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c1aa37107 deduplicate which("chargemol")
dfd2a560b refactor "Multiple files detected" warning
8e0b09967 use single dict assert instead of individual key asserts | {
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"@chiang-yuan: Thanks for highlighting. My opinion is that we should retain back-and-forth interconversion as much as possible, without any loss of information. This breaks that principle. Happy to review alternatives.",
"Also see slightly related comment: https://github.com/materialsproject/pymatgen/issues/3297 ... | 2023-09-28T01:33:50 | 2023-09-28T19:11:16 | 2023-09-28T19:11:16Z | CONTRIBUTOR | {
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} | I just merged this branch to my local and found that `jsanitize` breaks my code where I have `torch.multiprocessing` to convert `ase.Atoms` into `pymatgen.core.Strucuture`.
```
File "/global/homes/c/cyrusyc/.conda/envs/chace/lib/python3.9/site-packages/monty/json.py", line 585, in jsanitize
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"@chiang-yuan, @janosh: This is ready for your review.",
"Just want to offer thanks for this! @Andrew-S-Rosen you are so swift on this! (even on PTO 🫡",
"Had a spare moment and couldn't get it off my mind. I can go back to the beach life now. 😎🏖️"
] | 2023-09-28T03:29:16 | 2023-10-03T23:07:36 | 2023-09-28T19:11:15Z | MEMBER | {
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As raised in #3270, I stated:
> Currently, we have the mapping: `Atoms.info <--> Structure.properties`, since they serve the same purpose between ASE and Pymtatgen, respectively. However, I `jsanitize`-d the `atoms.info` before assigning it to `.properties` to ensure the `Structure`/`Molecule` objec... | {
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"Hi @janosh, this PR is ready to be merged. I would be happy to address if any specific changes are desired before merging."
] | 2023-09-29T11:52:09 | 2023-10-15T05:27:22 | 2023-10-14T14:24:20Z | CONTRIBUTOR | {
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1. Add a parser to read matrices written by Lobster like hamiltonMatrices.lobster, coefficientMatrices.lobster to outputs module
# Todo
- [x] Add tests and associated test files | {
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c1c9a1041 fix for loop overwriting hist variable in TransformedStructure.from_snl
596a56eea fix TestVasprun.test_update_potcar using wrong PotcarSingle hash: md5_computed_file_hash should be md5_header_hash | {
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major... | 2023-10-01T12:35:37 | 2023-10-01T16:34:13 | 2023-10-01T16:34:03Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<p>REL: v3.8.0</p>
<p>Highlights of this release include:</p>
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} | The breaking part of this PR is f09769b7a which probably sees little use, hence no deprecation period. Can always revert if that turns out to be wrong.
696008fff replace _parse_string with str.strip in PotcarSingle.parse_functions
328ae47c2 use keyword args to dict.update()
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"Hi. I think `pymatgen/io/vasp/potcar_summary_stats.json.gz` should be added to `setup.package_data` to use it via pip-installed version.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/44bf38318f1ff4265385eb6587bb713780732ff7/setup.py#L95-L119",
"Ah crap!",
"Not the first time don’t worry! I once adde... | 2023-10-02T21:35:44 | 2023-10-04T16:49:24 | 2023-10-03T23:11:53Z | CONTRIBUTOR | {
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} | ### Major changes:
- Follow-up to issue [#3342](https://github.com/materialsproject/pymatgen/issues/3342) and closed PR [#3351](https://github.com/materialsproject/pymatgen/pull/3351)
- Adds support for version 64 POTCARs
- Adds hidden function for PMG devs to continuously update potcar_summary_stats.json.gz used ... | {
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updates:
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/igorshubovych/markdownlint-cli: v0.36.0 → v0.37.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.36.0...v0.37.0)
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"@janosh this is failing in the most recent release right? My [workflows](https://github.com/AI-multimodal/Lightshow/pull/205) are failing because they can't find this file in `2023.10.3`. Thanks!",
"That's right, there will be a new release today.",
"I just released a bug fix release. v2023.10.4"
] | 2023-10-04T02:57:02 | 2023-10-04T13:22:53 | 2023-10-04T03:17:19Z | MEMBER | {
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"@epatyukova You're right, there is a problem here. Fwiw, the problem is more widespread than `pymatgen`.\r\n\r\n@esoteric-ephemera Did some investigation and it turns out `Vesta` and `ase` also parse this CIF file incorrectly. As @computron has said in the past, CIF is a troublesome format.\r\n\r\n`ase` completely... | 2023-10-04T13:04:20 | 2023-11-04T13:18:39 | NONE | {
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} | Structure with collection code 133424 from ICSD (Pr Sm Pb Si2 S8) is read incorrectly by `Structure.from_file()`. In particular there should be 18 Pb2+ sites, but there are 30 after the read. There is clearly a bug.
