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https://api.github.com/repos/materialsproject/pymatgen/issues/2404 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2404/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2404/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2404/events | https://github.com/materialsproject/pymatgen/pull/2404 | 1,119,659,470 | PR_kwDOACgets4x2YH1 | 2,404 | Finding Symmetrically Equivalent Bonds (Neighbors) in Structure | {
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"Thanks. I would suggest you go ahead and implement the PeriodicBond or Bond first. It shouldn't be a subclass of PeriodicNeighbor, but rather is a container of the starting site and the PeriodicNeighbor.",
"\n[](https://coveralls.io/builds/48680679)\n... | 2022-01-31T16:35:03 | 2022-04-28T21:19:32 | 2022-04-28T21:19:29Z | CONTRIBUTOR | {
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} | ## Summary
Added a method that gets all the neighbors up a maximum distance for a Structure, and groups these 'bonds' according to their symmetry. This is useful when building a physical model to see which bonds should have the same attributes by symmetry (like a tight-binding hopping amplitude). Furthermore, for ea... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2405 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2405/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2405/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2405/events | https://github.com/materialsproject/pymatgen/pull/2405 | 1,119,687,302 | PR_kwDOACgets4x2d7x | 2,405 | Remove more deprecated stuff | {
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"The get_neighbors old should not be removed. It is a debugging code that is very useful. Basically it is a brute force version of the get_neighbors that is very slow but guaranteed to be correct because of the very simple logic. ",
"@shyuep Yeah wasn't sure about whether that one should go. Put it back in.",
"... | 2022-01-31T17:01:06 | 2022-01-31T22:08:06 | 2022-01-31T21:36:10Z | MEMBER | {
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} | Follow up to #2397 and #2401.
Deletes some more code [@shyuep said is very old](https://github.com/materialsproject/pymatgen/pull/2397#issuecomment-1025976675). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2406 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2406/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2406/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2406/events | https://github.com/materialsproject/pymatgen/issues/2406 | 1,119,846,254 | I_kwDOACgets5Cv39u | 2,406 | Add mirroring of slabs to CoherentInterfaceBuilder | {
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"Yes this would be a helpful feature! But if you mirror, wouldn't that create a twin boundary?",
"Hmm I'm not sure that would happen. What the _CoherentInterfaceBuilder_ module does now is to take two specified slabs and make an interface out of them. If both slabs are symmetric, there is no issue with the orient... | 2022-01-31T19:29:07 | 2022-02-09T16:25:05 | NONE | {
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} | The _CoherentInterfaceBuilder_ works rather nicely when creating interfaces between various lattices. However, it seems like it currently doesn't consider mirroring non-symmetric slabs, which then leaves quite a few possible structures unexplored.
Not sure whether this would be easier to implement at this step or in ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2407 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2407/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2407/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2407/events | https://github.com/materialsproject/pymatgen/pull/2407 | 1,120,023,623 | PR_kwDOACgets4x3k-5 | 2,407 | Improve parsing of coupled-cluster calculations in Q-Chem | {
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"\n[](https://coveralls.io/builds/46106512)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **0632be938dae90de301a0c93f68fb1ca53f879d7 on espottesmith:qchem_cc** into **6dbdeec119491f21da88f3bdb7f4c33ee5fe7ff7 on materialsproject:master**.\n",
"T... | 2022-01-31T23:01:06 | 2022-02-01T18:47:34 | 2022-02-01T17:40:15Z | CONTRIBUTOR | {
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} | ## Summary
Currently, QCOutput will parse CCSD and CCSD(T) calculations, but will only grab the final energy, not the components (HF SCF, MP2, CCSD correlation, (T) correlation, etc.). This PR makes small changes to the QCOutput class to improve parsing of CC calculations.
An additional small change is made to ho... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2408 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2408/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2408/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2408/events | https://github.com/materialsproject/pymatgen/issues/2408 | 1,121,561,782 | I_kwDOACgets5C2ay2 | 2,408 | Vasprun().complete_dos.spin_polarization yields a KeyError for ISPIN=1 | {
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} | For the a ISPIN=1 calculation with VASP, the `complete_dos` from the `Vasprun` parser yields a `KeyError`. The `spin_polarization` property is not applicable for ISPIN=1, but we should make it clearer for the user rather than throwing a `KeyError`.
There are also no tests for this property.
