice, species, and coord. But, it had the same error in both of them.\r\n\r\nLet me know if it is due to some mismatch in different codes, or if I should make any changes in my workflow. I created a new environment and used the GitHub pymatgen and pip install atomate2 for checking it.\r\n"
] | 2024-01-01T17:37:26
| 2024-01-25T22:00:16
|
2024-01-22T19:39:30Z
|
CONTRIBUTOR
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atomate2 fails to create TaskDoc as it cannot parse the LOCPOT file generated after the VASP calculation. This happens if we use newer PBE 54 pseudopotential with hash or just using VASP version 6.4.2. The issue is where the element's name is printed in the LOCPOT file, which would be further used in the POSCAR file for the next steps.
Steps to reproduce the behavior:
1. Use any atomate2 workflow. (I'm using `MPMetaGGADoubleRelaxMaker`)
2. Use newer PBE 54 pseudopotentials with hash
OR
2. Use older PBE 54 pseudopotentials without hash but use VASP 6.4.2 version.
3. See error :
```
File "/home/ab6989/.conda/envs/my_pymatgen/lib/python3.12/site-packages/atomate2/vasp/jobs/base.py", line 292, in get_vasp_task_document
return TaskDoc.from_directory(path, **kwargs)
.....
File "/home/ab6989/.conda/envs/my_pymatgen/lib/python3.12/site-packages/pymatgen/core/periodic_table.py", line 1051, in from_str
properties = {tokens[0]: ast.literal_eval(tokens[1])}
IndexError: list index out of range
```
This is because of an extra ` “/”` coming after the element's name in the LOCPOT file. Or, an extra ` “/hashnumber”` in case of hash pseudopotentials. I've made sure of this by removing this extra bit and successfully running the `task_doc = get_vasp_task_document("/home/ab6989/MPScanRelaxSet/atomate2/Tests/job_2023-12-18-13-57-46-455621-69653")`
Examples:
LOCPOT file when using hashless pseudopotential but 6.4.2 version VASP.
```
Mg1 O1
1.00000000000000
-0.0000000000000000 2.1041807445817637 2.1041807445817637
2.1041807445817637 -0.0000000000000000 2.1041807445817637
2.1041807445817637 2.1041807445817637 0.0000000000000000
Mg/ O/
1 1
Direct
0.0000000000000000 0.0000000000000000 -0.0000000000000000
0.5000000000000000 0.5000000000000000 0.5000000000000000
```
LOCPOT file which works in creating task_doc and doesn't fail.
```
Mg1 O1
1.0
0.0000000000000000 2.1299999999999999 2.1299999999999999
2.1299999999999999 0.0000000000000000 2.1299999999999999
2.1299999999999999 2.1299999999999999 0.0000000000000000
Mg O
1 1
direct
0.0000000000000000 0.0000000000000000 0.0000000000000000 Mg
0.5000000000000000 0.5000000000000000 0.5000000000000000 O
```
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CONTRIBUTOR
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updates:
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
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Handle invalid selective dynamics info in POSCAR
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"Regarding the 1st POSCAR in the original issue. There is: https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/vasp/inputs.py#L121-L124\r\n\r\nMeaning selective dynamics array would only be written when there exists at least one degree of freedom (DOF) frozen. And the user used an example POSCAR where all DOFs are relaxed thus selective dynamics is dropped. \r\n\r\nShould we issue a warning to avoid confusion? I don't think it's necessary (but why would people relax all DOFs and toggle selective dynamics at the same time in the first place).\r\n\r\n",
"Meanwhile for the second POSCAR:\r\n```\r\nTest\r\n 1.000000000\r\n 20.0000000000000000 0.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 23.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 0.0000000000000000 15.0000000000000000\r\n C H \r\n 2 1\r\nSelective dynamics\r\nCartesian\r\n 2.201545747940 2.214990562232 1.000000000000 C T T T \r\n 3.625859708182 2.193941473662 1.000000000000 C T T T \r\n 4.326973622066 3.379594386626 1.000000000000 H T T T \r\n```\r\n\r\nWhich interprets to:\r\n```\r\nTest\r\n1.0\r\n 20.0000000000000000 0.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 23.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 0.0000000000000000 15.0000000000000000\r\nC H\r\n2 1\r\nSelective dynamics\r\ndirect\r\n 0.1100772873970000 0.0963039374883478 0.0666666666666667 F T T C\r\n 0.1812929854091000 0.0953887597244348 0.0666666666666667 F T T C\r\n 0.2163486811033000 0.1469388863750435 0.0666666666666667 F T T H\r\n```\r\n\r\nSeems still intended (anything other than \"T\" would be treated \"F\"):\r\nhttps://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/vasp/inputs.py#L430-L431\r\n\r\nI looked into the VASP source code `poscar.F (version 5.4.4.pl2)` line 385 to 392 (I cannot paste the code here, otherwise I would get sued for copyright), which defines the parsing mechanism of POSCAR. And it seems **VASP reads the 3-5 (0-indexed) elements of the line as selective dynamics, which deems such POSCAR invalid**. If so, I might proceed and issue a warning from our end.\r\n\r\n",
"I went ahead and tried to fix some minor issues and formats. Hope this is acceptable (let me know if I should be opening a new PR, but I think that might be too overkill). This time I runned unit tests and everything looks good.",
"Meanwhile I noticed this warning here: https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/lobster/inputs.py#L637-L644\r\n\r\nI had some experience with this issue, and was lucky enough to get direct input from Dr. Ryky Nelson @rnels12 (first author of the [LOBSTER paper](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26353)). When this imcompatibility issue happens, the charge spilling could jump from under 5% to as much as around 40%. Meanwhile the fix is pretty straightforward, by simply removing the lines in POTCAR with `SHA256` and `COPYR`, which is suggested by Dr. Nelson himself. I have tested this the fix and could confirm this could significant reduce charge spilling to normal range. \r\n\r\n~~Should I proceed and implement this fix directly in pymatgen (make a backup copy of POTCAR and modify the current POTCAR)? Meanwhile I think I might need to send Dr. Nelson another email to confirm the fix, because unfortunately my previous communication with Dr. Nelson is lost (my previous university set up an email purging policy for some reason).~~(maybe not worth patching after discussion with @JaGeo, fixed by latest Lobster)\r\n",
"> Meanwhile I noticed this warning here:\r\n> \r\n> https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/lobster/inputs.py#L637-L644\r\n> \r\n> I had some experience with this issue, and was lucky enough to get direct input from Dr. Ryky Nelson @rnels12 (first author of the [LOBSTER paper](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26353)). When this imcompatibility issue happens, the charge spilling could jump from under 5% to as much as around 40%. Meanwhile the fix is pretty straightforward, by simply removing the lines in POTCAR with `SHA256` and `COPYR`, which is suggested by Dr. Nelson himself. I have tested this the fix and could confirm this could significant reduce charge spilling to normal range.\r\n> \r\n> Should I proceed and implement this fix directly in pymatgen (make a backup copy of POTCAR and modify the current POTCAR)? Meanwhile I think I might need to send Dr. Nelson another email to confirm the fix, because unfortunately my previous communication with Dr. Nelson is lost (my previous university set up an email purging policy for some reason).\r\n\r\nWe implemented this warning after talking to @rnels12 and @QuantumChemist . If this happens, the POTCARs are not read correctly and the results you get are wrong. Of course, you can implement a fix but I am not sure what you are intending to do: generating POTCARs without the line?",
"Btw, many of the pymatgen implementations have been used for the above LOBSTER paper. 🙃",
"Side note: we should test if the latest LOBSTER version fixes this. If so, I would not spend time on this fix. ",
"Hi @JaGeo, thanks a lot for the input and the cool story (I'm new to the community). If I understand Dr. Nelson's information correctly, just **removing the lines with `SHA256` and `COPYR` from POTCAR** should resolve the compatibility issue with LOBSTER. An indicator should be a significant decrease in the charge spilling (but I could be wrong). If so, fixing should be quite straightforward by just making a backup POTCAR and removing those lines. What do you think?\r\n\r\nIt's certainly worth checking if the issue get solved in lastest version of LOBSTER, but I would personally prefer to improve the compatibility of pymatgen if the cost is not too high.\r\n\r\nBTW, I happend to find your LobsterPy package several weeks ago and it's awesome. I would see if I could make some contributions to that soon.",
"@naik-aakash might also be able to give further input and could probably check if the latest LOBSTER fixes the issue.\r\n\r\n> BTW, I happend to find your LobsterPy package several weeks ago and it's awesome. I would see if I could make some contributions to that soon.\r\n\r\nBtw, We work on a JOSS at the moment. (Basically now would be a perfect time for a contribution)\r\n\r\n",
"And, yes, the fix mentioned above is essentially the fix that we implemented manually. ",
"Hi @DanielYang59, I can test if the latest LOBSTER version fixes this issue and update you here asap ",
"@naik-aakash That would be much appreciated! My bad, I seem to be flooding this PR with irrelevant topic...",
"> And, yes, the fix mentioned above is essentially the fix that we implemented manually.\r\n\r\n@JaGeo Thanks for the input. If you have time you might open up some issues and I would see if I could solve any (as I'm not quite familiar with your package at this moment) so may not actually know where to get started. All the best with your paper then!",