[`ICSD_CollCode133424.cif`](https://github.com/materialsproject/pymatgen/files/12803589/ICSD_CollCode... | {
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"@mkhorton @shyuep It looks like `pymatgen/analysis/chemenv/coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json` is not used anywhere\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/32f032ca41afba1e353d8eb42a9a29dd0462873c/pymatgen/analysis/chemenv/coordination_environme... | 2023-10-04T15:52:54 | 2023-10-12T00:29:43 | 2023-10-04T18:15:55Z | MEMBER | {
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def test_egg_sources_txt_is_complete():
"""Check that all source and data files in pymatgen/ are listed in pymatgen.egg-info/SOURCES.txt."""
with open(src_txt_path) as file:
sources = file.read()
# check that all files listed in SOURCES.txt exist
f... | {
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} | 0bf11ebc7 bump pypa/cibuildwheel to v2.16.2
b5e375814 add apply_strain() arg inplace: bool=True
1209f2a17 test struct.apply_strain(inplace=False) | {
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"Good catch! Thanks for reporting. 👍 "
] | 2023-10-05T20:43:02 | 2023-10-07T02:01:21 | 2023-10-07T02:01:21Z | NONE | {
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} | The skewness and kurtosis should be dimensionless according to original mathematical definition. However, in pymatgen comment and documentation it is indicated that the unit is eV? Maybe there is some misunderstanding here?
```
def get_band_kurtosis(
self,
band: OrbitalType = OrbitalType.d,
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"Can you give some more details about your OS, pmg + Python version and code you're trying to run?\r\n\r\nI just confirmed [the symmetry package _is in_ the latest release](https://inspector.pypi.io/project/pymatgen/2023.10.4/packages/41/44/707494da35be2061dfb30d6b8b8cf179c558b35f09857fe6552921309a45/pymatgen-2023.... | 2023-10-05T23:14:43 | 2023-10-12T20:14:12 | 2023-10-12T20:14:11Z | NONE | {
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} | ## Summary
Major changes:
- Added (some) type annotations to `io/lammps` and fixed some typos.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
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"Cool yes. But practical purpose?",
"Sanity checking, seeing how the different Kpoint styles differ on your system of interest, that sort of thing.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/cf0be37137ea0c588b6558a2188f3f919d08e50a/pymatgen/io/vasp/inputs.py#L970-L979",
"Erm, really? If someone el... | 2023-10-06T15:11:58 | 2023-11-02T02:11:22 | 2023-11-02T02:11:22Z | MEMBER | {
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} | ### Problem
Would be cool to visualize `Kpoints` as a 3d scatter plot in the Brillouin zone.
### Proposed Solution
Something similar to https://materialscloud.org/work/tools/seekpath.
![Screenshot 2023-10-01 at 12 00 08 PM](https://github.com/materialsproject/pymatgen/assets/30958850/e972bfad-a80f-46b5-afa1-d8ff0... | {
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dcea6b6bb rename single-letter vars
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c2534c92d core/test_structure.py add add test_to_primitive and test_to_conventional | {
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"Just to leave a paper trail: this project of overhauling the pymatgen POTCAR validation to move away from hashes and towards checking several aggregations of numerical data in a POTCAR against reference values started in #3351, was updated in #3370 to support validating the latest 6.4 POTCARs and received this bug... | 2023-10-10T16:17:24 | 2023-10-10T22:34:43 | 2023-10-10T19:08:11Z | CONTRIBUTOR | {
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In some releases of VASP POTCARs, there exist multiple POTCARs with the same TITEL. The previous summary statistics used to uniquely ID POTCARs relied on the uniqueness of TITELs. The current implementation allows for multiple POTCARs within a single release to have the same TITEL field, but different dat... | {
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Major changes:
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## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
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<div type='discussions-op-text'>
<sup>Originally posted by **ZeW4tcher** October 11, 2023</sup>
Could it be possible to change a bit the CifWriter.write_file() method to make it possible to use append file mode 'a' or 'at' ? Like this... | {
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} | `LMAXMIX` controls expansion of the charge density up to spherical harmonics of order $Y_{lm}$ with $l$ = LMAXMIX, $l$ = 2 for p-block, 4 for d-block, 6 for f-block, etc.
Internal benchmarking by @esoteric-ephemera found little run time cost but improved energies from `LMAXMIX = 6`. See pages 7 and 8 in [2023-09-27-... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3401 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3401/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3401/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3401/events | https://github.com/materialsproject/pymatgen/pull/3401 | 1,938,576,586 | PR_kwDOACgets5cjvrE | 3,401 | Fix type annotations in phonon/ and lammps/ | {
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} | ## Summary
Major changes:
- Revert `Self` usage from #3393 and #3379 as mentioned by @janosh
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
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"Update. Everything worked well When I created a new environment with only pymatgen, matminer, and minimal necessary dependence."