```python
from pymatg... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2409 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2409/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2409/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2409/events | https://github.com/materialsproject/pymatgen/pull/2409 | 1,121,571,666 | PR_kwDOACgets4x8t8q | 2,409 | Return None for complete_dos.spin_polarization if ISPIN=1 | {
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"Thanks."
] | 2022-02-02T06:49:43 | 2022-02-03T17:39:19 | 2022-02-03T17:26:53Z | MEMBER | {
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} | Addresses #2408.
If a VASP calculation is carried out with ISPIN=1, the `Vasprun('vasprun.xml').complete_dos.spin_polarization` property throws a `KeyError`. This PR makes it so that `None` is returned instead.
The `.spin_polarization` property also had no tests. I added them. | {
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"Many thanks for addressing this issue @arosen93, this looks good.\r\n\r\nOn a technical note, I don't think this can be classed as a cosmetic change -- the return type is changing, this will have downstream consequences for anyone using the pymatgen parser (eg to store results in a database). However, I can't anti... | 2022-02-02T09:09:13 | 2022-02-28T07:45:44 | 2022-02-23T17:57:27Z | MEMBER | {
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} | Addresses #2361.
As noted by @RyanNKHall, the `Wavecar` class requires that ENCUT be an `int` when strictly speaking, this is not necessary within VASP. This PR implements the change suggested by @RyanNKHall to read ENCUT as a `float`.
If a test is requested, I can run a super cheap H2 calc, although I'm not su... | {
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"Thanks for fixing my `EnvironmentError`'s too. I just looked it up in response and it does not mean what I thought it meant.",
"There is a version difference for black between `.pre-commit-config.yaml` (21.12b0) and in requirements-dev.txt (22.1.0). Its also quite confusing that there is both a `.pre-commit-conf... | 2022-02-03T00:42:57 | 2022-02-04T16:12:24 | 2022-02-04T16:12:19Z | MEMBER | {
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} | Continuing on from #2379 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2412 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2412/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2412/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2412/events | https://github.com/materialsproject/pymatgen/issues/2412 | 1,123,083,769 | I_kwDOACgets5C8OX5 | 2,412 | "infinite" loop when importing pymatgen.core and MPRester | {
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"I can't reproduce this. Can you try renaming your .pmgrc.yaml file to sometjing else (e.g., .pmgrc.yaml.bak) and see if this still recurs. You can also try downgrading ruamel.yaml and see if that helps.",
"Thank you so much, renaming pmgrc.yaml worked! Why though?\r\n",
"Probably means your .pmgrc.yaml was cor... | 2022-02-03T13:25:02 | 2022-02-03T16:35:54 | 2022-02-03T16:35:54Z | NONE | {
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} | ## Bug description
The commands `import pymatgen.core` and `from pymatgen.ext.matproj import MPRester` are not completed, but result in a loop between two lines. Here follows the traceback after I interrupt the run with ctrl+c:
```
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2413 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2413/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2413/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2413/events | https://github.com/materialsproject/pymatgen/pull/2413 | 1,123,978,028 | PR_kwDOACgets4yEl6I | 2,413 | Update minimal basis | {
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"Not sure what is going on with the tests as I did not change anything on the code :).",
"\n[](https://coveralls.io/builds/46236468)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **338aa705ce794fe21aa2949dfde9ddca4e471025 on JaGeo:master** into... | 2022-02-04T09:16:54 | 2022-02-04T15:13:29 | 2022-02-04T14:49:09Z | MEMBER | {
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} | This is a very small change of the configuration files for the Lobster basis. We removed the 2p orbitals for Be as they led to problems in our computations and probably should be optional during the projection.
This should hopefully not affect any of the tests.
Best,
JG | {
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"@shyuep Better to leave the `flake8`, `autoflake` and `mypy` hooks in place so that users running `pre-commit` locally can still check new code they write against these hooks and only disable them in CI. As errors are fixed slowly over time, they can be re-enabled.",
"\n[![Coverage Status](https://coveralls.io/b... | 2022-02-04T15:21:45 | 2022-02-04T16:36:40 | 2022-02-04T16:17:17Z | MEMBER | {
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} | Nice to see you adopted pre-commit.ci!