"> > And, yes, the fix mentioned above is essentially the fix that we implemented manually.\r\n> \r\n> @JaGeo Thanks for the input. If you have time you might open up some issues and I would see if I could solve any (as I'm not quite familiar with your package at this moment) so may not actually know where to get started. All the best with your paper then!\r\n\r\nI don't have time to implement a fix. Sorry. Let's just see if the latest LOBSTER resolves it. Thanks in any case.",
"Sorry @JaGeo I didn't express myself clear enough. I mean I might dive into your Lobsterpy package and see if I could help contribute something. If you happen to have some work to be done for Lobsterpy, I might try to help (my knowledge is limited but I would try my best). Cheers!",
"> @naik-aakash That would be much appreciated! My bad, I seem to be flooding this PR with irrelevant topic...\r\n\r\nThe issue with high spilling when POTCARs have `SHA256` and `COPYR` seems to be solved in the latest [LOBSTER version 5.0.0](http://www.cohp.de/)\r\n",
"Great. Then, we just leave the warning for now (and potentially update the LOBSTER version in the text). I wouldn't attempt a fix as people should always use the latest LOBSTER version. It's also not hard to switch as it has an academic license and does not need much setup in contrast to codes like VASP.",
"Great! Thanks a lot for the confirmation @naik-aakash. Yes I agree with you, pymatgen should not patch every downstream issue, especially when it could be fixed with negligible cost by the user (it seems to be the `lobsterin` for 4.1.0 should also work for 5.0.0, but I could be wrong.). \r\n\r\nMeanwhile it might be good to implement a lobster version check before issuing a warning? What do you think? @JaGeoBut I currently cannot think of a better method than running command `lobster` (I don't like this idea though) or check the first line of `lobsterout` file (which is not possible when we are still generating `lobsterin`) ?",
"> Great! Thanks a lot for the confirmation @naik-aakash. Yes I agree with you, pymatgen should not patch every downstream issue, especially when it could be fixed with negligible cost by the user (it seems to be the `lobsterin` for 4.1.0 should also work for 5.0.0, but I could be wrong.).\r\n> \r\n> Meanwhile it might be good to implement a lobster version check before issuing a warning? What do you think? @JaGeoBut I currently cannot think of a better method than running command `lobster` or check the first line of `lobsterout` file?\r\n\r\nWe could do this. However, not sure how consistent versioning is ... Especially for test versions.",
"@JaGeo That would be wonderful. Meanwhile it appears to me lobster doesn't seem to have a version checking command? Maybe I'm wrong? I tried `lobster --version`/`lobster -v`/`lobster -V` and none seems to work. Also I didn't find any from the Manual.",
"Can you please review this? @janosh . I need confirmation on the handling of selective dynamics info by `VASP`. Thanks!",
"> I need confirmation on the handling of selective dynamics info by VASP\r\n\r\n@DanielYang59 I'm not the best person for that. @JaGeo @esoteric-ephemera @Andrew-S-Rosen and others are much more qualified here",
"Sorry I'm not quite familiar with git rebase and it seems I have messed up the commit history again. I'm working on rebase and squashing the above commits. Sorry for the inconvenience.",
"> I'm working on rebase and squashing the above commits. Sorry for the inconvenience.\r\n\r\nNo need. this PR is mergeable as is. once this is fully reviewed i'll take of any diverging git history",
"Thanks @janosh, it's so nice of you. I'm feeling so bad for messing with the commit history😭. I would go the learn all these again.\r\n\r\nUpdate: should be good now.",
"Sorry, I am still sick (third week) and therefore behind on many things. 🙃",
"So sorry to hear that @JaGeo. No rush at all. Hope you could get well soon.",
"Hey @DanielYang59 and @janosh - I just posted a reply to issue #3008. That issue can probably be closed with the explanation given\r\n\r\nThe short answer is yes, the author of 3008 had incorrectly-formatted POSCARs, and was unaware that at least one degree of freedom had to be disabled to use selective dynamics\r\n\r\nThe warning in this PR won't be raised if, e.g., a POSCAR contains fluorine and reverses the order of the site labels and selective dynamics tags, since the first letter is then F. The only way around that is to check if the labels at the end of the line match the expected composition, which they don't have to (might be wrong there)\r\n\r\nThe point of having specific warnings like `BadIncarWarning` is to help the user in debugging. Even if it's used quite sparingly within PMG, the warning points you to INCAR being incorrectly formatted. I don't see the rationale in removing this",
"Good point @esoteric-ephemera. I didn't realize `fluorine` would be a special case and it's quite tricky to handle. I cannot think it a good solution for this and might wait to see if others have a more elegant way around.\r\n\r\nSure I totally agree with your point to keep the `BadIncarWarning`. The reason I wish to remove it previously is that I browsed through the `inputs.py` module and notice custom warning is issued only for bad `INCAR`, and within the same method, not for any other input files (not `BadPoscarWarning` or such). I would reverse this deletion for now and maybe we can add a specific warning for each input file.\r\n\r\n",
"It appears to me the above checking should be able to capture most invalid POSCARs, except for some rare cases including Fluorine. But I think our safety margin is still generous.\r\n\r\nAs far as I can think of, only the following invalid POSCARs cannot be captured by the above check.\r\n\r\n### Some invalid POSCARs could bypass the check\r\n\r\n```POSCAR\r\nInvalid POSCAR with one Fluorine only\r\n1\r\n 0.50000000 0.50000000 0.00000000\r\n 0.00000000 0.50000000 0.50000000\r\n 0.50000000 0.00000000 0.50000000\r\n F\r\n 1\r\nSelective dynamics\r\nCartesian\r\n0.00000000 0.00000000 0.00000000 F T T F\r\n```\r\nThere is no way to tell whether the intended selective dynamics info is `F T T` or `T T F`. But why would people attempt to relax a single atom strutucre in the first place?\r\n\r\n```POSCAR\r\nInvalid POSCAR with multiple Fluorine only\r\n1\r\n 0.50000000 0.50000000 0.00000000\r\n 0.00000000 0.50000000 0.50000000\r\n 0.50000000 0.00000000 0.50000000\r\n F\r\n 3\r\nSelective dynamics\r\nCartesian\r\n0.00000000 0.00000000 0.00000000 F T T F\r\n0.00000000 0.00000000 0.15000000 F T T F\r\n0.00000000 0.00000000 0.30000000 F T T F\r\n```\r\nThis time the user has a good reason to relax the structure, but I'm not aware of any chemical structure consisting Fluorine only myself.\r\n\r\n```POSCAR\r\nInvalid POSCAR with Fluorine, but only Fluorine position line has tag\r\n1\r\n 0.50000000 0.50000000 0.00000000\r\n 0.00000000 0.50000000 0.50000000\r\n 0.50000000 0.00000000 0.50000000\r\n Na F\r\n 1 1\r\nSelective dynamics\r\nCartesian\r\n0.00000000 0.00000000 0.00000000 T T T # Does not has chemical symbol tag\r\n0.00000000 0.00000000 0.15000000 F T T F # Has a confusing chemical symbol tag\r\n```\r\nIn this case, if the user intend to apply a `T T F` selective dynamics constrain on Flurione, the check would be bypassed 😓. But...I'm out of it... There is no way to tell...\r\n\r\n### Some invalid POSCARs could not bypass the check\r\n\r\n```POSCAR\r\nInvalid POSCAR with Fluorine\r\n1\r\n 0.50000000 0.50000000 0.00000000\r\n 0.00000000 0.50000000 0.50000000\r\n 0.50000000 0.00000000 0.50000000\r\n Na F\r\n 1 1\r\nSelective dynamics\r\nCartesian\r\n0.00000000 0.00000000 0.00000000 Na T T T\r\n0.00000000 0.00000000 0.15000000 F T T F \r\n```\r\nIn this slightly rational case, `F T T F` would bypass the chec, but `Na T T T` would still be captured, and therefore a warning would be issued.\r\n\r\nSo this check should be robust overall, and only fail in some extreme cases. What do you think? @esoteric-ephemera \r\n\r\n"
] | 2024-01-02T05:29:51
| 2024-02-23T02:26:13
|
2024-02-13T08:20:07Z
|
CONTRIBUTOR
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## Summary
Major changes:
- Issue warning in `from_str` method when invalid selective dynamics info would found in POSCAR, to resolve #3008.
- Clean up INCAR tag checkings in `check_params` method.
- Fix missing type checkings in`test_check_params` of `tests/io/test_inputs.py`.
Minor changes:
- Issue warning if elements cannot be determined when reading POSCAR `from_file`
- Minor format improvements
## Analysis of "Invalid selective dynamics info in POSCAR"
In the second POSCAR provided in #3008:
```
Test POSCAR
1.000000000
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
Cartesian
2.201545747940 2.214990562232 1.000000000000 C T T T
3.625859708182 2.193941473662 1.000000000000 C T T T
4.326973622066 3.379594386626 1.000000000000 H T T T
```
Which interprets to:
```
Test POSCAR
1.0
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
direct
0.1100772873970000 0.0963039374883478 0.0666666666666667 F T T C
0.1812929854091000 0.0953887597244348 0.0666666666666667 F T T C
0.2163486811033000 0.1469388863750435 0.0666666666666667 F T T H
```
Seems intended by `pymatgen` (anything other than "T" would be treated "F"):
https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/vasp/inputs.py#L430-L431
I looked into the `VASP` source code `poscar.F (version 5.4.4.pl2)` line `385` to `392` (I cannot paste the code here for copyright reasons), which defines the parsing mechanism of POSCAR by `VASP`. And it seems `VASP` reads the 3-5 (0-indexed) elements of the position line as selective dynamics, which deems such POSCAR invalid.
## `Selective dynamics` tag dropped when all DOFs relaxed
Regarding the 1st POSCAR in the original issue. There is: https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/vasp/inputs.py#L121-L124
So selective dynamics array would only be kept when there exists at least one degree of freedom (DOF) frozen. And the user used an example POSCAR where all DOFs are relaxed.
