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https://api.github.com/repos/materialsproject/pymatgen/issues/2508 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2508/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2508/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2508/events | https://github.com/materialsproject/pymatgen/issues/2508 | 1,217,943,241 | I_kwDOACgets5ImFbJ | 2,508 | QUAD_EFG includes units for efg mode of MPNMRSet | {
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} | **Describe the bug**
The MPNMRSet (with mode="efg") writes units to file for the QUAD_EFG setting. This occurs because it is using FloatWithUnit class under the hood.
**To Reproduce**
``` python
from pymatgen.core import Structure
from pymatgen.io.vasp.sets import MPNMRSet
# Random structure to test with
s =... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2509 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2509/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2509/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2509/events | https://github.com/materialsproject/pymatgen/pull/2509 | 1,217,949,043 | PR_kwDOACgets425-Gc | 2,509 | fix bug with nmr set writing units | {
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"Please add a Unittest to catch this bug and prevent it from recurring. ",
"Yep, I'm working on that now :smile: ",
"\n[](https://coveralls.io/builds/48642946)\n\nCoverage decreased (-0.7%) to 83.279% when pulling **08daf1518e1c2377df7b149c866ee686a3... | 2022-04-27T22:35:52 | 2022-06-22T13:19:00 | 2022-04-28T15:03:11Z | CONTRIBUTOR | {
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} | resolves #2508
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https://api.github.com/repos/materialsproject/pymatgen/issues/2510 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2510/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2510/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2510/events | https://github.com/materialsproject/pymatgen/issues/2510 | 1,218,762,886 | I_kwDOACgets5IpNiG | 2,510 | LAMMPS IO: update to accomodate pandas deprecation | {
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"Thanks. Go ahead and submit a PR to fix this.",
"@manaslkht would you be able to tackle this?",
"@rkingsbury Yes, will get this done by this weekend. "
] | 2022-04-28T13:50:28 | 2022-10-22T17:41:42 | 2022-10-22T17:41:42Z | CONTRIBUTOR | {
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} | **Describe the bug**
Several lines in `pymatgen.io.lammps.data.py` make use of the pandas `DataFrame.append` method, which is being deprecated, causing many warnings along the lines of:
```
/Users/ryan/miniconda3/envs/md/code/pymatgen/pymatgen/io/lammps/data.py:1283:
FutureWarning: The frame.append method is dep... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2511 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2511/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2511/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2511/events | https://github.com/materialsproject/pymatgen/issues/2511 | 1,218,821,550 | I_kwDOACgets5Ipb2u | 2,511 | Packmol IO: Address which deprecation | {
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"Go ahead and submit a PR to change this.",
"Nvm I just puyshed a fix."
] | 2022-04-28T14:30:56 | 2022-04-28T15:05:49 | 2022-04-28T15:02:26Z | CONTRIBUTOR | {
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} | The `run` method of Packmol IO makes use of `monty.io.which` to detect whether packmol is installed, and this method will be deprecated soon. This should be changed to `shutil.which` from the standard library, or (perhaps a better solution), use the `monty.dev.requires` decorator as shown [here](https://github.com/mate... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2512 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2512/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2512/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2512/events | https://github.com/materialsproject/pymatgen/pull/2512 | 1,223,245,782 | PR_kwDOACgets43L55e | 2,512 | [pre-commit.ci] pre-commit autoupdate | {
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"\n[](https://coveralls.io/builds/48766999)\n\nCoverage decreased (-0.001%) to 84.04% when pulling **efd51159085d0fcea9452bf6d5e251266bc51812 on pre-commit-ci-update-config** into **6302e7db8c9c46d8a69b2a2888e9ca5880e43e5f on master**.\n"
] | 2022-05-02T19:12:44 | 2022-05-02T19:40:41 | 2022-05-02T19:14:29Z | CONTRIBUTOR | {
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} | <!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.31.1 → v2.32.0](https://github.com/asottile/pyupgrade/compare/v2.31.1...v2.32.0)
- [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.1.0...v4.2.0)
- [github.com/pre-commit/mirrors-m... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2513 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2513/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2513/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2513/events | https://github.com/materialsproject/pymatgen/issues/2513 | 1,225,156,651 | I_kwDOACgets5JBmgr | 2,513 | how to convert many cif file to poscar format in vasp? | {
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"Sorry, I found useful way in pymatgen tutorial. Thank you very much!",
"You might also have a look here: https://matsci.org/c/pymatgen/9\r\n\r\nThis is the discussion forum and the place where you can ask about the usage of pymatgen 🙂."
] | 2022-05-04T09:56:58 | 2022-05-04T10:13:55 | 2022-05-04T10:01:22Z | NONE | {
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} | Hi. I am a researcher in computational physics and I have been using pymatgen very well.
Recently, I have obtained hundreds (or even thousands of) of CIF files and I need to convert all CIF files to POSCAR format in vasp.
I already know how to convert single cif file to poscar format using VESTA, but I would like t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2514 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2514/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2514/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2514/events | https://github.com/materialsproject/pymatgen/pull/2514 | 1,226,053,650 | PR_kwDOACgets43UrcB | 2,514 | Replace IALGO with ALGO in MVLNPTMDSet | {
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"\n[](https://coveralls.io/builds/48846336)\n\nCoverage decreased (-0.7%) to 83.295% when pulling **5acde0edd9ca1730583c82084c33809439b34f42 on qianchenqc:master** into **61032a3365cfbae66d1aefae6c6606b66361ca80 on materialsproject:master**.\n",
"Thank... | 2022-05-04T23:12:44 | 2022-05-05T13:21:24 | 2022-05-05T13:21:17Z | CONTRIBUTOR | {
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} | ## Summary
* Replaced the IALGO tag with ALGO as recommended in the vasp documentation https://www.vasp.at/wiki/index.php/IALGO.
* Removed IALGO tag to enable Davidson first and then switch to the RMM-DIIS with ALGO=Fast. | {
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"\n[](https://coveralls.io/builds/51100719)\n\nCoverage decreased (-20.5%) to 63.575% when pulling **9d8a0cfc1b4e8fcc5e037a9aadf30c8a474a572a on mjwen:master** into **2b75957884934470962b56c644588eba1454dbaa on materialsproject:master**.\n",
"The chang... | 2022-05-06T06:30:51 | 2022-08-30T01:40:01 | 2022-08-30T01:29:50Z | MEMBER | {
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} | ## Summary
This PR cleans up the Trajectory class:
- add type annotation
- make doc string consistent with what the code is actually doing
- remove unused code pieces and slightly reorganize some parts
This breaks backward compatibility in one place. Previous `frame_properties` accepts a dict as input and ... | {
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"Hi @rkurchin, thanks for sharing this experience, this kind of feedback is useful!\r\n\r\nOne factor here is that you've caught us during a transition period where we're deploying a new API (first major change in 10+ years), which is going to cause some additional confusion since it changes some things, see https:... | 2022-05-06T21:43:04 | 2022-05-10T03:08:09 | 2022-05-10T03:08:09Z | CONTRIBUTOR | {
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} | **Describe the bug**
This is not _exactly_ a bug, so much as something I thought was a bug but was actually unclear documentation.
Basically, I wanted to download entries corresponding to stable materials with nonzero bandgap that have computed bandstructures. I'll describe what I did below...
**To Reproduce**
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2517 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2517/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2517/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2517/events | https://github.com/materialsproject/pymatgen/pull/2517 | 1,231,165,769 | PR_kwDOACgets43k8Iy | 2,517 | Fixed MSONable + InputSet's str(object) | {
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"\n[](https://coveralls.io/builds/48988239)\n\nCoverage decreased (-0.7%) to 83.319% when pulling **79e1a8770942671ec2b51dce7c0f6dccdca34f88 on davidwaroquiers:input_sets_strcast** into **2b75957884934470962b56c644588eba1454dbaa on materialsproject:maste... | 2022-05-10T13:29:34 | 2022-05-10T17:26:50 | 2022-05-10T17:26:50Z | CONTRIBUTOR | {
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} | ## Summary
* Added functionality to write the __str__ contents of an object in the contents of one of the InputSet's files, if this object is not an instance (subclass) of InputFile.
* Added unit tests for InputFile and InputSet.
* Fixed MSONable for InputSet when kwargs are given.
## Additional dependencies in... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2518 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2518/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2518/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2518/events | https://github.com/materialsproject/pymatgen/pull/2518 | 1,232,801,163 | PR_kwDOACgets43qO80 | 2,518 | Fix reading of orbitalwise ICOHPLIST.lobster | {
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"\n[](https://coveralls.io/builds/49030586)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **066299048cfb779c8edabc8792ff60e31aafdca1 on JaGeo:master** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"From my si... | 2022-05-11T15:03:51 | 2022-05-17T14:59:14 | 2022-05-17T14:59:08Z | MEMBER | {
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} | ## Summary
By accident, the wrong line in ICOHPLIST.lobster was read to assess whether orbitalwise interactions are included in these files. This lead to erros in case the first atom only has one relevant valence orbital. I fixed the problem. And, I included a test to fix this for the future.