Normally it auto-updates the hooks in `.pre-commit-config.yaml` weekly. Set it to monthly to keep down the noise. | {
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"\n[](https://coveralls.io/builds/46241233)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **ed995811800d6cd1f8fab9aebdde0c1b3679a2b3 on janosh:isort** into **df6515c1a55835aaee3c530c182e78cd651530a2 on materialsproject:master**.\n"
] | 2022-02-04T16:38:42 | 2022-02-04T18:13:56 | 2022-02-04T18:12:23Z | MEMBER | {
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"\n[](https://coveralls.io/builds/46241437)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **c58ed7f6766fb19fd5e1cdb8cc3feba31dc71df6 on janosh:docs-no-more-py37** into **df6515c1a55835aaee3c530c182e78cd651530a2 on materialsproject:master**.\n"
] | 2022-02-04T17:15:35 | 2022-02-04T17:36:28 | 2022-02-04T17:17:03Z | MEMBER | {
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"\n[](https://coveralls.io/builds/46255716)\n\nCoverage decreased (-0.6%) to 83.438% when pulling **07fa7114872fcdb0e46907bfe7cc267a57e223c3 on janosh:no-more-star-imports** into **0edacc7ee9c640202b12782315facb0967d12822 on materialsproject:master**.\n"... | 2022-02-04T20:55:48 | 2024-09-09T11:12:52 | 2022-02-05T16:45:05Z | MEMBER | {
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} | `flake8` complains about star imports (for good reason imo, they make code harder to understand and debug).
One step closer to enabling `flake8` in CI.
I noticed one odd thing,
```
pymatgen/io/abinit/netcdf.py
pymatgen/io/abinit/pseudos.py
```
both define `class AbinitHeader(dict)`. The 2nd starred impo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2418 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2418/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2418/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2418/events | https://github.com/materialsproject/pymatgen/issues/2418 | 1,125,182,249 | I_kwDOACgets5DEOsp | 2,418 | Parsing `vasprun.xml` with `RANDOM_SEED` tag | {
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} | **Describe the bug**
I consider this issue more of a `VASP` bug rather than `pyamtgen` bug. However, I think it would be good to have a mechanism in place within the `Vasprun` class to mitigate this issue and warn user too.
If user wants to use `RANDOM_SEED` tag in `VASP` and chooses numbers greater than `999999`, ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2419 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2419/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2419/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2419/events | https://github.com/materialsproject/pymatgen/issues/2419 | 1,125,320,688 | I_kwDOACgets5DEwfw | 2,419 | SpacegroupAnalyzer.get_crystal_system() does not raise on negative space group, returns 'monoclinic' | {
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} | Current implementation of `SpacegroupAnalyzer.get_crystal_system()` is meant to raise on invalid space groups but doesn't:
https://github.com/materialsproject/pymatgen/blob/03112486486c8203991b14dafeb3314a3f3c1ba7/pymatgen/symmetry/analyzer.py#L142-L167
Example
```py
from pymatgen.core import Lattice, Structu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2420 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2420/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2420/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2420/events | https://github.com/materialsproject/pymatgen/pull/2420 | 1,125,321,064 | PR_kwDOACgets4yIwxK | 2,420 | Ensure SpacegroupAnalyzer.get_crystal_system() raises ValueError on neg space groups | {
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"\n[](https://coveralls.io/builds/46269991)\n\nCoverage decreased (-0.6%) to 83.45% when pulling **8ede104926f5cfa46f5772de1332d65577975325 on janosh:fix-get-crys-sys** into **03112486486c8203991b14dafeb3314a3f3c1ba7 on materialsproject:master**.\n"
] | 2022-02-06T21:21:09 | 2022-02-07T06:49:38 | 2022-02-07T03:41:06Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2421 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2421/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2421/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2421/events | https://github.com/materialsproject/pymatgen/issues/2421 | 1,125,825,327 | I_kwDOACgets5DGrsv | 2,421 | Variables in `.pmgrc.yaml` file are no longer acessible since new update to pymatgen==2022.2.1 | {
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"I just want to add that I have the same problem as @naik-aakash. The .pmgrc.yaml gets overwritten while connecting to the Materials Project database. ",
"I had the same problem 2 weeks ago but I thought it was already fixed... @shyuep [said so](https://github.com/materialsproject/pymatgen/issues/2377#issuecommen... | 2022-02-07T10:56:26 | 2022-02-14T23:28:43 | 2022-02-07T15:07:32Z | CONTRIBUTOR | {
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} | **The bug**
Since the latest update the variables defined in `.pmgrc.yaml` file are no longer acessible after first usage of MPRester.