Should we issue a warning to avoid confusion? I think it's unnecessary (but why would people relax all DOFs and toggle selective dynamics at the same time in the first place).
## TODO list
- [x] Issue warning when invalid selective dynamics info detected in POSCAR
- [x] (**Need suggestions on this**) Confirm such POSCARs are truly invalid
- [x] Update unit tests for such invalid POSCARs
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[
"@materialsproject/pymatgen-maintainers is something amiss with the CI tests? They are all failing with\r\n\r\n```\r\n × Getting requirements to build wheel did not run successfully.\r\n │ exit code: 1\r\n ╰─> [20 lines of output]\r\n Traceback (most recent call last):\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 353, in <module>\r\n main()\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 335, in main\r\n json_out['return_val'] = hook(**hook_input['kwargs'])\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 118, in get_requires_for_build_wheel\r\n return hook(config_settings)\r\n ^^^^^^^^^^^^^^^^^^^^^\r\n File \"/tmp/pip-build-env-h4vu0vp5/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 325, in get_requires_for_build_wheel\r\n return self._get_build_requires(config_settings, requirements=['wheel'])\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/tmp/pip-build-env-h4vu0vp5/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 295, in _get_build_requires\r\n self.run_setup()\r\n File \"/tmp/pip-build-env-h4vu0vp5/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 480, in run_setup\r\n super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)\r\n File \"/tmp/pip-build-env-h4vu0vp5/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 311, in run_setup\r\n exec(code, locals())\r\n File \"<string>\", line 41, in <module>\r\n ModuleNotFoundError: No module named 'packaging'\r\n [end of output]\r\n \r\n note: This error originates from a subprocess, and is likely not a problem with pip.\r\nerror: subprocess-exited-with-error\r\n\r\n× Getting requirements to build wheel did not run successfully.\r\n│ exit code: 1\r\n╰─> See above for output.\r\n\r\nnote: This error originates from a subprocess, and is likely not a problem with pip.\r\n```",
"It appears to me the GitHub workflow might have some issue, as every commit auto-check seems to fail because of the same error: \r\n\r\n```\r\n × Getting requirements to build wheel did not run successfully.\r\n │ exit code: 1\r\n ╰─> [20 lines of output]\r\n Traceback (most recent call last):\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 353, in <module>\r\n main()\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 335, in main\r\n json_out['return_val'] = hook(**hook_input['kwargs'])\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py\", line 118, in get_requires_for_build_wheel\r\n return hook(config_settings)\r\n ^^^^^^^^^^^^^^^^^^^^^\r\n File \"/tmp/pip-build-env-d4g7fty8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 325, in get_requires_for_build_wheel\r\n return self._get_build_requires(config_settings, requirements=['wheel'])\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n File \"/tmp/pip-build-env-d4g7fty8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 295, in _get_build_requires\r\n self.run_setup()\r\n File \"/tmp/pip-build-env-d4g7fty8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 480, in run_setup\r\n super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)\r\n File \"/tmp/pip-build-env-d4g7fty8/overlay/lib/python3.11/site-packages/setuptools/build_meta.py\", line 311, in run_setup\r\n exec(code, locals())\r\n File \"<string>\", line 41, in <module>\r\n ModuleNotFoundError: No module named 'packaging'\r\n [end of output]\r\n\r\n```\r\n\r\nI was about to open an issue but realize maybe I could help fix this issue next week. ",
"Ready to merge, unless other comments / concerns from @materialsproject/pymatgen-maintainers ",
"Good work @rkingsbury ! Learned a lot from my side. And thanks for reviewing @janosh "
] | 2024-01-03T19:06:33
| 2024-10-10T01:55:04
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2024-01-08T16:06:41Z
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CONTRIBUTOR
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Fixes #3506
See discussion in #3534 which settled on moving the run type check and `raise` statement to `get_adjustments` itself and remove the other statements, as illustrated [here](https://github.com/materialsproject/pymatgen/pull/3540/files) as the cleanest fix.
The logic is the following:
- when `process_entries` is called, it calls `get_adjustments` for every entry provided
- Any entry which raises a `CompatibilityError` is excluded from the returned list.
- In the specific case of `MaterialsProjectCompatibility`, `get_adjustments` calls `get_corrections_dict`, which loop through the `get_correction` method of all 4 of the underlying `Correction` classes (we eliminated these in the newer scheme for simplicity)
- It just so happens that the `raise` statement that occurs in `UCorrection` (which processes any entry sent through `get_Adjustments`) serves the purpose of excluding incompatible entries.
- Strictly speaking, this `raise` statement could/should occur in `get_adjustments` itself, because that is really the only place that the run_type check needs to happen (an entry which is incompatible with one of the corrections is incompatible with all of them, for this purpose)
- The `return ufloat(0,0)` statements in the `Correction` classes do not serve an important purpose as far as I can tell.
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Fix bug in SQSTransformation
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[
"Thanks Aaron!",
"Also noting another (Pythonic) SQS generator in `icet` although I have not tried it myself."
] | 2024-01-03T20:56:21
| 2024-01-25T16:38:29
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2024-01-05T19:33:51Z
|
CONTRIBUTOR
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The `SQSTransformation` class in `pymatgen.transformations.advanced_transformations` has a `return_ranked_list` kwarg in `apply_transformation`.
Because this can be either boolean (return all best SQS structures from parallel runs) or an int (return only the `return_ranked_list` best SQS structures) and `bool` subclasses `int`in python, a previous check using `isinstance(return_ranked_list,int)` lead to returning only the first element in the ranked structure list (`int(True)=1`) rather than all structures in the list.
Fixed this bug and added to the existing TestSQSTransformation class to ensure this is checked.
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Improve CIF checking, support for isotopes, and correct handling of new VASP 6.4.2 POSCAR format incl. slashes in header
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[
"Thanks for these nice improvements @esoteric-ephemera \r\n\r\nSince you’re looking at this part of the code, do you have a view of how H2O or OH sites should be handled? It’s one remaining weakness of the CIF parser I think.",
"Also adding a note that the `mp` prefix has been registered with the IUCr, if we wanted to add support for writing out custom pymatgen fields (like site_properties). There’s definitely a way in which pymatgen could losslessly convert `Structure` to/from CIF. It’s been something on the back burner for me for a while.",
"> Since you’re looking at this part of the code, do you have a view of how H2O or OH sites should be handled? It’s one remaining weakness of the CIF parser I think.\r\n\r\nAre you thinking of experimental structures where the H sites are undetermined/unlisted? For organics, @Andrew-S-Rosen had a good suggestion of trying to mimic how Olex (used by crystallographers) [adds hydrogen atoms](https://www.olexsys.org/olex2/docs/tutorials/sucrose/refining/#add-hydrogen-atoms) to structures where their positions are unknown\r\n\r\n@kristinpersson had a suggestion that was based on a geometric construction - that would also be a cheap solution\r\n\r\nI have a few other ideas that would use a DFT charge density, but these are more intensive options\r\n\r\n> Also adding a note that the mp prefix has been registered with the IUCr, if we wanted to add support for writing out custom pymatgen fields (like site_properties). There’s definitely a way in which pymatgen could losslessly convert Structure to/from CIF. It’s been something on the back burner for me for a while.\r\n\r\nThat's great to know! The precision of atomic sites in CIFs seems to be a bottleneck to lossless conversion, since this can result in composition mismatches. Since a lot of CIFs are written by hand (especially ICSD ones), this happens frequently, see e.g., issue [#3373](https://github.com/materialsproject/pymatgen/issues/3373)",
"NIce work! One minor thing: does the cif assessor really need to be a class? I would think a CifParser.assess or CifParser.validate method would suffice. I am heavy proponent for OOP but in this case, the CifAssessor doesn't seem to conceptually an object per se.\r\n",
"> Are you thinking of experimental structures where the H sites are undetermined/unlisted?\r\n\r\nNot quite, there are two problems: (1) “implicit hydrogens” whereby the hydrogens are not listed in the atoms at all (so we might not realise hydrogens are missing unless we do a composition check as suggested), (2) the CIF files which list a molecule on a single atomic site, eg “OH” or “H2O” etc. Here, the CIF file at least tells us that a H should be present, but we still do not parse appropriately (I believe for OH, we parse as just O, and provide a warning).\r\n\r\nFor (2), it’s a difficult situation, because all options are unideal in some way. Omitting the H completely is wrong. Putting the H in an arbitrary location (eg correct bond length, perhaps do a bond valence sum or similar to find a plausible position) is tricky. Defining the site as containing a molecule is probably most correct, but does not fit with the current pymatgen object model.\r\n",
"> NIce work! One minor thing: does the cif assessor really need to be a class? I would think a CifParser.assess or CifParser.validate method would suffice. I am heavy proponent for OOP but in this case, the CifAssessor doesn't seem to conceptually an object per se.\r\n\r\nThanks! Yes I'll try to refactor the assessor",
