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PR_kwDOACgets5YSUBy
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Add VASP input set `MatPESStaticSet`
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[
"@SophiaRuan This looks good. But I would like @JiQi535 to go through it carefully and make sure everything is correct.",
"A few remarks given the updates to MP's GGA and r2SCAN WFs:\r\n- LREAL should be False for statics (consistent with how we do MP statics)\r\n- It says this is set is intended to r2SCAN, but the default is PBE? Otherwise, GGA = None and METAGGA = R2SCAN is needed (the GGA = None is needed for the more recent versions of VASP)\r\n- LAECHG should be False unless you plan on using the AECCAR* files\r\n- Same with LCHARG and the CHG/CHGCAR files\r\n- Same with LVTOT and the LOCPOT / POT files\r\n\r\nIf you want to contribute the statics to MP-core, then unfortunately you need LAECHG, LCHARG, and LOCPOT set to true for consistency with the r2SCAN WF. It'll just slow things down slightly with the file I/O\r\n\r\nWe're working on independently testing the differences in energies / forces / stresses for ISMEAR = 0 and -5. We may ultimately stay with ISMEAR = -5 for DOS / bandstructures / thermo properties, but that does mean incorrect forces for metals",
"@esoteric-ephemera this input set is for MatPES (as the name implies). While we are happy to contribute to MPstatics if MP wants them, forces are a priority here. Perhaps more so than even energies. \n\nI am unsure why MP would want to stick to ISMEAR -5 for all statics. The evidence is quite conclusive than 0 works as well for insulators and certainly better for metals. So what is the advantage of sticking with -5?",
"@shyuep I saw the work from your group for these differences, my only concern is that the average absolute energy differences between the two smearing methods is ~1 eV, which can be large on the scale of energy differences relevant for thermoprops (~5-10 meV/atom). Would be good to see these differences in eV/atom instead of eV\r\n\r\nI'm also not sure what the effect of ISMEAR is on the DOS / KS eigenvalues / bandgap. We usually assume ISMEAR = -5 gives a better description of the actual electronic structure, but we're testing this now",
"@esoteric-ephemera ok. Would be good to have independent validation. ",
"-5 should give a much better band gap based on DOS.",
"@esoteric-ephemera This is just my intuition. But if you use a small enough SIGMA, the DOS effect is small. After all, a smearing of 0.02 can't lead to more than a 0.04 eV error in band edges. In the grand scheme of DFT errors in band gaps, it is practically nothing. ",
"> @SophiaRuan This looks good. But I would like @JiQi535 to go through it carefully and make sure everything is correct.\r\n\r\nI have checked @SophiaRuan's implementation of MatPESStaticSet, and it looks nice to me. I have below questions.\r\n\r\n1. It seems to me that +U is by default not added. Isn’t this conflicting with the default in MPRelaxSet and MPStaticSet?\r\n2. In MPRelaxSet, there are 89 elements, same as the current coverage by MP. While for the new set, we have 97 elements. Some of the extra elements are Fr, Ra, Rn. @janosh I’m curious if and why they are added 😃 \r\n3. LVTOT=True. We don’t have this in MPStaticSet. Is MP storing this data? @janosh \r\n",
"Just adding this paper here for my comment on the DOS computations (a smearing of 0.05 was used):\r\nhttps://www.sciencedirect.com/science/article/pii/S277294942200002X",
"> 2 In MPRelaxSet, there are 89 elements, same as the current coverage by MP. While for the new set, we have 97 elements. Some of the extra elements are Fr, Ra, Rn. @janosh I’m curious if and why they are added 😃\r\n\r\n@JiQi535 They were copied from [`MPSCANRelaxSet`](https://github.com/materialsproject/pymatgen/blob/b874c73851d133e542c5a13183ce6f123147f13b/pymatgen/io/vasp/MPSCANRelaxSet.yaml#L28) IIRC.\r\n\r\n> 3 LVTOT=True. We don’t have this in MPStaticSet. Is MP storing this data? @janosh\r\n\r\nNo.",
"No. PBE default. U and r2scan as options. This is not MP. ",
"The lint and test failures are unrelated to the PR. I am merging.",
"They're not unrelated. The 1st `TestMatPESStaticSet ` `assert` fails:\r\n\r\n```sh\r\npytest tests/io/vasp/test_sets.py -k TestMatPESStaticSet -vv\r\n```\r\n\r\n```py\r\n_____________________________ TestMatPESStaticSet.test_init ______________________________\r\n\r\nself = <tests.io.vasp.test_sets.TestMatPESStaticSet testMethod=test_init>\r\n\r\n def test_init(self):\r\n prev_run = f\"{TEST_FILES_DIR}/relaxation\"\r\n \r\n vis = MatPESStaticSet.from_prev_calc(prev_calc_dir=prev_run)\r\n # Check that INCAR settings were load from yaml, check the default functional is PBE.\r\n CONFIG = _load_yaml_config(\"MatPESStaticSet\")\r\n> assert vis.incar == CONFIG[\"INCAR\"]\r\nE AssertionError: assert {'PREC': 'acc...ORBIT': False} == {'ALGO': 'Nor...5, 'Yb3+': 1}}\r\nE Omitting 3 identical items, use -vv to show\r\nE Differing items:\r\nE {'PREC': 'accurate'} != {'PREC': 'Accurate'}\r\nE {'ISMEAR': -5} != {'ISMEAR': 0}\r\nE {'MAGMOM': [0.6]} != {'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 0.6, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7,...4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}}\r\nE {'SIGMA': 0.2} != {'SIGMA': 0.05}\r\nE {'LORBIT': False} != {'LORBIT': 11}...\r\n```",
"I just noticed one problem. Why is the INCAR written as `return Incar(self.prev_incar or parent_incar)`? This is wrong. If the prev_incar is a relaxation, this will make it a relaxation calculator too."
] | 2023-08-19T00:05:50
| 2023-08-28T15:53:44
|
2023-08-28T15:47:03Z
|
CONTRIBUTOR
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## Summary
Major changes:
- feature 1: add MatPESStaticSet class
## Todos
If this is work in progress, what else needs to be done?
1. make sure all the input set default settings are right.
2. write unit tests
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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PR_kwDOACgets5YShPc
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Don't let tests pollute the `pymatgen` repo
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2023-08-19T15:21:16Z
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MEMBER
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All temporary test files should be written to temporary directories. This PR fixes the worst/most obvious offenders but probably many tests left writing to the current working or module directory.
f94f7a323 delete unused tests/files/chemenv/images/detailed_voronoi_container_coordination_numbers_1.png
bb4f4faf5 mv tests/files/chemenv/{json_test_files,json} mv tests/files/chemenv/structure_environments{_files,}
dec01937c remove all shutil.rmtree from tests
c3e11d6e1 pmg test_entrypoint run in tmp_path
7f4bd0357 refactor TestVampireCaller
b834872aa delete all def setUp(self): warnings.simplefilter("ignore")
e4a84c799 delete questionable def tearDown(self): del self.attrs
a0274dba8 remove all unused unittest.main()
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Fix bug in feff inputs.py
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"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`100.00%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`5f369ec`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/5f369ec4c1205fd158e8030281a8b5a9585bc957?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.69% compared to head [(`0018837`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.12%.\n> Report is 1 commits behind head on master.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3256 +/- ##\n==========================================\n- Coverage 74.69% 74.12% -0.57% \n==========================================\n Files 230 230 \n Lines 69375 69374 -1 \n Branches 16154 16154 \n==========================================\n- Hits 51818 51423 -395 \n- Misses 14490 14918 +428 \n+ Partials 3067 3033 -34 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/feff/inputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vZmVmZi9pbnB1dHMucHk=) | `82.69% <100.00%> (-0.04%)` | :arrow_down: |\n\n... and [7 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n",
"Thanks for the merge @janosh! "
] | 2023-08-19T03:04:38
| 2023-08-22T17:02:26
|
2023-08-22T16:52:50Z
|
CONTRIBUTOR
|
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## Summary
I found a small bug inside the feff.inputs module. The absorbing_atom index is misused in the following sentence, which generated a bug.
```python
atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
```
When I created a cluster using ```inputs.Atoms```,there is an error, since ```absorbing_atom``` in the argument is the index of the absorbing atom in the original structure, but the above sentence misused this index for the absorbing atom in the generated cluster, which should be 0. If we create a particle that has fewer atoms than the assigned index of the absorbing atom in the original structure, it can generate an IndexError.
For example:
the original structure has 55 U atoms and assigns a U atom with index 54 as the absorber, but we generate a particle that only has 30 atoms, so the index is mismatched and will prompt the following error.
I resubmitted this PR, since the previous one shows too many conflicts.
Major changes:
- feature: fix encountered IndexError error
- fix 1: delete
```python
atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
```
Firstly, I changed this ```absorbing_atom``` argument to 0. However, after scrutinizing the codes, I found that this sentence was redundant, so I deleted it.
- fix 2: modify one line:
```python
self.pot_dict = get_atom_map(self._cluster, self.absorbing_atom)
```
- add test file and updae ```test_set.py``` with a test function
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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PR_kwDOACgets5YVAoR
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Google-style doc string return types
|
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[] | 2023-08-20T20:42:55
| 2023-08-21T17:56:45
|
2023-08-21T17:56:44Z
|
MEMBER
|
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4276e4e90 delete analysis/solar/slme.py matrix_eigvals()
fcdd31188 fix whitespace
6d6026242 mv tests/io/lobster/test_{lobster,inputs}.py
89f454dd3 str concat to f-str
136590b4f use isinstance(x, Iterable) over hasattr(x, "__iter__")
4819d944c delete needless bool(...) calls
609cb75fc fix bad f-str conversion
ac1247dee fix typos, use f-strings, remove docs_rst from .gitattributes linguist-vendored
702b5f73b delete dead code in pymatgen/electronic_structure/boltztrap2.py
5411e52f7 google-style doc string return types
|
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I_kwDOACgets5u0Kzl
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NameError when importing dos from pymatgen.electronic_structure
|
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[
"Your import works for me. Try `pip uninstall pymatgen -y && pip install -U pymatgen` and then run your script again. Feel free to report back if that doesn't help."
] | 2023-08-21T11:26:45
| 2023-08-21T14:39:04
|
2023-08-21T14:38:37Z
|
NONE
|
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#### Description
When I try to import
```py
from pymatgen.electronic_structure import dos
```
I get:
```py
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 625, in <module>
class CompleteDos(Dos):
File "/usr/local/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 814, in CompleteDos
band: OrbitalType = OrbitalType.d,
NameError: name 'OrbitalType' is not defined
```
It is from a previously working script, so I am not sure if there was a change to the version or why it is not working any more.
#### Environment
Relevant versions and platform info:
- OS: Mac (macOS Catalina)
- Version (e.g. v2023.05.10)
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PR_kwDOACgets5YaGOC
| 3,260
|
Update `compatibility.md`
|
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[] | 2023-08-21T16:49:56
| 2023-08-21T17:36:53
|
2023-08-21T17:13:04Z
|
CONTRIBUTOR
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Add a note on the breaking changes made in https://github.com/materialsproject/pymatgen/commit/5b88fc181d8ab97a7d1d3c47692cefdf673888c5.
|
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Fix `Procar.get_projection_on_elements` for structures with multiple same-element ionic sites
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[
"Hello @janosh,\r\nI have added the test code for get_projction_on_elements() when the structure have multiple ionic sites with the same elements. Please check if it meets the requirements."
] | 2023-08-22T01:30:31
| 2023-08-23T16:07:08
|
2023-08-23T16:06:41Z
|
CONTRIBUTOR
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## Summary
Major changes:
Fixes a bug in the get_projection_on_elements function of Procar. In the current version, the code computes projections only for the final ion of each element when there are multiple ionic sites of the same element in the structure. To ensure projections are correctly computed and accumulated for all ions, I have corrected the assignment operator from '=' to '+='."
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I_kwDOACgets5u-I0R
| 3,262
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from pymatgen.analysis.graphs import MoleculeGraph gives ImportError: cannot import name 'which'
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[
"`which` was removed from `monty` in favor of std lib `shutil.which` a while ago. Please update your `pymatgen` version or downgrade your `monty`.",
"Many thanks! I was able to resolve the issue by downgrading my monty package as follows:\r\n\r\n pip install 'monty==2022.4.26' --force-reinstall\r\n\r\nNow it seems to work as expected!"
] | 2023-08-22T16:12:45
| 2023-08-24T14:09:21
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2023-08-23T22:30:30Z
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NONE
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#### Description
When running `from pymatgen.analysis.graphs import MoleculeGraph` , I get the error `ImportError: cannot import name 'which'`. Some googling suggests it is perhaps related to Python 2 compatibility? This system does not have Python 2 . I am using Python 3.6.8 from miniconda
#### Repro
```
[hussaif1@delltower48 VOID]$ python
Python 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pymatgen.analysis.graphs import MoleculeGraph
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/hussaif1/miniconda3/envs/VOID/lib/python3.6/site-packages/pymatgen/analysis/graphs.py", line 22, in <module>
from monty.os.path import which
ImportError: cannot import name 'which'
```
#### Expected behavior
No error on import
#### Environment
RedHat 8. Miniconda 3.8 ( also tried with Miniconda 3.11 ).
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Cancel concurrent CI runs to save budget
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[
"@henryiii More projects benefiting from https://learn.scientific-python.org/development/guides/repo-review/\r\n\r\nThanks again for such a useful tool!",
"@jarrodmillman Just curious if you guys have any tricks to suppress the \"Run cancelled\" email notifications from GitHub? Saw [this popular community discussion](https://github.com/orgs/community/discussions/13015) which looks like there's no way to configure that atm?",
"I've not seen one yet, other than setting up a filter in your mail application/service. :) But I haven't looked very hard or very recently."
] | 2023-08-23T03:21:54
| 2023-08-23T14:46:20
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2023-08-23T14:39:46Z
|
MEMBER
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If a PR receives commits in short succession, CI runs for previous commits are cancelled, leaving only the runs for the last commit to run to conclusion. This avoids wasted compute on testing outdated code.
As suggested by [https://scientific-python.github.io/repo-review](https://scientific-python.github.io/repo-review/?repo=materialsproject%2Fpymatgen&branch=master). Thanks @jarrodmillman for the pointer.
60617e2fc add concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true
019cb66a6 add commit hook https://github.com/adamchainz/blacken-docs
8349d2c8a use assignment for single-key dict.update()
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Add `properties` to Structure and Molecule
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[
"Thanks @gpetretto for taking this on! Looks promising. 👍 \r\n\r\nI think we need better file IO support before merging. Right now, the properties are written to JSON\r\n\r\n```py\r\njson_str = struct_with_props.to(fmt=\"json\")\r\nassert '\"test_property\": 42' in json_str\r\n```\r\n\r\nbut they're not read back in `Structure.from_str`, i.e. this fails:\r\n\r\n```py\r\nstruct = Structure.from_str(json_str, fmt=\"json\")\r\nassert struct.properties == props\r\n```\r\n\r\nAs I mentioned in https://github.com/materialsproject/pymatgen/issues/2884#issuecomment-1577522801 it would be nice to retain properties when reading and writing to as many file formats as possible. JSON at least is easy to do.",
"@arosen93 @utf Would you mind taking a look at this to ensure it addresses your use cases?",
"At a very quick glance, this seems reasonable. Once merged, I will need to update the ASE atoms adapter to ensure this is handled nicely. But that's for me to deal with. ",
"Thanks @gpetretto! 👍 ",
"@gpetretto: Any thoughts about (de)serialization with the new `.properties` flag? In principle, a user can define `.properties` such that it contains data that is not jsonable or that makes the following fail. Is this something where we put the onus on the user, or should we be incorporating some sort of check?\r\n\r\n```python\r\nd = jsanitize(structure, strict=True, enum_values=True)\r\nMontyDecoder().process_decoded(d)\r\n```",
"Good question! Not obvious what's the best solution here. We could issue a silenceable runtime warning when users set non-JSONable `properties`.",
"This is a good point. I actually did not think much about this kind of problems since in my view `properties` is somewhat equivalent to the `site_properties`, which suffer from the same limitation. \r\nIn general, adding non serializable properties could still be a valid use case, as long as the structure in not serialized. So, I would not strictly prevent a user from doing that. In any case one would get an error when trying to dump the structure to a file."
] | 2023-08-23T08:01:45
| 2023-08-31T13:20:21
|
2023-08-24T18:41:48Z
|
CONTRIBUTOR
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Closes #2884.
This PR implements a `properties` attribute for `Structure` and `Molecule`. I also modified the `Poscar` object to store the `predictor_corrector_preamble` in the structure properties.
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I_kwDOACgets5vCzNY
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Issues with properties of copied/modified structures/molecules
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[] | 2023-08-23T10:05:23
| 2023-08-24T17:44:45
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2023-08-24T17:44:45Z
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CONTRIBUTOR
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Hello,
#### Description
When modifying structures or molecules (e.g. with the replace_species method, but other modifications will likely be the same), some of the modified structures/molecules properties are wrong. Simple example for the number of electrons, it is defined in the __init__.
#### Repro
Steps to reproduce the behavior:
Create one molecule:
```
from pymatgen.core.structure import Molecule
mlc = Molecule(['Li','H'], [[0,0,0], [0,0,1]])
print(mlc.nelectrons)
```
This gives 4.0 electrons.
Modify the molecule:
```
mlc2 = mlc.replace_species({'Li': 'H'}, in_place=False)
print(mlc2.nelectrons)
```
This should give 2.0 electrons (gives 4.0).
Same goes with the in_place=True:
```
mlc.replace_species({'Li': 'H'}, in_place=True)
print(mlc.nelectrons)
```
This should also give 2.0 electrons (gives 4.0).
#### Expected behavior
See above.
#### Environment
Latest pymatgen version from pypi (2023.8.10)
#### Additional context
This is just one example for the nelectrons property, but there might be other things that may need to be checked (in particular those that are initialized during the __init__). One solution could be to move the "calculation" of the number of electrons (and other possible affected properties) inside their respective property methods. Another one could be to recompute these when there is a modification. In the latter case though, when adding new properties in the future (if any, and if they are "precomputed" at __init__ stage), all modification methods should be checked. I would be willing to provide a PR in one or another direction (or any other alternative proposed).
Thanks for the input!
|
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PR_kwDOACgets5YoaGW
| 3,266
|
Fix `TestMPScanStaticSet.test_as_from_dict()`
|
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[] | 2023-08-23T20:22:27
| 2023-08-23T21:13:30
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2023-08-23T21:13:29Z
|
MEMBER
|
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Thanks @SophiaRuan for catching!