Consider the vairables defined for eg in the `~/.pmgrc.yaml` file are as follows :
```
PMG_DEFAULT_FUNCTIONAL: PBE_54
PMG_VASP_PSP_DIR: /pathtopotcars/POTCAR
PMG_MAPI_KEY: you... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2422 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2422/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2422/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2422/events | https://github.com/materialsproject/pymatgen/issues/2422 | 1,126,111,545 | I_kwDOACgets5DHxk5 | 2,422 | Installation of pymatgen.core | {
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"The verison info is not longer in the root level. you should use `print(pymatgen.core.__version__)`. In any case, it is generally better to find out the version info using pkgutil.",
"how to import pymatgen.core?\n\nOn Mon, Feb 7, 2022 at 8:38 PM Shyue Ping Ong ***@***.***>\nwrote:\n\n> The verison info is not l... | 2022-02-07T15:03:30 | 2022-02-09T16:15:46 | 2022-02-07T15:08:49Z | NONE | {
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} | i have successfully installed pymatgen by import pymatgen but when want to print(pymatgen.__version__) getting error module 'pymatgen' has no attribute '__version___'. Not able to import pymatgen.core. pls help | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2423 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2423/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2423/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2423/events | https://github.com/materialsproject/pymatgen/pull/2423 | 1,126,148,977 | PR_kwDOACgets4yLeEV | 2,423 | Add --backup flag to pmg config | {
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"\n[](https://coveralls.io/builds/46305647)\n\nCoverage decreased (-0.6%) to 83.449% when pulling **045954cebceb2464f734a76624b0423b5e034e96 on janosh:pmg-config-backup-flag** into **c1335efbe8fe68f20427a5131dad4a0dc41e59ea on materialsproject:master**.\... | 2022-02-07T15:31:59 | 2022-02-07T20:11:34 | 2022-02-07T19:54:59Z | MEMBER | {
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} | Mostly to allow _not_ creating a backup file when modifying `.pmgrc.yaml`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2424 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2424/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2424/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2424/events | https://github.com/materialsproject/pymatgen/pull/2424 | 1,126,382,237 | PR_kwDOACgets4yMOgK | 2,424 | [pre-commit.ci] pre-commit autoupdate | {
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"\n[](https://coveralls.io/builds/46304522)\n\nCoverage decreased (-0.001%) to 84.086% when pulling **cb8b05f484040dfea3d61d416272aac8e74007ef on pre-commit-ci-update-config** into **c1335efbe8fe68f20427a5131dad4a0dc41e59ea on master**.\n"
] | 2022-02-07T19:06:43 | 2022-02-09T16:46:47 | 2022-02-09T16:46:47Z | CONTRIBUTOR | {
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updates:
- [github.com/pre-commit/mirrors-mypy: v0.930 → v0.931](https://github.com/pre-commit/mirrors-mypy/compare/v0.930...v0.931)
<!--pre-commit.ci end--> | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2425 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2425/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2425/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2425/events | https://github.com/materialsproject/pymatgen/issues/2425 | 1,126,671,808 | I_kwDOACgets5DJ6XA | 2,425 | install without internet connection | {
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"There are a lot of dependency packages. Sorry, but we do expect an internet connection when installing packages.",
"export CC=gcc before installing fixed the issue.\r\n\r\nThe issue I'm having now is that I don't have a pmgrc.yaml file; how to I get/create the file or specifically get a PMG_MAPI_KEY?",
"got it... | 2022-02-08T01:04:11 | 2022-02-08T15:27:27 | 2022-02-08T14:40:47Z | NONE | {
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} | Hi,
I'm having issues installing/running on a computer without internet connection so I can't just pip install. I believe I have installed all required dependencies. I can build and install "python setup.py build" and "python setup.py install"; I can even do "pip install pymatgen" (all: Requirement already satisfied... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2426 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2426/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2426/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2426/events | https://github.com/materialsproject/pymatgen/issues/2426 | 1,129,515,377 | I_kwDOACgets5DUwlx | 2,426 | sdist doesn't include `.c` files | {