"Sorry, sent that message too soon. I’m not familiar with the Olex method. My point anyway is just that there are cases where we have to figure out the hydrogen is missing based on composition, but also cases where we’re explicitly told a hydrogen should be there.\r\n\r\nIn terms of lossless conversion, correct me if I’m wrong but there’s no limit on the precision with which we write out atomic positions? We can write out as many significant figures as we do with JSON. I know the issue with the handwritten CIFs which is why we put in the rounding logic inside the parser (eg converting 0.333 -> 1/3 etc), but that seems like a separate issue.",
"@mkhorton @esoteric-ephemera I would just say that there are now universal potentials. For an OH, you can take the coordinates as the position of the O and then initialize a H at 0.5A bond distance (maybe away from other atom as well). Then use a UP to relax the H positions. :-) For this very constrained use case, I think it would lead to very reasonable results (much more than pure geometry / empirical constructions).",
"> (2) the CIF files which list a molecule on a single atomic site, eg “OH” or “H2O” etc. Here, the CIF file at least tells us that a H should be present, but we still do not parse appropriately (I believe for OH, we parse as just O, and provide a warning).\r\n\r\nOK I see what you mean. The best solution there in keeping with pymatgen's model is probably putting O on the site position and adding in H\r\n\r\n> My point anyway is just that there are cases where we have to figure out the hydrogen is missing based on composition, but also cases where we’re explicitly told a hydrogen should be there.\r\n\r\nThis PR warns the user in at least the latter case: if H is reported in the CIF but missing in the PMG structure, the user is warned. It **usually** seems to be the case that H's are reported in the CIF composition even when no H site positions are given. But if they're not, we might want to include a charge balance check\r\n\r\n> I know the issue with the handwritten CIFs which is why we put in the rounding logic inside the parser (eg converting 0.333 -> 1/3 etc), but that seems like a separate issue.\r\n\r\nWe can specify arbitrary position, but a lot of the ICSD CIFs seem to have lower precision than the default rounding tolerance in `CifParser` (4 digits). ICSD-191196 is a good example where the composition is only reported to two digits of precision\r\n\r\n> I would just say that there are now universal potentials.\r\n\r\nMight be good in this case to freeze the known positions and only relax the H atoms. My only concern here is that H is often underrepresented in ML-UIP training data. Maybe @janosh can comment more on that",
"Yes H is often underrepresented in UP training. But I think for a limited case like OH, it should be ok. Regardless, it is better than any of the rule of thumb alternatives. The only better option is DFT (with certain functionals).",
"Just adding the WIP tag for now, since I realized that oxidation state handling for isotopes isn't working as intended (also pending refactor of CifAssessor)",
"The hydrogen convex hull distance errors for MLIPs are definitely elevated based on Matbench Discovery testing.\r\nSee \"Per-Element Model Error Heatmaps\" at https://matbench-discovery.materialsproject.org/models with M3GNet and MACE at 260 meV/atom, CHGNet at 240.\r\n\r\nI think this not so much stems from underrepresentation (MPtrj contains 142k relaxation frames with hydrogen) but hints that the models are confused due to inconsistent training data, perhaps due to issues like the one (partially) addressed in this PR.\r\n\r\nBut I agree with @shyuep, doing H-only relaxation with any of the above mentioned models could still get you closer to true H positions.",
"This is almost ready for review, I think. One thing I'm not satisfied with: the user can manually specify an oxidation state for an isotope, however calling convenience functions like `Composition(...).add_charges_from_oxi_state_guesses()` or `Structure(...).add_oxidation_state_by_guess()` will convert any isotope to its parent bare `Element`\r\n\r\nFor example, The composition `Composition({\"D+\": 2, \"O2-\": 1})` includes D+ in the composition. However calling `add_charges_from_oxi_state_guesses()` on `Composition({\"D\": 2, \"O\": 1})` will return the equivalent of `Composition({\"H+\": 2 \"O2-\": 1})`.\r\n\r\nMaybe this isn't such an issue since this represents an extreme edge case. Issuing a warning to the user when calling any of the `add_*` oxi state methods would be sufficient?"
] | 2024-01-05T20:25:09
| 2024-01-29T19:27:11
|
2024-01-17T08:50:58Z
|
CONTRIBUTOR
|
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This PR does a few things:
- `pymatgen.io.cif.CifParser` now checks that the composition reported in a CIF matches that of the resulting `pymatgen` `Structure` and if not, warns the user what elements are missing (most often Hydrogens in experimental CIFs which are hard to locate without using neutron scattering), or when the parsing has gone awry and the stoichiometries differ
- Adds support for isotopes, particularly Deuterium and Tritium.
- `pymatgen.core.periodic_table.Element` now has a few more attributes, such as the atomic mass number (number of protons and neutrons) as the `.A` attr
- A structure containing an isotope will appear to only have the base element in it (e.g., D2O will look like H2O), and when files are written, the isotopes are converted to the element. However, the isotope names, mass, etc. are preserved in the element attr
- This closes issue [#2151](https://github.com/materialsproject/pymatgen/issues/2151)
- As of VASP version 6.4.2, when using POTCARs with a SHA, all files like CONTCAR, CHG*, LOCPOT, AECCAR* will have the element names followed by a slash
- This closes issue [#3503](https://github.com/materialsproject/pymatgen/issues/3503) and atomate2 issue [#662](https://github.com/materialsproject/pymatgen/issues/3571)
- Allow for correct parsing of these via changes to `pymatgen.io.vasp.inputs.Poscar`
- Tests for these additions
|
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PR_kwDOACgets5jYXbv
| 3,543
|
Fix failing CI due to broken BoltzTraP2 install
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[] | 2024-01-06T13:20:47
| 2024-01-06T13:34:34
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2024-01-06T13:34:33Z
|
MEMBER
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I commented out BoltzTraP2 in `setup.py` util broken install is fixed, hopefully following merge of https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18.
Pinging @esoteric-ephemera who helped troubleshoot this issue.
<details><summary>Install logs</summary>
```python
Collecting BoltzTraP2>=22.3.2 (from pymatgen==2023.12.18)
Downloading BoltzTraP2-22.12.1.tar.gz (81.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 81.8/81.8 MB 44.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [20 lines of output]
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-lb3tejv2/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-lb3tejv2/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-lb3tejv2/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 480, in run_setup
super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-lb3tejv2/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 41, in <module>
ModuleNotFoundError: No module named 'packaging'
[end of output]
```
</details>
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PR_kwDOACgets5jjCUq
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Phonon convenience imports
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[] | 2024-01-09T07:37:01
| 2024-01-09T07:51:33
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2024-01-09T07:51:32Z
|
MEMBER
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42b658b97 add `pymatgen/phonon/__init__.py` convenience imports
4c651752d `test_convenience_imports()`
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I_kwDOACgets57hgyr
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Issue with symmetrization (CifWrite) in newer pymatgen version
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[
"Note added: the bug persists in pymatgen version 2023.12.18. ",
"Hi @deecadance, can you explain why you expect to get space group 12 here? The space group of the POSCAR you attached is 8, and you're not directly symmetrizating the structure.\r\n\r\n`symprec` and `angprec` control the tolerance with which pymatgen handles equality of distances and angles, respectively. They maybe indirectly symmetrize a structure.\r\n\r\nI'll just note the following simpler syntax for writing CIFs than in your file:\r\n```\r\nfrom pymatgen.core import Structure\r\n\r\nstruct = Structure.from_file(\"POSCAR_src_166.vasp\")\r\ncif_writer_kwargs = {\"symprec\": symprec, \"angle_tolerance\" : angprec}\r\nstruct.to(\"filename.cif\", **cif_writer_kwargs)\r\n```",
"> can you explain why you expect to get space group 12 here? \r\n\r\nTwo reasons:\r\n1) Pasting the POSCAR file in a different symmetrizer (e.g. https://uspex-team.org/online_utilities/poscar2cif/#end) returns space group 12\r\n2) If you inspect the structure (e.g. using VESTA) before and after the symmetrization you can see that when space group 12 is return the structure correctly matches the original POSCAR. On the other hand, going through pymatgen 2023.11.12, when space group 8 is returned, the structure is just wrong (e.g. the W atoms are overlapping), see attached [structures.zip](https://github.com/materialsproject/pymatgen/files/13918308/structures.zip), I also re-added the poscar in a VESTA-friendly format.\r\n\r\n> symprec and angprec control the tolerance with which pymatgen handles equality of distances and angles, respectively. They maybe indirectly symmetrize a structure.\r\n\r\nYes, they do. I don't know if that was intentional or not, but the code does work as a symmetrizer (exceptionally well in the previous version), and I have been using it for that way for a long time. Even if you don't care about my use case, cif_writer is not reading this poscar correctly, though it used to. \r\n\r\n> I'll just note the following simpler syntax for writing CIFs than in your file:\r\n\r\nThanks\r\n",