JG | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2519 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2519/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2519/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2519/events | https://github.com/materialsproject/pymatgen/issues/2519 | 1,233,100,521 | I_kwDOACgets5Jf57p | 2,519 | `Atoms` --> `Structure` conversion fails for linear molecules | {
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"Never mind. This was a user error. I called `.get_structure()` on a non-PBC object. It should have been `.get_molecule()`. It could be worth adding a check for this."
] | 2022-05-11T19:36:50 | 2022-06-06T23:49:53 | 2022-05-11T19:44:30Z | MEMBER | {
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} | **Describe the bug**
For linear structures, the ASE `Atoms` to Pymatgen `Structure` conversion fails due to a singular matrix.
```python
from ase.build import molecule
from pymatgen.io.ase import AseAtomsAdaptor
atoms = molecule('CO2')
AseAtomsAdaptor.get_structure(atoms)
```
```python
--------------------... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2520 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2520/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2520/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2520/events | https://github.com/materialsproject/pymatgen/pull/2520 | 1,233,243,098 | PR_kwDOACgets43rr6p | 2,520 | Add rotational symmetry number property to `PointGroupAnalyzer` | {
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"\n[](https://coveralls.io/builds/49048738)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **05cbb1febd9b4e259d27ce381267f222694239fd on arosen93:rosen-symm** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"Tha... | 2022-05-11T22:28:02 | 2022-05-17T14:58:46 | 2022-05-17T14:58:41Z | MEMBER | {
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} | This PR adds a new property to the `PointGroupAnalyzer`: the rotational symmetry number.
Example:
```python
from pymatgen.core import Molecule
from pymatgen.symmetry.analyzer import PointGroupAnalyzer
CH4 = Molecule.from_file('methane.xyz')
pga = PointGroupAnalyzer(CH4)
print(pga.get_rotational_symmetry_numb... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2521 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2521/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2521/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2521/events | https://github.com/materialsproject/pymatgen/pull/2521 | 1,234,399,551 | PR_kwDOACgets43vfpq | 2,521 | Q-Chem updates to NBO and new geometry optimizer | {
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"\n[](https://coveralls.io/builds/49386982)\n\nCoverage decreased (-0.8%) to 83.285% when pulling **0bf3c4c4f3552db52da5465339332cdc6f4d64b0 on samblau:qchem** into **30e36f658aa121ee58caf962e230014e0e3fbbf9 on materialsproject:master**.\n",
"@mkhorton... | 2022-05-12T19:30:59 | 2022-05-24T14:06:13 | 2022-05-24T14:06:13Z | CONTRIBUTOR | {
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} | ## Summary
* Tweaks to Q-Chem - NBO functionality given latest Q-Chem release
* IO for new geometry optimizer that is hidden but present in latest Q-Chem release
* Parsing various new errors
Ready to merge!
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"\n[](https://coveralls.io/builds/49117949)\n\nCoverage decreased (-0.7%) to 83.324% when pulling **bb87db4c4fa73d731a21fae0433ba5c7db9e332c on jmmshn:pd_fix** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"Thanks @j... | 2022-05-13T23:23:09 | 2022-05-14T00:57:24 | 2022-05-14T00:57:24Z | CONTRIBUTOR | {
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} | JSON reconstruction bug:
The problem is: Because MSONables from_dict was replaced, there is no recursive reconstruction of the objects when you hit `el_ref` . When you do `as_dict` -> `from_dict` in python everything looks fine.
but the object was never completely serialized.
If you completely serialized it like p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2525 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2525/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2525/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2525/events | https://github.com/materialsproject/pymatgen/pull/2525 | 1,242,120,971 | PR_kwDOACgets44I29A | 2,525 | volumetric list -> array | {
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"\n[](https://coveralls.io/builds/49285272)\n\nCoverage decreased (-0.7%) to 83.323% when pulling **c034c3024d6259b1bea055576e53683e276d0cab on jmmshn:main** into **1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1 on materialsproject:master**.\n"
] | 2022-05-19T17:54:48 | 2022-05-20T20:47:43 | 2022-05-20T20:47:43Z | CONTRIBUTOR | {
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} | ## Allow lists to be used to construct the `data` field of `VolumetricData`
Depending on how the object was `jsantize` and store one might be reconstructing the `VolumetricData` object from a `list` rather than an `np.array`.
This small tweak just ensures that the reconstructive data is always an `np.array` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2526 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2526/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2526/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2526/events | https://github.com/materialsproject/pymatgen/issues/2526 | 1,243,181,852 | I_kwDOACgets5KGXMc | 2,526 | XRD as a function of q | {
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"Sure. By all means propose an implementation.",
"We will propose one via pull request once it is ready. Thanks!"
] | 2022-05-20T13:53:32 | 2022-05-20T14:04:44 | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
It concerns `pymatgen.analysis.diffraction.xrd`
Would there be interest to also offer XRD patterns as a function of q (1/Angstrom) instead of 2 Theta? It would be interesting to have this data for comparison with SAXS data. As the class currently star... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2527 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2527/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2527/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2527/events | https://github.com/materialsproject/pymatgen/issues/2527 | 1,244,125,842 | I_kwDOACgets5KJ9qS | 2,527 | Is there a way that I can get a layered pdos for the selected different atoms like that in p4vasp? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2528 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2528/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2528/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2528/events | https://github.com/materialsproject/pymatgen/issues/2528 | 1,245,312,529 | I_kwDOACgets5KOfYR | 2,528 | LAMMPS IO: update parse_lammps_log for thermo_style yaml | {
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} | **Is your feature request related to a problem? Please describe.**
The format of data output by LAMMPS is completely dependent on what a user specifies in the input file, making it difficult to parse the output text files in a robust way.
**Describe the solution you'd like**
LAMMPS has recently introduced `thermo_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2529 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2529/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2529/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2529/events | https://github.com/materialsproject/pymatgen/issues/2529 | 1,245,861,520 | I_kwDOACgets5KQlaQ | 2,529 | Magic Number of "max_sites=-20" in MP2020Compatibility Leads to Hidden Error | {
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"@JiQi535 thanks for posting. Your understanding of what's happening is 100% correct, and I hadn't realized that this wasn't documented (my apologies for that). The oxidation state guessing was a feature that we added somewhat at the last minute and the documentation must have slipped through the cracks. That said,... | 2022-05-24T01:25:34 | 2022-05-24T20:34:38 | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
Yes. The current get_adjustments() function in MP2020Compatibility fails to get the correct energy adjustments for compositions with over 20 atoms and specific mixed anions, e.g. Li20O9Cl2. For Li20O9Cl2, it can only get the energy correction for O2-, ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2530 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2530/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2530/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2530/events | https://github.com/materialsproject/pymatgen/issues/2530 | 1,246,431,746 | I_kwDOACgets5KSwoC | 2,530 | How to parse a complete dos object from DOSCAR but not from vasprun.xml by pymatgen | {
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"There is only a class to parse the Doscar from LOBSTER calculations. I am not sure why there is a need to do it from the DOSCAR since the vasprun.xml contains the same information as far as I can tell. To my knowledge, parsing the GW DOS from vasprun.xml should be the same as that from regular PBE. You should make... | 2022-05-24T11:54:42 | 2022-10-11T08:32:55 | 2022-05-24T13:52:20Z | NONE | {
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I have some trouble when I parse a DOS object with vasprun.xml obtained from GW calculation. The error is as follows:
“NotImplementedError: This vasprun.xml has >2 unlabelled dielectric functions”
So I want to parse it by using DOSCAR instead of the vasprun.xml. But I have not found a class that can do t... | {
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"\n[](https://coveralls.io/builds/49406524)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **a687dab12d754cefe44954ff0852d5218c7c02ba on janosh:fix-mprester-typeerror-on-empty-pmgrc** into **30e36f658aa121ee58caf962e230014e0e3fbbf9 on materialspro... | 2022-05-24T13:42:45 | 2022-05-24T14:15:12 | 2022-05-24T14:05:58Z | MEMBER | {
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```py
TypeError: 'NoneType' object is not iterable
```
if `.pmgrc.yaml` exists but is empty.