] | 2023-10-11T20:56:03 | 2023-10-12T16:02:57 | NONE | {
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} | HI! I was trying to use `CrystalNN` with a multiprocessing pool and found that the CPU usage was unexpected. I have given some small tests to figure out where the problems are and then found that when I import some modules from pymatgen, such as `from pymatgen.analysis.local_env import CrystalNN`, `from pymatgen.core i... | {
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} | dfd20f66a run `lint.yml` with python 3.9
dba615692 `OBAlign(includeH=False, symmetry=False) -> OBAlign(False, False)`
8716e4647 remove unused `np.abs(d, d)` in `pbc_coord_intersection` | {
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"FYI for developers, I have found it useful to be able to run `str()` on a PeriodicSite object, just as a way to compare sites to see if their species and coordinates are identical or not, and would prefer it not to be deprecated (if this was the intention)",
"Please post a minimal repro, i.e. the smallest piece ... | 2023-10-12T19:35:40 | 2023-10-19T18:45:22 | 2023-10-19T18:37:11Z | NONE | {
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I have some pymatgen code which worked previously. Essentially I have something like:
```
if str(site1) in [str(i) for i in list_of_sites]:
```
where `site1` is an instance of the `PeriodicSite` class and `list_of_sites` is a list of `PeriodicSite` objects.
However I recently upgraded my pymatgen an... | {
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"What should the new logic be for setting ISMEAR/SIGMA/KPOINTS? @esoteric-ephemera \r\n\r\nMaybe something like this?\r\n\r\n```py\r\nif self.bandgap == None:\r\n self._config_dict[\"INCAR\"].update({\"ISMEAR\": 0, \"SIGMA\": 0.05})\r\n self._config_dict[\"KPOINTS\"][\"reciprocal_density\"] = 200 #kpoint dens... | 2023-10-12T20:23:35 | 2024-04-17T23:51:01 | 2024-04-17T23:51:01Z | CONTRIBUTOR | {
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} | Follow-up to #3322.
- Change `LMAXMIX` to 6 for all MP input sets
- Change `LREAL` to `False` for MPRelaxSet and MPScanRelaxSet
- add logic to set `EDIFF = min(1e-4, NSITES * EDIFF_PER_ATOM)` as per [@esoteric-ephemera ](https://github.com/materialsproject/pymatgen/issues/3322#issuecomment-1723907332)
TODO:
- ... | {
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} | ## Summary
Major changes:
- Fix typo of using `+` instead of intended `*` to generate complex matrices : Led to incorrect outputs when non-zero imaginary values were there in the input files
- Added a more robust test to ensure file data is correctly read
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3410 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3410/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3410/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3410/events | https://github.com/materialsproject/pymatgen/pull/3410 | 1,945,896,555 | PR_kwDOACgets5c77Ms | 3,410 | Create jekyll-gh-pages.yml | {
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} | ## Summary
Major changes:
- feature 1: ...
- fix 1: ...
## 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`.
- [ ] Tests added for ne... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3411 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3411/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3411/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3411/events | https://github.com/materialsproject/pymatgen/issues/3411 | 1,947,184,738 | I_kwDOACgets50D65i | 3,411 | Thickness of generated slab is smaller than min_slab_size | {
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} | ### Bug Description
When using `generate_all_slabs` to generate surfaces by `primitive=True`, I have found some surfaces will have thickness smaller than the `min_slab_size` value.
### Reproduce the bug
```python
from pymatgen.core.surface import generate_all_slabs
from pymatgen.symmetry.analyzer import Spacegro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3412 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3412/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3412/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3412/events | https://github.com/materialsproject/pymatgen/issues/3412 | 1,947,241,399 | I_kwDOACgets50EIu3 | 3,412 | Inconsistency in oriented_unit_cell when generating (001)/(010)/(100) surface | {
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"I confirmed this problem as follows:\r\n```python\r\nfrom numpy.linalg import norm\r\nfrom numpy import cross\r\nfrom pymatgen.core.structure import Structure\r\nfrom pymatgen.core.surface import generate_all_slabs\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nimport numpy as np\r\n\r\ndef calcul... | 2023-10-17T11:56:17 | 2024-03-09T14:18:41 | NONE | {
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} | ### Bug description
When I generated the slab of TiNb(010) surface, I have found that the thickness of the slab (`6.95Å`) is smaller than `min_slab_size`, although `primitive=False` has been applied.
### Reproduce the bug
```python
from pymatgen.core.surface import generate_all_slabs
from pymatgen.symmetry.anal... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3413 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3413/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3413/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3413/events | https://github.com/materialsproject/pymatgen/issues/3413 | 1,950,566,945 | I_kwDOACgets50Q0oh | 3,413 | The current `py.typed` setup does not seem ideal | {
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"[Looks like it's not being shipped](https://inspector.pypi.io/project/pymatgen/2023.10.11/packages/1f/53/44b5986a59cef0fe28c88d84395c1656958ef8d7f523da60aa937127ed51/pymatgen-2023.10.11-cp310-cp310-macosx_10_9_x86_64.whl/) despite being included (incorrectly?) as `package_data` in `setup.py`\r\n\r\nhttps://github.... | 2023-10-18T20:10:20 | 2024-11-26T03:22:48 | MEMBER | {
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} | ### Problem
I am using `mypy` on a package with Pymatgen as a dependency and am getting back the following even though there is a `py.typed` marker in the base pymatgen directory. Any insights?