"Hey @deecadance, sorry if my message came across as dismissive! I'm trying to understand what might have changed so we can look into it further\r\n\r\nWhen I load in your POSCAR and write it to a CIF (still space group 8), I'm not getting overlapping W sites, so hopefully this is an issue of conflicting packages. You might want to try `pip install --upgrade spglib`, which handles PMG's symmetry determination\r\n\r\nI'm using spglib==2.2.0 and pymatgen==2023.12.18",
"Excuse me for interrupting. I am a maintainer of spglib.\r\n\r\nIt seems the POSCAR structure is rather distorted from C2/m.\r\nThe following script shows a detected space group type depends on `symprec` around 1e-2 to 1e-1.\r\nIf the behavior of CifWriter changed at some point, I guess a default symprec may be changed.\r\n```python\r\nfrom importlib.metadata import version\r\n\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nfrom pymatgen.io.vasp import Poscar\r\nimport spglib\r\n\r\nprint(f\"pymatgen: {version('pymatgen')}\")\r\nprint(f\"spglib: {spglib.__version__}\")\r\n\r\nstructure = Poscar.from_file('mwe/POSCAR_src_166.vasp').structure\r\ncell = SpacegroupAnalyzer(structure)._cell\r\n\r\nfor symprec in [1e-4, 1e-2, 3e-2, 1e-1]:\r\n dataset = spglib.get_symmetry_dataset(cell, symprec=symprec)\r\n print(f\"symprec={symprec}\")\r\n print(\" Space group type:\", dataset['international'])\r\n print(\" Number of atoms:\", len(dataset['std_types']))\r\n```\r\n\r\nOutput\r\n```\r\npymatgen: 2023.12.18\r\nspglib: 2.2.0\r\nsymprec=1e-08\r\n Space group type: Cm\r\n Number of atoms: 14\r\nsymprec=0.0001\r\n Space group type: Cm\r\n Number of atoms: 14\r\nsymprec=0.01\r\n Space group type: Cm\r\n Number of atoms: 14\r\nsymprec=0.03\r\n Space group type: C2/m\r\n Number of atoms: 14\r\nsymprec=0.1\r\n Space group type: C2/m\r\n Number of atoms: 14\r\n```",
"Much appreciated @lan496! While I can't clearly see a spot in pymatgen where symprec may have been lowered recently, that seems to be a reasonable fix. When I use a larger / looser symprec > 0.02, I get a space group of 12 for the symmetrized structure. Can you check that you get the same behavior @deecadance?",
"Hi, thanks to both for the nice replies, and sorry if I sounded salty, it was not my intention!\r\n@lan496 Thanks for joining the discussion! I tried to your script. Depending on the version of spglib/pymatgen that I'm using it runs or it doesn't. In particular:\r\nspglib 2.0.2, pymatgen 2023.5.31, numpy 1.23.5 I reproduce exactly your result\r\nspglib 2.2.0, pymatgen 2023.12.18, numpy 1.26.0 the code fails with error:\r\nspglib: ssm_get_exact_positions failed. (line 479, /private/var/folders/gb/48p5g82s29b2zzvm7yzcrwwh0000gn/T/pip-install-96qlk6rd/spglib_021622f088764b9bb72fef489c5e415e/src/refinement.c).\r\n\r\nI guess it's not so much a matter of exactly which space group, rather than a problem of overlapping atoms. Using a smaller symprec with the two versions of the libraries I can get to some cif file with both, and in both cases it has the same space group (8), except in the newer configuration the crystal structure is wrong (see png's/cifs in [new_mwe.zip](https://github.com/materialsproject/pymatgen/files/13966434/new_mwe.zip)). \r\n\r\n> I'm using spglib==2.2.0 and pymatgen==2023.12.18\r\n\r\n\r\nVery interesting. I am using the same when I get the wrong structure. What is your numpy version? Could it be something silly like a transpose in the wrong place?",
"Possibly related error:\r\n\r\n```python\r\nfrom pymatgen.ext.matproj import MPRester\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\\\r\nstruct = mpr.get_structure_by_material_id(\"mp-886\")\r\nsa = SpacegroupAnalyzer(struct)\r\nsstruct = sa.get_symmetrized_structure() #errors out\r\n```\r\n\r\nProduces:\r\n```\r\n 132 def get_space_group_number(self) -> int:\r\n 133 \"\"\"Get the international spacegroup number (e.g., 62) for structure.\r\n 134 \r\n 135 Returns:\r\n 136 int: International spacegroup number for structure.\r\n 137 \"\"\"\r\n--> 138 return int(self._space_group_data[\"number\"])\r\n\r\nTypeError: 'NoneType' object is not subscriptable\r\n```\r\n\r\nSo it looks like spglib is was not able to populate `_space_group_data`.\r\n\r\n",
"Just tested the code above using different managers:\r\n\r\n`pip install spglib` -> gives error\r\n\r\n`conda install -c conda-forge spglib` -> no error\r\n\r\nI’m guessing this is some weird interplay between the way data is represented in the numpy parts of the spglib python wrapper and the specific compilation of the C code. ~We probably have to ping one of their developer to resolve this one.~ nvm @lan496 is already here!",
"Hi @lan496 dear spglib developer, I recently had an issue related to this. For the same structure, I got a different number of symmetry operations after updating my pymatgen, let me reproduce the issue here\r\n```\r\nfrom importlib.metadata import version\r\nfrom pymatgen.analysis.structure_matcher import StructureMatcher\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nfrom pymatgen.ext.matproj import MPRester\r\nfrom pymatgen.io.vasp import Poscar\r\nimport spglib\r\nfrom pymatgen.core import Structure\r\n\r\nsm=StructureMatcher()\r\n\r\nprint(f\"pymatgen: {version('pymatgen')}\")\r\nprint(f\"spglib: {spglib.__version__}\")\r\n\r\nmpr=MPRester()\r\ns1=mpr.get_structure_by_material_id(\"mp-2133\")\r\ns2 = Poscar.from_file('./ZnO_2133/ZnO.poscar').structure ## poscar downloaded from MP website\r\nprint (f\"structure_matcher={sm.fit_anonymous(s1,s2)}\")\r\n\r\nfor symprec in [1e-5,1e-1]:\r\n for s in [s1,s2]:\r\n spg=SpacegroupAnalyzer(structure=s,symprec=symprec)\r\n print(f\"symprec={symprec}\")\r\n print(\"Space group type:\", spg.get_space_group_symbol())\r\n print(\"Number of operations:\", len(spg.get_space_group_operations()))\r\n```\r\n\r\nThe output is\r\n```\r\npymatgen: 2023.8.10\r\nspglib: 2.3.0\r\nstructure_matcher = True\r\nsymprec=1e-05\r\nSpace group type: P6_3mc\r\nNumber of operations: 24\r\nsymprec=1e-05\r\nSpace group type: P6_3mc\r\nNumber of operations: 12\r\nsymprec=0.1\r\nSpace group type: P6_3mc\r\nNumber of operations: 24\r\nsymprec=0.1\r\nSpace group type: P6_3mc\r\nNumber of operations: 12\r\n```\r\nTwo things that I want to confirm are:\r\n1. Anyone knows whether `mpr.get_structure_by_material_id()` switched the default`conventional_unit_cell` setting (`from True to False`)? \r\n2. For the same structure (passed structure_matcher), the symmetry operation numbers might be different (depending on whether it is a conventional unit cell or not)? Here we exclude the reasoning from symprec setting by tuning it from 1e-5 to 1e-1, plus the space group type remains the same.\r\n\r\n[ZnO_2133.zip](https://github.com/materialsproject/pymatgen/files/14105313/ZnO_2133.zip)\r\n",
"Just locate the bug from spglib update (`from 1.16.5 to 2.3.0`). \r\nI have submitted a new issue there [https://github.com/spglib/spglib/issues/413](https://github.com/spglib/spglib/issues/413)",
"@esoteric-ephemera \r\nFor the first case of this issue, the distinction between Cm and C2/m would be challenging for such a large symprec. It may be helpful to check atoms are not overlapped in pymatgen's cif parser side.",
"@jmmshn \r\nI could not reproduce your result with spglib==2.3.1 and pymatgen==2024.1.27. If your error still presents in the latest, please open an issue at spglib. In that case, please use a raw input for spglib by `SpacegroupAnalyzer(structure)._cell`."
] | 2024-01-09T13:34:45
| 2024-02-01T10:40:46
|
NONE
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### Python version
Python 3.10.13
### Pymatgen version
Version: 2023.11.12
### Operating system version
Mac OSX 13.2.1
### Current behavior
```Python
I try to symmetrize a POSCAR file. The symmetrization is successful but the structure produced is wrong: space group is 8 and the atoms are clearly overlapping. Using an older version of pymatgen (2023.5.31) gives the right structure instead.
```
### Expected Behavior
I expect the structure to be correctly symmetrized (space group 12).
### Minimal example
```Python
Using the zip file provided run from terminal:
python3 poscar2cif POSCAR_src_166.vasp 0.05 5
Using pymatgen 2023.5.31 gives the right cif
Using pymatgen 2023.11.12 gives the wrong cif
```
### Relevant files to reproduce this bug
[mwe.zip](https://github.com/materialsproject/pymatgen/files/13874281/mwe.zip)
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PR_kwDOACgets5jrxtq
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Add diffusive thermal conductivity model proposed by Agne et al.
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[
"Hi @janosh , This PR can be reviewed",
"@JaGeo , just tagging you here incase you have comments on this.",
"> lgtm! 👍\r\n\r\nThanks! I missed adding it as decorator so did not seem to work. Good to know how to correctly use it 😃 "
] | 2024-01-10T13:15:58
| 2024-03-13T18:02:00
|
2024-01-10T17:34:16Z
|
CONTRIBUTOR
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Add diffusive thermal conductivity empirical model as proposed by [Agne et al.](https://pubs.rsc.org/en/content/articlelanding/2018/EE/C7EE03256K)
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I_kwDOACgets5726c1
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Broken unit test `tests/io/vasp/test_inputs.py`? Broken `monty` maybe?
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[
"It seems some other unit tests (for example `tests/io/vasp/test_outputs.py`) are broken as well? (Or something with my environment?) Can you please look into this? @janosh ",
"Closed as everything seems to work just fine in my home PC. Might be something wrong with my office PC. I would double check from my side."
] | 2024-01-12T03:20:28
| 2024-01-12T05:08:44
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2024-01-12T05:07:13Z
|
CONTRIBUTOR
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### Python version
Python 3.10.13
### Pymatgen version
Version: 2023.12.18
### Operating system version
Ubuntu 20.04.6 LTS (Codespace Container)
### Current behavior
Not sure if I'm missing anything, the unit test of `tests/io/vasp/test_inputs.py` seems broken? I tried to run the unittest in a brand new codespace container in master branch (no personal commits). I got the following output (full output is enclosed below). It appears `monty` is broken?