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"Nevermind, was missing cython :)"
] | 2022-02-10T06:25:04 | 2022-02-10T06:26:48 | 2022-02-10T06:26:48Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
Trying to build from sdist
**To Reproduce**
```
pip install --no-binary --user https://files.pythonhosted.org/packages/00/eb/fc120e9c0d006788015cff8a6e8650bce18e23c5f24811f7a71f1ffab01b/pymatgen-2022.2.7.tar.gz
```
**Expected behavior**
Builds with C toolchain and other dependencies.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2427 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2427/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2427/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2427/events | https://github.com/materialsproject/pymatgen/pull/2427 | 1,129,519,383 | PR_kwDOACgets4yWiVh | 2,427 | Move cython to setup_requires | {
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"Thanks.",
"\n[](https://coveralls.io/builds/46419483)\n\nCoverage decreased (-0.6%) to 83.449% when pulling **542067ecbd0a5a61416d9942d173da77fd980af5 on jonringer:patch-1** into **a160fca5669e95ddb700b1fef0323b58b96532ce on materialsproject:master**.... | 2022-02-10T06:30:18 | 2022-02-10T17:09:01 | 2022-02-10T15:06:11Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Move cython to `setup_requires`. Allows for availability to be checked before attempting to build native extensions. Avoiding #2426
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2428 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2428/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2428/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2428/events | https://github.com/materialsproject/pymatgen/issues/2428 | 1,130,484,448 | I_kwDOACgets5DYdLg | 2,428 | Ih point group symmetry operations | {
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"The list of point group symmetry operations in pymatgen are mainly dealing with the crystallographic point groups (Ih is not crystallographic since it has 5-fold rotations). So you will need to look for them in texts. That said, it is relatively easy to generate the whole list if you define the main 5-fold, 3-fold... | 2022-02-10T17:08:05 | 2022-02-10T17:14:04 | 2022-02-10T17:14:04Z | NONE | {
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I was trying to find out the symmetry operations of the point of Ih. But I did not find a symbol corresponding to it to generate a PointGroup object.
I would really appreciate the symbol to generate the symmetry operations of Ih point group.
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2429 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2429/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2429/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2429/events | https://github.com/materialsproject/pymatgen/pull/2429 | 1,132,712,109 | PR_kwDOACgets4yh2x_ | 2,429 | Partial periodic boundary conditions | {
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"\n[](https://coveralls.io/builds/49489353)\n\nCoverage decreased (-0.7%) to 83.291% when pulling **9dfe1665eef558d5b8511c1055a682ebdc5b1e99 on gpetretto:ppbc** into **6bbe18e33348ba0175c423ac8f9533d02b7fbc75 on materialsproject:master**.\n",
"Thanks f... | 2022-02-11T14:56:56 | 2022-05-26T18:06:21 | 2022-05-26T18:06:14Z | CONTRIBUTOR | {
"total": 0,
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} | ### Summary
As a follow up to #2364 I am opening this PR to discuss about the introduction of partial periodic boundary conditions (PPBC).
### Details
This first draft is based on these main points:
* PPBC are introduced at the level of `Lattice` with a tuple of three bool in the `pbc` attribute, defining the p... | {
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"\n[](https://coveralls.io/builds/46570777)\n\nCoverage remained the same at 83.481% when pulling **14df0164b47f30a047cd362febc18abb01f0277f on janosh:unpin-dev-reqs** into **6ec393bdfa5bdbc3548bc47b89b9c9fb159793b5 on materialsproject:master**.\n"
] | 2022-02-12T15:27:14 | 2022-02-15T17:40:48 | 2022-02-15T17:18:17Z | MEMBER | {
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} | Also unpins dev requirements. I noticed they are kept very close to the latest versions anyway which `pip` auto-installs by default so this simply removes the need to update the version numbers manually. | {
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} | **Describe the bug**
Accessing `atomic_numbers` on a disordered structure throws `AttributeError: specie`.