```
schemas/_aliases/emmet.py:11: error: Skipping analyzing "pymatgen.core.composition": module is installed, but missing... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3414 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3414/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3414/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3414/events | https://github.com/materialsproject/pymatgen/issues/3414 | 1,953,935,540 | I_kwDOACgets50drC0 | 3,414 | Dirty print in CifParser.get_structures | {
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} | https://github.com/materialsproject/pymatgen/blob/cfd47add8958af795dabcfe1661cf8890ad56415/pymatgen/io/cif.py#L1171
Hi, there is a dirty print in the get_structures function. I assume this is a forgotten debug log. Can we please remove this? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3415 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3415/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3415/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3415/events | https://github.com/materialsproject/pymatgen/issues/3415 | 1,956,519,804 | I_kwDOACgets50nh98 | 3,415 | Error in the battery explorer using the legacy MPRester | {
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"Please report this to the materialsproject.org people, specifically @munrojm . Pymatgen maintainers have no control over the front end or the API end points, especially the legacy end points."
] | 2023-10-23T07:22:13 | 2023-10-23T15:08:17 | 2023-10-23T15:08:17Z | NONE | {
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} | The follow codes work well previously, but now error comes out in something like "/var/www/python/matgen_prod/materials_django/battery_explorer/rest.py". Using mp_api
seems to bypass the problem in this case, however, it would be appreciated that the legacy MPRester still works for a while.
mpr = MPRester("16-... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3416 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3416/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3416/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3416/events | https://github.com/materialsproject/pymatgen/issues/3416 | 1,956,523,724 | I_kwDOACgets50ni7M | 3,416 | py4vasp for VASP output parsing | {
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"Agreed. Some people might still use VASP 5.4. Hdf5 support requires extra efforts to compile, if I am not mistaken. I think we should wait.",
"> Some people might still use VASP 5.4. Hdf5 support requires extra efforts to compile, if I am not mistaken. \r\n\r\nThis is correct. Certainly, one should not even con... | 2023-10-23T07:24:43 | 2023-10-23T15:12:06 | 2023-10-23T15:12:06Z | MEMBER | {
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} | I wanted to open up a point of (potentially contentious!) discussion here. It has now been quite some time since the VASP company released [py4vasp](https://github.com/vasp-dev/py4vasp) for VASP output parsing. I was initially skeptical about if it would be well-maintained or not, but things seem to be promising in tha... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3417 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3417/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3417/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3417/events | https://github.com/materialsproject/pymatgen/pull/3417 | 1,958,158,087 | PR_kwDOACgets5dlUw6 | 3,417 | Fix `test_relax_chgnet` | {
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} | 8ab226159 fix doc string indentations
b6fd1c0e2 fix variable names shadowing python builtins
72326ae70 del parens around doc string return type
9a696371f fix `docs/fetch_pmg_contributors.py` numpy import broken due to `secrets.py` shadowing `randints.secrets`
76461a17f add `TestPeriodicSite.test_str()`
411d62e5f f... | {
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"I fear this will break a lot of code! Can one alert users about this change? ",
"@JaGeo Definitely! See [22f6201](https://github.com/materialsproject/pymatgen/pull/3419/commits/22f6201bc949aaeeca4e266386b36a952ae52120).",
"Pls do not do this kind of thing. No breaking change unless absolutely necessary. ",
"... | 2023-10-24T18:21:50 | 2023-11-10T21:18:49 | 2023-11-08T16:13:14Z | MEMBER | {
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} | ### Motivation
`CifParser.get_structures('some.cif')[0]` and `Structure.from_file('some.cif')` currently return different cells. And `primitive=True` seems like a bad default. Cell reduction seems like something the user should request explicitly.
### Context
This came up in the MP ingestion of new ICSD struct... | {
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"Black literally takes milliseconds for pymatgen. I think making this change took possibly 1000000 iterations of black time. ",
"You know most of these are auto-changes? Just ran `time black pymatgen --check`. Takes 2 sec on my machine and several times that to install in CI.",
"`ruff` has ~10x the development ... | 2023-10-24T19:50:34 | 2023-10-25T14:39:45 | 2023-10-24T20:35:36Z | MEMBER | {
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} | `ruff format` [was just released](https://astral.sh/blog/the-ruff-formatter) as part of [v0.1.2](https://github.com/astral-sh/ruff/releases/tag/v0.1.2). It's in preview but considered production-ready. About 30x faster than `black` and 99% compatible (counted by lines of code with conflicting format in empirical testin... | {
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"These different functionals are related to the INCAR settings, not the POTCAR. There are currently only two types of POTCARs supported by VASP: the PBE and LDA POTCARs. Could you clarify why you wish to modify this from the POTCAR side of things?\r\n",
"I wanted to do it from INCAR tags, just don't know how to d... | 2023-10-24T22:29:11 | 2023-12-20T02:01:43 | NONE | {
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} | ### Problem
I want to use different versions of GGA-tag in INCAR, e.g. PBEsol or revPBE, how to specify that in pymatgen?