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Bump activesupport from 7.0.6 to 7.0.7.2 in /docs
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[] | 2023-08-23T21:50:16
| 2023-08-23T21:51:24
|
2023-08-23T21:51:23Z
|
CONTRIBUTOR
|
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Bumps [activesupport](https://github.com/rails/rails) from 7.0.6 to 7.0.7.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/rails/rails/releases">activesupport's releases</a>.</em></p>
<blockquote>
<h2>7.0.7.2 release</h2>
<p>No changes between this and 7.0.7.2. This release was just to fix file permissions in the previous release.</p>
<h2>7.0.7.1</h2>
<h2>Active Support</h2>
<ul>
<li>
<p>Use a temporary file for storing unencrypted files while editing</p>
<p>[CVE-2023-38037]</p>
</li>
</ul>
<h2>Active Model</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Active Record</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Action View</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Action Pack</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Active Job</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Action Mailer</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Action Cable</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/rails/rails/blob/v7.0.7.2/activesupport/CHANGELOG.md">activesupport's changelog</a>.</em></p>
<blockquote>
<h2>Rails 7.0.7.2 (August 22, 2023)</h2>
<ul>
<li>No changes.</li>
</ul>
<h2>Rails 7.0.7.1 (August 22, 2023)</h2>
<ul>
<li>
<p>Use a temporary file for storing unencrypted files while editing</p>
<p>[CVE-2023-38037]</p>
</li>
</ul>
<h2>Rails 7.0.7 (August 09, 2023)</h2>
<ul>
<li>
<p>Fix <code>Cache::NullStore</code> with local caching for repeated reads.</p>
<p><em>fatkodima</em></p>
</li>
<li>
<p>Fix <code>to_s</code> with no arguments not respecting custom <code>:default</code> formats</p>
<p><em>Hartley McGuire</em></p>
</li>
<li>
<p>Fix <code>ActiveSupport::Inflector.humanize(nil)</code> raising <code>NoMethodError: undefined method `end_with?' for nil:NilClass</code>.</p>
<p><em>James Robinson</em></p>
</li>
<li>
<p>Fix <code>Enumerable#sum</code> for <code>Enumerator#lazy</code>.</p>
<p><em>fatkodima</em>, <em>Matthew Draper</em>, <em>Jonathan Hefner</em></p>
</li>
<li>
<p>Improve error message when EventedFileUpdateChecker is used without a
compatible version of the Listen gem</p>
<p><em>Hartley McGuire</em></p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/rails/rails/commit/3668b4b5978822f1e6311c7fd7a32f58daee136a"><code>3668b4b</code></a> Preparing for 7.0.7.2 release</li>
<li><a href="https://github.com/rails/rails/commit/2294b8b27a95f12bb25a891d1ce8f3f68c6af601"><code>2294b8b</code></a> Bumping version</li>
<li><a href="https://github.com/rails/rails/commit/c92caefc2bdf856845a72b8608d5603b330e8c3e"><code>c92caef</code></a> Preparing for 7.0.7.1 release</li>
<li><a href="https://github.com/rails/rails/commit/936587d49b3d490462c794b30fb672cef43e1bd0"><code>936587d</code></a> updating version / changelog</li>
<li><a href="https://github.com/rails/rails/commit/a21d6edf35a60383dfa6c4da49e4b1aef5f00731"><code>a21d6ed</code></a> Use a temporary file for storing unencrypted files while editing</li>
<li><a href="https://github.com/rails/rails/commit/522c86f35ccc80453ed9fb6ca8b394db321f9a69"><code>522c86f</code></a> Preparing for 7.0.7 release</li>
<li><a href="https://github.com/rails/rails/commit/5610cbacc5630d775a1a7be78ccb17e561908cba"><code>5610cba</code></a> Sync CHANGELOG with the changes in the repository</li>
<li><a href="https://github.com/rails/rails/commit/7e9ffc2e137b649c6fd2ca1c580cdfffc9845b55"><code>7e9ffc2</code></a> Fix to_s not using :default format with no args</li>
<li><a href="https://github.com/rails/rails/commit/a8e88e2e4f157e47050d4ba17ea936902f6a2994"><code>a8e88e2</code></a> Fix <code>Cache::NullStore</code> with local caching for repeated reads</li>
<li><a href="https://github.com/rails/rails/commit/b18b9df65eb7d4e5dfa9a6982a8709c0c94b0b97"><code>b18b9df</code></a> Merge pull request <a href="https://redirect.github.com/rails/rails/issues/48800">#48800</a> from robinjam/fix-humanize-nil</li>
<li>Additional commits viewable in <a href="https://github.com/rails/rails/compare/v7.0.6...v7.0.7.2">compare view</a></li>
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PR_kwDOACgets5Yo2Dj
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Fix `TestMPStaticSet` using `MPRelaxSet` in `test_user_incar_kspacing` and `test_kspacing_override`
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[] | 2023-08-23T22:14:24
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2023-08-23T22:19:23Z
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MEMBER
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d568f04aa fix `TestMPStaticSet` running with `MPRelaxSet` instead of `MPStaticSet` in `test_user_incar_kspacing` and `test_kspacing_override`
86f03dec7 add `self.set` attribute to `InputSetTests` to make it harder to use the wrong `InputSet` in a test
Again, thanks for reporting @SophiaRuan.
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PR_kwDOACgets5Yt3xW
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Fix `nelectrons` not updating when replacing species in `Molecule`
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[] | 2023-08-24T17:18:22
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2023-08-24T17:44:44Z
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Closes #3265.
I briefly checked for other `Molecule` attributes that are currently static but might need to change when modifying in place but didn't find any.
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PR_kwDOACgets5Yuhhv
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Breaking: Update `AseAtomsAdaptor` to handle `Structure.properties`/`Molecule.properties`
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[
"I see you @shyuep! 👀😅\n\nI plan to finish this PR later today.",
"@janosh: When you're back on GitHub, would you mind helping me out with the `mypy` issue? I think it might be because `.properties` is not a `@property` attribute of `Structure` or `Molecule`, but I'm not 100% sure. Thank you 🙏 Not urgent!"
] | 2023-08-24T19:37:34
| 2023-09-28T01:49:42
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2023-08-31T09:56:22Z
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Ensure `Structure.properties` and `Molecule.properties` do not get lost with ASE `Atoms` interconversion.
Recent PR that added `properties`: #3264
Breaking because `IMolecule.__eq__` and `IStructure.__eq__` were changed to check `self.properties == other.properties`. See https://github.com/materialsproject/pymatgen/pull/3270#discussion_r1311253937.
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I_kwDOACgets5vNdd2
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line 1118 in cif.py needs removed
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[] | 2023-08-24T19:59:47
| 2023-08-24T23:56:27
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2023-08-24T23:56:27Z
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CONTRIBUTOR
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https://github.com/materialsproject/pymatgen/blob/5409db9655516fd3b23ea6993c48d673ae567872/pymatgen/io/cif.py#L1118
This prevents you from getting a symmetrized structure that does not check the occupancy.
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PR_kwDOACgets5YvV4i
| 3,272
|
Fix `CifParser.get_structures(check_occu=False)`
|
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[] | 2023-08-24T23:13:52
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2023-08-24T23:56:26Z
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MEMBER
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Closes #3271.
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PR_kwDOACgets5Y1Xna
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Add `PotcarSingle.__repr__`
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2023-08-25T23:19:32Z
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MEMBER
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a35f8a8ff add WIP PotcarSingle.__repr__
321c04914 test_repr()
6c0267aaf ruff . --fix
77056eeb3 delete repeated words
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PR_kwDOACgets5Y2qg3
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`__str__` to `__repr__`
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MEMBER
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33af062fc use self-documenting f-string in reprs
07b1256f4 `TestLibxcFunc` add `test_repr`
03dc9318b use python behavior that `__str__` falls back to `__repr__` if not defined
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PR_kwDOACgets5Y8Foc
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Ion: handle dissolved gas formulas
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[
"@materialsproject/pymatgen-maintainers there are a handful of test failures here that seem unrelated to the changes in this PR. I believe I am up to date with the latest `master` branch; please advise if further changes are needed. Thanks!"
] | 2023-08-28T14:02:53
| 2023-08-28T15:32:25
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2023-08-28T15:32:25Z
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CONTRIBUTOR
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## Summary
`Ion.reduced_formula` does not correctly handle dissolved gas molecules, such as `O2`, for example:
```
>>> Ion.from_formula('O2').get_reduced_formula_and_factor()
('O', 2)
>>> Ion.from_formula('O2').formula
'O2 (aq)'
>>> Ion.from_formula('O2').reduced_formula
'O(aq)'
```
This PR modifies `Ion.get_reduced_formula_and_factor` to correctly report dissolved formulas of dissolved gases H2, N2, O2, F2, Cl2, and O3. It also updates the docstrings of `formula` and `reduced_formula`.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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PR_kwDOACgets5Y8plF
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Fix `test_valid_magmom_struct()` error message regex
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[] | 2023-08-28T15:34:55
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2023-08-28T15:58:15Z
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MEMBER
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0d86dd110 psps->PSPs in doc strings
798953cfd fix typo
0323c473b try fix test_valid_magmom_struct() err msg regex
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PR_kwDOACgets5Y9K7_
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Add F* diagram generator to pymatgen
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[
"@janosh \r\nEverything on this pull request looks good from my end. Let me know if there are any changes you want me to make.",
"@janosh \r\nI got the tests to work with just one cif that is already in the test files directory. Please let me know if there are other changes you would like.",
"@jonathanjdenney There are still 33 changed files and 23k changed lines which make this PR very hard to review. The purpose of these 3 files is obvious.\r\n\r\n\r\n\r\nCould you either explain the purpose of or remove the other 30 files?",
"@janosh \r\nSorry, I didn't realize it thinks I changed/added all those files. The ones you highlighted are the only ones I deliberately added. I'm guessing the others are the remnants of some merge error or something. I will get rid of them.",
"> @janosh Sorry, I didn't realize it thinks I changed/added all those files. The ones you highlighted are the only ones I deliberately added. I'm guessing the others are the remnants of some merge error or something. I will get rid of them.\r\n\r\nI'm looking through the extra files and in all of them they are treated as changed files but the addition and deletion lines are identical. I don't what happened, but the files are supposed to be there as they are in the main pymatgen code as well. I'm not quite sure how to move forward. Should I just delete those files from my local version and make that as a pull request? I feel like that would have the same problem of showing as 30 edited files. ",
"I think you need to run sth like\r\n\r\n```sh\r\ngit checkout master -- space/separated paths/to/files you/want/to/revert\r\n```",
"@jonathanjdenney I removed all the excess files and gzipped `pymatgen/analysis/fstar/neutron_factors.csv`. The tests look a bit meagre. Maybe you can think of more things to test? E.g. uncovered edge cases?",
"> @jonathanjdenney I removed all the excess files and gzipped `pymatgen/analysis/fstar/neutron_factors.csv`. The tests look a bit meagre. Maybe you can think of more things to test? E.g. uncovered edge cases?\r\n\r\nI added a few ValueError messages for situations I know won't work. Specifically structures with less than 3 unique sites, and neutron scattering for atomic numbers greater than 96. I'm having trouble thinking of any more edge cases than that. I'm not sure of any specific tests I can add. \r\n\r\nAlso I would like to set up a tutorial for this, as some of it's features are not all that intuitive. What would be the best way to go about setting that up?",
"Thanks. One thing I would like you to do is to instead of a `pymatgen/analysis/fstar/fstar.py` structure, choose either `pymatgen/analysis/fstar.py` or `pymatgen/analysis/fstar/__init__.py`. Right now the import requires an additional nesting, which is unnnecessary. I prefer the former unless you believe there will be many more modules to be implemented within fstar."
] | 2023-08-28T17:20:17
| 2024-11-13T17:53:23
|
CONTRIBUTOR
|
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I have written code that takes a list of symmetrized structure objects and generates an f* diagram automatically with the plotly library.
## 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_kwDOACgets5Y-gTP
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[WIP] revise MatPESStaticSet, inherit from DictSet
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[
"I was not able to directly commit to this PR, so I opened #3280 ",
"> I was not able to directly commit to this PR, so I opened #3280\r\n\r\nYou can push directly to this PR after @SophiaRuan adds you as a collaborator to her fork."
] | 2023-08-28T21:42:55
| 2023-08-29T15:20:35
|
2023-08-29T13:41:16Z
|
CONTRIBUTOR
|
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## Summary
Related PR: #3254
Major changes:
- feature 1: Revise MatPESStaticSet, inherit from DictSet
## Todos
Check if the previous Incar will override the default MatPESStaticSet Incar.
Check if the new settings added by Custodian will be updated.
## 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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```sh
pip install -U pre-commit
pre-commit install
```
|
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404 code for using the new MPRester
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[
"Pls report this to the mpapi repo. Pymatgen maintainers are not responsible for mpapi. "
] | 2023-08-29T00:11:12
| 2023-08-29T00:20:41
|
2023-08-29T00:20:41Z
|
NONE
|
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#### Description
When I run the following code under home internet
```
from mp_api.client import MPRester
USER_API_KEY='XXXX'
mpr = MPRester(USER_API_KEY)
mp_entries = mpr.get_entries_in_chemsys(['Li','Mn','O'])
```
The following message shows up:
```
MPRestError: REST query returned with error status code 404 on URL https://api.materialsproject.org/thermo/?_fields=entries&chemsys=Li-O&_limit=143 with message:
Response {"message":"no Route matched with those values"}
```
#### Environment
Relevant versions and platform info:
- Python: 3.9.13
- OS: Mac OS 12.6
- Version: pymatgen 2023.7.20, mp_api 0.29.7
|
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| 1,870,895,537
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PR_kwDOACgets5Y_qC3
| 3,280
|
Corrections for MatPESStaticSet and its tests
|
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[
"Linting and test workflows are failing. When you add a new input set, the hash test needs to be updated. The linting errors are easy to fix. Fix both first.",
"New PR #3281 was opened as the superset of the PR #3280 , so this #3280 can be closed."
] | 2023-08-29T05:12:08
| 2023-08-30T02:44:36
|
2023-08-30T02:44:36Z
|
CONTRIBUTOR
|
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Related PR: #3278 #3254
Tests now covers all MatPESStaticSet parameters.
Remaining question: While the default setting of MatPESStaticSet is without Hubbard U, when +U is enabled, the Hubbard U related parameters will be the same as MPRelaxSet. As I have noticed that MITRelaxSet and MPRelaxSet have different default parameters, I'm not sure if setting the defaults same as MPRelaxSet is the most correct.
|
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PR_kwDOACgets5ZFB0j
| 3,281
|
fix tests of MatPESStaticSet
|
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[
"The relevant tests pass. I merged."
] | 2023-08-29T21:31:05
| 2023-08-30T15:05:46
|
2023-08-30T15:05:38Z
|
CONTRIBUTOR
|
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## Summary
Related: #3280
Major changes:
- fix 1: fix test_sets.py
## Todos
Check if all the incar, kpoints and potcars are tested.
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
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I_kwDOACgets5vsX_M
| 3,282
|
as_dict returns a non-json serializable dictionary
|
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[
"In general, we recommend serialization and deserialization with the MontyJSONEncoder and MontyJSONDecoder, which support more types than just python primitives. The as_dict function is not meant to return a json serializable dict directly since there are many situations where we merely want a dictionary representation of non-primitives. E.g., numpy arrays are especially ubiquitous in science."
] | 2023-08-30T15:21:10
| 2023-08-30T15:31:39
|
2023-08-30T15:30:46Z
|
NONE
|
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#### Description
Calling the as_dict() method on a structure loaded in from a POSCAR returns a dictionary that can't be serialized. It appears the issue is with the selective dynamics that are stored as a numpy array.
#### Repro
I included my example script and the POSCAR I initialized the structure from in a zipped folder.
[pymatgen_as_dict_test.zip](https://github.com/materialsproject/pymatgen/files/12477187/pymatgen_as_dict_test.zip)
When running the script, I get this error:
```
Traceback (most recent call last):
File "c:\Users\coopy\OneDrive - UCB-O365\Research\my_scripts\pymatgen_as_dict_test.py", line 12, in <module>
json_object = json.dumps(struct.as_dict())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\coopy\anaconda3\envs\pymat\Lib\json\__init__.py", line 231, in dumps
return _default_encoder.encode(obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\coopy\anaconda3\envs\pymat\Lib\json\encoder.py", line 200, in encode
chunks = self.iterencode(o, _one_shot=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\coopy\anaconda3\envs\pymat\Lib\json\encoder.py", line 258, in iterencode
return _iterencode(o, 0)
^^^^^^^^^^^^^^^^^
File "C:\Users\coopy\anaconda3\envs\pymat\Lib\json\encoder.py", line 180, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type ndarray is not JSON serializable
```
#### Expected behavior
The script should write a json to the current working directory.
#### Environment
Relevant versions and platform info:
- OS: Windows 10
- Pymatgen Version: 2023.8.10
- Python Version: 3.9.7.final.0
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PR_kwDOACgets5ZKTcF
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|
Breaking: bump minimum Python version to 3.9
|
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[] | 2023-08-30T17:05:24
| 2023-08-30T17:56:15
|
2023-08-30T17:56:14Z
|
MEMBER
|
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Following suit with [`numpy` v1.25.0](https://numpy.org/doc/stable/release/1.25.0-notes.html) and [`pandas` v 2.1.0](https://pandas.pydata.org/pandas-docs/version/2.1.0/whatsnew/v2.1.0.html).
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PR_kwDOACgets5ZMOde
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|
[WIP] add custodian modified incar settings to incar and modify tests
|
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[] | 2023-08-31T01:54:38
| 2023-08-31T13:42:06
|
2023-08-31T13:42:05Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- feature 1: incar will update custodian added incar settings but will not change default incar settings
Problem:
I cannot update the incar settings with a new incar() method overriding DictSet incar. The test will all fail.
|
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PR_kwDOACgets5ZN_8J
| 3,285
|
Slightly relax the constraint satisfy condition of get_primitive_structure()
|
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[] | 2023-08-31T09:38:10
| 2023-08-31T13:02:24
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2023-08-31T13:02:23Z
|
CONTRIBUTOR
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## Summary
Context [here](https://matsci.org/t/varying-results-with-get-primitive-structure/41663). I finally took some time to figure out why this was happening and it turned out to be the check that compares the lattice parameters of the primitive structures found against the constraints. The equivalency check in the current implementation is too strict to account for small changes in the constraints, which is why I went with `np.isclose()` with its default `atol` and `rtol` parameters which should still be strict enough.
I also include two unit tests, one for a general `get_primitive_structure()` call with `constrain_latt` which was missing, and #another to ensure two very similar constraints result in the same primitive structure.
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PR_kwDOACgets5ZPYVC
| 3,286
|
`np.(arange->linspace)` in `io/vasp/optics.py` `get_delta`, `get_setp` and `epsilon_imag`
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[] | null |
[
"Thanks @LucasGVerga!"
] | 2023-08-31T13:42:11
| 2023-08-31T15:22:57
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2023-08-31T15:22:46Z
|
CONTRIBUTOR
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`np.linspace` ensures the array size is numerically stable. See the [`numpy.arange` warning](https://numpy.org/doc/stable/reference/generated/numpy.arange.html).
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PR_kwDOACgets5ZPmzH
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Add keyword `bandgap_tol: float = 1e-4` to `MPScanRelaxSet`
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[] | 2023-08-31T14:14:29
| 2023-08-31T14:35:38
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2023-08-31T14:35:37Z
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MEMBER
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159493440 add keyword `bandgap_tol: float = 1e-4` to `MPScanRelaxSet`
6decb99da add `test_bandgap_tol()` to `TestMPScanRelaxSet`
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MatPESStaticSet restore GGA tag removal if xc_functional.upper() == "R2SCAN"
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2023-09-01T12:04:22Z
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MEMBER
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13883af9c use str.split for INHERITED_INCAR_PARAMS
9d6ee83cb add MatPESStaticSet init type hints
a89090aaf move ValueError Unrecognized {xc_functional=} to top
aeebf008f refactor MatPESStaticSet def incar(self) -> Incar:
bfd947676 leave user-defined ALGO if set, always apply LADU if xc_functional.upper().endswith("+U") and restore removing GGA tag if xc_functional.upper() == "R2SCAN"
5b7ab3fa3 fix test_functionals
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Bump plotly from 5.11.0 to 5.16.1
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[//]: # (dependabot-start)
⚠️ **Dependabot is rebasing this PR** ⚠️
Rebasing might not happen immediately, so don't worry if this takes some time.