<details>
<summary>full error trace</summary>
```py
AttributeError Traceback (most recent call last)
~/.venv/py310/lib/python3.10/site-packages/pymatgen/core/structure.py i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2432 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2432/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2432/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2432/events | https://github.com/materialsproject/pymatgen/pull/2432 | 1,137,820,572 | PR_kwDOACgets4y0Cpa | 2,432 | Fix and add some type annotations | {
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"\n[](https://coveralls.io/builds/46555065)\n\nCoverage decreased (-0.6%) to 83.443% when pulling **7a53d56ccbd6086050b7e6f421ae0bbceebfd9d6 on janosh:fix-type-annos** into **555a788348d5aa8e1d5fdfa20cffa859ec1e475e on materialsproject:master**.\n"
] | 2022-02-14T20:43:07 | 2022-02-15T17:26:57 | 2022-02-15T17:17:31Z | MEMBER | {
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} | [Docs](https://docs.python.org/3/library/typing.html#typing.Tuple):
> To specify a variable-length tuple of homogeneous type, use literal ellipsis, e.g. [Tuple](https://docs.python.org/3/library/typing.html#typing.Tuple)[int, ...]. A plain Tuple is equivalent to Tuple[Any, ...], and in turn to [tuple](https://docs.p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2433 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2433/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2433/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2433/events | https://github.com/materialsproject/pymatgen/pull/2433 | 1,138,517,076 | PR_kwDOACgets4y2XhV | 2,433 | Fix Structure.apply_operation() return val | {
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"\n[](https://coveralls.io/builds/46555597)\n\nCoverage decreased (-0.6%) to 83.439% when pulling **c44f0d5c547817103fda935e9e400bce285a0f75 on janosh:fix-struct-apply_operation** into **555a788348d5aa8e1d5fdfa20cffa859ec1e475e on materialsproject:master... | 2022-02-15T10:52:58 | 2022-02-15T17:25:36 | 2022-02-15T17:17:09Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2434 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2434/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2434/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2434/events | https://github.com/materialsproject/pymatgen/pull/2434 | 1,138,944,845 | PR_kwDOACgets4y3xkm | 2,434 | Small changes to Lobster classes | {
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"\n[](https://coveralls.io/builds/46582749)\n\nCoverage decreased (-0.6%) to 83.482% when pulling **f2caba9f57f9a4c17c7379aefacfb792dcb1a2a8 on JaGeo:master** into **df44a54129f468e2a506cb3ed674a75b70d344b3 on materialsproject:master**.\n"
] | 2022-02-15T16:47:11 | 2022-02-16T00:14:20 | 2022-02-15T23:43:17Z | MEMBER | {
"total": 0,
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} | ## Summary
I have changed the energy range for the standard Lobster computation. This is partially related to a VASP 6.0 problem with Fermi levels at the bottom of the band gap.
Furthermore, I have enabled the use of Loewdin charges to determine cation and anions and respective coordination environments based on t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2435 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2435/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2435/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2435/events | https://github.com/materialsproject/pymatgen/pull/2435 | 1,139,854,347 | PR_kwDOACgets4y6u8_ | 2,435 | Remove unused mypy ignores | {
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"\n[](https://coveralls.io/builds/48165920)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **db6268f413cffca8cf79ec1f159afb4c9253efbe on janosh:no-unused-mypy-ignore** into **1a2bf238bf87123b09ab8a207f50a9f4eeb13d68 on materialsproject:master**.\n... | 2022-02-16T10:54:48 | 2022-04-11T20:58:18 | 2022-04-11T20:58:06Z | MEMBER | {
"total": 0,
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} | Might want to add
```cfg
[mypy]
warn_redundant_casts = true
warn_unused_ignores = true
check_untyped_defs = true
```
to `setup.cfg` in future though currently emits too many type errors to deal with. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2436 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2436/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2436/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2436/events | https://github.com/materialsproject/pymatgen/pull/2436 | 1,140,934,975 | PR_kwDOACgets4y-DR_ | 2,436 | [WIP] Add comments and type hints | {
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"\n[](https://coveralls.io/builds/46629515)\n\nCoverage decreased (-0.6%) to 83.481% when pulling **39f203529819f151827c9c147c331af9a5cd7209 on penicillin0:add-type-vasp-input** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**... | 2022-02-17T06:38:41 | 2022-06-14T00:07:38 | 2022-06-14T00:07:38Z | CONTRIBUTOR | {
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} | ## Summary
The function for vasp's io is used often, so I made the type more explicit.
This is also for the safety and uniformity of the types.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2437 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2437/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2437/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2437/events | https://github.com/materialsproject/pymatgen/issues/2437 | 1,143,819,585 | I_kwDOACgets5ELU1B | 2,437 | Structure doesn't recognize Yaml files it writes | {
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"total": 0,
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} | ```py
from pymatgen.core import Structure
from pymatgen.ext.matproj import MPRester
mp_id = "mp-2201"
struct = MPRester().get_structure_by_material_id(mp_id)
struct.to(filename=f"{mp_id}.yml")
Structure.from_file(filename=f"{mp_id}.yml")
>>> ValueError: Unrecognized file extension!