I didn't find the functionality of specifying functional_tags in writing POTCAR file.
### Proposed Solution
Maybe modify the function from_symbol_and_functional in PotcarSingle class.
### Alt... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3422 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3422/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3422/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3422/events | https://github.com/materialsproject/pymatgen/pull/3422 | 1,960,298,425 | PR_kwDOACgets5dsgW1 | 3,422 | Add functionality to read ASE *.traj file in Trajectory class method from_file() | {
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} | Summary:
Add functionality to read ASE *.traj file in Trajectory class method from_file(), located in core/trajectory.py.
Purpose:
As ASE *.traj file is a standard format for generating and storing relaxation / MD trajectories, it would be nice to have a method which can read a Pymatgen Trajectory instance from an... | {
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} | Hi all, this is a small PR that makes sure labels are passed when a `SymmetrizedStructure` is initialized. This follows-up on earlier work in #3183
## Summary
Major changes:
- fix 1: Propagate site labels through `SymmetrizedStructure()`
## Checklist
- [x] Google format doc strings added. Check with `ru... | {
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"This breaks legacy code. We don't do that. I would rather you create a separate BaderData class that stores the analysis and you can write the init whatever way you want. \n\nBasic principle of writing a code base used by others - don't break stuff unless you have no choice. ",
"@shyuep Thanks for the quick feed... | 2023-10-25T22:22:13 | 2024-03-08T05:32:06 | 2024-03-08T05:32:06Z | CONTRIBUTOR | {
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This PR reformats the __init__ function of BaderAnalysis class and adds new functionality without changing its default behaviors.
## Major changes:
1. Allow users to load from existing bader charge analysis results from folder. This means that when users already have bader analysis results, pymatgen do... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3425 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3425/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3425/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3425/events | https://github.com/materialsproject/pymatgen/issues/3425 | 1,962,685,250 | I_kwDOACgets50_DNC | 3,425 | MP2020Compatibility not applying correct anion correction | {
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"Code from [here](https://github.com/CederGroupHub/chgnet/blob/main/examples/fine_tuning.ipynb)",
"@janosh @kristinpersson feel free to tag whoever is supposed to be dealing with this in MP. ",
"@shyuep The person to tag would be @rkingsbury or myself. I thought I fixed this problem in https://github.com/mater... | 2023-10-26T04:34:13 | 2023-10-26T21:01:32 | 2023-10-26T19:58:49Z | NONE | {
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```
from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
from pymatgen.entries.computed_entries import ComputedStructureEntry
params = {"hubbards": {"Mn": 3.9, "O": 0, "Li": 0}, "run_type": "GGA+U"}
cse = ComputedStructureEntry(lmo, vasp_raw_energy, parameters=para... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3426 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3426/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3426/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3426/events | https://github.com/materialsproject/pymatgen/pull/3426 | 1,963,950,729 | PR_kwDOACgets5d47Mb | 3,426 | Fix `Atoms.cluster_from_file()` in `io.feff.inputs` giving wrong number of atoms | {
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Atoms.cluster_from_file() generates a cluster with a wrong number of atoms because it skips wrong lines when the format of feff input file in the Atom parts is different.
Major changes:
- feature 1(old): skipped 3 lines from the line having "ATOMS"
- fix 1(new): only skip 1 line(ignore ATOMS line)
- f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3427 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3427/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3427/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3427/events | https://github.com/materialsproject/pymatgen/pull/3427 | 1,964,235,290 | PR_kwDOACgets5d56pi | 3,427 | Breaking: return sum of `Species` with matching `Element` in `Composition.__getitem__` | {
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} | Closes #3425.
Follow up to https://github.com/materialsproject/pymatgen/pull/3184 since that turns out to only have been a partial fix for not applying anion corrections to `ComputedEntries` with oxidation states.
The bug comes from `Composition` indexing behaving differently for `Elements`/`str` vs. `Species`. C... | {
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} | ## Summary
NpT MD simulation in VASP provide additional information about lattice dynamics in the CONTCAR that are used when restarting.
In order to allow restarting of generic MD simulations in workflows (https://github.com/materialsproject/atomate2/pull/489) I added the parsing and writing of this section to th... | {
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"Hi @fraricci,\r\n\r\nThanks for bringing this up. Can you confirm this only applies to compositions with 2 or more magnetic species, and only for orderings of the type `afm_by_XX`? Regarding this:\r\n\r\n> some of the magnetic configurations won't be actually computed and some will be computed multiple times.\r\n\... | 2023-10-28T18:04:01 | 2023-11-15T22:28:27 | CONTRIBUTOR | {
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} | I noticed this bug while ago while using the MagWF in atomate and discussed it
with @mkhorton at that time. I see that this bug is still present in the last pmg version.
Here is an example of what happens with Mn₂FeWO₆.