Note: if you make any changes to this PR yourself, they will take precedence over the rebase.
---
[//]: # (dependabot-end)
Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.16.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.16.1</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed issue with necessary columns from complex arguments dropped when interchanging dataframes [<a href="https://redirect.github.com/plotly/plotly.py/pull/4324">#4324</a>]</li>
</ul>
<h2>v5.16.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.24.1 to version 2.25.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2252----2023-08-11">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module. Notable changes include:
<ul>
<li>Add "Equal Earth" projection to geo subplots [<a href="https://redirect.github.com/plotly/plotly.js/pull/6670">#6670</a>],
with thanks to <a href="https://github.com/apparebit"><code>@apparebit</code></a> for the contribution!</li>
<li>Add options to include legends for shapes and <code>newshape</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6653">#6653</a>]</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <a href="https://data-apis.org/dataframe-protocol/latest/index.html">dataframe interchange protocol</a>, such as polars, vaex, modin etc. This protocol has priority on <code>to_pandas</code> call, but will only be used if pandas>=2.0.2 is installed in the environment.</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>toPandas()</code> method, such as Spark DataFrames, or a <code>to_pandas_df()</code> method, such as Vaex DataFrames.</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed Pandas performance warning issue caused by multiple <code>frame.insert</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4246">#4246</a>]</li>
</ul>
<h2>v5.15.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.20.0 to version 2.24.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2241----2023-06-07">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add pattern to pie, funnelarea, sunburst, icicle and treemap traces [<a href="https://redirect.github.com/plotly/plotly.js/pull/6601">#6601</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6619">#6619</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6622">#6622</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6626">#6626</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6627">#6627</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6628">#6628</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6629">#6629</a>], with thanks to <a href="https://github.com/thierryVergult"><code>@thierryVergult</code></a> for the contribution!</li>
<li>Add <code>texttemplate</code> to shape.label for parametric shapes i.e. line, rect and circle [<a href="https://redirect.github.com/plotly/plotly.js/pull/6527">#6527</a>],
with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add strict option to custom bundle command [<a href="https://redirect.github.com/plotly/plotly.js/pull/6557">#6557</a>],
with thanks to <a href="https://github.com/CallumNZ"><code>@CallumNZ</code></a> for the contribution!</li>
<li>Add <code>legend</code> references to traces and <code>legend2</code>, <code>legend3</code>, etc. to layout,
also add <code>visible</code> to legend i.e. to allow positioning multiple legends on a graph [<a href="https://redirect.github.com/plotly/plotly.js/pull/6535">#6535</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>legend.xref</code> and <code>legend.yref</code> to enable container-referenced positioning of legends [<a href="https://redirect.github.com/plotly/plotly.js/pull/6589">#6589</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>colorbar.xref</code> and <code>colorbar.yref</code> to enable container-referenced positioning of colorbars [<a href="https://redirect.github.com/plotly/plotly.js/pull/6593">#6593</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>to_pandas()</code> method, such as polars, cudf, vaex etc</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed another compatibility issue with Pandas 2.0, just affecting <code>px.*(line_close=True)</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4190">#4190</a>]</li>
<li>Empty pandas dataframe with facet row/column set no longer fails [<a href="https://redirect.github.com/plotly/plotly.py/pull/4038">#4038</a>]</li>
<li>Added some rounding to the <code>make_subplots</code> function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts [<a href="https://redirect.github.com/plotly/plotly.py/pull/4153">#4153</a>]</li>
<li>Sanitize JSON output to prevent an XSS vector when graphs are inserted directly into HTML [<a href="https://redirect.github.com/plotly/plotly.py/pull/4196">#4196</a>]</li>
<li>Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the <code>yref</code> parameter [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
<li>Remove <code>use_2to3</code> setuptools arg, which is invalid in the latest Python and setuptools versions [<a href="https://redirect.github.com/plotly/plotly.py/pull/4206">#4206</a>]</li>
<li>Fix <a href="https://redirect.github.com/plotly/plotly.py/issues/4066">#4066</a> JupyterLab v4 giving tiny default graph height [<a href="https://redirect.github.com/plotly/plotly.py/pull/4227">#4227</a>]</li>
<li>Fixed issue with <code>colors.n_colors</code> where generated RGB color values were not being constrained to stay between 0 and 255 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4110">#4110</a>]</li>
<li>Fix streamline figure factory with recent versions of Numpy</li>
<li>Fix issue with shapes and annotations not drawing on correct axis [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
</ul>
<h2>v5.14.1</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<h2>v5.14.0</h2>
<h3>Updated</h3>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.16.1] - 2023-08-16</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed issue with necessary columns from complex arguments dropped when interchanging dataframes [<a href="https://redirect.github.com/plotly/plotly.py/pull/4324">#4324</a>]</li>
</ul>
<h2>[5.16.0] - 2023-08-11</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.24.1 to version 2.25.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2252----2023-08-11">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module. Notable changes include:
<ul>
<li>Add "Equal Earth" projection to geo subplots [<a href="https://redirect.github.com/plotly/plotly.js/pull/6670">#6670</a>],
with thanks to <a href="https://github.com/apparebit"><code>@apparebit</code></a> for the contribution!</li>
<li>Add options to include legends for shapes and <code>newshape</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6653">#6653</a>]</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <a href="https://data-apis.org/dataframe-protocol/latest/index.html">dataframe interchange protocol</a>, such as polars, vaex, modin etc. This protocol has priority on <code>to_pandas</code> call, but will only be used if pandas>=2.0.2 is installed in the environment.</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>toPandas()</code> method, such as Spark DataFrames, or a <code>to_pandas_df()</code> method, such as Vaex DataFrames.</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed Pandas performance warning issue caused by multiple <code>frame.insert</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4246">#4246</a>]</li>
</ul>
<h2>[5.15.0] - 2023-06-08</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.20.0 to version 2.24.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2241----2023-06-07">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add pattern to pie, funnelarea, sunburst, icicle and treemap traces [<a href="https://redirect.github.com/plotly/plotly.js/pull/6601">#6601</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6619">#6619</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6622">#6622</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6626">#6626</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6627">#6627</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6628">#6628</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6629">#6629</a>], with thanks to <a href="https://github.com/thierryVergult"><code>@thierryVergult</code></a> for the contribution!</li>
<li>Add <code>texttemplate</code> to shape.label for parametric shapes i.e. line, rect and circle [<a href="https://redirect.github.com/plotly/plotly.js/pull/6527">#6527</a>],
with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add strict option to custom bundle command [<a href="https://redirect.github.com/plotly/plotly.js/pull/6557">#6557</a>],
with thanks to <a href="https://github.com/CallumNZ"><code>@CallumNZ</code></a> for the contribution!</li>
<li>Add <code>legend</code> references to traces and <code>legend2</code>, <code>legend3</code>, etc. to layout,
also add <code>visible</code> to legend i.e. to allow positioning multiple legends on a graph [<a href="https://redirect.github.com/plotly/plotly.js/pull/6535">#6535</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>legend.xref</code> and <code>legend.yref</code> to enable container-referenced positioning of legends [<a href="https://redirect.github.com/plotly/plotly.js/pull/6589">#6589</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>colorbar.xref</code> and <code>colorbar.yref</code> to enable container-referenced positioning of colorbars [<a href="https://redirect.github.com/plotly/plotly.js/pull/6593">#6593</a>], with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
</ul>
</li>
<li><code>px</code> methods now accept data-frame-like objects that support a <code>to_pandas()</code> method, such as polars, cudf, vaex etc [<a href="https://redirect.github.com/plotly/plotly.py/pull/4244">#4244</a>], [<a href="https://redirect.github.com/plotly/plotly.py/pull/4286">#4286</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed another compatibility issue with Pandas 2.0, just affecting <code>px.*(line_close=True)</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4190">#4190</a>]</li>
<li>Empty pandas dataframe with facet row/column set no longer fails [<a href="https://redirect.github.com/plotly/plotly.py/pull/4038">#4038</a>]</li>
<li>Added some rounding to the <code>make_subplots</code> function to handle situations where the user-input specs cause the domain to exceed 1 by small amounts [<a href="https://redirect.github.com/plotly/plotly.py/pull/4153">#4153</a>]</li>
<li>Sanitize JSON output to prevent an XSS vector when graphs are inserted directly into HTML [<a href="https://redirect.github.com/plotly/plotly.py/pull/4196">#4196</a>]</li>
<li>Fixed issue with shapes and annotations plotting on the wrong y axis when supplied with a specific axis in the <code>yref</code> parameter [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
<li>Remove <code>use_2to3</code> setuptools arg, which is invalid in the latest Python and setuptools versions [<a href="https://redirect.github.com/plotly/plotly.py/pull/4206">#4206</a>]</li>
<li>Fix <a href="https://redirect.github.com/plotly/plotly.py/issues/4066">#4066</a> JupyterLab v4 giving tiny default graph height [<a href="https://redirect.github.com/plotly/plotly.py/pull/4227">#4227</a>]</li>
<li>Fixed issue with <code>colors.n_colors</code> where generated RGB color values were not being constrained to stay between 0 and 255 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4110">#4110</a>]</li>
<li>Fix streamline figure factory with recent versions of Numpy</li>
<li>Fix issue with shapes and annotations not drawing on correct axis [<a href="https://redirect.github.com/plotly/plotly.py/pull/4177">#4177</a>]</li>
</ul>
<h2>[5.14.1] - 2023-04-05</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<!-- raw HTML omitted -->
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<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/bbbf5eff75883511a1126b11205bef34f1cf0ff9"><code>bbbf5ef</code></a> version changes for v5.16.1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/402c9b42003a14426cd891523504733f7fdf9002"><code>402c9b4</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4324">#4324</a> from guyrosin/fix-necessary-columns</li>
<li><a href="https://github.com/plotly/plotly.py/commit/1625d35aa0c7cca227ebcf0bf9ead746165820d5"><code>1625d35</code></a> Support python<3.8</li>
<li><a href="https://github.com/plotly/plotly.py/commit/f251f0825031a6c1960ada7308e0f1df96920e70"><code>f251f08</code></a> Add changelog entry</li>
<li><a href="https://github.com/plotly/plotly.py/commit/83c2260f1d7e26feace3c911dcbc0f6cf245031a"><code>83c2260</code></a> Necessary columns can be unordered</li>
<li><a href="https://github.com/plotly/plotly.py/commit/e2a7cb4d97c6ee4086cd5984cbf8a7b71837b8a4"><code>e2a7cb4</code></a> No type check for array_attrables, add test for a hover_data dictionary</li>
<li><a href="https://github.com/plotly/plotly.py/commit/a457f0ee5acda7d10a91fa7d1a2fac725bd06be4"><code>a457f0e</code></a> Consider necessary columns from complex arguments when interchanging dataframes</li>
<li><a href="https://github.com/plotly/plotly.py/commit/91060d3a840e66e65f47da941eebb16dab1a3b04"><code>91060d3</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4322">#4322</a> from plotly/update-master</li>
<li><a href="https://github.com/plotly/plotly.py/commit/3b561c28c94bcaebb2469c048d085a82db2e02ba"><code>3b561c2</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4321">#4321</a> from plotly/update-production-docs</li>
<li><a href="https://github.com/plotly/plotly.py/commit/feb50c9cd423578904f26d04b2f770c4cf1d72f9"><code>feb50c9</code></a> Merge branch 'doc-prod' into update-production-docs</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.16.1">compare view</a></li>
</ul>
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PR_kwDOACgets5ZVUjg
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Bump joblib from 1.3.1 to 1.3.2
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[] | 2023-09-01T12:09:07
| 2023-09-01T15:11:03
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2023-09-01T15:11:02Z
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CONTRIBUTOR
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Bumps [joblib](https://github.com/joblib/joblib) from 1.3.1 to 1.3.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/joblib/joblib/releases">joblib's releases</a>.</em></p>
<blockquote>
<h2>Joblib 1.3.2</h2>
<p>Bug fix release</p>
<h2>What's Changed</h2>
<ul>
<li>
<p>FIX treat n_jobs=None as if left to its default value by <a href="https://github.com/jeremiedbb"><code>@jeremiedbb</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1475">joblib/joblib#1475</a></p>
</li>
<li>
<p>FIX Init logger parent class in Parallel by <a href="https://github.com/fcharras"><code>@fcharras</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1494">joblib/joblib#1494</a></p>
</li>
<li>
<p>MNT remove unnecessary .bck file by <a href="https://github.com/lesteve"><code>@lesteve</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1480">joblib/joblib#1480</a></p>
</li>
<li>
<p>MTN adjust test regex for Python 3.12 improved error message by <a href="https://github.com/hroncok"><code>@hroncok</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1476">joblib/joblib#1476</a></p>
</li>
<li>
<p>DOC add public documentation for parallel_backend by <a href="https://github.com/glemaitre"><code>@glemaitre</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1481">joblib/joblib#1481</a></p>
</li>
<li>
<p>FIX flake8 new E721: type comparison by <a href="https://github.com/tomMoral"><code>@tomMoral</code></a> in <a href="https://redirect.github.com/joblib/joblib/pull/1492">joblib/joblib#1492</a></p>
</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/hroncok"><code>@hroncok</code></a> made their first contribution in <a href="https://redirect.github.com/joblib/joblib/pull/1476">joblib/joblib#1476</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/joblib/joblib/compare/1.3.1...1.3.2">https://github.com/joblib/joblib/compare/1.3.1...1.3.2</a></p>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/joblib/joblib/blob/master/CHANGES.rst">joblib's changelog</a>.</em></p>
<blockquote>
<h2>Release 1.3.2 -- 2023/08/08</h2>
<ul>
<li>
<p>Fix a regression in <code>joblib.Parallel</code> introduced in 1.3.0 where
explicitly setting <code>n_jobs=None</code> was not interpreted as "unset".
<a href="https://redirect.github.com/joblib/joblib/pull/1475">joblib/joblib#1475</a></p>
</li>
<li>
<p>Fix a regression in <code>joblib.Parallel</code> introduced in 1.3.0 where
<code>joblib.Parallel</code> logging methods exposed from inheritance to
<code>joblib.Logger</code> didn't work because of missing logger
initialization.
<a href="https://redirect.github.com/joblib/joblib/pull/1494">joblib/joblib#1494</a></p>
</li>
<li>
<p>Various maintenance updates to the doc, the ci and the test.
<a href="https://redirect.github.com/joblib/joblib/pull/1480">joblib/joblib#1480</a>,
<a href="https://redirect.github.com/joblib/joblib/pull/1481">joblib/joblib#1481</a>,
<a href="https://redirect.github.com/joblib/joblib/pull/1476">joblib/joblib#1476</a>,
<a href="https://redirect.github.com/joblib/joblib/pull/1492">joblib/joblib#1492</a></p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/joblib/joblib/commit/942a41084dbe79743d3114a475dc9e390b8718f1"><code>942a410</code></a> RELEASE 1.3.2 - bugfix release (<a href="https://redirect.github.com/joblib/joblib/issues/1493">#1493</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/85ab83640a31bd74437e4ebd286873c10f0b3d21"><code>85ab836</code></a> FIX init logger parent class in Parallel (<a href="https://redirect.github.com/joblib/joblib/issues/1494">#1494</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/3d56c25125d8bc5dbd2840de710244240fce0b08"><code>3d56c25</code></a> MTN fix flake8 new error E721: type comparison (<a href="https://redirect.github.com/joblib/joblib/issues/1492">#1492</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/0c57c18c906b60002b394d91600e6189d98c0caa"><code>0c57c18</code></a> TST adjust test_regex for Python 3.12 abstract method error (<a href="https://redirect.github.com/joblib/joblib/issues/1476">#1476</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/4ccc02d9bceaea4e09c0d0c211858bcf13bf2b89"><code>4ccc02d</code></a> FIX n_jobs=None behavior in Parallel and config contexts (<a href="https://redirect.github.com/joblib/joblib/issues/1475">#1475</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/8be8d32b0d52c2204d081001b02a95e137cf0db5"><code>8be8d32</code></a> DOC add public documentation for parallel_backend (<a href="https://redirect.github.com/joblib/joblib/issues/1481">#1481</a>)</li>
<li><a href="https://github.com/joblib/joblib/commit/3c314c12356a80409ccf0f1e487e4fb2ec8c7d4e"><code>3c314c1</code></a> MNT remove unnecessary file (<a href="https://redirect.github.com/joblib/joblib/issues/1480">#1480</a>)</li>
<li>See full diff in <a href="https://github.com/joblib/joblib/compare/1.3.1...1.3.2">compare view</a></li>
</ul>
</details>
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PR_kwDOACgets5ZVUrL
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Bump scipy from 1.11.1 to 1.11.2
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[] | 2023-09-01T12:09:30
| 2023-09-01T15:10:39
|
2023-09-01T15:10:38Z
|
CONTRIBUTOR
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Bumps [scipy](https://github.com/scipy/scipy) from 1.11.1 to 1.11.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
<blockquote>
<h1>SciPy 1.11.2 Release Notes</h1>
<p>SciPy <code>1.11.2</code> is a bug-fix release with no new features
compared to <code>1.11.1</code>. Python <code>3.12</code> and musllinux wheels
are provided with this release.</p>
<h1>Authors</h1>
<ul>
<li>Name (commits)</li>
<li>Evgeni Burovski (2)</li>
<li>CJ Carey (3)</li>
<li>Dieter Werthmüller (1)</li>
<li>elbarso (1) +</li>
<li>Ralf Gommers (2)</li>
<li>Matt Haberland (1)</li>
<li>jokasimr (1) +</li>
<li>Thilo Leitzbach (1) +</li>
<li>LemonBoy (1) +</li>
<li>Ellie Litwack (2) +</li>
<li>Sturla Molden (1)</li>
<li>Andrew Nelson (5)</li>
<li>Tyler Reddy (39)</li>
<li>Daniel Schmitz (6)</li>
<li>Dan Schult (2)</li>
<li>Albert Steppi (1)</li>
<li>Matus Valo (1)</li>
<li>Stefan van der Walt (1)</li>
</ul>
<p>A total of 18 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/scipy/scipy/commit/686422c4f0a71be1b4258309590fd3e9de102e18"><code>686422c</code></a> REL: 1.11.2 release [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/dede0d3cb7f271a1b015fa2308701c9c1b5ff77d"><code>dede0d3</code></a> Merge pull request <a href="https://redirect.github.com/scipy/scipy/issues/19040">#19040</a> from tylerjereddy/treddy_backports_1_11_2</li>
<li><a href="https://github.com/scipy/scipy/commit/bbf69b28f8b78e22d2fa4025cf525bff961fc717"><code>bbf69b2</code></a> TST: PR 19040 revisions [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/b505ab1e17d369b6eb89944cf833ebdbd695b45a"><code>b505ab1</code></a> BLD: PR 19040 revisions [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/0ab03c0aba7d6b1be69eea12d3edfa68f26b454e"><code>0ab03c0</code></a> DEBUG: PR 19040 [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/8ee9b00cda558ffbe818331e01d93ff9eea4c2dd"><code>8ee9b00</code></a> MAINT: PR 19040 revisions</li>
<li><a href="https://github.com/scipy/scipy/commit/b256ffb302044fe99f488b73c786bf779b8f7974"><code>b256ffb</code></a> DOC: update 1.11.2 relnotes</li>
<li><a href="https://github.com/scipy/scipy/commit/0641a73ae4fbb1ee377518d3054ef7123b1c0f88"><code>0641a73</code></a> LINT</li>
<li><a href="https://github.com/scipy/scipy/commit/a8b825af44d7ad2187d3cafb2247c17acf0ae709"><code>a8b825a</code></a> MAINT: ensure cobyla objective returns scalar</li>
<li><a href="https://github.com/scipy/scipy/commit/4dd233372f30327a101331af8dab4a8a9b9c2659"><code>4dd2333</code></a> MAINT: fixup dep warning</li>
<li>Additional commits viewable in <a href="https://github.com/scipy/scipy/compare/v1.11.1...v1.11.2">compare view</a></li>
</ul>
</details>
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PR_kwDOACgets5ZVU0v
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Bump cython from 3.0.0 to 3.0.2
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[] | 2023-09-01T12:10:00
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2023-09-01T15:10:28Z
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CONTRIBUTOR
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Bumps [cython](https://github.com/cython/cython) from 3.0.0 to 3.0.2.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/cython/cython/blob/master/CHANGES.rst">cython's changelog</a>.</em></p>
<blockquote>
<h1>3.0.2 (2023-08-27)</h1>
<h2>Bugs fixed</h2>
<ul>
<li>
<p>Using <code>None</code> as default value for arguments annotated as <code>int</code> could crash Cython.