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2438 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2438/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2438/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2438/events | https://github.com/materialsproject/pymatgen/pull/2438 | 1,143,825,167 | PR_kwDOACgets4zIBDu | 2,438 | Fix `Structure.from_file()` for `.yml` extension | {
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"\n[](https://coveralls.io/builds/46704312)\n\nCoverage decreased (-0.6%) to 83.483% when pulling **8427738c341d2230647c83e7b3924920f1a1faeb on janosh:fix-structure-from-yml** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\... | 2022-02-18T21:54:44 | 2022-02-24T14:49:01 | 2022-02-24T14:47:49Z | MEMBER | {
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} | Also adds a test for this.
Closes #2437. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2439 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2439/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2439/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2439/events | https://github.com/materialsproject/pymatgen/pull/2439 | 1,145,268,231 | PR_kwDOACgets4zM4qb | 2,439 | added wswq parser | {
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"\n[](https://coveralls.io/builds/46720329)\n\nCoverage decreased (-0.6%) to 83.486% when pulling **a3f8f941ab48daaee588de4929573da75ca4c9ce on jmmshn:parse_WSWQ** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thank... | 2022-02-21T03:15:21 | 2022-02-23T16:16:27 | 2022-02-22T23:31:42Z | CONTRIBUTOR | {
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} | # WSWQ Parsing
VASP has a "secret" file WSWQ representing the matrix elements of <W | S | W(Q)>
Where W is the plane-wave wavefunction of the present calculation and W(Q) is the wavefunction of some perturbed calculation.
These matrix elements can be used to calculate the finite-difference of the wavefunction ov... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2440 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2440/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2440/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2440/events | https://github.com/materialsproject/pymatgen/pull/2440 | 1,146,138,813 | PR_kwDOACgets4zPwES | 2,440 | Add pydocstyle pre-commit hook | {
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"\n[](https://coveralls.io/builds/46744919)\n\nCoverage decreased (-0.6%) to 83.48% when pulling **326af0eb1a1926a398a1f7379c535ce301fa5099 on janosh:pydocstyle** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks... | 2022-02-21T19:04:39 | 2022-02-24T18:20:10 | 2022-02-24T17:05:03Z | MEMBER | {
"total": 0,
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} | Brings pre-commit.ci more in line with GHA `lint.yml` so people can be more confident CI won't complain once checks pass locally.
Adds a few type hints along the way. | {
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"\n[](https://coveralls.io/builds/46746727)\n\nCoverage decreased (-0.6%) to 83.482% when pulling **a78eb0ce018fd5a10c7bbac7c050c8361e551f41 on janosh:citation** into **394e0d71bf1d1025fcf75498cbb16aa3f41ce78c on materialsproject:master**.\n",
"Thanks.... | 2022-02-21T19:42:40 | 2022-02-22T11:06:51 | 2022-02-22T00:18:18Z | MEMBER | {
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} | GitHub supports adding citation metadata to repos. This PR moves instructions on how to cite `pymatgen` from readme into the `CITATION.cff` file which GH uses to then display citations in BibTeX and APA formats in the side bar. See [docs for details](https://docs.github.com/en/repositories/managing-your-repositorys-se... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2442 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2442/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2442/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2442/events | https://github.com/materialsproject/pymatgen/issues/2442 | 1,146,175,007 | I_kwDOACgets5EUT4f | 2,442 | Missing ``kpath`` property in ``HighSymmKPath`` breaks VASP Kpoints | {
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} | **Describe the bug**
The ``kpath`` property was removed from the ``pymatgen.symmetry.bandstructure.HighSymmKPath``. This now breaks the VASP Kpoints object ``pymatgen.io.vasp.inputs.Kpoints`` if one tries to instantiate a Kpoints instance using the ``automatic_linemode()`` method as it makes use of the ``kpath`` pro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2444 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2444/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2444/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2444/events | https://github.com/materialsproject/pymatgen/issues/2444 | 1,148,441,020 | I_kwDOACgets5Ec9G8 | 2,444 | pmgrc.yaml not created when installing pymatgen (Python 3.8, pymatgen 2022.2.10) | {
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"This is a warning, not an error. The pmgrc file stores certain settings that is needed if you are generating VASP input files, using the materials project, etc. This warning can be ignored if you are not planning on using those.",
"This warning was also updated in https://github.com/materialsproject/pymatgen/com... | 2022-02-23T18:31:13 | 2022-02-23T22:20:25 | 2022-02-23T18:50:23Z | NONE | {
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After installing pymatgen using 'pip pre-commit pymatgen' from my environment in bash and trying to import a function (OCPCalculator from the ocp module) I receive the following message from the terminal.