Plus add some more type hints for frequently used functions. | {
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} | **Is your feature request related to a problem? Please describe.**
I have a module that takes a [`BandStructureSymmLine`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/electronic_structure/bandstructure.py#:~:text=class%20BandStructureSymmLine(BandStructure%2C%20MSONable)%3A) object obtained fr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2533 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2533/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2533/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2533/events | https://github.com/materialsproject/pymatgen/pull/2533 | 1,250,084,881 | PR_kwDOACgets44jE8I | 2,533 | Fix function to produce continuous line-mode band structures | {
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"\n[](https://coveralls.io/builds/49611807)\n\nCoverage decreased (-0.7%) to 83.29% when pulling **a586eff982d3ee4f45aa2c286738560714b7a445 on munrojm:continuous_bs_fix** into **aa0e9cf43bdae3df4a87fd77d5bbfd6dc1603eec on materialsproject:master**.\n"
] | 2022-05-26T21:04:19 | 2022-06-06T19:10:10 | 2022-06-06T19:10:10Z | MEMBER | {
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} | ## Summary
This PR fixes a bug in the `get_continuous_path` method of `HighSymmKpath` which formats line-mode band structure to ensure the k-path is continuous. Previously, the last segment of the path was not correctly being added to the new one in all cases. This fix ensures the final k-point is always the same as... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2534 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2534/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2534/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2534/events | https://github.com/materialsproject/pymatgen/issues/2534 | 1,251,428,459 | I_kwDOACgets5Kl0hr | 2,534 | Need to add `enthalpy is TOTEN` to `pymatgen.io.vasp.outputs` module? | {
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} | When the calculation of VASP is performed under pressure conditions, the `PSTRESS` parameter needs to be added to `INCAR`, and the `enthalpy is TOTEN` item will be obtained in OUTCAR. Sometimes we need to extract the value of this item, so I wonder if we need to implement this operation to `pymatgen.io.vasp.outputs` mo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2536 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2536/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2536/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2536/events | https://github.com/materialsproject/pymatgen/pull/2536 | 1,252,006,361 | PR_kwDOACgets44pUnG | 2,536 | Pandas fix and Black version update in pre-commit YAML file | {
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"Closing as I can't push to this fork to fix CI:\r\n\r\n> remote: Permission to manaslkht/pymatgen.git denied to janosh.\r\nfatal: unable to access 'https://github.com/manaslkht/pymatgen.git/': The requested URL returned error: 403"
] | 2022-05-29T22:20:04 | 2022-10-22T17:14:27 | 2022-10-22T17:14:26Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2537 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2537/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2537/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2537/events | https://github.com/materialsproject/pymatgen/issues/2537 | 1,252,213,546 | I_kwDOACgets5Ko0Mq | 2,537 | Voronoi charges in `pymatgen.command_line.bader_caller` | {
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"Closing this because I thought `bader` output the voronoi deformation density, but the voronoi analysis is simpler here."
] | 2022-05-30T05:31:46 | 2022-06-01T07:13:27 | 2022-06-01T07:13:27Z | MEMBER | {
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} | The `bader` code by the Henkelman group, which is currently used in `pymatgen.command_line.bader_caller`, can also compute Voronoi charges for basically free simply by adding the `-c voronoi` command-line argument. It would be ideal to add support for this to the `bader_caller` and to have it store the Voronoi charges ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2538 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2538/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2538/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2538/events | https://github.com/materialsproject/pymatgen/pull/2538 | 1,252,871,916 | PR_kwDOACgets44sMR5 | 2,538 | Allow compressed lammps and xyz files in io.lammps.data | {
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"Thanks.",
"\n[](https://coveralls.io/builds/49568292)\n\nCoverage decreased (-0.7%) to 83.293% when pulling **fe1eb5d15c149a2196081105d50a665b29d6feaf on ab5424:lammps-zopen** into **aa0e9cf43bdae3df4a87fd77d5bbfd6dc1603eec on materialsproject:master*... | 2022-05-30T15:14:32 | 2022-05-30T15:59:31 | 2022-05-30T15:30:55Z | CONTRIBUTOR | {
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} | ## Summary
* Add `zopen()` to `LammpsData`
* Spelling & updated links
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2539 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2539/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2539/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2539/events | https://github.com/materialsproject/pymatgen/pull/2539 | 1,256,669,436 | PR_kwDOACgets445PD_ | 2,539 | small bug in gruneisen.py | {
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"\n[](https://coveralls.io/builds/49647815)\n\nCoverage decreased (-0.7%) to 83.294% when pulling **4c13d29b13644a122b1b7921fb163d4a7d374a21 on antonf-ekb:master** into **2c62d53588e70b22e8e0f6352a7d1974f3cfcb16 on materialsproject:master**.\n",
"Thank... | 2022-06-01T18:03:10 | 2022-08-04T18:11:39 | 2022-08-04T18:11:39Z | NONE | {
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} | At converting adt from K to Hz we get numbers of the order 10^12 (TeraHz) but since w are not yet multiplied by 10^12, the value adt * const.value ("Boltzmann constant in Hz/K") should be divided by the const.tera. The error lead to that all values of w satisfy the condition while this should not be the case.
## Sum... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2540 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2540/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2540/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2540/events | https://github.com/materialsproject/pymatgen/issues/2540 | 1,258,692,925 | I_kwDOACgets5LBiE9 | 2,540 | Feature Suggestion: Add ZVAL to POTCAR metadata | {
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"Sorry, I see this is under `nelectrons`. It just doesn't make its way into the POTCAR spec.",
"I have no objection to adding a ZVAL as a alternative name or in the spec.",
"Thanks! I might consider adding it to the spec. But I also think it's mostly a non-issue if the data is present elsewhere already."
] | 2022-06-02T20:42:40 | 2022-06-02T20:46:36 | 2022-06-02T20:43:34Z | MEMBER | {
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} | Currently, the `Potcar()` object in pymatgen does not store the `ZVAL` as a property. However, when carrying out partial charge calculations (e.g. a Bader analysis), having information about the `ZVAL` is crucial. Since the `ZVAL` isn't stored anywhere other than the POTCAR file or OUTCAR file itself, this means that d... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2541 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2541/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2541/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2541/events | https://github.com/materialsproject/pymatgen/issues/2541 | 1,260,870,290 | I_kwDOACgets5LJ1qS | 2,541 | [FEATURE REQUEST] Python 3.7 support | {
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"Well, any version of pymatgen pre 2022.X would support python 3.7. Unless you are planning to demo some cutting feature, you can just install one of those? I would say 99% of users do not need the latest version of pymatgen. ",
"@shyuep thanks for the quick response. An alternative is for me to switch back to th... | 2022-06-04T19:06:03 | 2022-06-17T10:27:39 | 2022-06-04T19:52:24Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
It would be nice to have Python 3.7 support for exposing code examples that depend on `mp_api` on Google Colab. See https://github.com/materialsproject/api/issues/600
**Describe the solution you'd like**
Support for Python 3.7 until Colab starts su... | {
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"Hi @Anny-tech, thanks for the report. To be able to reproduce, could you supply the input structure too?\r\n\r\nMy suggestions are:\r\n\r\n1. Try `st1_1.diff(st2_1)` first. This calls the `.diff()` method which needs to work for the drawing method to work, and if this gives an error it may be more helpful.\r\n2. B... | 2022-06-05T04:54:39 | 2022-06-06T18:40:32 | NONE | {
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} | **Describe the bug**
'diff' parameter not working in 'draw_graph_to_file' from StructureGraph class of the pymatgen.analysis.graphs module
**To Reproduce**
Steps to reproduce the behavior:
1. Generated structure using *.cif file
2. Generated structuregraph using 'with_local_env_strategy', with strategy=CrystalN... | {
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"@mkhorton Tests are passing now. :)",
"\n[](https://coveralls.io/builds/49983249)\n\nCoverage decreased (-0.7%) to 83.285% when pulling **09b7c308fc86dcb83fe5cafa7186e087ba6bd029 on ab5424:gruneisen-bug** into **9c0fe8ed4a1719f59bef901726c746c2a4a8323... | 2022-06-06T14:07:31 | 2022-06-14T20:04:08 | 2022-06-14T18:01:50Z | CONTRIBUTOR | {
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} | ## Summary
* Fix bug in `average_gruneisen` with a wrong unit @JaGeo #2539
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
... | {
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updates:
- [github.com/asottile/pyupgrade: v2.32.0 → v2.32.1](https://github.com/asottile/pyupgrade/compare/v2.32.0...v2.32.1)
- [github.com/pre-commit/mirrors-mypy: v0.950 → v0.960](https://github.com/pre-commit/mirrors-mypy/compare/v0.950...v0.960)
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} | Currently, the `AseAtomsAdaptor()` conversion of an `Atoms` object to a Pymatgen `structure` object includes duplicate site properties for initial magnetic moments. This PR resolves the duplication -- the docs indicate that the initial magmoms should only be stored under `magmom` and that `initial_magmoms` should not e... | {
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"You can handle periodic systems by taking a supercell, applying qhull to the super cell and then folding the images back into the unit cell. This is the approach used in pymatgen."