```Python
/usr/local/python/3.10.13/lib/python3.10/site-packages/monty/io.py:45: FileNotFoundError
________________________________________________ test_gen_potcar_summary_stats _________________________________________________
tmp_path = PosixPath('/tmp/pytest-of-codespace/pytest-2/test_gen_potcar_summary_stats0')
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7f8393ec15d0>
def test_gen_potcar_summary_stats(tmp_path: Path, monkeypatch: MonkeyPatch) -> None:
"""Regenerate the potcar-summary-stats.json.bz2 file used to validate POTCARs with scrambled POTCARs."""
psp_path = f"{TEST_FILES_DIR}/fake_potcar_library/"
summ_stats_file = f"{tmp_path}/fake-potcar-summary-stats.json.bz2"
_gen_potcar_summary_stats(append=False, vasp_psp_dir=psp_path, summary_stats_filename=summ_stats_file)
# only checking for two directories to save space, fake POTCAR library is big
summ_stats = loadfn(summ_stats_file)
expected_funcs = {"LDA_64", "PBE_54_W_HASH"}
> assert set(summ_stats) == expected_funcs
E AssertionError: assert set() == {'LDA_64', 'PBE_54_W_HASH'}
E Extra items in the right set:
E 'LDA_64'
E 'PBE_54_W_HASH'
E Use -v to get more diff
test_inputs.py:1291: AssertionError
----------------------------------------------------- Captured stderr call -----------------------------------------------------
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_GGA_PAW_PBE POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_GGA_PAW_PBE_52 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POTPAW_PBE_52 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_GGA_PAW_PBE_54 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POTPAW_PBE_54 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_PAW_PBE_64 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_LDA_PAW POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_LDA_PAW_52 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POTPAW_LDA_52 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_LDA_PAW_54 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POTPAW_LDA_54 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_LDA_PAW_64 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_GGA_PAW_PW91 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_LDA_US POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
/usr/local/python/3.10.13/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py:2396: UserWarning: missing POT_GGA_US_PW91 POTCAR directory
warnings.warn(f"missing {PotcarSingle.functional_dir[func]} POTCAR directory")
===================================================== slowest 30 durations =====================================================
0.38s call tests/io/vasp/test_inputs.py::test_potcar_summary_stats
0.07s call tests/io/vasp/test_inputs.py::TestPoscar::test_init
0.02s call tests/io/vasp/test_inputs.py::TestKpoints::test_automatic_kpoint
0.01s setup tests/io/vasp/test_inputs.py::TestIncar::test_get_str
0.01s call tests/io/vasp/test_inputs.py::TestPoscar::test_cart_scale
(25 durations < 0.005s hidden. Use -vv to show these durations.)
51 failed, 10 passed in 13.83s
```
### Expected Behavior
NA
### Minimal example
```Python
`pytest test_inputs.py`
```
### Relevant files to reproduce this bug
[test_inputs.txt](https://github.com/materialsproject/pymatgen/files/13911138/test_inputs.txt)
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I_kwDOACgets574gj1
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Allow for custom `_atom_site_` fields in `CifWriter`
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[] | 2024-01-12T09:20:11
| 2024-01-14T15:51:18
|
2024-01-14T15:51:18Z
|
MEMBER
|
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### Feature Requested
Right now, there is not too much flexibility with the `CifWriter` when it comes to what fields can be written out to the resulting CIF. It does have a keyword argument for writing out magnetic moments, but that's really it. It would be ideal to support a more generic option where the user can write out custom `_atom_site_<NAME>` fields based on the `Structure` object's site properties.
### Proposed Solution
The solution is I will do it myself imminently and open a PR.
### Relevant Information
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I_kwDOACgets57_sar
| 3,549
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Interpretation and Handling of Unique SHA256 Identifiers in the CONTCAR/CHGCAR/CHG Files Generated by VASP.6.4.2 Compiled with HDF5 Support when using Pymatgen.
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[] | null |
[
"Hey @hongyi-zhao, sorry for the slow response. This issue may have been recently fixed by PR #3542, see also (potentially duplicate) issue #3571\r\n\r\nIf you're still having issues parsing VASP I/O after upgrading PMG (the latest release should have these fixes), please let me know!",
"closing this as assumed fixed by #3542. @hongyi-zhao please ping back if issues persist after updating"
] | 2024-01-13T13:14:49
| 2024-01-31T12:57:12
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2024-01-31T12:57:11Z
|
CONTRIBUTOR
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Dear Pymatgen Team,
While using vasp.6.4.2 compiled with HDF5 support, I've encountered an issue while working with pymatgen for handling some of the output files, aka, CONTCAR/CHGCAR/CHG, where I found some strings in these files that I hadn't seen before, as shown below:
```
$ ug -a Re/5e0f28cc669
CONTCAR: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHGCAR: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
CHG: Re/5e0f28cc669 S/0fc7481fb069 N/e053789ff3a6 Ga_d/a60ddf36e
```
As discussed [here](https://www.vasp.at/forum/viewtopic.php?p=24935) and [here](https://www.vasp.at/forum/viewtopic.php?f=4&t=19108), this information has something to do with pseudopotentials' sha256 hashes as the unique identifiers. However, I am at a loss as to whether pymatgen can handle this case correctly. I would appreciate any insight or guidance you could provide to help me understand and overcome this issue.
Your time and help in addressing my questions are deeply appreciated.
Attached please find the related input and output files for the computation discussed here.
[vasp-test.zip](https://github.com/materialsproject/pymatgen/files/13928080/vasp-test.zip)
Thank you,
Zhao
|
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PR_kwDOACgets5kAzCF
| 3,550
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Add flag `write_site_properties = False` in `CifWriter` for writing `Structure.site_properties` as `_atom_site_{prop}`
|
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[
"@janosh: This is ready for review!\r\n\r\nEdited because I solved the issue."
] | 2024-01-13T23:11:32
| 2024-01-26T12:41:55
|
2024-01-14T15:51:16Z
|
MEMBER
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## Summary
Closes #3548 by adding a `write_site_properties: bool = False` keyword argument to `CifWriter`. Existing behavior is unchanged, but if `write_site_properties = True`, then the `Structure` object's site properties will be written out to the CIF file as atom site entries.
In principle, it would be nice to add a parser of custom site properties in `CifParser`, but I'll leave that to a separate PR.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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I_kwDOACgets58Am9r
| 3,551
|
The `Structure.to()` command fails if the `filename` keyword argument is of type `Pathlib.Path`
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[] | 2024-01-14T00:58:31
| 2024-01-15T11:45:42
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2024-01-15T11:45:42Z
|
MEMBER
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### Python version
Python 3.11.7
### Pymatgen version
Version: 2023.12.18
### Operating system version
Ubuntu
### Current behavior
```Python
Version: 2023.12.18
```
### Expected Behavior
When using a `Path` as the `filename` in `Structure.to()`, a file should be written. Instead, the following error occurs because `.lower()` is being called on `filename`.
This is _technically_ not a bug because the typehint is `str`, but it's not ideal behavior.
```python
AttributeError Traceback (most recent call last)
Cell In[10], line 9
2 from pathlib import Path
4 struct = Structure(
5 lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
6 species=["Mg", "O"],
7 coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
8 )
----> 9 struct.to(filename=Path("test.cif"))
File ~/software/miniconda/envs/quacc/lib/python3.11/site-packages/pymatgen/core/structure.py:2678, in IStructure.to(self, filename, fmt, **kwargs)
2657 """Outputs the structure to a file or string.
2658
2659 Args:
(...)
2674 is provided, the same string is written to the file.
2675 """
2676 fmt = fmt.lower()
-> 2678 if fmt == "cif" or fnmatch(filename.lower(), "*.cif*"):
2679 from pymatgen.io.cif import CifWriter
2681 writer = CifWriter(self, **kwargs)
AttributeError: 'PosixPath' object has no attribute 'lower'
```
### Minimal example
```Python
from pymatgen.core import Structure
from pathlib import Path
struct = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
struct.to(filename=Path("test.cif"))
```
### Relevant files to reproduce this bug
_No response_
|
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| 2,081,546,827
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PR_kwDOACgets5kENNG
| 3,552
|
Retain `Structure.properties` in `structure_from_abivars()`/`structure_to_abivars()` round trip
|
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[] | 2024-01-15T08:57:07
| 2024-01-15T12:05:19
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2024-01-15T12:05:18Z
|
MEMBER
|
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734a8d24e retain Structure.properties in structure_from_abivars()/structure_to_abivars() round trip
4cd59493a test_structure.py add self.struct.properties["foo"] = "bar" for test_to_from_abivars()
|
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PR_kwDOACgets5kEQxG
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Accept `Path` objects as `filename` in `IStructure.to()`
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[] | 2024-01-15T09:05:02
| 2024-01-15T11:45:42
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2024-01-15T11:45:41Z
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MEMBER
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Closes #3551.