(Github issue :issue:<code>5643</code>)</p>
</li>
<li>
<p>Default values of fused types that include <code>complex</code> could generate invalid C code
with <code>-DCYTHON_CCOMPLEX=0</code>.
(Github issue :issue:<code>5644</code>)</p>
</li>
<li>
<p>Using C++ enum class types in extension type method signatures could generate invalid C code.
(Github issue :issue:<code>5637</code>)</p>
</li>
</ul>
<h1>3.0.1 (2023-08-25)</h1>
<h2>Features added</h2>
<ul>
<li>The error messages regarding exception declarations were improved in order to give
better help about possible reasons and fixes.
(Github issue :issue:<code>5547</code>)</li>
</ul>
<h2>Bugs fixed</h2>
<ul>
<li>
<p>Memory view types in Python argument annotations no longer accept <code>None</code>. They now
require an explicit <code>Optional[]</code> or a <code>None</code> default value in order to allow <code>None</code>
to be passed. This was an oversight in the 3.0.0 release and is a BACKWARDS INCOMPATIBLE
change. However, since it only applies to code using Python syntax, it probably only
applies to newly written code that was written for Cython 3.0 and can easily be adapted.
In most cases, we expect that this change will avoid bugs in user code rather than
produce problems.
(Github issue :issue:<code>5612</code>)</p>
</li>
<li>
<p><code>nogil</code> functions using parallel code could freeze when called with the GIL held.
(Github issues :issue:<code>5564</code>, :issue:<code>5573</code>)</p>
</li>
<li>
<p>Relative cimports could end up searching globally and find the same package installed
elsewhere, potentially in another version.
(Github issue :issue:<code>5511</code>)</p>
</li>
<li>
<p>Attribute lookups on known standard library modules could accidentally search
in the module namespace instead.
(Github issue :issue:<code>5536</code>)</p>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/cython/cython/commit/fc5b199fcec1db0922364d351203a7d5205a4ca1"><code>fc5b199</code></a> Prepare release of 3.0.2.</li>
<li><a href="https://github.com/cython/cython/commit/e4c70439ada81536d0c996554ee6481dbfa63911"><code>e4c7043</code></a> Minor code cleanup.</li>
<li><a href="https://github.com/cython/cython/commit/96390aef239d5c3fcd7c2a6b2d3d951e28d3e0b1"><code>96390ae</code></a> Move an enum class macro before the types block which might need it (<a href="https://redirect.github.com/cython/cython/issues/5656">GH-5656</a>)</li>
<li><a href="https://github.com/cython/cython/commit/0bdfb97f905520e778a169146d54007836fd678f"><code>0bdfb97</code></a> Fix typo in declaration (<a href="https://redirect.github.com/cython/cython/issues/5655">GH-5655</a>)</li>
<li><a href="https://github.com/cython/cython/commit/351e13cab0ff4d5aae7289e859f0f7a62cb70ca1"><code>351e13c</code></a> Avoid useless runtime type checks when coercing a None default argument to a ...</li>
<li><a href="https://github.com/cython/cython/commit/584078a371ef412554a2cd0b96fcc20fb3b9c476"><code>584078a</code></a> Avoid using an unescaped name in the code (however unlikely it is that someon...</li>
<li><a href="https://github.com/cython/cython/commit/61535cf93cb76efac3d8f18a5e105301a8e13be3"><code>61535cf</code></a> Fix invalid C code with -DCYTHON_CCOMPLEX=0 when assigning a simple (integer)...</li>
<li><a href="https://github.com/cython/cython/commit/0870f6b1904381e9211ccc97208455eac7af2660"><code>0870f6b</code></a> Fix test in Py2.</li>
<li><a href="https://github.com/cython/cython/commit/310720fdeff34e20b33af02f57451da7b4701f9b"><code>310720f</code></a> Convert a test to language_level=3.</li>
<li><a href="https://github.com/cython/cython/commit/7c3d175babbc59880b1b6cf5d9d01c14c504f442"><code>7c3d175</code></a> Remove useless shebang in Cython/Build/Cythonize.py (<a href="https://redirect.github.com/cython/cython/issues/5647">GH-5647</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/cython/cython/compare/3.0.0...3.0.2">compare view</a></li>
</ul>
</details>
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5ZVU2l
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|
Bump mp-api from 0.33.3 to 0.35.1
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[] | 2023-09-01T12:10:06
| 2023-09-01T15:11:33
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2023-09-01T15:11:33Z
|
CONTRIBUTOR
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[//]: # (dependabot-start)
⚠️ **Dependabot is rebasing this PR** ⚠️
Rebasing might not happen immediately, so don't worry if this takes some time.
Note: if you make any changes to this PR yourself, they will take precedence over the rebase.
---
[//]: # (dependabot-end)
Bumps [mp-api](https://github.com/materialsproject/api) from 0.33.3 to 0.35.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/materialsproject/api/releases">mp-api's releases</a>.</em></p>
<blockquote>
<h2>v0.35.1</h2>
<p>Small deployment fixes</p>
<h2>v0.35.0</h2>
<p>Version 0.35.0</p>
<h3>Commits</h3>
<ul>
<li>[57d8acfe] General repo and tooling cleanup (<a href="https://redirect.github.com/materialsproject/api/issues/839">#839</a>)</li>
<li>[f8cfd822] Linting</li>
<li>[0a2c36d6] Optional botocore</li>
<li>[7cbf363e] use create_user_settings for new users posting settings for the first time (<a href="https://redirect.github.com/materialsproject/api/issues/837">#837</a>)</li>
<li>[5f15be17] Keep boto3 optional (<a href="https://redirect.github.com/materialsproject/api/issues/836">#836</a>)</li>
<li>[2352288b] Update setup.py</li>
<li>[01983caf] Update setup.py</li>
<li>[46cb50e0] Nest all resters (<a href="https://redirect.github.com/materialsproject/api/issues/833">#833</a>)</li>
<li>[38555057] Update docs link</li>
<li>[b2431e8a] replace method post with patch for user setting to avoid wiping out certain fields (<a href="https://redirect.github.com/materialsproject/api/issues/829">#829</a>)</li>
<li>[b2f2bc01] fix MPRester doc string for notify_db_version (<a href="https://redirect.github.com/materialsproject/api/issues/746">#746</a>)</li>
<li>[f0fb74ae] Revert pmg bump</li>
<li>[68f769b0] Bump pmg</li>
<li>[1989f031] Add sorting and projecting to private resters (<a href="https://redirect.github.com/materialsproject/api/issues/826">#826</a>)</li>
<li>[c32d0717] Remove existing warning</li>
<li>[98443a06] Merge branch 'main' of <a href="https://github.com/materialsproject/api">https://github.com/materialsproject/api</a></li>
<li>[da0f4df5] Add warning when accessing new molecules data</li>
<li>[bf5bfee1] Accommodate cloudflare errors (<a href="https://redirect.github.com/materialsproject/api/issues/823">#823</a>)</li>
<li>[8709deca] add a patch method to update the message_last_read field in _user_set… (<a href="https://redirect.github.com/materialsproject/api/issues/821">#821</a>)</li>
<li>[a1512bb9] Automated dependency upgrades (<a href="https://redirect.github.com/materialsproject/api/issues/822">#822</a>)</li>
<li>[5da8ed28] unsigned boto3 (<a href="https://redirect.github.com/materialsproject/api/issues/818">#818</a>)</li>
<li>[928a6969] Linting</li>
<li>[8f0358aa] Fix de-serlization of dos object</li>
<li>[bf390c76] Integrate AWS open data buckets (<a href="https://redirect.github.com/materialsproject/api/issues/815">#815</a>)</li>
<li>[f7e2a4e8] Automated dependency upgrades (<a href="https://redirect.github.com/materialsproject/api/issues/816">#816</a>)</li>
<li>[de162d5f] Merge branch 'main' of <a href="https://github.com/materialsproject/api">https://github.com/materialsproject/api</a></li>
<li>[d5fb3907] Add messages client and 400,404 warnings</li>
<li>[9976131b] Fix molecules summary tests</li>
<li>[3e514cf1] Overload model dict to fix monty dumping (<a href="https://redirect.github.com/materialsproject/api/issues/813">#813</a>)</li>
<li>[04f06620] Add 504 and 502 responses to retry settings</li>
<li>[e4a07341] New molecules resters (<a href="https://redirect.github.com/materialsproject/api/issues/803">#803</a>)</li>
<li>[3ffecd21] get_ion_reference_data_for_chemsys: fix bug in str chemsys (<a href="https://redirect.github.com/materialsproject/api/issues/756">#756</a>)</li>
<li>[a7097c7a] Automated dependency upgrades (<a href="https://redirect.github.com/materialsproject/api/issues/800">#800</a>)</li>
<li>[9e5be9f9] More test fixes</li>
<li>[307e9db0] Fix traj test</li>
<li>[6e225dc8] More chemenv test fixes</li>
<li>[5997ff5c] Fix chemenv test</li>
<li>[e5b6e176] Linting</li>
<li>[138057f2] Fix setup</li>
<li>[37763cb7] Add testing reqs</li>
<li>[06e4f4ea] Fix gh token</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/materialsproject/api/commit/7109a4464b0192d5b63419ff6abeb2bac3f60b8c"><code>7109a44</code></a> Update build wflow</li>
<li><a href="https://github.com/materialsproject/api/commit/57d8acfeb89c43ba2fcc79020af61acd801ecef0"><code>57d8acf</code></a> General repo and tooling cleanup (<a href="https://redirect.github.com/materialsproject/api/issues/839">#839</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/f8cfd8223b5b4098f66f27142c845ff2025775cf"><code>f8cfd82</code></a> Linting</li>
<li><a href="https://github.com/materialsproject/api/commit/0a2c36d6f6de225de9d7706c5d73926adb87435e"><code>0a2c36d</code></a> Optional botocore</li>
<li><a href="https://github.com/materialsproject/api/commit/7cbf363e2f87edd3c84ad7f6486f7b6cc7aff758"><code>7cbf363</code></a> use create_user_settings for new users posting settings for the first time (#...</li>
<li><a href="https://github.com/materialsproject/api/commit/5f15be176c01cafc521b0d665b30afd706faade6"><code>5f15be1</code></a> Keep boto3 optional (<a href="https://redirect.github.com/materialsproject/api/issues/836">#836</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/2352288bb220e7daaeb1eb9c5137b970a2fed465"><code>2352288</code></a> Update setup.py</li>
<li><a href="https://github.com/materialsproject/api/commit/01983caf5b01df32facc6bd15662b745c56fa790"><code>01983ca</code></a> Update setup.py</li>
<li><a href="https://github.com/materialsproject/api/commit/46cb50e05a59db0a837f8d920ddc5d113403c111"><code>46cb50e</code></a> Nest all resters (<a href="https://redirect.github.com/materialsproject/api/issues/833">#833</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/38555057c1fc36ce8306e196762b55db3912e49f"><code>3855505</code></a> Update docs link</li>
<li>Additional commits viewable in <a href="https://github.com/materialsproject/api/compare/v0.33.3...v0.35.1">compare view</a></li>
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PR_kwDOACgets5ZVWwU
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Bump pypa/cibuildwheel from 2.14.1 to 2.15.0
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2023-09-01T15:10:04Z
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CONTRIBUTOR
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.14.1 to 2.15.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.15.0</h2>
<ul>
<li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li>
<li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.15.0</h3>
<p><em>8 August 2023</em></p>
<ul>
<li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li>
<li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li>
</ul>
</blockquote>
</details>
<details>
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<ul>
<li><a href="https://github.com/pypa/cibuildwheel/commit/39a63b5912f086dd459cf6fcb13dcdd3fe3bc24d"><code>39a63b5</code></a> Bump version: v2.15.0</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/47e5d3c2cdee9d5324b6abe18c380c5ee33fd8f9"><code>47e5d3c</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1565">#1565</a> from henryiii/henryiii/feat/312rc</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/a63e11a1c40bf45810a29b0837a72312202cb00b"><code>a63e11a</code></a> feat: build using 3.12 RC by default</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/df94b5db6769eb8c3abb164caa9ab84c763570da"><code>df94b5d</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1553">#1553</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/36049d86a2e21d74382d84d7a423e20e49a2ca91"><code>36049d8</code></a> feature: add musllinux_1_2 support (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/229f8570b497b5fa4a201f7dd28c4f52c104218e"><code>229f857</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1562">#1562</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/5b32ee7d7bcd9433f559d8b43e9f9a180288c227"><code>5b32ee7</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1559">#1559</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/3f3bd9cff62eb311ed99891cc65132731c0a1c6f"><code>3f3bd9c</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1554">#1554</a> from pypa/pre-commit-ci-update-config</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/8df6d59adf7f9c7876ece95d0f908b53e2014ff2"><code>8df6d59</code></a> [pre-commit.ci] pre-commit autoupdate</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/4135c0a01dc11910ce118f58acc7caf4ac5c524a"><code>4135c0a</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1546">#1546</a>)</li>
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PR_kwDOACgets5ZYxbj
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Deprecate overlooked `from/as_..._string` methods
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| 2023-09-02T05:14:16
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2023-09-02T05:14:15Z
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MEMBER
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f01d38d14 rename variables: `toks->tokens`
42b7451e1 deprecate overlooked `from/as_..._string` methods (these were missed in https://github.com/materialsproject/pymatgen/issues/3230 and https://github.com/materialsproject/pymatgen/pull/3158 due to extra characters between `from_..._str`.
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I_kwDOACgets5v9S5F
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`InputSet` optional structure refactor introduced missing warning and `W_sv` PSP default
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"The warning still comes when the incar and POTCARs are generated. I think it is fine. ",
"Actually, I'm wrong. This line\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/49083cc93f5d2bb5633aabab094f025b047d591c/pymatgen/io/vasp/sets.py#L376-L377\r\n\r\ncalls the structure `@setter` and so all that logic runs even on `InputSet.__init__`. As it must have since this test was still passing:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/49083cc93f5d2bb5633aabab094f025b047d591c/tests/io/vasp/test_sets.py#L73-L91"
] | 2023-09-02T04:30:10
| 2023-09-02T05:09:34
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2023-09-02T05:09:23Z
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MEMBER
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@shyuep The recent [Allow structure=None in inputsets](https://github.com/materialsproject/pymatgen/commit/fabdd276497493f87f72348a3573bbe8a6c38f26#diff-e59a3ba79a120caa18efeceef5f857faf5a1d798c9efd1345746079941a2b471R433-R440) commit introduced an issue. Putting all structure-dependent logic inside the new `InputSet.structure` `@setter` means it no longer runs if people pass in the structure immediately on `InputSet` creation. So e.g. the warning about using `Yb_2` PSPs won't be issued if people use the old way of passing structure immediately.
Same with [defaulting the tungsten PSP to `W_sv`](https://github.com/materialsproject/pymatgen/blob/4b705801a3128ddf95ae5b4c79218ad735ef7d39/pymatgen/io/vasp/sets.py#L401).
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I_kwDOACgets5v_D8p
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Any thoughts on how to handle non-serializable `Structure.properties`?
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[
"I would assume properties must be something that can be handled by MontyEncoder. This can be made explicit in the doc."
] | 2023-09-02T18:42:51
| 2023-09-05T21:47:29
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2023-09-05T21:47:29Z
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Recently, a `.properties` attribute was added to the `Structure`/`Molecule` objects in #3264. However, since the user can provide any data they want here, it has the potential to break serialization (same thing with the pre-existing `.site_properties`, technically, but `.properties` is more open-ended).
We should think about how we best want to handle this (e.g. do we raise a warning to the user, do nothing at all, sanitize the data, something else?). It's possible that "do nothing at all" is the best approach, as the user will get an error when they try to dump the object if there is something non-serializable in it, but I wanted to open this up for broader discussion anyway.
---------------
On a related note, in the `ASEAtomsAdapter`, I have the following line:
https://github.com/materialsproject/pymatgen/blob/a5b82b5a2c6dd66fef6bfea87f39d3b6656770cb/pymatgen/io/ase.py#L221
The `jsanitize` part was added because oftentimes the `atoms.info` dictionary contains an entry that is not serializable, like the [ASE `Spacegroup` object](https://gitlab.com/ase/ase/-/blob/master/ase/atoms.py?ref_type=heads#L88-94) when you read in a CIF. By using `jsanitize`, it ensures that things are always clean. However, it makes me slightly uncomfortable because if someone converts back and forth between `Atoms` and `Structure`/`Molecule`, it's possible that the starting object is not the same due to `jsanitize` being called on some aspect of the data. Given how often there is non-serializable data in `atoms.info`, I felt it necessary to not simply ignore it, but I am not convinced that the current approach is ideal and am open to suggestions.
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PR_kwDOACgets5ZaPH_
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Fix code comment in ASE adapter
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2023-09-02T21:21:07Z
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There was a code comment I added in the ASE Atoms Adapter that was slightly inaccurate. This PR will just save future me a bit of headache by correcting it.
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Add an input arg check for `Kpoints.automatic_density_by_lengths`
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## Summary
The function `Kpoints.automatic_density_by_length()` takes in a sequence of values, e.g. `[50, 50, 1]`, to set the k-point density for each dimension. However, the function does not raise any kind of error if a sequence of dimensions != 3 is supplied.
This PR adds a `ValueError` if the `len` is != 3, along with a test for it.
## 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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[] | 2023-09-05T01:45:16
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2023-09-05T05:45:58Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/igorshubovych/markdownlint-cli: v0.35.0 → v0.36.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.35.0...v0.36.0)
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I_kwDOACgets5wJBgr
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Add support for pydantic > 2
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[] | 2023-09-05T07:52:45
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2023-09-05T15:54:58Z
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MEMBER
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This is simply to track when Pydantic 2+ is supported by Pymatgen. I know this depends on upstream dependencies.
Related:
- https://github.com/materialsvirtuallab/monty/pull/548
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PR_kwDOACgets5ZljSO
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Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt`
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[] | 2023-09-05T15:28:49
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2023-09-05T15:53:28Z
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MEMBER
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We don't need the version pin anymore, right @janosh? Emmet has this taken care of upstream.
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I_kwDOACgets5wOGxL
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Updating `sets.py` docstrings
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[] | 2023-09-05T21:26:47
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2023-09-05T21:37:25Z
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CONTRIBUTOR
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https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/vasp/sets.py#L26
Is the first 'unbreakable' rule for sets no longer true / should this be updated?