] | 2022-06-08T19:21:34 | 2022-06-17T21:23:18 | NONE | {
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I had been trying to use the VoronoiNN class to find nearest neighbors w.r.t a particular site within the structures I am studying. However, I found from literature, that the quickhull algorithm used to create VoronoiNN does not take care of periodic boundary conditions. In that case, how can I be sure whether th... | {
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"Thanks.",
"\n[](https://coveralls.io/builds/49940384)\n\nCoverage decreased (-0.7%) to 83.288% when pulling **643f34f0c61f2c6c926e6796d97df20df4ed4e32 on turrisxyz:Pinned-Dependencies-GitHub** into **f61869ed20f942c00e7ba592d44ca5338ffbbb2f on materia... | 2022-06-11T00:32:13 | 2022-06-11T03:05:25 | 2022-06-11T02:43:58Z | CONTRIBUTOR | {
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- Included permissions for the action. https://github.com/ossf/scorecard/blob/main/docs/checks.md#token-permissions
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} | This should help with keeping the GitHub actions updated on new releases. This will also help with keeping it secure.
Dependabot helps in keeping the supply chain secure https://docs.github.com/en/code-security/dependabot
GitHub actions up to date https://docs.github.com/en/code-security/dependabot/working-with-depen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2549 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2549/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2549/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2549/events | https://github.com/materialsproject/pymatgen/pull/2549 | 1,270,094,815 | PR_kwDOACgets45mL8C | 2,549 | allow a comment on KPOINTS line 4 | {
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"\n[](https://coveralls.io/builds/49990245)\n\nCoverage decreased (-0.7%) to 83.288% when pulling **d2ec302523544ee35606f6fef5e542384eff572d on xivh:fix-kpoints-from-string** into **9c0fe8ed4a1719f59bef901726c746c2a4a83230 on materialsproject:master**.\n... | 2022-06-14T00:13:38 | 2022-08-26T19:56:58 | 2022-06-22T14:21:01Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Ignore the comment on the last line of a KPOINTS file.
## Additional dependencies introduced (if any)
## TODO (if any)
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Befor... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2550 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2550/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2550/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2550/events | https://github.com/materialsproject/pymatgen/issues/2550 | 1,270,095,186 | I_kwDOACgets5LtB1S | 2,550 | A comment on the last line of KPOINTS cannot be parsed. | {
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} | **Describe the bug**
A KPOINTS file with a comment on the last line cannot be parsed by Kpoints.from_string().
**To Reproduce**
Example KPOINTS file that fails:
> Automatic mesh
0 ! number of k-points = 0 -> automatic generation scheme
Auto ! fully automatic
40 ! length (R_k parameter)
Error:
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2551 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2551/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2551/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2551/events | https://github.com/materialsproject/pymatgen/pull/2551 | 1,270,552,752 | PR_kwDOACgets45ns6l | 2,551 | Add `flake8` plugin `bugbear` as pre-commit hook | {
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"Something keeps shaving off the last line from `requirements.txt` and then pre-commit.ci adds it back. @shyuep What's that 1st thing doing the shaving?",
"No idea....",
"Didn't realize this would turn into such a hornets' nest of `mypy` errors... 😅 ",
"\n[![Coverage Status](https://coveralls.io/builds/50966... | 2022-06-14T09:55:18 | 2022-07-21T17:21:48 | 2022-07-21T17:08:55Z | MEMBER | {
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} | Just discovered [`flake8-bugbear`](https://github.com/PyCQA/flake8-bugbear) and tried it out on pymatgen. I think it makes sense to add it to `pre-commit`. it points out a lot of mutable function default values, unused loop control variables (stuff like `for i, val in enumerate(values): print(value)` where `i` is never... | {
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"\n[](https://coveralls.io/builds/50146362)\n\nCoverage decreased (-0.8%) to 83.285% when pulling **cd860eb890ff026c2977cd3f61c62a20ef6d41e6 on acrutt:voltage_profile** into **e0c1ee845e7131213055c5b4fc6df2cb12fcc667 on materialsproject:master**.\n",
"... | 2022-06-17T23:37:30 | 2022-06-22T13:25:27 | 2022-06-22T13:25:22Z | CONTRIBUTOR | {
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} | Change VoltageProfilePlotter.get_plotly_figure() so connecting vertical lines are not drawn in voltage profile. These vertical lines are misleading for interpreting voltage profile plots.
@mkhorton this change was discussed with Kristin at the Jun 13 meeting on the current state of the battery code infrastructure. ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2553 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2553/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2553/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2553/events | https://github.com/materialsproject/pymatgen/issues/2553 | 1,279,378,105 | I_kwDOACgets5MQcK5 | 2,553 | `Composition.replace` incorrect with complex mappings | {
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"fyi -- I don't have a dev env for pymatgen set up at the moment, and it's late here -- so I'll open the PR and add unittests for this tomorrow. ",
"I think there are two issues - one which I think I can fix, but the other one is a logic problem. \r\nThe problem with a substitution like `{\"Ca\": \"Sr\", \"N\": \... | 2022-06-22T02:21:00 | 2022-06-23T01:41:51 | 2022-06-22T14:00:12Z | CONTRIBUTOR | {
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} | **Describe the bug**
If an element is present in multiple places of the `elem_map`, the `Composition.replace` will return an incorrect result.
**To Reproduce**
``` python
from pymatgen.core import Composition
c = Composition("Ca2NF")
example_sub_1 = {"Ca": "Sr", "N": "O", "F": "O"}
c_new_1 = c.replace(ex... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2555 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2555/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2555/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2555/events | https://github.com/materialsproject/pymatgen/pull/2555 | 1,280,193,133 | PR_kwDOACgets46H5PL | 2,555 | fix replace method for complex mappings | {
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"closed in favor of https://github.com/materialsproject/pymatgen/commit/c676b6f115d2e9e696ffb6ebc0335cba5c564152",
"\n[](https://coveralls.io/builds/50279121)\n\nCoverage increased (+0.003%) to 63.534% when pulling **43b039723c8709964066e22db7ba255cca9... | 2022-06-22T13:59:03 | 2022-06-23T02:32:00 | 2022-06-23T01:41:32Z | CONTRIBUTOR | {
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"\n[](https://coveralls.io/builds/50264654)\n\nCoverage decreased (-19.8%) to 63.526% when pulling **f17ebefa7fcbc6434203b459cb1701899a46a75c on dependabot/github_actions/actions/download-artifact-3** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on ma... | 2022-06-22T17:02:05 | 2022-06-22T17:26:52 | 2022-06-22T17:02:22Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p>
<blockquote>
<h2>v3.0.0</h2>
<h2>What's Changed</... | {
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"\n[](https://coveralls.io/builds/50264584)\n\nCoverage decreased (-0.002%) to 83.287% when pulling **97ec22645ec549b12b0cad374b5c8050dcba5fc1 on dependabot/github_actions/actions/upload-artifact-3** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on mas... | 2022-06-22T17:02:07 | 2022-06-22T17:25:48 | 2022-06-22T17:02:33Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's releases</a>.</em></p>
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<h2>v3.0.0</h2>
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https://api.github.com/repos/materialsproject/pymatgen/issues/2558 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2558/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2558/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2558/events | https://github.com/materialsproject/pymatgen/pull/2558 | 1,280,556,980 | PR_kwDOACgets46JI37 | 2,558 | Bump actions/setup-python from 3 to 4 | {
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"\n[](https://coveralls.io/builds/50264901)\n\nCoverage remained the same at 83.289% when pulling **d0cb3b1481e19dfa224b3d66732508761b4aaade on dependabot/github_actions/actions/setup-python-4** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on master**... | 2022-06-22T17:02:12 | 2022-06-22T17:32:15 | 2022-06-22T17:02:45Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/setup-python/releases">actions/setup-python's releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h3>What's Changed</h3>
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https://api.github.com/repos/materialsproject/pymatgen/issues/2559 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2559/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2559/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2559/events | https://github.com/materialsproject/pymatgen/pull/2559 | 1,284,214,163 | PR_kwDOACgets46VnlO | 2,559 | Minor changes | {
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"\n[](https://coveralls.io/builds/50350919)\n\nCoverage decreased (-0.002%) to 63.532% when pulling **0abcd1c818204caa7b3c7586ce1cc7ea49c78ddb on jmmshn:main** into **96aa3c028b29bf656640a14579ad0e24a2003105 on materialsproject:master**.\n"
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1. Change the background color on the chemical potential plots (for dark backgrounds)
2. Added warning that the `pymatgen.analysis.defects` module will be replaced with a namespace package. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2560 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2560/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2560/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2560/events | https://github.com/materialsproject/pymatgen/issues/2560 | 1,284,670,129 | I_kwDOACgets5MkoKx | 2,560 | Parsing AIRSS results into structures | {
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"Closed in #2625, thanks @ScottNotFound.\r\n\r\nI think [`matador`](https://github.com/ml-evs/matador) by @ml-evs deserves an honorable mention here since its [`matador.scrapers.res2dict`](https://docs.matador.science/en/latest/matador.scrapers.html#matador.scrapers.res2dict) also offers `.res` file parsing."