```
st = rester.get_structure_by_material_id("mp-107827")
mo = MagneticStructureEnumerator(st... | {
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"@espottesmith: Do you have any insight on this one?",
"Actually, I have been told that this is @rkingsbury's area perhaps.",
"Yeah, those are related to the ISOSVP/CMIRS solvent models, I believe. Hopefully @rkingsbury can address, but if not, I'm sure I could add docstrings.",
"> Yeah, those are related to ... | 2023-10-30T02:38:53 | 2023-12-17T15:47:56 | 2023-12-17T15:47:56Z | MEMBER | {
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} | ### Problem
https://github.com/materialsproject/pymatgen/blob/2709068a2b01cfbbfda4e2dcd62361678c30c10f/pymatgen/io/qchem/inputs.py#L55-L56
The `svp` and `pcm_nonels` kwargs in the Q-Chem `QCInput` class are currently undocumented. I was looking to know a bit more about them. The input type is `dict | None`, but t... | {
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"Hi @janosh, I added a check on the format of the produced POSCAR. It should be noted that in this case it just checks that the format is equivalent to the one written from the `Poscar` object. This seems to be the only option that is correctly parsed by VASP, even though it is not exactly equilant to what is produ... | 2023-10-30T15:15:59 | 2023-11-30T16:09:36 | 2023-10-31T14:00:40Z | CONTRIBUTOR | {
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This PR fixes a problem in #3428 that I encountered while performing some more tests with NpT MD simulations: in the case of lattice velocities VASP seems to be strict in the format when reading the POSCAR. After some tests it seems that this should be the best format to allow the correct parsing of this ... | {
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"@esoteric-ephemera is there any chance you could add the ZVALs to the summary_stats.json file in this PR too? We talked about this a while ago offline"
] | 2023-10-30T16:12:47 | 2023-11-01T22:58:19 | 2023-11-01T22:58:18Z | CONTRIBUTOR | {
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} | Given the new POTCAR validation introduced in [PR #3351](https://github.com/materialsproject/pymatgen/pull/3351), it makes sense to include a `summary_stats` key in the `Vasprun.potcar_spec` dict (from `io.vasp.outputs`). This will help with validation of outputs using the new summary stats method.
I also removed a ... | {
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"I think everything is now typehinted with google docstrings",
"@janosh I think this is ready to review as well ",
"Tests should now work",
"I updated to master if those changes are needed for the docker images (errors are in tests I did not touch)",
"Do we need to write a tutorial for the aims IO or are th... | 2023-10-30T20:12:13 | 2023-11-08T20:20:02 | 2023-11-08T20:20:02Z | CONTRIBUTOR | {
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} | ## Summary
Creates an FHI-aims interface for pymatgen based off of the ASE parser and input generating structures. Part of this work was done in atomate2 originally for this PR (https://github.com/materialsproject/atomate2/pull/562) where @ansobolev contributed.
This PR was made by the request of atomate2 so the... | {
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"Is this a proprietary file format?",
"Do you mean if it's not from ithe ICCD database?\r\nIf that is what you meant by proprietary file format, then yes.",
"If I use structure.from_file or from_str, it keep throwing unknown file extension as error",
"The file opens in topaz and diffrac.eva if this informatio... | 2023-10-31T17:48:36 | 2023-11-02T13:33:32 | 2023-11-02T12:54:28Z | NONE | {
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} | ### Problem
My XRD files are in .STR and I'm trying to convert all to cif but having issues loading the files
### Proposed Solution
A library that can load str directly or a library that can help convert it to cif for use in pymatgen
### Alternatives
_No response_ | {
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"Thanks for looking at the Lobster part of the code. @naik-aakash and I will check your suggestion carefully. \r\n",
"I think the bug is coming from the fact that the overwriting of the dict. We will look into it more carefully to not break other parts of the code!",
"Hi @RedStar-Iron, Thanks for the suggestion... | 2023-10-31T23:14:37 | 2023-11-02T20:29:01 | 2023-11-02T20:29:01Z | CONTRIBUTOR | {
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} | https://github.com/materialsproject/pymatgen/blob/15dc77da508c6824a2e7cc41e983f797c64815c4/pymatgen/io/lobster/inputs.py#L271-L272
`key` in `self.get(key)` should be lower, then it can be found in Lobsterin.FLOAT_KEYWORDS.
And the cohpsteps might need to be a positive integer.
So I just revised it to:
```
if... | {
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"Tagging @JaGeo.",
"We are on it as a part of https://github.com/materialsproject/pymatgen/pull/3439. Thank you, @Andrew-S-Rosen !",
"@janosh can also be closed. It was adressed as a part of #3439"
] | 2023-10-31T23:19:52 | 2023-11-02T21:55:07 | 2023-11-02T21:55:07Z | CONTRIBUTOR | {
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It will fail if there is a '\t' in my lobsterin file.
I recommand to use the `re`.