1a39d626f accept Path objects as filename in IStructure.to()
5afdf01c7 add test case for saving structure to pathlib.Path
|
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PR_kwDOACgets5kFDkX
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Support `magmoms` in `get_phonopy_structure()`
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[
"Tagging @JonathanSchmidt1 as I have seen a similar fix in one of his atomate2 branches. ",
"@JaGeo My solution basically was the same as here.\r\n Maybe sth relevant for you is that when I added magnetic moments it broke sth in atomate2 because some of the functionalities of phonopy did not work with magnetic moments at the time.\r\nI assume this change in the materials project will lead to the workflow accepting magnetic structures automatically.\r\n``` \r\n get_phonopy_structure(structure)\r\n if use_symmetrized_structure == \"primitive\" and kpath_scheme != \"seekpath\":\r\n primitive_matrix: list[list[float]] | str = [\r\n [1.0, 0.0, 0.0],\r\n [0.0, 1.0, 0.0],\r\n [0.0, 0.0, 1.0],\r\n ]\r\n else:\r\n primitive_matrix = \"auto\"\r\n```\r\nFor me auto was not working with magmoms so I had to remove it. If this is still the case, it might be an option to give a warning in atomate2 and specifically disable auto for magnetic structures. \r\n",
"@JonathanSchmidt1 Thanks! I will keep the potential issue for atomate2 in mind."
] | 2024-01-15T11:03:32
| 2024-01-15T14:09:14
|
2024-01-15T14:08:43Z
|
CONTRIBUTOR
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## Summary
Phonopy needs magnetic moments to calculate the symmetry etc, currently pymatgen does not send it.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
python -m pytest tests/io/test_phonopy.py fails with "ImportError: cannot import name 'coord_cython' from 'pymatgen.util'", any ideas?
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I_kwDOACgets58GgKo
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`pymatgen.io.vasp` docs page is very slow to load and scroll
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[
"Oof thanks for reporting this @kuwabara74 and @janosh! Yes I've made this a private attr in #3491, which hopefully fixes the docs issue. Huge oversight on my part!",
"> Huge oversight on my part!\r\n\r\nNo worries. I didn't even know it would end up as 10k lines in the docs as a non-private attribute.\r\n\r\nAnyway, thanks for fixing in #3491."
] | 2024-01-15T13:52:06
| 2024-01-17T08:33:12
|
2024-01-17T08:33:12Z
|
MEMBER
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### Discussed in https://github.com/materialsproject/pymatgen/discussions/3554
<div type='discussions-op-text'>
<sup>Originally posted by **kuwabara74** January 15, 2024</sup>
Hello,
The documentation web page of pymatgen.io.vasp package (https://pymatgen.org/pymatgen.io.vasp.html) is too heavy to open immediately. I suppose that the contents of the Potcar class, the description of "potcarpotcar_summary_stats", are very very long.
Could you change the contents so that they do not appear on the web page or only part of the contents are shown?</div>
Thanks a lot for reporting this @kuwabara74. It's definitely the huge string repr of `potcar_summary_stats` that's causing this problem. No idea why it's showing that value in the first place. I assume if we turn this into a private class attribute, it would not be shown in the docs? What do you think @esoteric-ephemera?
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PR_kwDOACgets5kKsDM
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Fix `ValueError: Invalid fmt` with `Structure.to(fmt='yml')`
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2024-01-16T09:55:39Z
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96bbf50eb fix Structure.to(fmt='yml'), add Structure.FileFormats to ensure consistent format support and value err msg in Structure.to and Structure.from_file
02593cd21 test_structure.py cover fmt='yml' in test_to_from_file_string
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pymatgen.io.pwscf add symmetry
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[
"I am not a pymatgen developer, but I am working on a class that does basically this. \r\n\r\nMy two cents are that I would discourage crystal_sg as the amount of handpicked information you need to correctly provide the coordinates in terms of Wyckoff positions to QE is too large, and also you don't get the information back in terms of Wyckoff positions when you relax the structure. I have a prototype version that determines the right ibrav from the space group and gives the atomic coordinates in crystal coordinates. The symmetry is then used anyway.\r\n\r\nI cannot estimate when I could polish this enough to directly push it to pymatgen on my own, but I am happy to share what I have done so far if a developer wants to build on it. ",
"> I cannot estimate when I could polish this enough to directly push it to pymatgen on my own, but I am happy to share what I have done\r\n\r\nsounds good! if you can provide a good unit tests, i can take care of polishing"
] | 2024-01-16T14:37:00
| 2024-01-22T16:48:41
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NONE
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### Feature Requested
Hi! When would the pymatgen.io.pwscf support for symmetry be added? It would greatly reduce the computational complexity of the input files generated.
### Proposed Solution
Implementing a function to read symmetrised CIFs, and using the crystal_sg tag in quantum espresso
### Relevant Information
_No response_
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Error in Parsing Complex Chemical Formulas with Parentheses in pymatgen's Composition Class
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[
"thanks for the detailed bug report! should be a straightforward fix by turning the `if match` statement in `_parse_formula()` into a `while` loop to keep unpacking nested parens\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/20475b6e2ba9f7304f9cc2094b9fa4685c094c58/pymatgen/core/composition.py#L561-L571"
] | 2024-01-17T06:37:10
| 2024-01-22T16:27:53
|
2024-01-22T16:27:53Z
|
NONE
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### Python version
Python 3.10.12
### Pymatgen version
2023.12.18
### Operating system version
Ubuntu 22.04.3 LTS
### Current behavior
The `Composition` class in `pymatgen` fails to correctly parse strings containing complex chemical formulas, resulting in a `ValueError`. An example of such a formula that causes an error is as follows:
```python
pmg.Composition("(Bi2(Mg0.667Nb1.333)O7)((Bi2(Mg0.667Nb1.333)O7)0.9(SrCO3)0.1)((Bi2(Mg0.667Nb1.333)O7)0.7(SrCO3)0.3)")
```
The error seems to stem from the usage of parentheses in the expression, which is not properly interpreted by the `pymatgen` parser.
### Expected Behavior
The `Composition` class in `pymatgen` is expected to correctly parse and calculate the composition for complex chemical formulas, even those using parentheses. However, it has been observed that modifying the formula from
`(Bi2(Mg0.667Nb1.333)O7)((Bi2(Mg0.667Nb1.333)O7)0.9(SrCO3)0.1)((Bi2(Mg0.667Nb1.333)O7)0.7(SrCO3)0.3)`
to
`(Bi2(Mg0.667Nb1.333)O7)1((Bi2(Mg0.667Nb1.333)O7)0.9(SrCO3)0.1)((Bi2(Mg0.667Nb1.333)O7)0.7(SrCO3)0.3)`
allows for correct interpretation. However, this should be considered a workaround rather than a solution. The parser should ideally handle the original format without requiring such modifications.
### Minimal example
The following is a minimal example that reproduces the issue:
```Python
import pymatgen as pmg
# This chemical formula triggers the error
pmg.Composition("(C)((C)0.9(B)0.1)")
```
This code leads to a `ValueError: could not convert string to float: '1.00.9'`.
### Relevant files to reproduce this bug
No special files are needed to reproduce this issue. The problem can be replicated by running the above code in an environment where `pymatgen` is installed.
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| 2,086,053,717
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PR_kwDOACgets5kTlDg
| 3,560
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Pass file IO modes as kwarg
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[] | 2024-01-17T12:07:32
| 2024-01-17T12:36:58
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2024-01-17T12:36:57Z
|
MEMBER
|
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More explicit. Example:
```diff
- with open(path, "w") as file:
+ with open(path, mode="w") as file
```
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PR_kwDOACgets5kTotZ
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Remove deprecated `(to|from|as|get)_string` methods
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[
"Hi @janosh, thanks for keeping on top of deprecation notices. I think we may have been a bit premature here:\r\n\r\n* There was no notice on the [compatibility](https://pymatgen.org/compatibility.html) page.\r\n* An updated atomate2 has not been released yet. I see your PR https://github.com/materialsproject/atomate2/pull/690 got merged but since there was no subsequent release, the latest atomate2 is not compatible with latest pymatgen.\r\n\r\nI realize from a pymatgen maintainer point of view that it's not our responsibility to keep downstream codes working, but I do want to make sure we're mindful of community usage, especially for breaking changes which are not critical.",
"apologies, i had forgotten about the existence of the compatibility page. both the [initial deprecation](https://github.com/materialsproject/pymatgen/releases/tag/v2023.8.10) and [the recent removal](https://github.com/materialsproject/pymatgen/releases/tag/v2024.1.26) were in the release notes of course but perhaps a bit buried.\r\n\r\nthe deprecation period of 6 months was agreed upon with @shyuep who also green-lighted making the to-string API consistent (i.e. replace mixture of `get_str` and `get_string` with `get_str` everywhere).\r\ni suspect in `atomate2`, the deprecation warnings did not prompt any code updates until it actually broke because the warnings only show up in the logs when executing a workflow. the logs are quite verbose and so usually only inspected when a workflow fails. other community codes may have transitioned earlier and faster on account of the warnings being less buried. i suspect waiting longer would not have made much difference ito community transition (though I could be wrong)\r\n\r\ni'll add an entry to the compatibility page right now",
"Thanks @janosh! No worries, these things happen. But we should be careful, any breaking change has the potential to create a lot of work for a lot of people downstream, so we need to make sure such changes are strongly motivated (in this example, removing the deprecated functions does improve code cleanliness but given that the functions were already marked as deprecated, and their inclusion does not cause any performance issue, they could have been left around longer).\r\n\r\nThe point on logs is well taken. Ultimately, the lack of full, real integration tests has always been an atomate issue, but one that is difficult to address!",
"> The point on logs is well taken. Ultimately, the lack of full, real integration tests has always been an atomate issue, but one that is difficult to address!\r\n\r\ni was chatting with @Andrew-S-Rosen about that at some point who managed to setup very sophisticated CI which we tested in https://github.com/Quantum-Accelerators/quacc/pull/1285. it triggers integration tests on Princeton HPC that actually run VASP (even on 3rd party PRs). IIRC he suggested to run a small subset of atomate2 tests as well just to keep a tap on it. but long-term would be better to setup sth similar in `atomate2` itself",
"Yes, I do have a variety of integration tests going, which is how I caught https://github.com/materialsproject/pymatgen/issues/3586 so quickly (actually, many of my bug reports lately come from this since I am running less calculations myself these days...). I'm now taking advantage of on-prem HPC tests to such a degree that I should probably avoid adding on any other compute for things I don't actively use (i.e. atomate2). But indeed, having some sort of regular integration tests set up and synced to GitHub has been extremely valuable. Always happy to brainstorm with MP team about possible avenues."