] | 2022-06-25T17:44:46 | 2022-09-01T19:39:34 | 2022-09-01T19:39:26Z | MEMBER | {
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} | [Ab initio random structure searching (AIRSS)](https://airss-docs.github.io) run creates a directory of `.res` result files describing final structures and some high-level properties like Pressure, Volume, Enthalpy, Symmetry for each randomly sampled crystal relaxation.
I saw https://github.com/materialsproject/pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2561 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2561/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2561/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2561/events | https://github.com/materialsproject/pymatgen/pull/2561 | 1,284,758,470 | PR_kwDOACgets46XQty | 2,561 | Fix typos in pymatgen.symmetry.analyzer docstrings | {
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"\n[](https://coveralls.io/builds/50360788)\n\nCoverage decreased (-0.002%) to 63.535% when pulling **bef64d16fe2543f2f4f695cd336431499dd2b222 on dgaines2:master** into **d2042532624b363d5ace8c4199d22d4503e853dd on materialsproject:master**.\n"
] | 2022-06-26T00:44:34 | 2022-06-26T03:46:40 | 2022-06-26T03:26:11Z | CONTRIBUTOR | {
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"Thanks Sudarshan! Flagging @samblau for comment. I don't use these features so don't have much to say other than I think it's great when our IO classes support as many features of the underlying code as possible.",
"\n[](https://coveralls.io/builds/53... | 2022-06-29T01:09:22 | 2022-11-01T16:47:12 | 2022-11-01T16:47:01Z | CONTRIBUTOR | {
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} | ## Summary
I am not sure if this typically required output to be parsed from a QChem file, so please feel free to let me know if this is not of interest.
This PR includes changes to `qchem/outputs.py` and `qchem/utils.py` files. In case the Fock-matrix and eigenvalues are requested by the user (though the flags ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2563 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2563/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2563/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2563/events | https://github.com/materialsproject/pymatgen/pull/2563 | 1,289,616,042 | PR_kwDOACgets46nUTR | 2,563 | Molecule: warn when writing charged mol to xyz | {
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"Again, I have to question whether this is necessary at all. Surely a user would know the XYZ format doesn't store charge and use something else if he wants the charge?",
"> Again, I have to question whether this is necessary at all. Surely a user would know the XYZ format doesn't store charge and use something e... | 2022-06-30T05:44:34 | 2024-10-10T01:54:46 | 2022-07-06T23:59:49Z | CONTRIBUTOR | {
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} | ## Summary
`Molecule.to()` supports many formats including .xyz; however .xyz format does not store charge information; only atomic positions. For users not intimately familiar with details of the .xyz format, this can lead to unexpected behavior when working with charged `Molecule`, e.g.
```
>>> m = Molecule([E... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2564 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2564/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2564/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2564/events | https://github.com/materialsproject/pymatgen/issues/2564 | 1,289,648,027 | I_kwDOACgets5M3neb | 2,564 | InterstitialGenerator Wrongly Counts Interstitial Sites Due to Overlapped Interstitials | {
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"The likely reason is the tolerance in symmetry finding. This can easily be solved with using Structure.merge_sites after you generate the interstitials. Or maybe refining the structure before you run the defect analysis."
] | 2022-06-30T06:13:43 | 2022-06-30T06:25:35 | 2022-06-30T06:25:35Z | CONTRIBUTOR | {
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} | **Describe the bug**
The InterstitialGenerator can identify octahedral and tetrahedral interstitials, however, it overestimates the number of interstitial sites due to overlapping interstitials. _**More than that, the method of create_saturated_interstitial_structure creates structures with overlapped interstitial sit... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2565 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2565/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2565/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2565/events | https://github.com/materialsproject/pymatgen/pull/2565 | 1,289,654,453 | PR_kwDOACgets46ncuH | 2,565 | Molecule: warn user about non-triplet O2 | {
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"No harm in a warning. Seems good to me. ",
"No issue from me. Let's consider it a reprimanding instead of a warning though. 😉 ",
"Sorry to take an alternative position, but I am not sure this is necessary at all. It is strange to do this specially for O2. What if someone sets H2 to be in a triplet state? The ... | 2022-06-30T06:21:48 | 2024-10-10T01:54:47 | 2022-06-30T16:53:32Z | CONTRIBUTOR | {
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} | ## Summary
When a user creates a `Molecule` to represent O2 with default keyword arguments, the spin_multiplicity will be set to 1. However, the ground state of the O2 molecule is triplet (unlike most molecules with a single covalent bond).
```
>>> mol = Molecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]])
>>> m.spin_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2566 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2566/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2566/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2566/events | https://github.com/materialsproject/pymatgen/pull/2566 | 1,289,666,911 | PR_kwDOACgets46nfXx | 2,566 | Ion: pass charge to oxi_state_guesses | {
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"This is a great edit @rkingsbury, thanks!"
] | 2022-06-30T06:36:20 | 2022-07-26T21:04:13 | 2022-06-30T19:00:47Z | CONTRIBUTOR | {
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} | ## Summary
`Ion.oxi_state_guesses()` currently inherits from `Composition`, and generally fails to provide useful information unless the user specifies the `target_charge` (which is an optional kwarg):
```
>>> i=Ion.from_formula('SO4-2')
>>> i.oxi_state_guesses()
[]
```
This PR overloads the parent method... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2567 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2567/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2567/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2567/events | https://github.com/materialsproject/pymatgen/pull/2567 | 1,289,684,041 | PR_kwDOACgets46njAF | 2,567 | Element: add from_name() | {
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} | Adds an `Element.from_name` convenience function to make it possible to init an `Element` from its long name, in addition to existing methods based on symbol (default), atomic number (`Element.from_Z`), or row and group (`Element.from_row_and_group``)
```
>>> Element.from_name('Sodium')
Element Na
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2568 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2568/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2568/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2568/events | https://github.com/materialsproject/pymatgen/pull/2568 | 1,290,437,325 | PR_kwDOACgets46qE78 | 2,568 | allow to change voronoi_distance_cutoff in ChemEnv | {
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"\n[](https://coveralls.io/builds/50501842)\n\nCoverage decreased (-0.003%) to 63.532% when pulling **87bec49eee0fe3f5f3c711966fa5cde77fb3adc3 on JaGeo:fix_voronoi** into **57075245189b05f6eaba356dffc39e1ec58812a7 on materialsproject:master**.\n",
"Tha... | 2022-06-30T17:23:20 | 2022-06-30T20:43:46 | 2022-06-30T18:57:28Z | MEMBER | {
"total": 0,
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} | ## Summary
This pull-request allows to change the voronoi_distance cutoff in ChemEnv. Otherwise, molecules in too large boxes cannot be investigated. I have added a test and a warning for users in case the cutoff is too small. (Issue found by @rlaplaza) | {
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"\n[](https://coveralls.io/builds/50532847)\n\nCoverage decreased (-0.002%) to 63.534% when pulling **90d1b5afc573232509b39245dc774634ddd0c4d2 on orioncohen:small_docs_fix** into **99a65ac4a49a7a9c20aa7969f5b7f1db773143eb on materialsproject:master**.\n"... | 2022-07-01T16:25:01 | 2022-07-01T17:12:53 | 2022-07-01T17:12:44Z | CONTRIBUTOR | {
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} | ## Summary
Tiny addition to documentation. This was a gotcha for me. | {
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"Thanks,",
"\n[](https://coveralls.io/builds/50656255)\n\nCoverage increased (+0.002%) to 63.539% when pulling **3da0e594551dd4a429e9f8503344559854290214 on mjwen:hotfix** into **38666c384fa3a0ae78d55a3e002f20c140f72fc5 on materialsproject:master**.\n"... | 2022-07-01T21:14:28 | 2022-07-07T00:20:12 | 2022-07-06T23:58:02Z | MEMBER | {
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} | ## Summary
- Do not report not converted warnings on MD runs. | {
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## Summary
Incorrect use of "respectively" fixed
Made terminology and formatting consistent (e.g., k-path vs kpath)
It's conventional (ha-ha!) to abbreviate "Latimer and Munro convention" to "Latimer-Munro convention", and so on... | {
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"\n[](https://coveralls.io/builds/50562835)\n\nCoverage decreased (-0.002%) to 63.581% when pulling **e2b1aea7f131969b82bc96442f9b85053e82fa61 on cajfisher:patch-5** into **85796d24190aca51a2674a7895430eb7c561b0a9 on materialsproject:master**.\n"
] | 2022-07-04T07:12:51 | 2022-07-04T12:31:33 | 2022-07-04T12:31:33Z | CONTRIBUTOR | {
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} | Minor English corrections and improved descriptions/reduced ambiguity
## Summary
"can be incorrect" should be "may be incorrect"
The "lattice" is infinite in all dimensions and remains unchanged; only the "cell" or "lattice vectors" are reduced
Other minor improvements for clarity/ease-of-reading | {
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"\n[](https://coveralls.io/builds/50582833)\n\nCoverage decreased (-0.002%) to 63.581% when pulling **75ddae179369742d1fd07c86be839be526d7e312 on pre-commit-ci-update-config** into **723260b181734337cbd75fc4ec8f55382b91dc90 on master**.\n"
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updates:
- [github.com/asottile/pyupgrade: v2.32.1 → v2.34.0](https://github.com/asottile/pyupgrade/compare/v2.32.1...v2.34.0)
- [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.2.0...v4.3.0)
- [github.com/psf/black: 22.3.0 → ... | {
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"\n[](https://coveralls.io/builds/50648810)\n\nCoverage increased (+0.007%) to 63.591% when pulling **ab9d4e51a5a15b3a942b882539729f9885b37bec on rkingsbury:inputset_eq** into **723260b181734337cbd75fc4ec8f55382b91dc90 on materialsproject:master**.\n",
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} | ## Summary
This pull request fixes two items in `InputSet`:
1. `__iter__` was previously iterating an iterator over `self.inputs.items()` rather than `self.inputs`. This was not a correct implementation (see example for implementing a `dict`-like class from `MutableMapping` [here](https://stackoverflow.com/questi... | {
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"Fixed in #2577 "
] | 2022-07-06T22:32:05 | 2022-07-08T06:12:18 | 2022-07-08T06:12:18Z | CONTRIBUTOR | {
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} | Here the sign convention is more electrons bigger number:
https://github.com/materialsproject/pymatgen/blob/723260b181734337cbd75fc4ec8f55382b91dc90/pymatgen/io/vasp/outputs.py#L1170
Here `nelect` is the number computed from the potcar so it is exactly the opposite of the definition above:
https://github.com/mater... | {
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"Unittest needed.",
"\n[](https://coveralls.io/builds/50656286)\n\nCoverage decreased (-0.001%) to 63.589% when pulling **5f2ce21b223837d300624cdf1fb16bf0be4f490d on jmmshn:charge_sign** into **72d6e8b4df2a7e76ac5bba4ccc834df3683637c0 on materialsproje... | 2022-07-06T23:52:46 | 2023-01-03T01:06:13 | 2022-07-07T14:15:13Z | CONTRIBUTOR | {
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} | ## The sign convention of the net charge parsed by Vasprun should be changed.