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Consistent casing `setup->setUp` across test classes
|
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[] | 2023-09-08T19:55:16
| 2023-09-10T09:03:39
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2023-09-10T08:42:13Z
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MEMBER
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d3dbd5097 fix typo matricies -> matrices
ebad8c2d0 fix `TestVaspInput.test_write()` polluting repo dir
58925e5a9 `def setup()` -> `def setUp()`
|
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I_kwDOACgets5wk8b0
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[Bug]: Error parsing GaussianOutput from frequency job with g09
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[] | 2023-09-09T12:58:51
| 2023-09-10T06:52:09
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2023-09-10T06:52:09Z
|
NONE
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### Email (Optional)
_No response_
### What happened?
Error when parsing the Hessian from a frequency job. Finding number of coordinates / atoms by using wrong structure list (`input_structures `instead of `std_structures`). Error can be circumvented by a simple check:
```
if len(input_structures):
ndf = 3 * len(input_structures[0])
else:
ndf = 3 * len(std_structures[0])
```
### Version
v2023.9.2
### What OS(es) are you seeing the problem on?
_No response_
### Relevant log output
```shell
File ~\micromambaenv\envs\protein_ir_spectroscopy\lib\site-packages\pymatgen\io\gaussian.py:696, in GaussianOutput.__init__(self, filename)
691 """
692 Args:
693 filename: Filename of Gaussian output file.
694 """
695 self.filename = filename
--> 696 self._parse(filename)
File ~\micromambaenv\envs\protein_ir_spectroscopy\lib\site-packages\pymatgen\io\gaussian.py:993, in GaussianOutput._parse(self, filename)
988 elif parse_hessian:
989 # read Hessian matrix under "Force constants in Cartesian coordinates"
990 # Hessian matrix is in the input orientation framework
991 # WARNING : need #P in the route line
992 parse_hessian = False
--> 993 ndf = 3 * len(input_structures[0])
994 self.hessian = np.zeros((ndf, ndf))
995 j_indices = range(5)
IndexError: list index out of range
```
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
|
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| 1,888,838,581
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PR_kwDOACgets5Z8Bst
| 3,307
|
Move `py.typed` to package root
|
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[] | null |
[
"Since the goal is to add type hints all across `pymatgen` (although some areas still fall short), I moved the `py.typed` into the package root."
] | 2023-09-09T18:34:32
| 2023-09-10T08:40:18
|
2023-09-10T08:40:18Z
|
MEMBER
|
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When using `mypy` on packages that rely on Pymatgen, it often complains like follows:
> Skipping analyzing "pymatgen.io.vasp.inputs": module is installed, but missing library stubs or py.typed marker
Since `pymatgen.io` is such a commonly used module, let's add a `py.typed` there unless there's a reason to avoid doing so.
Is there a reason why it wasn't included? And should one be included in other directories (e.g. `pymatgen.symmetry`)?
|
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PR_kwDOACgets5Z8iGg
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Fix IndexError when parsing Hessian from Gaussian frequency job
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[] | 2023-09-10T06:37:07
| 2023-09-10T06:52:09
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2023-09-10T06:52:08Z
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MEMBER
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Closes #3306.
013a1da58 add _parse_hessian method to GaussianOutput
55031490b snake_case vars
35c952e86 fix typo in test name: paramaters->parameters
|
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v2023.9.10
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"Thank you very much! "
] | 2023-09-10T09:13:29
| 2023-09-10T14:01:26
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2023-09-10T09:15:00Z
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New release as requested by @Andrew-S-Rosen to propagate `pydantic<2` pin removal across MP stack.
Also thanks @utf for the inspiration to add `.github/release.yml`.
7ec6221b1 add .github/release.yml
83701e2f1 remove @dependabot PRs from changelogs
3712380dc fix doc str indent
285655146 add release note categories Performance, Refactoring, Tests
8cd58f4fe add release categories Breaking Changes 💥, Security Fixes 🔒, Package Health 🏥
2a461429e update CHANGES.md and docs/CHANGES.md
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PR_kwDOACgets5Z82bh
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Fix `MPSOCSet` raising ValueError on `structure=None`
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PR_kwDOACgets5Z9LZv
| 3,311
|
Update @arosen93 to @Andrew-S-Rosen
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| 2023-09-10T18:15:13
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2023-09-10T18:10:12Z
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I changed my username and did a find-and-replace to update it where it's mentioned in Pymatgen.
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PR_kwDOACgets5Z-sO2
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Fix ruff PERF401
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PR_kwDOACgets5aAdX3
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Remove redundant my_? prefix from variables
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PR_kwDOACgets5aDhOX
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Allow usage of `calculate_ng` with a custom ENCUT and PREC values for VASP input sets
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[
"Unit test pls. Thanks.",
"of course @shyuep , was already on it before your comment!",
"@shyuep ready for merging"
] | 2023-09-11T19:11:02
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2023-09-12T06:24:19Z
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CONTRIBUTOR
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Add in new kwarg to `calculate_ng` to reduce redundancy with new VASP calculation validator in Emmet.
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PR_kwDOACgets5aGvuv
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Fix internal `SymmOp.from_xyz_string` and `MagSymmOp.from_xyzt_string` deprecation warnings
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I_kwDOACgets5wytUR
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Incorrect atomic mass of element Og in periodic_table.json
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"Thanks for letting us know @trachote, fixed in https://github.com/materialsproject/pymatgen/pull/3317/commits/463cc248974b66f5a0766e7365e2b1846dc6b511"
] | 2023-09-12T11:45:59
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2023-09-12T14:15:37Z
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NONE
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The atomic mass of Og should be 294u, but it is reported as 2949u.
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PR_kwDOACgets5aIfAL
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Fix atomic mass for Og
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2023-09-12T13:54:20Z
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MEMBER
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Closes https://github.com/materialsproject/pymatgen/issues/3316.
Thank you @trachote.
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PR_kwDOACgets5aIxQ3
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Fix copy-paste error in `MagSymmOp.as_xyzt_string` (`@staticmethod` should be `@classmethod`)
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[] | 2023-09-12T14:30:39
| 2023-11-20T14:11:49
|
2023-09-12T14:48:18Z
|
MEMBER
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I merged #3315 prematurely.
|
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I_kwDOACgets5w3WTF
| 3,319
|
Not sure this is a bug for Phasedigram.get_element_profile
|
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[
"Hi Bin (@Jeff-oakley),\r\n\r\nThis issue is caused by `MPRester.get_entries`, not pymatgen. This function returns entries of different thermo_types. This has been clarified in the latest release of mp-api (https://github.com/materialsproject/api/commit/83b27a0899101f5d0cb73fa16352e082adb264a3). Thanks @munrojm!\r\n\r\nSo with these lines here\r\n\r\n```python\r\nentries = mpr.get_entries(open_ele)\r\nenergies = [entry.energy_per_atom for entry in entries]\r\nmiu0 = min(energies)\r\n```\r\n\r\nYou might be getting an R2SCAN entry that is non-compatible with the GGA/GGA+U phase diagram. For example, for Na this corresponds to this entry:\r\n```\r\nmp-10172-R2SCAN ComputedStructureEntry - Na2 (Na)\r\nEnergy (Uncorrected) = -7.1284 eV (-3.5642 eV/atom)\r\nCorrection = 0.0000 eV (0.0000 eV/atom)\r\nEnergy (Final) = -7.1284 eV (-3.5642 eV/atom)\r\nEnergy Adjustments:\r\n None\r\nParameters:\r\n potcar_spec = [{'titel': 'PAW_PBE Na_pv 19Sep2006', 'hash': '0abb5935ffb9cb16b2a78f04e4174f32'}]\r\n is_hubbard = False\r\n hubbards = {}\r\n run_type = R2SCAN\r\n```\r\n\r\nTo fix everything, you can delete the 3 lines mentioned above and use this one-liner instead:\r\n\r\n```python\r\nmiu0 = pd.el_refs[Element(open_ele)].energy_per_atom\r\n```\r\n\r\nDoes this fix your issue?\r\n",
"Yes. Now it works and generates reasonable results. Thank you!"
] | 2023-09-13T01:12:04
| 2023-09-28T00:54:16
|
2023-09-28T00:54:15Z
|
NONE
|
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### Email (Optional)
bouyang@fsu.edu
### Version
2023.7.17
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
Not sure this is because of pymatgen, new api of MP or my incorrect understanding . Below is the sample code.
By running the code below, it will show a negative stability window for the case of Na and K, but normal results for Li. Which means the chemical potential can go above Na elemental metal and K elemental metal. Can you look into that?
### Code snippet
```python
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.core.periodic_table import Element
from mp_api.client import MPRester
from pymatgen.entries.computed_entries import ComputedEntry
from copy import deepcopy
from pymatgen.apps.borg.hive import SimpleVaspToComputedEntryDrone
from pymatgen.io.vasp.inputs import *
from copy import deepcopy
from pymatgen.core.composition import Composition
def getWindow(comp, open_ele='Li'):
"""
Obtain electrochemical window
Args:
comp: A string of composition
open_ele: The open element
"""
mpr = MPRester('my_api_key')
eles = list(Composition(comp).as_dict().keys())
entries = mpr.get_entries_in_chemsys(eles)
pd = PhaseDiagram(entries)
el_profile = pd.get_element_profile(Element(open_ele),Composition(comp))
entries = mpr.get_entries(open_ele)
energies = [entry.energy_per_atom for entry in entries]
miu0 = min(energies)
for i, d in enumerate(el_profile):
v = - (d["chempot"] - miu0)
print(f'v={v}, reaction={d["reaction"]}')
x1 = v
y1 = d["evolution"]
if i != len(el_profile) - 1:
x2 = - (el_profile[i + 1]["chempot"] - miu0)
else:
x2 = 5.0
y_red_min, y_oxi_max = 1e10, -1e10
oxi_reaction, red_reaction = None, None
if abs(y1) < 0.0001:
print(f'electrochemical window is {x1}V - {x2}V')
elif y1 > 0.0001 and y1 < y_red_min:
red_reaction = d['reaction']
elif y1 > y_oxi_max and y1 < -0.0001:
oxi_reaction = d['reaction']
print(f'Reduction reaction is {red_reaction}')
print(f'Oxidation reaction is {oxi_reaction}')
getWindow('Na3YCl6','Na')
getWindow('Li3YCl6','Li')
getWindow('K3YCl6','K')
```
```
### Log output
```shell
Retrieving ThermoDoc documents: 100%|█████████████████████████████████████████████████████████████████████████████████████| 43/43 [00:00<00:00, 409897.89it/s]
Retrieving ThermoDoc documents: 100%|████████████████████████████████████████████████████████████████████████████████████| 37/37 [00:00<00:00, 1326403.83it/s]
v=-2.2416552765517244, reaction=Na3YCl6 + 3 Na -> Y + 6 NaCl
v=-1.7188283677777778, reaction=Na3YCl6 + 1.5 Na -> 0.5 Y2Cl3 + 4.5 NaCl
v=-1.658641016666667, reaction=Na3YCl6 -> Na3YCl6
electrochemical window is -1.658641016666667V - 1.515256235000002V
v=1.515256235000002, reaction=Na3YCl6 -> NaCl3 + YCl3 + 2 Na
v=2.5369849624999996, reaction=Na3YCl6 -> 0.4286 NaCl7 + YCl3 + 2.571 Na
v=3.4422044700000023, reaction=Na3YCl6 -> YCl3 + 1.5 Cl2 + 3 Na
Reduction reaction is None
Oxidation reaction is Na3YCl6 -> YCl3 + 1.5 Cl2 + 3 Na
Retrieving ThermoDoc documents: 100%|████████████████████████████████████████████████████████████████████████████████████| 25/25 [00:00<00:00, 1191563.64it/s]
Retrieving ThermoDoc documents: 100%|█████████████████████████████████████████████████████████████████████████████████████| 25/25 [00:00<00:00, 953250.91it/s]
v=-0.4777835466666669, reaction=Li3YCl6 + 3 Li -> Y + 6 LiCl
v=0.09965877388888833, reaction=Li3YCl6 + 1.5 Li -> 0.5 Y2Cl3 + 4.5 LiCl
v=0.17498946500000168, reaction=Li3YCl6 -> YCl3 + 3 LiCl
electrochemical window is 0.17498946500000168V - 3.7960650216666667V
v=3.7960650216666667, reaction=Li3YCl6 -> YCl3 + 1.5 Cl2 + 3 Li
Reduction reaction is None
Oxidation reaction is Li3YCl6 -> YCl3 + 1.5 Cl2 + 3 Li
Retrieving ThermoDoc documents: 100%|████████████████████████████████████████████████████████████████████████████████████| 42/42 [00:00<00:00, 1835008.00it/s]
Retrieving ThermoDoc documents: 100%|████████████████████████████████████████████████████████████████████████████████████| 53/53 [00:00<00:00, 2315605.33it/s]
v=-4.90786498925, reaction=K3YCl6 + 3 K -> Y + 6 KCl
v=-4.170335528472221, reaction=K3YCl6 -> K3YCl6
electrochemical window is -4.170335528472221V - -0.3252949437500039V
v=-0.3252949437500039, reaction=K3YCl6 -> K2YCl5 + 0.5 Cl2 + K
v=-0.25898547208333245, reaction=K3YCl6 -> 0.5 KY2Cl7 + 1.25 Cl2 + 2.5 K
v=-0.19964401375000307, reaction=K3YCl6 -> YCl3 + 1.5 Cl2 + 3 K
Reduction reaction is None
Oxidation reaction is K3YCl6 -> YCl3 + 1.5 Cl2 + 3 K
```
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
|
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| 1,893,840,541
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PR_kwDOACgets5aMttT
| 3,320
|
Google-style doc strings for class attributes
|
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[] | 2023-09-13T06:33:38
| 2023-09-13T06:48:12
|
2023-09-13T06:48:12Z
|
MEMBER
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|
[Bug]: Unexpected values/errors when accessing specific attributes of `Element`(s)
|
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[] | null |
[
"I have fixed some of the obvious ValueErrors. But there are some things which are not worth the time to fix. For example, the data on the artificial elements like Og, Lv, etc. are sparse (they exist for fractions of a second). None of these elements are used in any usual sense of the world. Quite simply, they are not worth the time to debug. \r\n\r\nAs for the wrong values, pls provide the correct ones and a source. Thanks.\r\n\r\n",
"@shyuep Thanks for the quick response. Of course I agree that most of these missing values are not useful. \r\nI only created the issue because if you want to use them more a programmatic way you do not get what you \"expect\". \r\nI would simply expect `None` for them...\r\n\r\nI think the correct values are there (I cannot provide any extra source now) but it is not interpreted in the right way:\r\n- For the `refractive_index` I would just use the value belongs the gas phase \r\n- For the `C`'s `mineral_hardness` I would use the the value of the diamond (similarly as in case of the `refractive_index` of C)\r\n- For the `Fr` I would simply drop the `maybe` similarly you do with the `about`\r\n\r\nPlease note that these are suggestion based on technical point of view only...",
"Ok, I fixed those. I am not doing anything about the artificial elements since in most cases you can get around it by simply not calling them."
] | 2023-09-13T12:55:01
| 2023-09-13T16:03:01
|
2023-09-13T16:01:58Z
|
CONTRIBUTOR
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### Email (Optional)
_No response_
### Version
v2023.2.28
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
- There are about 80 ValueErrors, 400 TypeError(s), 120 KeyError(s) and 10 IndexError(s) when Trying to access the specific attributes of the Elements (shortened log available below).
- I would expect to return with None (with some warning). Using try/expect block to access an attribute doesn't sound very efficient.
- Even after getting the value there are 7 cases when it is a wrong value:
```
Element.H.refractive_index: 1.000132 (gas; liquid 1.12)(no units)
Element.He.refractive_index: 1.000035 (gas; liquid 1.028)(no units)
Element.C.refractive_index: 2.417 (diamond)(no units)
Element.C.mineral_hardness: 0.5 (graphite; diamond is 10.0)(no units)
Element.N.refractive_index: 1.000298 (gas; liquid 1.197)(no units)
Element.O.refractive_index: 1.000271 (gas; liquid 1.221)(no units)
Element.Fr.melting_point: maybe about 300 K
```
### Code snippet
```python
from typing import Optional
from pydantic import BaseModel, ValidationError
from pymatgen.core.periodic_table import Element
properties = (
"X",
"atomic_radius",
"atomic_mass",
"mendeleev_no",
"electrical_resistivity",
"velocity_of_sound",
"reflectivity",
"refractive_index",
"poissons_ratio",
"molar_volume",
"thermal_conductivity",
"boiling_point",
"melting_point",
"critical_temperature",
"superconduction_temperature",
"liquid_range",
"bulk_modulus",
"youngs_modulus",
"brinell_hardness",
"rigidity_modulus",
"mineral_hardness",
"vickers_hardness",
"density_of_solid",
"atomic_radius_calculated",
"van_der_waals_radius",
"atomic_orbitals",
"coefficient_of_linear_thermal_expansion",
"ground_level",
"ionization_energies",
"ionization_energy",
"electron_affinity",
"electronic_structure",
"average_ionic_radius",
"average_cationic_radius",
"average_anionic_radius",
"ionic_radii",
"number",
"max_oxidation_state",
"min_oxidation_state",
"oxidation_states",
"common_oxidation_states",
"icsd_oxidation_states",
"metallic_radius",
"full_electronic_structure",
"valence",
"term_symbols",
"ground_state_term_symbol",
"row",
"group",
"block",
"is_noble_gas",
"is_transition_metal",
"is_post_transition_metal",
"is_rare_earth_metal",
"is_metal",
"is_metalloid",
"is_alkali",
"is_alkaline",
"is_halogen",
"is_chalcogen",
"is_lanthanoid",
"is_actinoid",
"is_quadrupolar",
"nmr_quadrupole_moment",
"iupac_ordering"
)
class PymatgenData(BaseModel):
atomic_mass: float
atomic_orbitals: Optional[dict[str,float]]
atomic_radius: Optional[float]
atomic_radius_calculated: Optional[float]
average_anionic_radius: float
average_cationic_radius: float
average_ionic_radius: float
block: str
boiling_point: Optional[float]
brinell_hardness: Optional[float]
bulk_modulus: Optional[float]
coefficient_of_linear_thermal_expansion: Optional[float]
common_oxidation_states: set[int]
critical_temperature: Optional[float]
density_of_solid: Optional[float]
electrical_resistivity: Optional[float]
electron_affinity: Optional[float]
electronic_structure: Optional[str]
full_electronic_structure: Optional[list[tuple[int,str, int]]]
ground_level: Optional[str]
ground_state_term_symbol: Optional[str]
group: int
icsd_oxidation_states: set[int]
ionic_radii: dict[int,float]
ionization_energies: list[Optional[float]]
ionization_energy: Optional[float]
is_actinoid: bool
is_alkali: bool
is_alkaline: bool
is_chalcogen: bool
is_halogen: bool
is_lanthanoid: bool
is_metal: bool
is_metalloid: bool
is_noble_gas: bool
is_post_transition_metal: bool
is_quadrupolar: bool
is_rare_earth_metal: bool
is_transition_metal: bool
iupac_ordering: Optional[int]
liquid_range: Optional[float]
max_oxidation_state: int
melting_point: Optional[float]
mendeleev_no: Optional[float]
metallic_radius: Optional[float]
min_oxidation_state: int
mineral_hardness: Optional[float]
molar_volume: Optional[float]
nmr_quadrupole_moment: dict[str,float]
number: int
oxidation_states: set[int]
poissons_ratio: Optional[float]
reflectivity: Optional[float]
refractive_index: Optional[float]
rigidity_modulus: Optional[float]
row: int
superconduction_temperature: Optional[float]
term_symbols: Optional[list[list[str]]]
thermal_conductivity: Optional[float]
valence: set[float]
van_der_waals_radius: Optional[float]
velocity_of_sound: Optional[float]
vickers_hardness: Optional[float]
X: Optional[float]
youngs_modulus: Optional[float]
for element in Element:
data = {}
for prop in properties:
try:
data[prop] = getattr(element, prop)
except ValueError as err:
print(f'Element: {element}, attribute: {prop}, ValueError: {err}')
except TypeError as err:
print(f'Element: {element}, attribute: {prop}, TypeError: {err}')
except KeyError as err:
print(f'Element: {element}, attribute: {prop}, KeyError: {err}')
except IndexError as err:
print(f'Element: {element}, attribute: {prop}, IndexError: {err}')
try:
PymatgenData(**data)
except ValidationError as err:
print(f'Element: {element}, ValidationError: {err}')
# Some of the problematic values
print(f'Element.H.refractive_index: {Element.H.refractive_index}')
print(f'Element.He.refractive_index: {Element.He.refractive_index}')
print(f'Element.C.refractive_index: {Element.C.refractive_index}')
print(f'Element.C.mineral_hardness: {Element.C.mineral_hardness}')
print(f'Element.N.refractive_index: {Element.N.refractive_index}')
print(f'Element.O.refractive_index: {Element.O.refractive_index}')
print(f'Element.Fr.melting_point: {Element.Fr.melting_point}')
```
### Log output
```shell
Raised exceptions:
Element: H, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: He, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: B, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: C, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: N, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: O, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: F, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Ne, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Si, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: P, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: S, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Cl, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Ar, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Cr, attribute: ground_state_term_symbol, ValueError: Ambiguous valence
Element: Cr, attribute: valence, ValueError: Ambiguous valence
Element: Cr, attribute: valence, ValueError: Ambiguous valence
Element: Cr, attribute: term_symbols, ValueError: Ambiguous valence
Element: Cr, attribute: ground_state_term_symbol, ValueError: Ambiguous valence
Element: As, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Se, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Kr, attribute: metallic_radius, ValueError: could not convert string to float: 'no data'
Element: Nb, attribute: ground_state_term_symbol, ValueError: Ambiguous valence
Element: Nb, attribute: valence, ValueError: Ambiguous valence
...