] | 2024-01-17T12:17:46
| 2024-02-15T11:34:45
|
2024-01-17T13:42:07Z
|
MEMBER
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Deprecation period started with #3158 on Jul 15 2023 (6+ months ago).
Migration to the new API in all cases is to replace `(to|from|as|get)_string` with `(to|from|as|get)_str`.
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PR_kwDOACgets5kWE4G
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Deprecate `Structure.ntypesp` replaced by `Structure.n_elems`
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[] | 2024-01-17T18:55:43
| 2024-01-17T19:11:49
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2024-01-17T19:11:48Z
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MEMBER
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f202b7970 deprecate Structure.ntypesp replaced by Structure.n_elems
8b893efb0 fix structure_to_abivars() for non-hexagonal structures
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minimizing import overhead
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[
"@mturiansky thanks for profiling! such analysis is hugely appreciated!\r\n\r\nlazy-loading seems like a good UX improvement here. PR incoming",
"Actually, I'm not sure this solves the problem. Sorry, I probably could have been more clear in my description.\r\n\r\nThe reason this doesn't work is because the importing of pandas is not actually being done within `pymatgen.core.structure`. Pandas will be imported at the first invocation and then later invocations will simply read from the cached module. If you print out the full tree structure of `python -Ximporttime` (not putting here because of length), you'll see that pandas is actually being within `monty.json`. In monty, pandas is just an optional dependency though. If it exists, however, [it will be imported](https://github.com/materialsvirtuallab/monty/blob/5d37679e1f0cd58a8d165d76f3a095cb71266831/monty/json.py#L22C1-L25C30).\r\n\r\nPerhaps I should raise the issue with monty instead. If monty implements lazy loading also, then the change made here should work.\r\n\r\nThoughts?",
"By the way, here is the output from running importtime to show that the problem still exists:\r\n```\r\nimport time: self [us] | cumulative | imported package\r\nimport time: 2518 | 100511 | numpy\r\nimport time: 242 | 129682 | pandas.core.api\r\nimport time: 511 | 176807 | pandas\r\nimport time: 411 | 284171 | monty.json\r\nimport time: 732 | 327149 | pymatgen.core.composition\r\nimport time: 343 | 109818 | scipy.spatial\r\nimport time: 644 | 112443 | pymatgen.core.lattice\r\nimport time: 3964 | 534195 | pymatgen.core\r\n```",
"@mturiansky thanks for following up. https://github.com/materialsvirtuallab/monty/pull/604 refactors to lazy loading in `monty` also",
"This has become way more complicated than I had originally anticipated. The change implemented in monty is actually a significant regression:\r\n```\r\nimport time: self [us] | cumulative | imported package\r\nimport time: 2044 | 100229 | numpy\r\nimport time: 347 | 106559 | monty.json\r\nimport time: 713 | 151276 | pymatgen.core.composition\r\nimport time: 338 | 101914 | scipy.spatial\r\nimport time: 677 | 104410 | pymatgen.core.lattice\r\nimport time: 210 | 121982 | pandas.core.api\r\nimport time: 441 | 164693 | pandas\r\nimport time: 472242 | 6429146 | pymatgen.symmetry.groups\r\nimport time: 778 | 6432398 | pymatgen.symmetry.maggroups\r\nimport time: 4142 | 6450731 | pymatgen.core.structure\r\nimport time: 3584 | 6760861 | pymatgen.core\r\n```\r\nIt seems that not only is pandas still getting imported, it's getting imported with considerably higher overhead. Furthermore, since pydantic, bson, and torch are not installed in my environment, the interpreter attempts to import them over and over. The try except statement allows it to make this attempt over and over rather than just failing.",
"ok, so this is too much effort. I don't think a startup is an issue for most people. One shouldn't be starting up pymatgen again and again in most use cases anyway. I will revert the change. If you have a solution, feel free to implement in monty and release.",
"The use case that comes to mind is in a CLI, where you might call a script several times.\r\n\r\nI will take a look at monty and see what I can do when I have some free time. Are you opposed to removing the try-except statements or if my solution does away with them would that be okay?",
"I would be opposed to removing try except because I want monty to be usable without those dependencies. If your solution keeps that and does not require try except, it is fine iwth me.",
"I think @mturiansky raises a good point overall, we want pymatgen to be lean, and that includes startup times. As long as the fix doesn’t create a mess, I’m in favor of it.",
"I would just say that anything that requires calling a script several times probably is better off looping in python, in which the import is done only once. Anyway, I am all for a solution that reduces startup times without mess. \r\n",
"> I would just say that anything that requires calling a script several times probably is better off looping in python, in which the import is done only once.\r\n\r\nSure that's an obvious thing to say, but that's not always possible if you're trying to develop modular code, allowing the user to choose how they would like to interact with it. Returning to my original example of CLI, consider a script which can be used to do preprocessing and postprocessing of data, while running some other program in between. Sure, you could \"throw it in a loop\" and have python run the program for you, but that's not feasible for everyone. That also may entail developing significant amounts of automation code to run the program. Not everyone has a data-centric approach.\r\n\r\nYou could argue that two imports isn't a big deal for performance, and I'd agree. This is mainly a UX issue: half a second load times is noticeable for a user, especially when the import time is longer than the time it takes for the code to process the data. Half a second was just the number on my computer, some clusters have slow home directories for which import times can be much longer. @mkhorton hit the nail on the head with my intention for this request."
] | 2024-01-18T06:52:15
| 2024-01-25T00:41:06
|
2024-01-22T16:13:29Z
|
CONTRIBUTOR
|
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### Feature Requested
I noticed that pymatgen can have quite an overhead when importing relatively simple pieces of code from within. From a computing point of view, it's a rather small cost (and something inherent to python), but from a UX perspective, it can be quite noticeable. Take the simple example of importing the `Structure` class. This is something fairly fundamental to pymatgen, and I find myself using quite frequently in my own code. However, just importing Structure takes half a second on my computer:
```sh
» python -Ximporttime -c 'from pymatgen.core import Structure' 2>&1 | awk '($5 > 100000) {print}'
import time: self [us] | cumulative | imported package
import time: 259 | 142336 | pandas.core.api
import time: 658 | 197000 | pandas
import time: 412 | 298831 | monty.json
import time: 808 | 329711 | pymatgen.core.composition
import time: 4451 | 523381 | pymatgen.core
```
38% of the time is spent just importing pandas! Looking at `pymatgen.core.structure`, only [one line](https://github.com/materialsproject/pymatgen/blob/e6cc11c1c1832e9cdb56d7e09bbc97a23f495cae/pymatgen/core/structure.py#L2637) uses pandas.
### Proposed Solution
In this specific example, one solution would be to make pandas an optional dependency. Then only people who need pandas would pay the import penalty. Another solution would be implementing lazy loading [[1]](https://github.com/pytest-dev/apipkg) [[2]](https://github.com/scientific-python/lazy_loader), which would allow pandas to be a required dependency while avoiding the overhead. If implemented more broadly across pymatgen, lazy loading could have a more significant reduction in overhead, but would obviously require more work and may not be worth the effort.
### Relevant Information
_No response_
|
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| 2,091,950,831
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PR_kwDOACgets5knuRY
| 3,564
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Ruff fixes
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[] | null |
[
"Hi @janosh, I found some bugs on Ruff when it recently upgraded to `0.1.14`.\r\nWhen I firstly run `ruff format --check .` locally, it has the warning of \"The following rules may cause conflicts when used with the formatter: `ISC001`.\"\r\nThus I added the conflict formatter `ISC001` into `pyproject.toml` ignore configuration,\r\nhttps://github.com/Zhuoying/pymatgen/blob/90700f92adcdd74137565f3ed1088a00004c44af/pyproject.toml#L80\r\n[https://github.com/Zhuoying/pymatgen/blob/90700f92adcdd74137565f3ed1088a00004c44af/pyproject.toml#L88](url)\r\nthen the warning disappear but still with the error below:\r\n<img width=\"525\" alt=\"Screenshot 2024-01-24 at 12 31 33 AM\" src=\"https://github.com/materialsproject/pymatgen/assets/10410019/5c4cbdfd-c63a-41db-8c4f-0d764b416460\">\r\nAny idea on this? Thanks~",
"exit code 1 means the file you were editing needs formatting changes. i think we can ignore the warning about `ISC001` but either way, it's independent from the exit code you're getting"
] | 2024-01-20T07:43:33
| 2024-01-24T10:05:55
|
2024-01-20T14:32:08Z
|
MEMBER
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47b91ebc9 fix ruff SIM300 Yoda asserts
2d8571f4c fix ruff F841 local var assigned but never used
6c278aa33 fix ruff SIM113 use enumerate() for index variable
c9d67d973 fix ruff RUF021 parenthesize `a and b` when chaining `and` and `or` together
386b969ec fix likely unintentional operator precedence in LobsterEnv._find_relevant_atoms_additional_condition()
b60e68a72 fix ruff E226 missing whitespace around arithmetic op
882452e48 fix super.__init__() call missing parens
|
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