The current value of the parsed charge for Vasprun.structure is more positive if NELECT is higher.
If we used the electron -> negative charge convention then this expression should have the other sign
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"addressed in #2579 "
] | 2022-07-08T06:45:24 | 2022-07-08T06:58:39 | 2022-07-08T06:58:39Z | CONTRIBUTOR | {
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The charge is missing in `Vasprun.final_structure` and `Vasprun.initial_structure`.
Is it possible to just use `Vasprun.structures[-1]` and `Vasprun.structures[0]` for these as oppose... | {
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"\n[](https://coveralls.io/builds/50701699)\n\nCoverage increased (+0.003%) to 63.593% when pulling **29706c90fc55d6aec4f0be4b9d09f7da2091d84d on jmmshn:charge_sign** into **d10c460b2b20b8802e345491bfe2301d1376650e on materialsproject:master**.\n"
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} | ## Bug Fix in Vasprun
The current code does not decorate the initial and final structures in `Vasprun` with the charge. This affects Atomate2
https://github.com/materialsproject/atomate2/issues/154
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"\n[](https://coveralls.io/builds/50707453)\n\nCoverage remained the same at 63.591% when pulling **f9d38dfee844b0017ee4121cc030b6958fa66939 on janosh:typo** into **d10c460b2b20b8802e345491bfe2301d1376650e on materialsproject:master**.\n"
] | 2022-07-08T11:02:31 | 2022-07-08T11:55:17 | 2022-07-08T11:34:46Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2581 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2581/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2581/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2581/events | https://github.com/materialsproject/pymatgen/pull/2581 | 1,299,656,562 | PR_kwDOACgets47JAXP | 2,581 | Add "External tools" section to `docs_rst/addons.rst` | {
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"\n[](https://coveralls.io/builds/51098196)\n\nCoverage decreased (-0.001%) to 63.579% when pulling **078479d67967ef6af4cd22edb8362ffa635d9e23 on janosh:pymatviz-addon** into **780788270550fe4febeeac50ae00dbc2167a1b47 on materialsproject:master**.\n",
... | 2022-07-09T12:08:48 | 2022-07-28T18:00:30 | 2022-07-28T17:58:34Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2582 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2582/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2582/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2582/events | https://github.com/materialsproject/pymatgen/pull/2582 | 1,301,162,265 | PR_kwDOACgets47N6TI | 2,582 | Preparing to replace defects module | {
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"\n[](https://coveralls.io/builds/50804688)\n\nCoverage increased (+0.05%) to 63.64% when pulling **30e0977f9c3f9357503d6e090377960cd1f16c78 on jmmshn:replace_defects** into **23421524e1ac567358144b74825be14b2b1a7af6 on materialsproject:master**.\n",
"... | 2022-07-11T20:04:39 | 2022-07-28T16:14:41 | 2022-07-13T18:02:49Z | CONTRIBUTOR | {
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} | ## Moving code that overlap the current defects module
Some parts of the current defect module have parts that leak into other parts of our code.
This PR moves all the codes and tests inside the current (old) defects module.
The warning message has also been moved into the `core` submodule. This allows the old ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2583 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2583/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2583/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2583/events | https://github.com/materialsproject/pymatgen/issues/2583 | 1,306,100,461 | I_kwDOACgets5N2YLt | 2,583 | Scaling of velocities in Poscar file | {
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"Thanks. I agree and I have made the change."
] | 2022-07-15T14:23:46 | 2022-07-30T15:47:31 | 2022-07-30T15:47:25Z | CONTRIBUTOR | {
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I have a question about the sampling of velocities on this line. It corresponds to the `set_temperature()` method in the Poscar class.
https://github.com/materialsproject/pymatgen/blob/23421524e1ac567358144b74825be14b2b1a7af6/pymatgen/io/vasp/inputs.py#L597
I wonder why, the velocities are scaled before the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2584 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2584/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2584/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2584/events | https://github.com/materialsproject/pymatgen/pull/2584 | 1,306,306,090 | PR_kwDOACgets47fDkF | 2,584 | Structure __eq__ bugfix | {
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"I can reproduce in `pymatgen==2022.7.8`\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\n\r\ncoords = [[0.5, 0.5, 0.5], [0, 0, 0]]\r\nspecies = [\"Na\", \"Cl\"]\r\nlattice = Lattice.from_parameters(a=4, b=4, c=4, alpha=90, beta=90, gamma=90)\r\nstructure = Structure(lattice, species, coords)\r\n... | 2022-07-15T17:27:19 | 2022-07-21T01:28:13 | 2022-07-21T01:28:13Z | CONTRIBUTOR | {
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} | Ran into an obscure bug where `other` was a length-18 string and `self` was a structure with 18 atoms
## Summary
Include a summary of major changes in bullet points:
* Check that the structure being compared against has a lattice parameter before trying to access the lattice parameter.
## Additional depende... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2585 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2585/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2585/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2585/events | https://github.com/materialsproject/pymatgen/pull/2585 | 1,306,720,789 | PR_kwDOACgets47gcp- | 2,585 | Added 'get_ir_reciprocal_mesh_map'-method | {
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"\n[](https://coveralls.io/builds/50922191)\n\nCoverage decreased (-0.01%) to 63.627% when pulling **6fe9396b8e3491b4327f53631ce4a6e290ddcf68 on nheinsdorf:master** into **58b8bd589ec6b39b22007e536d5a8a38281d824f on materialsproject:master**.\n",
"Than... | 2022-07-16T06:08:44 | 2022-07-21T00:50:47 | 2022-07-21T00:50:46Z | CONTRIBUTOR | {
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} | ## Summary
In physical simulations it is often desirable to make use of the lattice symmetries to save computational time. The 'get_ir_reciprocal_mesh' function (which is basically an interface to spglib) returns an irreducible mesh and the weight, which just tells how many other kpoints a given irreducible kpoint i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2587 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2587/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2587/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2587/events | https://github.com/materialsproject/pymatgen/issues/2587 | 1,313,376,988 | I_kwDOACgets5OSIrc | 2,587 | `IStructure.__eq__` fails for integers | {
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"I am confused. Isn't comparing Structure and a string/int/whatever that is not Structure-like supposed to fail?",
"Comparison across types is supposed to return false. E.g.\r\n\r\n```py\r\n'foo' == 5\r\n>>> False\r\n```",
"Then the current PR implementation is not correct. I would actually do something like \r... | 2022-07-21T14:45:16 | 2022-07-21T17:07:39 | 2022-07-21T17:07:39Z | MEMBER | {
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} | There are more edge cases like #2584 in `IStructure.__eq__`. E.g. comparing against `int`s also throws.