Element: He, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: He, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: He, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Ne, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Ne, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: Ne, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Ar, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Ar, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: Ar, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Kr, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Kr, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: Kr, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Xe, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Xe, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: Xe, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Rn, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
Element: Rn, attribute: term_symbols, TypeError: 'float' object cannot be interpreted as an integer
Element: Rn, attribute: ground_state_term_symbol, TypeError: 'float' object cannot be interpreted as an integer
...
Element: Rf, attribute: ground_state_term_symbol, KeyError: 'Electronic structure'
Element: Rf, attribute: valence, KeyError: 'Electronic structure'
Element: Rf, attribute: electronic_structure, KeyError: 'Electronic structure'
Element: Rf, attribute: metallic_radius, KeyError: 'Metallic radius'
Element: Rf, attribute: full_electronic_structure, KeyError: 'Electronic structure'
Element: Rf, attribute: valence, KeyError: 'Electronic structure'
Element: Rf, attribute: term_symbols, KeyError: 'Electronic structure'
Element: Rf, attribute: ground_state_term_symbol, KeyError: 'Electronic structure'
Element: Rf, attribute: iupac_ordering, KeyError: 'IUPAC ordering'
Element: Db, attribute: ground_state_term_symbol, KeyError: 'Electronic structure'
Element: Db, attribute: valence, KeyError: 'Electronic structure'
Element: Db, attribute: electronic_structure, KeyError: 'Electronic structure'
Element: Db, attribute: metallic_radius, KeyError: 'Metallic radius'
Element: Db, attribute: full_electronic_structure, KeyError: 'Electronic structure'
Element: Db, attribute: valence, KeyError: 'Electronic structure'
Element: Db, attribute: term_symbols, KeyError: 'Electronic structure'
Element: Db, attribute: ground_state_term_symbol, KeyError: 'Electronic structure'
Element: Db, attribute: iupac_ordering, KeyError: 'IUPAC ordering'
Element: Sg, attribute: ground_state_term_symbol, KeyError: 'Electronic structure'
Element: Sg, attribute: valence, KeyError: 'Electronic structure'
Element: Sg, attribute: electronic_structure, KeyError: 'Electronic structure'
...
Element: Rg, attribute: ionization_energy, IndexError: list index out of range
Element: Cn, attribute: ionization_energy, IndexError: list index out of range
Element: Nh, attribute: ionization_energy, IndexError: list index out of range
Element: Fl, attribute: ionization_energy, IndexError: list index out of range
Element: Mc, attribute: ionization_energy, IndexError: list index out of range
Element: Lv, attribute: ionization_energy, IndexError: list index out of range
Element: Ts, attribute: ionization_energy, IndexError: list index out of range
Element: Og, attribute: ionization_energy, IndexError: list index out of range
```
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
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I_kwDOACgets5w9Kg1
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Changing MP Input Sets
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[
"Thanks. I have no problems with most of this, but I would point out a few issues. \r\n\r\nThe MPRelaxSet is generally used as the *first* calculation for a new structure. So the assumptions are (a) we do not know whether it is a metal or not, and (b) too strict criteria result in extremely long ionic convergence. Hence, I would still argue for keeping EDIFF_PER_ATOM, no EDIFFG and an assumption of insulator (unless someone wants to code a rough estimator, such as any compound containing only metallic elements are considered to be metals and everything else are assumed insulators. Alternatively, we can use one of the ML band gap models to make an initial estimate of the band gap). I have done relaxations before and my tests show that a loose first relaxation followed by a strict second relaxation is much faster and yields just as accurate results than immediately doing a strict relaxation.\r\n\r\nFor second relaxations, I believe the practice is actually to use EDIFF (no per atom), set EDIFFG and also determine ISMEAR based on band gap. \r\n\r\nOne possible compromise is to have a \"strict\" mode for MPRelaxSet, which defaults to False. People who want to immediately start with stricter criteria can just set it to True and EDIFF, EDIFFG will automatically be set.",
"@JiQi535 @SophiaRuan I have changed `LREAL` to `False` in `MatPESStaticSet`.\r\n",
"> So the assumptions are (a) we do not know whether it is a metal or not\r\n\r\nCouldn't we just use ISMEAR = 0, SIGMA = 0.05, and a higher KPOINTS in such cases? The first two could probably be done regardless of whether or not the \"strict mode\" stuff you are talking about is implemented, as they are the recommended settings by VASP when the bandgap is unknown.\r\n\r\n>I have done relaxations before and my tests show that a loose first relaxation followed by a strict second relaxation is much faster and yields just as accurate results than immediately doing a strict relaxation.\r\n\r\nPerhaps this should be built into an Atomate2 workflow rather than the pymatgen sets? I expect most of the users of pymatgen do not use a package like Atomate2, so they are probably more likely to just use an input set for a single calc (rather than doing a \"loose\" calc --> \"strict\" calc type of workflow, which I expect is more tedious to do without workflow orchestration)\r\n",
"Just from the times when I ran such computations by hand: I have always done a loose and then strict calculation. I therefore think it is a good idea. I mostly, however, only adapted kpoints and not EDIFF.",
"@matthewkuner Also, re the recommendations on ISMEAR, I think it should be clarified that you are recommending -5 based on mostly the discrepancy in band gaps? I completely agree that band gaps are better with ISMEAR=-5. But for energies, the only result shown is that ISMEAR=0 and ISMEAR=-5 differ in a small number of cases, but I have no idea which is the correct one. \r\n\r\nAnd yes, the design of MPRelaxSet is for the first of the two relaxations as implemented in Custodian and Atomate2. The second relaxation overrides EDIFF. A EDIFF_PER_ATOM has no real effect in small systems (which I would guess is the majority of structures out there). ",
"I also add that the strict vs loose has smaller effects on PBE of course. But in HSE calculations for instance, a loose relaxation vs strict relaxation can be a huge difference in terms of convergence (in some cases, whether a calculation even succeeds or not).",
"> @matthewkuner Also, re the recommendations on ISMEAR, I think it should be clarified that you are recommending -5 based on mostly the discrepancy in band gaps? I completely agree that band gaps are better with ISMEAR=-5. But for energies, the only result shown is that ISMEAR=0 and ISMEAR=-5 differ in a small number of cases, but I have no idea which is the correct one.\r\n\r\nI'm advocating for using ISMEAR = 0 when we do not know the bandgap of a material (except for static calcs, where we always use ISMEAR=-5 for good energies/DOS). In subsequent relaxation calculations, ISMEAR could be set to -5 for non-metals, and to 1 or 2 for metals. The logic I'm advocating for already exists in the Atomate2 r2SCANRelaxSet that is going to be merged into pmg (see https://github.com/materialsproject/atomate2/blob/ecf80af781ee754f0f918a5ed90cf7d1247f62a5/src/atomate2/vasp/sets/base.py#L669)\r\n*Note that I disagree with the choice of SIGMA used in the code above for the case where the bandgap is unknown--I think it should be set to 0.05. I've been dragging my feet on doing benchmarking tho",
"OK. But I just want to note that ISMEAR=0 does not affect insulator negatively at all. So for MatPES (where we don't really care about DOS, bandgap, etc.), we are going to do ISMEAR=0 for everything.",
"> Hence, I would still argue for keeping EDIFF_PER_ATOM\r\n\r\nThis doesn't seem to matter too much if the r2SCAN workflow is used since the EDIFFG in the second step of the workflow will fix things up even for larger systems. But for a GGA workflow, is it indeed true that EDIFFG is always set explicitly (and EDIFF without per atom)? Just want to confirm that's indeed the case. As long as the per-atom business isn't being used in the final relax, I personally don't care what happens in terms of the first relax. (EDIFF_PER_ATOM is a horrible choice for the systems I typically study, which often have hundreds of atoms... but I am not MP 😅 ).\r\n\r\n@esoteric-ephemera, could you confirm? Thanks!",
"@Andrew-S-Rosen for the GGA workflow, EDIFF_PER_ATOM is always set in each step of the WF (initial relax, second relax, static), and EDIFFG is never set explicitly (VASP defaults to EDIFFG = 10*EDIFF).\r\n\r\nPer @shyuep's and @Andrew-S-Rosen's comments on EDIFF: we could do an initial coarse relax with EDIFF_PER_ATOM set, and a final tighter relax with EDIFF set. To balance this for larger structures, setting EDIFF = min( 1.e-4, NSITES * EDIFF_PER_ATOM) might be a better choice\r\n\r\nI agree with @matthewkuner that setting ISMEAR = 0 with an appropriate SIGMA (we're discussing how to proceed with this) is best for the initial relax. If that returns a metal, we switch to ISMEAR = 2, SIGMA = 0.2, and if not, we stick with ISMEAR = 0\r\n\r\nTo see which value of ISMEAR is most correct, I can try to run some tests like in [this Jorgensen and Hart paper ](https://iopscience.iop.org/article/10.1088/1361-651X/ac13ca/meta) recommended by @computron . Will just be costly to do such a high density of k-points",
"I agree with setting `EDIFF = min(1e-4, NSITES * EDIFF_PER_ATOM)`\r\nEDIT: I am now unsure as of Oct 26, 2023)",
"I think we need to be deliberate in the amount of benchmarking we do to avoid it sapping too much time and effort. At least for the pre-relax step, maybe we can pick a setting that everyone agrees is _good enough_ without more benchmarking?",
"@rkingsbury regarding EDIFFG in the R2SCAN input set-- how was the value of 0.02 chosen? In your paper \"Performance comparison of r2SCAN and SCAN metaGGA density functionals for solid materials via an automated, high-throughput computational workflow\", I can't find justification for that specific value being used",
"> @rkingsbury regarding EDIFFG in the R2SCAN input set-- how was the value of 0.02 chosen? In your paper \"Performance comparison of r2SCAN and SCAN metaGGA density functionals for solid materials via an automated, high-throughput computational workflow\", I can't find justification for that specific value being used\r\n\r\nHi @matthewkuner I dug back through old notes and determined that we initially used EDIFFG=-0.05, and later decided to tighten the convergence to -0.02 for the 2nd relaxation (the r2SCAN one) in the workflow. My recollection at the time was that there was some precedent for these values, but I can't find what now. We tested different workflows with and without force-convergence (see Table A.1 in the SI of the paper), but we didn't do a systematic evaluation of different EDIFFG values. I know from some of the old emails I dug up that we did look at the forces on selected structures to sanity check our value, but that's all I can remember. @mkhorton do you recall any additional context about `EDIFFG=-0.02`?\r\n",
"@mkhorton just a follow-up ping for the above comment",
"> Per @shyuep's and @Andrew-S-Rosen's comments on EDIFF: we could do an initial coarse relax with EDIFF_PER_ATOM set, and a final tighter relax with EDIFF set. To balance this for larger structures, setting EDIFF = min( 1.e-4, NSITES * EDIFF_PER_ATOM) might be a better choice\r\n\r\n@esoteric-ephemera but wouldn't `min( 1.e-4, NSITES * EDIFF_PER_ATOM)` just set EDIFF=1e-4 for all structures with _2_ or more atoms? At that point, it would be better to just set a static EDIFF for all calculations.",
"Thanks for initiating/sharing the benchmarking document. I’m in favor of most of this but want to query the ENCUT — is this not very large for a GGA?\r\n\r\nRe. EDIFFG, I do not recall. I think perhaps 0.01 was tried initially but was too difficult to converge.\r\n\r\nI’d add the standard caveat that the older input set yaml is retained somewhere for historical reference.\r\n",
"For EDIFF, if we’re adding force convergence, my hunch is that a decent EDIFF will also be required. I would abandon the EDIFF_PER_ATOM. However, this opinion should certainly be overruled by anyone who has data to support an alternative view.",
"> Thanks for initiating/sharing the benchmarking document. I’m in favor of most of this but want to query the ENCUT — is this not very large for a GGA?\r\n\r\nThe idea for changing ENCUT/ENAUG to match the r2SCAN set was floated offline (I forget by who). We haven't conducted any benchmarking for this, though, so will probably forego this unless anyone objects (or unless anyone performs this benchmarking).\r\n\r\nThanks for the info regarding EDIFFG! @mkhorton "
] | 2023-09-13T18:57:53
| 2023-10-27T00:38:19
|
CONTRIBUTOR
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There have been internal talks with @munrojm @Janosh @esoteric-ephemera, among others, about changing the MP Input Sets. We want to open the discussion up before moving forward with such changes.
Currently, we are in favor of the following changes:
For **all** MP sets:
- Set LMAXMIX = 6 for all structures. This is based on a benchmarking study @esoteric-ephemera performed (attached below) which showed that the VASP manual recommendations for setting LMAXMIX based on the element block is actually _not_ sufficient in all cases.
- Set `LREAL=False`, because the current `LREAL=Auto` seems to be less reliable for structures further from equilibrium (regardless of # of sites). Data supporting this is also in the attached benchmark by @esoteric-ephemera.
- Get rid of EDIFF_PER_ATOM and instead replace it with a flat value. `EDIFF = 1e-5` is a reasonable starting point for discussion.
For MPRelaxSet (and the MPMetalRelaxSet):
- Use a force-based convergence criterion.` EDIFFG = -0.05` is standard. We could also use `-0.02` to match the value from the MPScanRelaxSet
- Include additional functionality similar to the MPSCANRelaxSet wherein certain parameters are set according to bandgap, if known (see https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/vasp/sets.py#L950). This would likely involve merging the MPMetalRelaxSet and MPRelaxSet.
- Change the ENCUT and ENAUG of MPRelaxSet to match the r2SCAN values of 680 and 1360, respectively.
Here is the current draft of @esoteric-ephemera's benchmarking study: [bench_vasp_pars.docx](https://github.com/materialsproject/pymatgen/files/12600987/bench_vasp_pars.docx).
@shyuep see the final section of the attached doc regarding LREAL (which we discussed earlier today)
@computron @Andrew-S-Rosen @JaGeo @utf would love to hear your thoughts as well!
|
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PR_kwDOACgets5aUeaK
| 3,323
|
More Google-style class attribute doc strings
|
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[] | 2023-09-14T09:19:09
| 2023-09-14T11:29:25
|
2023-09-14T11:29:23Z
|
MEMBER
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Missed some in #3320.
819b65771 rename variables: d->dct
47f1ed7f3 :param to google-style
46d4aba4c fix typos
a6c0569c8 staticmethod to classmethod
19f89bdf7 more class attribute doc strings to google style
f72ac9a31 fix doc str indentation
|
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I_kwDOACgets5xFj74
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|
[Bug]: oxi_state_guesses does not work for selected diatomic gases
|
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[] | null |
[
"Looks like oxidation state of 0 for diatomic molecules isn't specified in `Element.icsd_oxidation_states` or `Element.oxidation_states` here\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/047ce69fe111d53fd6776f8773216bd9a042f987/pymatgen/core/composition.py#L912-L916\r\n\r\nNot sure if the better solution is to update that data or just hard-code a special case for single-element diatomic molecules in `oxi_state_guesses()`:\r\n\r\n```py\r\n if len(self.elements) == 1 and self.element_composition[self.elements[0]] == 2:\r\n return ({self.elements[0].symbol: 0.0},)\r\n```\r\n\r\nMaybe @shyuep or @mkhorton want to weigh in?",
"I discovered this morning that this can be partially solved by passing `all_oxi_states=True`, but there still appears to be data missing for `F2`. \r\n\r\nGiven how commonly diatomic gases arise in, e.g., formation energy calcs, I also think we should not require a non-default kwarg just to get the correct oxidation state for these substances.\r\n\r\n```\r\n>>> Composition('O2').oxi_state_guesses(all_oxi_states=True)\r\n({'O': 0.0},)\r\n>>> Composition('Cl2').oxi_state_guesses(all_oxi_states=True)\r\n({'Cl': 0.0},)\r\n>>> Composition('F2').oxi_state_guesses(all_oxi_states=True)\r\n[]\r\n>>> Composition('I2').oxi_state_guesses(all_oxi_states=True)\r\n({'I': 0.0},)\r\n>>> Composition('Br2').oxi_state_guesses(all_oxi_states=True)\r\n({'Br': 0.0},)\r\n>>> Composition('N2').oxi_state_guesses(all_oxi_states=True)\r\n({'N': 0.0},)\r\n>>> Composition('H2').oxi_state_guesses(all_oxi_states=True)\r\n({'H': 0.0},)\r\n```",
"I am not actually sure who relies on oxi_state_guesses. As their name implies, they are guesses. The guesses are probably not very useful. For diatomic gases, I would simply set oxidation state to 0 since that's the only possible charge neural solution. In fact, all elemental systems (be it metals, gases or whatever) should have an oxidation state of 0. @janosh Can you correct your recent PR to reflect this?",
"Thanks for the quick action @janosh and @shyuep 👍🏻 "
] | 2023-09-14T20:44:46
| 2023-09-18T17:36:59
|
2023-09-18T16:21:41Z
|
CONTRIBUTOR
|
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### Email (Optional)
_No response_
### Version
latest from git as of 2023.09.14
### Which OS(es) are you using?
- [ ] MacOS
- [X] Windows
- [X] Linux
### What happened?
1. I was using `Ion.oxi_state_guesses` to determine oxidation states of elements in aqueous species. This method inherits from `Composition`
2. No results were given for `O2`. Subsequent testing revealed that `O2,`, `Cl2`, and `F2` return empty lists `[]`, whereas `N2` and `H2` return tuples of dicts, as expected.