```
raw_datum = re.findall(r'(?i)\b[a-z]+(?:\d+)?\b|\b\d+[a-z]+\b|[-]?\d*\.?\d+', datum)
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"@naik-aakash , I have started with the fix. I will test methods like update, delete as well. \r\n\r\nWe could also directly implement a fix for reading lobsterins with \\t",
"Thanks! Thats great. So you will also fix the `reading lobsterins with \\t` issue in this PR itself? ",
"@naik-aakash You are invited to... | 2023-11-01T06:13:33 | 2023-11-02T20:29:00 | 2023-11-02T20:29:00Z | MEMBER | {
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} | ## Summary
Closes https://github.com/materialsproject/pymatgen/issues/3437 and https://github.com/materialsproject/pymatgen/issues/3438.
Inheritance of the dict was not carried out correctly. I have started here with inheriting from UserDict. We will add more tests to avoid similar issues in the future.
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`.\n\nIf you change your mind, j... | 2023-11-01T12:49:44 | 2023-11-01T14:17:26 | 2023-11-01T14:17:16Z | CONTRIBUTOR | {
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<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>v5.18.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.26.0 t... | {
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} | ### Problem
The link for "matgenie web app" at https://pymatgen.org/#matgenie--examples is dead.
### Proposed Solution
Remove or update the link, I don't know which is appropriate as I cannot find the latest version of matgenie.
### Alternatives
_No response_ | {
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"Thanks @ml-evs! 👍 \r\n\r\nI expect new deps, esp. `pydantic` might be a blocker. We might consider a soft dependency that prompts the user to `pip install pydantic` when actually using functionality that requires it.",
"> Thanks @ml-evs! 👍\r\n> \r\n> I expect new deps, esp. `pydantic` might be a blocker. We mi... | 2023-11-01T18:35:30 | 2023-11-01T19:06:56 | 2023-11-01T19:06:56Z | CONTRIBUTOR | {
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} | ## Summary
*Apropos* of nothing in particular... here is PR that makes some updates to the OPTIMADE client (and maybe starts a discussion about its future).
Major changes:
- Refreshes the baked-in OPTIMADE providers list with the latest new APIs
- Expands upon some of the docstrings
Happy to talk about how... | {
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"I think it's a good idea to do this for such an obvious error. However, you cannot prevent everything. If you run this after a very low precision computation in VASP, the results are probably also not reliable. ",
"It's true we can't catch everything. However, in this case, the kwargs for AECCAR files is optiona... | 2023-11-02T01:59:48 | 2023-11-06T04:38:25 | 2023-11-06T04:38:24Z | MEMBER | {
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In pymatgen, it's possible to run Bader both with and without the AECCARs as reference. However, in the latter case, the results of a Bader analysis can be severely inaccurate. I don't have statistics off-hand, but U had discussed this with _someone_ in Kristin's group (can't remember who... @janosh?) wh... | {
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"May I work on this?",
"Fixed in #3528."
] | 2023-11-02T07:35:25 | 2024-01-15T08:38:08 | 2024-01-15T08:38:08Z | MEMBER | {
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} | There is only one template right now, which is for a feature request. At the very least, a bug report template should be added along with some fields about necessary reporting details (e.g. pymatgen version, Python version, OS), a minimal example, etc. I thought that existed at some point but perhaps not? | {
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"Closed in #3451."
] | 2023-11-02T19:33:29 | 2023-11-03T17:01:51 | 2023-11-03T17:01:51Z | MEMBER | {
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If I can chime in here, I noticed a bug potentially introduced by this pull request.
As mentioned [here](https://matsci.org/t/bsplotterprojected-get-elt-projecte-plots-method-broken/51434/4?u=fraricci), there is a "ax =" missing [he... | {
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Closes #3450. | {
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"Good to see you around these parts, @tawe141!!!",
"Added test and confirmed it passes on my end!"
] | 2023-11-03T02:36:01 | 2023-11-08T17:39:06 | 2023-11-08T17:39:05Z | CONTRIBUTOR | {
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} | VASP will sometimes print "***********" when there's a float overflow. There's already a function in here to interpret these as `np.nan`, but it looks like it wasn't applied everywhere. I found one place where it wasn't used (ie just using Python's `float` function) that helped me process a large batch of `vasprun.xml`... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3453 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3453/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3453/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3453/events | https://github.com/materialsproject/pymatgen/issues/3453 | 1,977,004,279 | I_kwDOACgets511rD3 | 3,453 | [Issue]: NDCalculator does not support Deuterium? | {
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"Yes D is not supported. But feel free to add the scattering factors to support it.",
"Okay sounds good. Thank you."