```py
from pymatgen.core import Lattice, Structure
coords = [[0.5, 0.5, 0.5], [0, 0, 0]]
species = ["Na", "Cl"]
lattice = Lattice.from_parameters(a=4, b=4, c=4, alpha=90, beta=90, gamma=90)
structure = St... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2588 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2588/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2588/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2588/events | https://github.com/materialsproject/pymatgen/pull/2588 | 1,313,393,264 | PR_kwDOACgets473K5w | 2,588 | Fix edge cases in Structure equality | {
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"\n[](https://coveralls.io/builds/51060609)\n\nCoverage decreased (-0.0007%) to 63.571% when pulling **fb45c40867fff0413d7bb21cc2bdb609128ec5ae on janosh:test-structure-equality** into **c4e0552c2fdb14bb02152fced8ef7fcbb0de8007 on materialsproject:master... | 2022-07-21T14:54:39 | 2022-07-21T17:21:02 | 2022-07-21T17:07:39Z | MEMBER | {
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} | Closes #2587.
Related #2584.
Also adds tests for `IStructure.__eq__()`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2589 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2589/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2589/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2589/events | https://github.com/materialsproject/pymatgen/pull/2589 | 1,313,834,327 | PR_kwDOACgets474rGJ | 2,589 | fixed serialization bug | {
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"\n[](https://coveralls.io/builds/51069669)\n\nCoverage decreased (-0.0008%) to 63.58% when pulling **ff4696c29a81888bec93828da28db8c363027686 on jmmshn:symm_fix** into **cd47594bab856ecc70e427e99ed77e9990f14d8b on materialsproject:master**.\n"
] | 2022-07-21T21:39:15 | 2022-07-21T22:18:01 | 2022-07-21T22:18:01Z | CONTRIBUTOR | {
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} | ## Summary
This should fix the underlying serialization bug related to this PR:
https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/pull/264
I think the other PR
https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/pull/312
still fails if `symm_structure` is provided due to this b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2590 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2590/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2590/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2590/events | https://github.com/materialsproject/pymatgen/pull/2590 | 1,315,303,610 | PR_kwDOACgets479zJ7 | 2,590 | Update absorption coefficient | {
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"\n[](https://coveralls.io/builds/51094622)\n\nCoverage remained the same at 63.58% when pulling **3acc67b6d66c6c02e423c6728d94b40d528b3d5b on yang-ruoxi:absorption** into **780788270550fe4febeeac50ae00dbc2167a1b47 on materialsproject:master**.\n",
"Th... | 2022-07-22T18:29:54 | 2022-07-22T23:09:19 | 2022-07-22T23:08:51Z | MEMBER | {
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The previous absorption coefficient lack a 2*pi constant. It is corrected in this PR and the results compare well with experiments. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2591 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2591/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2591/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2591/events | https://github.com/materialsproject/pymatgen/issues/2591 | 1,318,106,385 | I_kwDOACgets5OkLUR | 2,591 | Atom position overlap after repairing the slab | {
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"I could confirm I'm able to reproduce this issue with the provided structure and code in `v2023.12.18`, and I'm looking into this.\r\n\r\nIn the following generated `POSCAR-1`, there are at least a pair of overlapped atoms (didn't check the others):\r\n<details>\r\n <summary>POSCAR-1 with overlap atoms</summary>\... | 2022-07-26T11:31:50 | 2024-01-15T05:37:19 | NONE | {
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} | Hey, I'm trying to generate the (010) facet structures of α-Al2O3 with pymatgen 2022.5.26
```python
from pymatgen.core.surface import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.structure import Structure
struct = Structure.from_file('Al2O3CONTCAR')
struct = SpacegroupAnalyzer... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2592 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2592/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2592/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2592/events | https://github.com/materialsproject/pymatgen/issues/2592 | 1,321,901,357 | I_kwDOACgets5Oyp0t | 2,592 | Please add to README how to run tests | {
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"I am not sure how your pymatgen is installed. But tests are included only in the dev version of pymatgen cloned from Github. After that, it is just `pytest pymatgen` like all other codes."
] | 2022-07-29T08:04:44 | 2022-07-30T15:09:57 | 2022-07-30T15:09:57Z | NONE | {
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} | pytest used to run tests, but now it fails to find any tests:
```
==================================================================================== test session starts =====================================================================================
platform freebsd13 -- Python 3.9.13, pytest-7.1.2, pluggy-1.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2593 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2593/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2593/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2593/events | https://github.com/materialsproject/pymatgen/issues/2593 | 1,322,721,734 | I_kwDOACgets5O1yHG | 2,593 | Faster structure matching via `StructureMatcher` (and by extension, `group_structures`) | {
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"Speed ups are always welcome. But I want to note a few things:\r\n1. Hashing is already done. E.g., if the fractional composition are not equal, two structures would immediately evaluate to not being equal without any matrix comparisons.\r\n2. Most of the code is already vectorized in numpy. Any GPU optimizations ... | 2022-07-29T22:19:38 | 2024-10-09T19:13:25 | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
Using `StructureMatcher` repeatedly causes a large overhead (in my use-case, ~40 hrs to check the performance of a generative benchmark via [`matbench-genmetrics`](https://github.com/sparks-baird/matbench-genmetrics)).
**Describe the solution you'... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2594 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2594/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2594/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2594/events | https://github.com/materialsproject/pymatgen/pull/2594 | 1,322,898,660 | PR_kwDOACgets48Wjem | 2,594 | Change lattice equality | {
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"\n[](https://coveralls.io/builds/51284315)\n\nCoverage increased (+0.003%) to 63.547% when pulling **f178d555ae5762d49ca490116807446398bddf9e on janosh:change-lattice-equality** into **1335a14ffc9ef0f50d782316cd6a8abfdfad1b54 on materialsproject:master*... | 2022-07-30T04:38:21 | 2022-07-30T15:06:57 | 2022-07-30T15:06:57Z | MEMBER | {
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} | Same treatment for `Lattice` as `IStructure` received in #2588, i.e. return `NotImplemented` rather than `False` in `Lattice.__eq__()` if other lacks expected attributes.
Related #2587, #2584.
Also adds test to `Lattice.__eq__()` plus some `flake8` fixes. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2595 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2595/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2595/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2595/events | https://github.com/materialsproject/pymatgen/pull/2595 | 1,322,926,498 | PR_kwDOACgets48Wowx | 2,595 | Correct doc description of electron affinity | {
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"\n[](https://coveralls.io/builds/51284823)\n\nCoverage increased (+0.005%) to 63.549% when pulling **176495aceb9d8bfdfca0e12786a09f1554cd7693 on 755452800:master** into **1335a14ffc9ef0f50d782316cd6a8abfdfad1b54 on materialsproject:master**.\n",
"than... | 2022-07-30T07:34:54 | 2022-07-30T15:06:41 | 2022-07-30T15:06:33Z | CONTRIBUTOR | {
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} | The electron affinity description is duplicate with ionization energy. Updated the definition according to wiki (https://en.wikipedia.org/wiki/Electron_affinity).
| {
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"\n[](https://coveralls.io/builds/51288725)\n\nCoverage increased (+0.002%) to 63.549% when pulling **00d81f1fe22ca669cc72de81d9d40a0f2a91731d on janosh:fix-for-loop-assigning-its-iterable** into **fd88d820820d57cd370eaf88ce89e9283dc19f11 on materialspro... | 2022-07-30T19:18:12 | 2022-07-31T01:38:27 | 2022-07-31T01:37:52Z | MEMBER | {
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} | Two small bug fixes in a7f5fb226ede0cfc57fc81b71b61ce98cf310f58 and 5246c19845f9ef7ddfa366b1bf0510d1bc8e663e.