3. I examined `Element.common_oxidation_states` for each of these elements, but none contains 0 as a common oxi state. Nevertheless, 0 is correctly returned by `Composition.oxi_state_guesses` for two of them.
### Code snippet
```python
>>> Composition('O2').oxi_state_guesses()
[]
>>> Composition('H2').oxi_state_guesses()
({'H': 0.0},)
>>> Composition('N2').oxi_state_guesses()
({'N': 0.0},)
>>> Composition('F2').oxi_state_guesses()
[]
>>> Composition('Cl2').oxi_state_guesses()
[]
>>> Element('O').common_oxidation_states
(-2,)
>>> Element('H').common_oxidation_states
(-1, 1)
>>> Element('N').common_oxidation_states
(-3, 3, 5)
>>> Element('F').common_oxidation_states
(-1,)
>>> Element('Cl').common_oxidation_states
(-1, 1, 3, 5, 7)
```
### Log output
_No response_
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
|
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Readme notice regarding updated pymatgen publication
|
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[
"And thanks @janosh! :)"
] | 2023-09-15T06:52:05
| 2023-09-15T17:53:14
|
2023-09-15T06:52:34Z
|
MEMBER
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Thanks @mkhorton!
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AttributeError in BSPlotter.get_plot(): 'Axes' object has no attribute 'gcf'
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[] | 2023-09-15T11:57:19
| 2023-09-15T12:16:00
|
2023-09-15T12:16:00Z
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MEMBER
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> It would potentially break 100s of projects, scripts. (😬) Mine included.
Sorry to open this issue again. In our project updated to latest pymatgen, we encounter unexpected errors in various scripts customizing the window title and size after using get_plot(). After updating all the scripts according to the above breaking changes, we still get the following error:
Traceback (most recent call last):
.../pymatgen/electronic_structure/plotter.py", line 711, in fix_layout
ax.gcf().tight_layout()
^^^^^^
AttributeError: 'Axes' object has no attribute 'gcf'
This error seems to be due to Line 711/712 in pymatgen/electronic_structure/plotter.py:
def fix_layout(event):
if (event.name == "key_press_event" and event.key == "t") or event.name == "resize_event":
ax.gcf().tight_layout()
ax.gcf().canvas.draw()
since ax is now an Axes object, not a pyplot object.
_Originally posted by @goodwilling in https://github.com/materialsproject/pymatgen/issues/3138#issuecomment-1720850463_
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PR_kwDOACgets5abtsx
| 3,327
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Fix `AttributeError` in `BSPlotter.get_plot()`
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[] | 2023-09-15T11:59:24
| 2023-09-15T12:16:00
|
2023-09-15T12:15:59Z
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MEMBER
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Closes #3326.
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I_kwDOACgets5xJYYA
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|
BSPlotter.plot_brillouin() returns empty window
|
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[] | null |
[
"According to the following URL, it seems to be solved by the replacement of \r\n ax = axes3d.Axes3D(fig) \r\nwith\r\n ax = fig.add_subplot(projection='3d')\r\n\r\nin pymatgen/utils/plotting.py.\r\n\r\nmatplotlib and Axes3D give a blank picture\r\nhttps://stackoverflow.com/questions/76069849/matplotlib-and-axes3d-give-a-blank-picture"
] | 2023-09-15T12:02:19
| 2023-09-16T14:45:04
|
2023-09-16T14:45:04Z
|
MEMBER
|
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```python
from pymatgen.ext.matproj import MPRester
mpr = MPRester("32-digit key")
bs = mpr.get_bandstructure_by_material_id("mp-3748")
plotter = BSPlotter(bs)
plotter.plot_brillouin()
```
Result: an empty window comes out.
_Originally posted by @goodwilling in https://github.com/materialsproject/pymatgen/issues/3138#issuecomment-1721020134_
|
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PR_kwDOACgets5aflZY
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|
Breaking: rename `get_ax3d_fig_plt->get_ax3d_fig` and `get_ax_fig_plt->get_ax_fig` plus no longer return `plt`
|
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[] | 2023-09-16T13:54:59
| 2023-09-16T14:24:03
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2023-09-16T14:24:02Z
|
MEMBER
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7fc6bb5d6 breaking: rename get_ax3d_fig_plt->get_ax3d_fig and stop returning matplotlib.pyplot
cd7567481 breaking: same for get_ax_fig_plt->get_ax_fig
0a58b782b remove :class:`SomeObject` from doc strings
bf1a65e3c simplify doc strings: pymatgen.core.(lattice.->'')Lattice
0f4214013 blank line before all Args: and Returns: doc string section headers
cbaa1002c use dict.setdefault() instead of checking key presence first
74e5f854e doc string indentation and line break fixes
45d18cc1b fix doc string Returns: sections
62c06f0e8 define reusable LatticeType and CrystalSystem types
039b4b1c2 simplify with_local_env_strategy() sg.add_edge() call
|
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PR_kwDOACgets5afnU7
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|
Use `ax = fig.add_subplot(projection='3d')` to create `Axes3D`
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[] | 2023-09-16T14:30:07
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2023-09-16T14:45:02Z
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Closes #3328.
As suggested by @goodwilling in https://github.com/materialsproject/pymatgen/issues/3328#issuecomment-1722076836. Thanks! 👍
Applies to `BSPlotter.plot_brillouin()` and `WulffShape.get_plot()`.
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PR_kwDOACgets5af08c
| 3,331
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Fix `ruff` A001 violations: Variable is shadowing a Python builtin
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[] | 2023-09-16T18:15:37
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PR_kwDOACgets5af1Xp
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Always return 0 for `Composition.oxi_state_guesses()` of diatomic molecules
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[] | 2023-09-16T18:23:47
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2023-09-18T16:21:40Z
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Closes #3324.
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PR_kwDOACgets5agD8p
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Delete unused or numpy-provided routines from `pymatgen.util.num`
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Use `np.clip` instead.
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I_kwDOACgets5xOuu_
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Coherent interface builder: too strict tolerance in assert_allclose
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[
"This is due to #3253. Should be easy to fix by reinstating explicit `atol=1e-08`. Thanks for reporting!"
] | 2023-09-17T07:20:29
| 2023-09-17T20:04:14
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2023-09-17T20:04:14Z
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NONE
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#### Issue: Coherent Interface Builder Fails in pymatgen 2023.9.10 on Windows 10
##### Description
When building Si(100)/Au(100) interfaces using `coherent_interface_builder` on Windows 10, we encounter an `AssertionError` in pymatgen version 2023.9.10. The issue didn't exist in previous versions. We're using `mp-149` for Si bulk and `mp-81` for Au bulk structures.
##### Error Details
Here's the relevant stack trace:
```python
pymatgen\analysis\interfaces\coherent_interfaces.py", line 217, in get_interfaces
assert_allclose(
File numpy\testing\_private\utils.py, line 1504, in assert_allclose
assert_array_compare(compare, actual, desired, err_msg=str(err_msg),
File contextlib.py, line 81, in inner
return func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File numpy\testing\_private\utils.py, line 797, in assert_array_compare
raise AssertionError(msg)
```
**AssertionError Details:**
- **Tolerance**: rtol=1e-07, atol=0
- **Mismatched Elements**: 3/6 (50%)
- **Max Absolute Difference**: \(4.4408921 \times 10^{-16}\)
##### Current Workaround
Explicitly setting `atol` to a small non-zero value in `assert_allclose` within `pymatgen/analysis/interfaces/coherent_interface.py` bypasses the error.
---
Please investigate why this issue has appeared in the latest version. Thank you.
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PR_kwDOACgets5agsGd
| 3,335
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fix ruff FBT003: Boolean positional value in function call
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PR_kwDOACgets5agxMe
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Fix breaking change to `CoherentInterfaceBuilder.get_interfaces`
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Closes #3334.
Fix accidental breaking change introduced in https://github.com/materialsproject/pymatgen/pull/3253 by reinstating explicit `atol=1e-08` (default for `np.allclose` whereas `np.testing.assert_allclose` sets this to 0).
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PR_kwDOACgets5ag6Uq
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Add `properties` @property/docstring to `IStructure`
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[
"Adding a note that, while reviewing this, I noticed a lot of methods on `SiteCollection` reference a \"structure\", even though these methods are also used by `IMolecule`/`Molecule`. Might cause some confusion. "
] | 2023-09-17T19:33:31
| 2023-09-17T23:26:27
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2023-09-17T23:22:53Z
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Addendum to #3264, notifying @gpetretto, @janosh.
Two things I think we missed in #3264:
* A formal `@property` so that we get a docstring for the new `IStructure.properties`
* An edge-case for backwards compatibility. While I strongly recommend people _do not_ use pickle as an archival format, nevertheless this is a very core pymatgen class, and I don't want to break people's workflows if they upgrade. Specifically, if you pickle a `Structure` from a previous pymatgen version, and then un-pickle it with the new pymatgen version, the `__init__` will not be called, so the `.properties` instance variable is never set: this will then break code that relies upon it, like `as_dict()`. Luckily, adding the `@property` interface allows us to trivially catch this edge case.
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PR_kwDOACgets5ag-2m
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Snake case test method names
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[Bug]: Inconsistent behaviour with `get_symmetrized_structure`
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[
"Hi @kavanase! It seems that your supercell is quite large and if you are saving it as a `POSCAR` with default settings you may be running into numerical precision issues. I suggest you look into either (1) increasing export accuracy or (2) playing with the `SpacegroupAnalyzer`'s `symprec` parameter, to allow for larger basis distortions from ideal positions. Good luck!",
"It might also be worth talking to the developers of `spglib` if it might seem like a legitimate bug in symmetry determination, rather than a precision issue (of course, they would need a minimal reproducible example using spglib directly rather than pymatgen—the easiest way to do this is typically to add a print statement before the spglib call inside pymatgen to see the exact values passed to spglib).\r\n\r\nFor symmetry issues, it’s also worth trying some different versions of spglib just in case there’s been a regression etc.",
"As spglib developer side, I think it may be possible that spglib returns another space group for a supercell than that for the primitive structure. Spglib only returns rotation matrices with integers. So if the supercell matrix breaks the symmetry, corresponding result may change.\r\nI am also wondering what space group types does spglib return for this issue's structure.",
"Btw, I checked that this issue is still not fixed with the latest versions of `pymatgen` or `spglib`.\r\n\r\nThese are the relevant structures, needed to reproduce this issue (to run the code in the notebook):\r\n[Sb2Si2Te6_POSCARs.zip](https://github.com/user-attachments/files/17080090/Sb2Si2Te6_POSCARs.zip)\r\n\r\nRegarding @lan496 :\r\n> I am also wondering what space group types does spglib return for this issue's structure.\r\nThe space groups returned in all cases are the correct `R-3`, as shown in the notebooks I attached above:\r\n<img width=\"444\" alt=\"image\" src=\"https://github.com/user-attachments/assets/8e24bf9f-8679-4c7c-a62d-01b5aef4cdd5\">\r\n<img width=\"434\" alt=\"image\" src=\"https://github.com/user-attachments/assets/3cfaa3df-c960-4f93-857b-17c10a36b5e8\">\r\n<img width=\"525\" alt=\"image\" src=\"https://github.com/user-attachments/assets/539dfe46-e79e-4504-8a6b-95d24d080bc8\">\r\n\r\n"
] | 2023-09-18T11:21:28
| 2024-09-20T19:34:30
|
CONTRIBUTOR
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### Email (Optional)
sean.kavanagh.19@ucl.ac.uk
### Version
v2023.9.2
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
When using `SpacegroupAnalyzer.get_symmetrized_structure()`, I noticed some odd behavior.
If the input structure is a non-diagonal supercell of the primitive structure, the space group symmetry of the material is correctly determined (and returns the correct primitive structure), but the `SymmetrizedStructure` _differs_ from that obtained when inputting the primitive structure.
In the example case below, this now outputs additional 'inequivalent' sites, which are in fact equivalent in the primitive structure. I've witnessed this now in a couple of different material systems, with non-diagonal supercells.
I'm not sure if this is the desired behaviour, but I wouldn't have guessed so.
Notebook and PDF attached below.
[pymatgen_symm_structure_PR.pdf](https://github.com/materialsproject/pymatgen/files/12647147/pymatgen_symm_structure_PR.pdf)
[pymatgen_symm_structure_PR.ipynb.zip](https://github.com/materialsproject/pymatgen/files/12647180/pymatgen_symm_structure_PR.ipynb.zip)
### Code snippet
_No response_
### Log output
_No response_
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
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I_kwDOACgets5xdD-l
| 3,341
|
[Bug]: `converged_ionic` does not account for stopped calculation
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[
"I agree this is misleading behavior. A PR that modifies `converged_ionic` to also check `EDIFFG` sounds like an improvement.\r\n\r\nThough as @Andrew-S-Rosen pointed out, some calculations keep some atoms fixed in which case you may end up with large forces even though VASP is done. @shyuep @esoteric-ephemera curious to hear your thoughts. Is there some better heuristic we should use instead?",
"The fixed atoms isn't a big deal. We would \n compute the max force on the non-fixed atoms. Just something to be cognizant of.\n\nIn general, this seems like a change that is important but could easily break things if we aren't careful. ",
"Similar logic is implemented in `converged_electronic`, it relies on `NELM` steps performed vs specified rather than `EDIFF`:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/46c71963b1c15c9bf7a7964a0908c602f7b67758/pymatgen/io/vasp/outputs.py#L509-L524\r\n\r\nA calculation will stop at the next electronic step if `STOPCAR` has `LABORT = .TRUE.` ([ref](https://www.vasp.at/wiki/index.php/STOPCAR)). I think the property should need to account for it.",
"Agree with @Andrew-S-Rosen, we should check and see how converged_ionic and converged_electronic are being used in, e.g., PMG, custodian, and atomate, to make sure we don't break expected behaviors. Custodian very likely uses this for the unconverged error handler\r\n\r\nThe \"correct\" check for electronic self-consistency would be to make sure that |E(IELM) - E(IELM - 1)| < EDIFF, where 1 <- IELM <= NELM is the electronic step. A calculation could converge on the NELM-th step, probably exceedingly rare though. \r\n\r\nSimilar for forces/EDIFFG, but with those caveats about full vs. partial relaxation"
] | 2023-09-19T17:33:06
| 2023-09-21T20:21:44
|
CONTRIBUTOR
|
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### Email (Optional)
_No response_
### Version
v2023.6.28
### Which OS(es) are you using?
- [ ] MacOS
- [ ] Windows
- [X] Linux
### What happened?
I have a long VASP calculation and I use `STOPCAR` to stop the calculation early before reaching wall time limit. Once the vasp finishes, I use the `pymatgen.io.vasp.outputs.Vasprun` to parse the `vasprun.xml` and check if the calculations converged based on that I make a decision to resubmit the calculation or not.
However, `converged_ionic` logic checks if the calculations reached the specified NSW steps and not respects the `EDIFFG` criteria.: https://github.com/materialsproject/pymatgen/blob/f4e605776b7afc6e74bd6e855f94280268aeb698/pymatgen/io/vasp/outputs.py#L619-L626
So, for my case because the calculation will be stopped early and ionic steps < specified `NSW` steps, the `converged_ionic` is always `True`. Is there something I am missing or is it the desired behavior?
### Code snippet
```python
vasprun = Vasprun(vasprun_path, parse_dos=False, parse_eigen=False)
if vasprun.converged:
return # resubmission not required
else:
# resubmit calculation
```
### Log output
_No response_
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
|
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I_kwDOACgets5xk0ze
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Support VASP 64 pseudopotentials
|
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[
"Besides adding new POTCAR hashes (or whatever future validation technique we migrate to), are we expecting additional TODOs?",
"Here are a few questions:\r\n\r\n- Everything works as-expected with the `pmg config` command-line utility? \r\n- Parsing of the POTCAR spec in the `Potcar` class fetches all the metadata appropriately?\r\n\r\nIt's very possible that there are no changes needed. Part of this issue was also to decide if that's the case :)",
"Is there a link to release notes from VASP on these pseudopotentials? I was hoping to find a news item or a wiki page or similar.",
"If you find one, let me know. This is all i could find. The `README.UPDATES` file they mention offers no further details either.\r\n\r\n\r\n",
"Thanks @janosh, I haven't found any mention myself but if I do I'll make sure to share.",
"Seems the most recent update of https://www.vasp.at/wiki/index.php?title=Available_PAW_potentials&type=revision&diff=14415&oldid=12650 was the addition of the Yb_3 line in Jan 2022.",
"Are the changes from the new \"Cs_sv\" on structural optimizations drastic? I guess we would expect the largest impact here.",
"Why would you expect Cs_sv specifically to be largest impact @JaGeo? (I have no intuition here.)",
"@mkhorton should have phrased it more carefully. \"Cs_pv\" and potentially all lanthanides but I assume that the \"Cs_pv\" potential is used more frequently.",
"Is this closed by [PR #3370](https://github.com/materialsproject/pymatgen/pull/3370)?",
"Sounds like it. Thanks! ",
"We haven't really run anything with the new 6.4 POTCARs yet so I left this open in case we encounter issues. We can re-open if that's the case."
] | 2023-09-20T17:59:29
| 2023-10-20T19:22:28
|
2023-10-20T19:21:11Z
|
MEMBER
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### Email (Optional)
_No response_
### Problem
VASP has now released v64 pseudopotentials (PBE and LDA). This is an issue tracker to monitor progress related to ensuring that Pymatgen plays nicely with them.