] | 2023-11-03T22:23:18 | 2023-11-06T15:42:52 | 2023-11-05T22:15:25Z | NONE | {
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I was using a cif file and I received this error when using it:
**ValueError: Unable to calculate ND pattern as there is no scattering coefficients for D.**
Here is my code:
```
struct = parser.get_structures(primitive=False, symmetrized=True)[0]
nd_calculator = NDCalculator(wavelength=1.6)
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} | Also, fix `MPScanRelaxSet` not using `bandgap_tol` kwarg. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3455 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3455/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3455/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3455/events | https://github.com/materialsproject/pymatgen/issues/3455 | 1,977,118,108 | I_kwDOACgets512G2c | 3,455 | [Feature Request]: Vasprun.xml needs to be updated to be compatible vasp > 6.3 | {
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"For us to work on this, I need an example vasprun.xml with 6.3 and the two band structures. Just a simple one for say Si will do.",
"Thanks. Here is the zip file for a calculation with Si. Multiple output files have different formats, e.g. vasprun.xml (has both band structures from KPOINTS and KPOINTS_OPT), OUTC... | 2023-11-04T02:10:35 | 2024-03-09T01:03:40 | NONE | {
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} | ### Problem
The new vasp allows to provide KPOINTS_OPT so that a non-self-consistent run will be done automatically after self-consisten run on KPOINTS file. This is the new feature starting from vasp.6.3. As a result, the vasprun.xml will generate two "band structures" rather than just one, can anyone update this f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3456 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3456/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3456/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3456/events | https://github.com/materialsproject/pymatgen/pull/3456 | 1,977,555,452 | PR_kwDOACgets5em1Md | 3,456 | Add a save parameter for chargemol calculation to select whether save the output files, use "link" rather than "copy" for the input file of chargemol calc, add mpi function to run chargemol. | {
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"```\r\nfrom pymatgen.command_line.chargemol_caller import *\r\n\r\nchargemol = ChargemolAnalysis(mpi=True,ncores=32, save=True)\r\n```\r\nJob script to run chargemol program.",
"Hi Dr. @Andrew-S-Rosen,\r\n\r\nAre you available to have look the remaining problem in this commit?\r\n\r\nI have tried several methods... | 2023-11-04T23:38:44 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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} | ## Revised Content
1. Add `save` parameter to control whether save the output files from `chargemol` calculation
2. Use `link` rather than `copy` for `CHGCAR, POTCAR, ARCCAR0 and ARCCAR2` during the calculation
3. Support `mpirun` for `chargemol` calculation
| {
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"Your code makes no sense. Your lattice parameter is 0.0006 but your radius is 0.0025? This will result in a huge number of periodic images. The error message is precisely what it says - there are just too many images. Either your computer RAM is too little or your system is just way too large."
] | 2023-11-05T20:59:58 | 2023-11-05T21:47:49 | 2023-11-05T21:47:49Z | NONE | {
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} | While calculating electrostatic forces using analysis.ewald.EwaldSummation I encountered the following error with version 2023.8.10, Python 3.11.4, and on MacOS.
```
forces = ewald_sum.forces
.../lib/python3.11/site-packages/pymatgen/analysis/ewald.py:272: in forces
self._calc_ewald_terms()
.../lib/pytho... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3458 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3458/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3458/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3458/events | https://github.com/materialsproject/pymatgen/pull/3458 | 1,977,984,031 | PR_kwDOACgets5eoIit | 3,458 | Issue stronger warning if `bader` is run without the `AECCAR`s | {
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"@JiQi535 you're right, thanks for reporting. the reason this wasn't caught is that the only test for `bader_analysis_from_path` is skipped\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/5514ff5418b23da809b23056ea876c0a4c244c96/tests/command_line/test_bader_caller.py#L84-L99"
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https://api.github.com/repos/materialsproject/pymatgen/issues/3459 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3459/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3459/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3459/events | https://github.com/materialsproject/pymatgen/issues/3459 | 1,980,493,236 | I_kwDOACgets52C-20 | 3,459 | [Feature Request]: SubstrateAnalyzer class does not save the oringinal vector orientation | {
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} | ### Problem
In the SlabGenerator class, the vectors used to do lattice matching were extracted from the slab model made by the SlabGenerator. This reorient the vectors and in this way from the final results of lattice matching, the user might get lost of this information. As shown below:
print(around(dot(inv(Ni3S2.la... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3460 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3460/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3460/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3460/events | https://github.com/materialsproject/pymatgen/issues/3460 | 1,980,544,125 | I_kwDOACgets52DLR9 | 3,460 | [Feature Request]: missing potcar_summary_stats.json.bz2 error using my forked version | {
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"This is the git link of my forked version:https://github.com/jinlhr542/pymatgen",
"The [file is actually there](https://github.com/jinlhr542/pymatgen/blob/master/pymatgen/io/vasp/potcar_summary_stats.json.bz2) so I assume it's a Windows path issue. Could you try replacing\r\n\r\n```diff\r\n- potcar_summary_stats... | 2023-11-07T04:53:06 | 2023-11-10T23:04:54 | 2023-11-10T23:04:54Z | CONTRIBUTOR | {
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} | ### Problem
To use the version I made some modification myself, I forked the master package and made some modification to the SubstrateAnalyzer module. After I install this version, I got this error:
<details><summary>Details</summary>
```py
Li2S = Structure.from_file('lattice_vasp/Li2S/CONTCAR')
-----------... | {
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