Plus address some linter errors in 86d08dcfe46bca993d06519e6c4a392f7deefde0. | {
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"Thanks for the contribution. You can simply create a pull request and we will provide feedback on it. The steps are in the pymatgen documentation under the \"contributing\" section. ",
"Thanks, would that be under the master branch?",
"Doesn't matter what branch. Whatever you prefer on your fork. The master br... | 2022-07-31T15:27:12 | 2022-08-01T03:22:47 | 2022-08-01T03:22:47Z | NONE | {
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As part of my research I created a unit cell transformation algorithm that I thought might be useful to others. I'm not used to working on collaberative open source projects like this. I'd like to ask if there is anywhere / anyone I should send my code to for the purposes of getting external confirmation my co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2598 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2598/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2598/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2598/events | https://github.com/materialsproject/pymatgen/pull/2598 | 1,324,959,832 | PR_kwDOACgets48dXiq | 2,598 | [pre-commit.ci] pre-commit autoupdate | {
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"\n[](https://coveralls.io/builds/51328233)\n\nCoverage remained the same at 63.549% when pulling **e83f546ea995fa60c291065ca7cc516aa8b58f6c on pre-commit-ci-update-config** into **013b70530ead3ede744dbda3b691f9c502036f7d on master**.\n"
] | 2022-08-01T20:43:38 | 2022-08-01T21:31:06 | 2022-08-01T21:31:06Z | CONTRIBUTOR | {
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updates:
- [github.com/asottile/pyupgrade: v2.34.0 → v2.37.3](https://github.com/asottile/pyupgrade/compare/v2.34.0...v2.37.3)
- [github.com/PyCQA/flake8: 4.0.1 → 5.0.2](https://github.com/PyCQA/flake8/compare/4.0.1...5.0.2)
- [github.com/pre-commit/mirrors-mypy: v0.961 → v0.971](https://gith... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2599 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2599/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2599/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2599/events | https://github.com/materialsproject/pymatgen/issues/2599 | 1,325,188,605 | I_kwDOACgets5O_MX9 | 2,599 | Allow the user to set SpacegroupAnalyzer parameters when writing FEFF input files | {
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"Since it is a relatively quick fix, I have implemented it. Pls see latest commits.",
"@shyuep Perfect thank you. Quick followup question: are you open to using the FEFF writers to handle amorphous materials and clusters (i.e. very low symmetry systems)? I think that would be quite useful for people (though perha... | 2022-08-02T02:07:29 | 2022-08-02T14:31:10 | 2022-08-02T03:39:52Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
Currently when writing FEFF input files, if [SpacegroupAnalyzer](https://github.com/materialsproject/pymatgen/blob/baf62b77788fc43387e15b1e0b60094132815c47/pymatgen/io/feff/inputs.py#L177) fails at any point, it prevents the user from writing anythin... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2600 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2600/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2600/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2600/events | https://github.com/materialsproject/pymatgen/issues/2600 | 1,326,310,451 | I_kwDOACgets5PDeQz | 2,600 | Add low-symmetry structure/cluster support for FEFF writers | {
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} | # Is your feature request related to a problem? Please describe
Currently, the `FEFFDictSet` object utilizes the `SpacegroupAnalyzer` in various contexts to produce header files. The `is_ordered` property is also called quite a few times. I don't think any of these will work properly if the provided structure is eit... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2601 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2601/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2601/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2601/events | https://github.com/materialsproject/pymatgen/pull/2601 | 1,327,639,942 | PR_kwDOACgets48mVoH | 2,601 | Remove `__ne__` methods | {
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"To quote [this SO answer](https://stackoverflow.com/a/30676267): \r\n\r\n> should I implement `__ne__()` operator based on `__eq__`?\r\n> \r\n> Short Answer: Don't implement it, but if you must, use `==`, not `__eq__`",
"Wait! Still need to fix a test. :)",
"Don't worry about it.",
"I'm in a call atm, will d... | 2022-08-03T18:39:37 | 2022-08-03T19:47:41 | 2022-08-03T19:24:05Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2602 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2602/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2602/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2602/events | https://github.com/materialsproject/pymatgen/pull/2602 | 1,327,701,804 | PR_kwDOACgets48mjBb | 2,602 | Fix CI AssertionError: `False` is not `True` in `self.assertTrue(Magmom([0, 0, 10]) == 10)` | {
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Fixes `pymatgen/electronic_structure/tests/test_core.py:131: AssertionError`. | {
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"\n[](https://coveralls.io/builds/51417780)\n\nCoverage increased (+0.008%) to 63.533% when pulling **d7aba46501cc07e8ca6b3627f3901960f8cd51fc on JaGeo:supercell_transformation** into **6ea3ec8d055dd7cd4e8e0e4008e866e288c693a1 on materialsproject:master*... | 2022-08-04T12:31:51 | 2022-08-04T19:03:27 | 2022-08-04T18:44:26Z | MEMBER | {
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} | ## Summary
I have added an additional option to the CubicSupercellTransformation to only return cells with three 90 degree angles. I think this might be useful for tasks where supercells are required.
I have also added two test cases and documentation. | {
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"Thanks @henriquemiranda. This change breaks quite a number of tests. They need to be fixed before I can merge it.",
"Ok, I see... I don't see where to start to fix those issues.\r\n@shyuep Do you think any of the devs could help me?\r\n",
"Click on the failed tests and look at the logs. There will be error mes... | 2022-08-04T15:14:43 | 2022-08-08T21:31:04 | 2022-08-08T21:31:04Z | CONTRIBUTOR | {
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} | ## Summary
* Changed the default number of significant digits to be used when writing the POSCAR file.
Writing the POSCAR with the current default can cause all kinds of different nasty issues in VASP for example:
- VASP might not be able to find the correct space group
- VASP might lose the symmetry during rel... | {
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"@shyuep Not sure the remaining CI error is related to my changes.\r\n\r\n<details>\r\n<summary>CI logs</summary>\r\n\r\n```py\r\n================================== FAILURES ===================================\r\n____________________________ TestQCOutput.test_all ____________________________\r\n\r\nself = <qchem.te... | 2022-08-05T18:07:39 | 2022-08-05T19:59:58 | 2022-08-05T19:33:32Z | MEMBER | {
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} | Remove unneeded `dict.keys()` calls for conciseness. Finishes up some loose ends from #2596. | {
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"I do not have a super strong opinion. The only thing is that unittest is included as part of python and I don't find a big problem with it. Pytest is used right now as a dev requirement, but there is no guarantee that we will continue to use it in future.",
"> but there is no guarantee that we will continue to u... | 2022-08-06T02:44:34 | 2022-08-17T01:43:27 | 2022-08-17T01:43:27Z | MEMBER | {
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} | @shyuep What's your stance on converting `pymatgen` tests from `unittest` to `pytest`?
I find `pytest`'s functional style to be more concise and easier to read than `unittest`.
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} | **Describe the bug**
when I use the BSDosPlotter model to draw BAND and DOS figure,I am fail with a “band = cast(list[float], band)” . then I modified the code with "band = cast(list band) " and got a result.
**To Reproduce**
Steps to reproduce the behavior:
Follows are my script of DosPlotter:
from pymatgen... | {
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"The test failures seem to be related to `bader` installation (which afaik is not related to the changes here)",
"Thanks"
] | 2022-08-06T18:04:24 | 2022-08-10T14:01:15 | 2022-08-06T22:24:24Z | CONTRIBUTOR | {
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} | ## Summary
Assorted enhancements to `metal_edge_extender` to increase its flexibility for use in contexts beyond the LIBE dataset (e.g., water-ion coordination)
* Adds `metals`, `coordinators`, and `cutoff` as keyword arguments so that metal edge extender settings can be customized for different applications (e.g... | {
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"Thanks,"
] | 2022-08-06T22:03:18 | 2022-08-13T07:22:16 | 2022-08-06T22:22:48Z | CONTRIBUTOR | {
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} | The link in the docs was mistakenly interpreted as relative inside the pymatgen documentation. Also added `rel/`, which will always point to the documentation for the latest version of the code
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"A few suggestions:\r\n\r\n1. Pls change low_symmetry to just skip_symmetry.\r\n2. Pls add a unittest (in test_sets.py) to test the new argument functionality.\r\n\r\nA note about the rest. A symmetry calculation is actually fast. By specifying symmetry, we reduce the cost of the FEFF calculation itself. It is true... | 2022-08-06T23:24:47 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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Allows passing of a `low_symmetry_system` keyword argument to `FEFFDictSet` which skips the `SpacegroupAnalyzer` runs in constructing the header.
# Comments
* Frankly I think the entire feature should be deprecated. There's no reason to do such a heavy calculation just for a header comment. If the us... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2612 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2612/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2612/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2612/events | https://github.com/materialsproject/pymatgen/issues/2612 | 1,332,303,559 | I_kwDOACgets5PaVbH | 2,612 | `IndexError` when unassigned ID passed to `MPRester().get_entry_by_material_id()` | {
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} | ```py
from pymatgen.ext.matproj import MPRester
MPRester().get_entry_by_material_id("mp-2022")
```
raises
```py
777 """
778 data = self.get_entries(
779 material_id,
780 compatible_only=compatible_only,
(...)
783 conventional_unit_cell=conventional_unit_cell,
784... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2613 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2613/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2613/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2613/events | https://github.com/materialsproject/pymatgen/pull/2613 | 1,332,308,474 | PR_kwDOACgets481llF | 2,613 | Fix `MPRester.get_entry_by_material_id()` for missing ID | {
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"\n[](https://coveralls.io/builds/51504706)\n\nCoverage increased (+0.003%) to 63.516% when pulling **f469cbe587e006816631849d8f268a8b39ee37f5 on janosh:fix-get-entry-by-id-for-missing-id** into **ebfdde14598795a90ad3e6b7a2f0bf2ae6a36858 on materialsproj... | 2022-08-08T19:34:51 | 2022-08-08T21:31:48 | 2022-08-08T21:31:48Z | MEMBER | {
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} | Closes #2612. | {
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