### Proposed Solution
N/A
### Alternatives
_No response_
### Code of Conduct
- [X] I agree to follow this project's Code of Conduct
|
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Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file`
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[
"tag @tschaume you might be interested to comment since I mentioned this bug to you 😄 ",
"The error I received is \r\n```\r\n-> 3585 f.write(\"\".join(self.data_aug.get(data_type, [])))\r\n\r\nTypeError: can only join an iterable\r\n```\r\n@janosh this is a file output bug, so do you want me to check if the file looks identical to itself after read in and output? ",
"> @janosh this is a file output bug, so do you want me to check if the file looks identical to itself after read in and output?\r\n\r\nSounds good! Just writing to disk would be enough to test this fix but checking for equality after re-read is even better.",
"Test added :) @janosh "
] | 2023-09-20T20:33:45
| 2023-09-30T20:30:32
|
2023-09-30T20:30:32Z
|
CONTRIBUTOR
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Context: I was trying to download `AECCAR`s from aws and save them locally as vasp compatible format. `CHGCAR`s can pass successfully but `AECCAR` will yield error when `aeccar.write_file` like following
```python
mp_id = 'mp-1523380'
prefix = 'aeccar0s'
suffix = prefix.rstrip("s")
fpath = f'{mp_id}-{suffix}.json.gz'
with zopen(fpath) as f:
json_string = f.read()
data = json.loads(json_string, cls=MontyDecoder)['data']
data.write_file(f'{mp_id}.{suffix.upper()}')
```
Modify `io/vasp/outputs.py` to do the Iterable check first and only write to file when `self.data_aug.get(data_type, [])` is not empty
# Checklist
- [x] ruff
- [x] mypy
- [x] pre-commit
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Fix: `TestMITMPRelaxSet.test_nelect` claimed to but wasn't testing disordered structure
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Remove rounding during FEFF writing
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[
"> I'm also happy to use this PR to help make the other codes consistent. Thoughts?\r\n\r\nThanks @matthewcarbone. Which other codes are you referring to?",
"@janosh \r\n\r\n> Thanks @matthewcarbone. Which other codes are you referring to?\r\n\r\nWell, selfishly the ones I use [here](https://github.com/AI-multimodal/Lightshow): FEFF, EXCITING, Xspectra, OCEAN and VASP. But that can just be a starting point!",
"I think I can see both sides. Why not write geometries as is, as you're suggesting.\r\n\r\nOn the other side, there's usually no point in recording higher float precision than what your data has i.t.o. significant digits. Is yours more accurate than 1e-6? If not, maybe a rounded equality check or using something like `np.allclose` would be a better option for you?",
"> I think I can see both sides. Why not write geometries as is, as you're suggesting.\r\n\r\nIt's more just write them at the precision specified by `self._cluster` instead of constraining the precision in a way that _seems_ arbitrary.\r\n\r\n> On the other side, there's usually no point in recording higher float precision than what your data has i.t.o. significant digits. Is yours more accurate than 1e-6? If not, maybe a rounded equality check or using something like `np.allclose` would be a better option for you?\r\n\r\nCertainly true. This is really a nitpick, but when doing some sanity checks on my end, the problem is that the precision differences cause sorting issues which scramble the order of atoms! I can give you the long story \"long\", if you want, but that's the long story short.\r\n\r\nIs it a big deal? No absolutely not. But why not be consistent!\r\n",
"> But why not be consistent!\r\n\r\nSure, I'm happy to go ahead with this. I'm also not a user of these parts of pymatgen myself so just trying to get an idea on what's the best course of action. The other option that comes to mind is to add an explicit `fmt: str = ''` keyword. So the old behavior could still be retained when users pass `fmt=\".f\"`.",
"> Sure, I'm happy to go ahead with this. I'm also not a user of these parts of pymatgen myself so just trying to get an idea on what's the best course of action. The other option that comes to mind is to add an explicit `fmt: str = ''` keyword. So the old behavior could still be retained when users pass `fmt=\".f\"`.\r\n\r\nYes we definitely could do that too! What would you like to do? If you want I can implement this. We'd have to have a lot of passthroughs from the `FEFFDictSet` -> `Atoms` -> etc. so it will take another commit or two.",
"Please go ahead."
] | 2023-09-21T16:50:01
| 2024-03-03T18:26:41
|
2024-02-26T09:11:31Z
|
CONTRIBUTOR
|
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`pymatgen/io/feff/inputs.py` lines 504-506 rounded the FEFF geometry to 6 decimal places by default. This also occurs in 518-520. Other writers (such as the one for EXCITING) do not appear to do this. This commit makes a simple change and removes the `":f"` from the string representation in the lines formatting. Thus FEFF clusters will now be saved with default precision (or whatever `self._cluster` uses).
I'm implementing this fix because it's actually causing me some precision issues when testing save spectroscopy input files for FEFF against other codes, and also because this would make the FEFF writers consistent.
I'm also happy to use this PR to help make the other codes consistent. Thoughts?
## 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))
Note I don't think that there are any new tests to run here.
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Q-Chem initial_hessian handling
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[
"was this accidentally left in draft mode?"
] | 2023-09-21T21:34:59
| 2024-08-03T19:01:57
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CONTRIBUTOR
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Small change to sets.py to better handle initial hessian for new geometry optimizer
Still need to add a test to go along with it
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PR_kwDOACgets5bC2z7
| 3,347
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Fix `TestPotcar.test_write` polluting git repo on failure
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[] | 2023-09-23T17:41:09
| 2023-09-23T17:55:27
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2023-09-23T17:55:26Z
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MEMBER
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036770c99 improve StructureError msg on species/coord length mismatch
20c8b1693 fix TestPotcar.test_write polluting git repo on failure
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I_kwDOACgets5x-E4W
| 3,348
|
[Bug]: `v2023.9.25` pip install fail on MacOS (in specific cases)
|
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[
"Hmm... the error suggests it is a problem with your gcc and not pymatgen? I just installed it on my mac and there were no issues. Also, your numpy seems to be really old. I would upgrade numpy first using `pip install --upgrade numpy`.",
"The above occurred with numpy-1.26.0-cp39-cp39-macosx_10_9_x86_64, from a week ago, installed earlier in the workflow run. Environment is a clean GitHub `macos-latest` runner with default configuration.",
"We are running CI on the same environment. You can check it out in the Actions tab. There is no issue on our end. I guess the question is whether rpy is installing something that conflicts with the pymatgen requirements.",
"Right! I checked first to see if your tests were passing. On my side, all of my other packages utilizing pymatgen, but not rpy2, have passed as well with the new release. \r\n\r\nI probably should have been more clear. The reason I brought this up is that this issue seemed to indicate pymatgen's dependencies might be underspecified, allowing for too old Numpy, given changes done in the new release. When installing pymatgen on its own, like in the test matrix, or with other highly-maintained packages, this wouldn't show up, as pip solves for the latest versions of everything, but some other installations might force older versions while still resolving dependencies.\r\n\r\nIf you think there is no problem, please don't hesitate to close. And big thanks for such a quick response!",
"> The reason I brought this up is that this issue seemed to indicate pymatgen's dependencies might be underspecified, allowing for too old Numpy\r\n\r\nYou're right, we should require the oldest numpy to have 3.9 as oldest supported Python. This appears to be [v1.25.0](https://github.com/numpy/numpy/releases)."
] | 2023-09-25T18:53:02
| 2023-09-26T18:19:11
|
2023-09-26T18:19:11Z
|
CONTRIBUTOR
|
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Hi! I noticed that the just-released pymatgen `v2023.9.25` [in this specific configuration cannot `pip install` correctly on **MacOS X86_64 GitHub runner**](https://github.com/amkrajewski/pqam-dparamhu2021/actions/runs/6302862819/job/17112125672) for Python 3.9 and Python 3.10, but can for Python 3.11.
**Notes:**
- Issue re-occurs when workflow is re-run.
- Issue does _not_ occur on Linux (Ubuntu).
- [Installs correctly under `v2023.9.10`](https://github.com/amkrajewski/pqam-dparamhu2021/actions/runs/6226021670/job/16897635425) on the same system.
- The only other dependency alongside it is `rpy2>3.5.0`. With `rpy2==3.5.14`, all dependency versions seem satisfied.
- It seems to be `numpy`-related. I attach a relevant snippet at the end. [Full log is here.](https://github.com/amkrajewski/pqam-dparamhu2021/actions/runs/6302862819/job/17112125672)
- When I tested 3 other packages that do not use `rpy2`, `v2023.9.25` installs as usual.
```
Compiling pymatgen/optimization/linear_assignment.pyx because it changed.
[1/1] Cythonizing pymatgen/optimization/linear_assignment.pyx
building 'pymatgen.optimization.linear_assignment' extension
creating build/temp.macosx-11.7-x86_64-cpython-310
creating build/temp.macosx-11.7-x86_64-cpython-310/pymatgen
creating build/temp.macosx-11.7-x86_64-cpython-310/pymatgen/optimization
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/sqlite/include -I/usr/local/opt/sqlite/include -I/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/pip-build-env-1za7ze_a/overlay/lib/python3.10/site-packages/numpy/core/include -I/Users/runner/hostedtoolcache/Python/3.10.13/x64/include/python3.10 -c pymatgen/optimization/linear_assignment.c -o build/temp.macosx-11.7-x86_64-cpython-310/pymatgen/optimization/linear_assignment.o
<built-in>: error: unknown value ‘11.7’ of -mmacosx-version-min
In file included from /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/pip-build-env-1za7ze_a/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
from /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/pip-build-env-1za7ze_a/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/pip-build-env-1za7ze_a/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pymatgen/optimization/linear_assignment.c:1167:
/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/pip-build-env-1za7ze_a/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
error: command '/usr/local/gfortran/bin/gcc' failed with exit code 1
[end of output]
```
Have a lovely day!
Adam
|
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I_kwDOACgets5x-tBr
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Wrong name of Pourbaix Entry
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[
"What is your MPRester version? Also, this should be reported to the mp-api package since it has nothing to do with pymatgen. ",
"@yuxin-chang I thought this was an issue in `Ion.reduced_formula`, but I'm not able to reproduce:\r\n\r\n```\r\n>>> from pymatgen.core.ion import Ion\r\n>>> i=Ion.from_formula('SnHO2+')\r\n>>> print(i.reduced_formula, i.composition)\r\nSnHO2[+1] Sn1 H1 O2\r\n>>> i=Ion.from_formula('SnHO2-')\r\n>>> print(i.reduced_formula, i.composition)\r\nSnHO2[-1] Sn1 H1 O2\r\n```\r\n\r\nPlease update your `pymatgen` and `mp-api` clients to the latest versions and let us know if this is still a problem."
] | 2023-09-25T20:50:03
| 2023-09-26T13:28:36
|
2023-09-25T20:59:06Z
|
NONE
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The ion entry of Sn was in a wrong name:
the ion entry with composition Sn1 O2 H1 has name SnOH2[+1]
the ion entry with composition H1 Sn1 O2 has name SnOH2[-1]
As printed out, the number of O and H are opposite
```
mpr = MPRester()
entries = mpr.get_pourbaix_entries([ "Sn"])
for entry in entries:
print(entry.name,entry.composition )
```
The output is:
Sn[+2] Sn1
SnOH[+1] Sn1 O1 H1
SnOH2[+1] Sn1 O2 H1
SnO3[-2] Sn1 O3
SnOH2[-1] H1 Sn1 O2
Sn[+4] Sn1
…
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Ion: default hydrates=False in reduced_formula
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[
"@rkingsbury Is this intentionally in draft mode?",
"@janosh it was intentional, but I think it's good to go. All tests pass, but I wanted to make sure that this didn't mess up anything on the API side. When we re-did the [Pourbaix ion data](https://next-gen.materialsproject.org/contribs/projects/ion_ref_data?_limit=75), I used `Ion.reduced_formula` as the database keys (the MPContribs identifiers). However, it doesn't appear that any of the ions in the dataset were formatted as hydrates (for example, `Be3(OH)3[3+]` is listed there, but could be written `Be3OH2.1H2O`).\r\n\r\nIn the API client, the only call is `Ion.from_formula()` ([here](https://github.com/materialsproject/api/blob/ffd9713ec0847466eae858a802d6692dfc476159/mp_api/client/mprester.py#L1032C13-L1032C17)) followed by `Ion.composition` so I don't think this change will cause any problems."
] | 2023-09-26T15:03:42
| 2024-10-10T01:55:02
|
2023-10-09T14:41:58Z
|
CONTRIBUTOR
|
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## Summary
Major changes:
- default to `hydrates=False` in `Ion.get_reduced_formula_and_factor()`
- explicitly use `Ion.get_reduced_formula_and_factor()` rather than `super().get_reduced_formula_and_factor()` in `reduced_formula
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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PR_kwDOACgets5bQQDq
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Breaking: New method of POTCAR validation
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[
"Thanks for taking a fresh look at this problem @esoteric-ephemera, it's been unsatisfactory for a while. These warnings frequently confuse or alarm people unnecessarily, but the underlying motivation of rigorously checking pseudopotential compatibility is of course very important.\r\n\r\n> However FORTRAN is space-insensitive, thus two POTCARs that differ by spaces are read identically by VASP.\r\n\r\nI imagine there's a way around this, to normalize the POTCAR file, but it might be slow and perhaps there'd still be brittleness in other ways so I like your suggestions.\r\n\r\nWhen the original POTCAR hash database was assembled we tried to find as many examples as we could, but I'm still surprised there are files out there that might differ by e.g. spaces within the file itself, since I can't imagine why these edits would have been made.\r\n\r\n ",
"Thanks both @janosh and @mkhorton! Tried to address your comments. \r\n\r\nIt is possible just to completely strip a POTCAR of spaces and hash it that way, but I see one issue with that: in the PSCTR / header section of the POTCAR, there are comments. Normally, in fortran, in-line comments would be indicated by a leading \"!\", but these are omitted in the proprietary POTCAR format. One could add comments without changing any numeric values, and get the same POTCAR\r\n\r\nThere was actually a test of PotcarSingle in PMG that did just that - it basically added comments to a PSCTR tag. A hash would report these as different, but the numeric values are identical to vasp",
"Thank you, @esoteric-ephemera, for helping me sleep better at night with this PR.",
"At the risk of asking a stupid question, I saw the MPRelaxSet defaults changed Yb_2 to Yb_3 recently (see #2968).\r\n\r\nHowever, as far as I can tell, only `Yb_2` is in the POTCAR database for the `PBE` functional (i.e., the MPRelaxSet default). The `Yb_3` only exists for the `PBE_52`/`PBE_54`.\r\n\r\nSo my questions are, (1) is this correct?, and (2), if so, is it even possible to run MPRelaxSet with Yb-containing materials at present?",
"> So my questions are, (1) is this correct?, and (2), if so, is it even possible to run MPRelaxSet with Yb-containing materials at present?\r\n\r\n@mkhorton I think you forgot about https://github.com/materialsproject/pymatgen/pull/2972 which reverted the `Yb_2` -> `Yb_3` migration for `MPRelaxSet`:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/8e0b09967d4135e33675bc7615c2b4d5e5613162/pymatgen/io/vasp/MPRelaxSet.yaml#L175",
"Indeed I did, thanks @janosh! This was not reverted in [atomate2](https://github.com/materialsproject/atomate2/blob/8c151790ec1db7b6e7a55e15f2d5a1fd34235e97/src/atomate2/vasp/sets/BaseMPGGASet.yaml#L202-L204) so the two sets are currently inconsistent (I realise this is an active topic of discussion right now).\r\n\r\nApologies to @esoteric-ephemera for bringing a tangent to this PR.",
"@mkhorton Good catch! yes, `POTCAR_FUNCTIONAL: PBE` might change to `PBE_54` in `atomate2` as soon as next week so I'll refrain from any fixes now."
] | 2023-09-26T16:57:20
| 2023-09-30T01:53:23
|
2023-09-30T00:03:15Z
|
CONTRIBUTOR
|
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## Summary
**Issues:**
current method of POTCAR validation is too brittle to work well in high-throughput calculations. For example, hashes are sensitive to subtle changes in spaces (addition/deletion). However FORTRAN is space-insensitive, thus two POTCARs that differ by spaces are read identically by VASP.
**Goals**:
Develop less brittle method for validating POTCARs that reflects how POTCAR metadata and numeric values are read by FORTRAN.
Major changes:
- *is_valid* function in *pymatgen.io.vasp.inputs.PotcarSingle*, which checks POTCAR metadata and values against a database of these
- To respect copyright, only statistics on the numerical values are stored separately for the PSCTR / POTCAR header and pseudopotential numeric values
- Keywords found within the PSCTR header and pseudopotential body are stored as well for comparison. For example, older POTCARs may have lacked the kinetic energy density (needed for meta-GGA calcs), and were later updated to include this. The check distinguishes the older and newer version of the same POTCAR
- Tests have been updated (*TestPotcarSingle* class in *tests/io/vasp/test_inputs.py*)
## Todos
- While I generated POTCAR metadata from those available to our group, might be beneficial to expand the database of POTCAR metadata to older / newer releases
|
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PR_kwDOACgets5bQlax
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Bump min `numpy` to v1.25.0
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[] | 2023-09-26T18:02:34
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2023-09-26T18:19:10Z
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MEMBER
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Closes #3348.
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PR_kwDOACgets5bQozW
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Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry`
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[] | 2023-09-26T18:12:23
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2023-09-26T18:28:49Z
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Thanks @munrojm for reporting. [This change](https://github.com/materialsproject/pymatgen/blame/4bff21d33625bc9f7077c7b4eb06098d1f50277c/pymatgen/analysis/molecule_matcher.py#L146) (although it improved code readability) caused errors in emmet CI.
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[WIP] Adding alias `.to_file()` for `.to()` method of site collections, structures and molecules
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[
"Sorry but we cannot do this. Whatever the merits of the renaming, this will cause all other packages that depends on pymatgen to break. Writing out files is probably one of the main uses. At best, we can allow write_file as an alias for to so that we preserve backwards compatibility. ",
"> Sorry but we cannot do this. Whatever the merits of the renaming, this will cause all other packages that depends on pymatgen to break. Writing out files is probably one of the main uses. At best, we can allow write_file as an alias for to so that we preserve backwards compatibility.\r\n\r\nSure, I can totally understand that! Then I will rewrite it that it is simply added as alias! ",
"I have to close this PR and will open a new one...."
] | 2023-09-27T09:16:22
| 2023-09-27T17:15:26
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2023-09-27T17:15:25Z
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CONTRIBUTOR
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## Summary
I have noticed that many beginners (including myself a while ago) find it very unintuitive to write e.g. structures to a file by using `.to()`, especially with the `.from_file()` method counterpart. That's why I refactored each instance/occurrence using the [pycharm](https://www.jetbrains.com/pycharm/) built-in refactoring feature to `.write_to_file()` and suggest this change in this PR. Of course I made sure not to change any of the unit conversion `.to()` instances.
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Fix MPMD set bug
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[
"Thanks"
] | 2023-09-27T14:16:12
| 2023-10-03T23:06:28
|
2023-09-27T14:41:46Z
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CONTRIBUTOR
|
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## Summary
Small bugfix for the MPMD vasp input set. The input parameter `time_step` was added in fabdd276497493f87f72348a3573bbe8a6c38f26 (it was in the docstring before that), but it was not added as a class attribute, leading to an `NotImplementedError` raised when trying to convert the object to a dict:
~~~
NotImplementedError: Unable to automatically determine as_dict format from class. MSONAble requires all args to be present as either self.argname or self._argname, and kwargs to be present under a self.kwargs variable to automatically determine the dict format. Alternatively, you can implement both as_dict and from_dict.
~~~
Major changes:
- feature 1: `time_step` is now usable and is passed on to `POTIM`. It defaults to None, in which case, the MPMDSet behaves as previously and `POTIM` is set to 0.5fs for compounds containing hydrogen, 2fs for anything else.
- fix 1: time_step is now also a class attribute, making the set MSONAble.
Both the time steps, as well as the dict conversion are tested in a new unit test for the MPMD set.
## 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_kwDOACgets5bXYx_
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Add alias `.to_file()` for `.to()` method of structures and molecules
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[
"You don't actually need to write it this way. All that needs to be done is to add `to_file = to` and `write_file = to` in SiteCollection. That will create the aliases without so much code.",
"> You don't actually need to write it this way. All that needs to be done is to add `to_file = to` and `write_file = to` in SiteCollection. That will create the aliases without so much code.\r\n\r\nI know, that's how I started, but when I tried to call the alias in pycharm, it wouldn't give me the input hints and at least for me they are really important. If you think that's not necessary, then I can change it to the simple alias.\r\n\r\nAlso when I only added `to_file = to` in SiteCollection, it would throw an error saying something like \"cannot call abstract method\" (I'm writing this from my phone, I would need to check the details tomorrow again if you wanna know the exact error)",
"> We definitely need a test for the new alias.\r\n\r\nAye aye! 🫡",
"hi @janosh I hope the tests are ok like that?"
] | 2023-09-27T17:40:49
| 2023-10-03T23:07:57
|
2023-09-30T17:17:06Z
|
CONTRIBUTOR
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## Summary
I have noticed that many beginners (including myself a while ago) find it very unintuitive to write e.g. structures to a file by using .to(), especially with the .from_file() method counterpart. That's why I added aliases `to_file` for structures and molecules.
PS: This is the second attempt of #3354 as something went wrong there...
|
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