**warnings.warn(f"Error loading .pmgrc.yaml: {ex}. You may need to reconfigure your yaml file.")**
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2445 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2445/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2445/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2445/events | https://github.com/materialsproject/pymatgen/issues/2445 | 1,148,728,053 | I_kwDOACgets5EeDL1 | 2,445 | `ChemicalPotentialDiagram` fails on interior point selection for some systems | {
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"Just for posterity, here is a copy of the kind of error that is produced in Qhull when selecting an incorrect interior point (Zr-O-N system as before, with `default_min_limit=-20`)\r\n\r\n```\r\nscipy.spatial._qhull.QhullError: QH6023 qhull input error: feasible point is not clearly inside halfspace\r\nfeasible po... | 2022-02-24T00:38:54 | 2022-02-25T18:58:45 | 2022-02-25T18:58:45Z | MEMBER | {
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} | **Describe the bug**
The `ChemicalPotentialDiagram` class currently fails upon initialization for some systems using MP data (e.g., Zr-O-N) due to improper selection of an interior point to be passed to Qhull.
The current logic implemented in pymatgen is to use the mean of the elemental limits/bounds as the interio... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2446 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2446/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2446/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2446/events | https://github.com/materialsproject/pymatgen/issues/2446 | 1,148,758,220 | I_kwDOACgets5EeKjM | 2,446 | `ChemicalPotentialDiagram.get_plot()` needs better default limits for cleaner plotting | {
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"Thanks for taking care of this @mattmcdermott, it was actually an issue in our website issue tracker :)\r\n\r\nPart of the issue also seems to be font size related too, I wonder if we can pull the axes labels further from the plot so they don't overlap.",
"@mkhorton For sure, gonna try to address that as well in... | 2022-02-24T01:28:11 | 2022-02-25T18:58:21 | 2022-02-25T18:58:20Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
Chemical potential diagrams tend to look pretty gross with the current defaults, especially for MP data. See screenshot from the new MP website below:
![Screen Shot 2022-02-23 at 5 23 42 PM](https://user-images.githubusercontent.com/40469694/1554392... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2447 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2447/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2447/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2447/events | https://github.com/materialsproject/pymatgen/pull/2447 | 1,148,764,673 | PR_kwDOACgets4zYOi5 | 2,447 | Fix bug in `ChemicalPotentialDiagram` initialization (interior point), improve default plots | {
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"\n[](https://coveralls.io/builds/46873292)\n\nCoverage decreased (-0.7%) to 83.374% when pulling **961f2cd298e3b3575d7998f794ca6c72515e1b7e on mattmcdermott:cpd_fix** into **03e8b9981535acace1fc84406c8c027626ebbad4 on materialsproject:master**.\n",
"@... | 2022-02-24T01:40:52 | 2022-02-25T18:56:41 | 2022-02-25T18:56:11Z | MEMBER | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Bug fix: changed method of determining interior point for Qhull algorithm to improve stability (see Issue #2445)
* Bug fix: better default plotting by re-assignment of minimum limit when `get_plot()` is called (see Issue #2446)
## Additional de... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2448 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2448/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2448/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2448/events | https://github.com/materialsproject/pymatgen/pull/2448 | 1,149,500,139 | PR_kwDOACgets4zapgH | 2,448 | Allow to switch off print of ChemEnv citation | {
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"I would say - why print citations at all? I don't think any other part of the code prints citations. E.g., pymatgen doesn't print a citation everytime something is done. I would suggest turning it off by default. I think the citation is prominently displayed in all the documentation.",
"I would be fine with this... | 2022-02-24T16:33:20 | 2022-02-24T17:04:44 | 2022-02-24T17:04:44Z | MEMBER | {
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} | ## Summary
I am adding a small parameter to switch off the ChemEnv citation print. This will make it easier to use ChemEnv in other program packages. I am also updating the citation of ChemEnv.
I am tagging @davidwaroquiers here, so that he knows.
Let me know if I should do anything additionally. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2449 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2449/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2449/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2449/events | https://github.com/materialsproject/pymatgen/pull/2449 | 1,157,034,909 | PR_kwDOACgets4z0g1k | 2,449 | Bump `actions/checkout` in GitHub CI to v3 | {
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"\n[](https://coveralls.io/builds/47007120)\n\nCoverage decreased (-0.8%) to 83.369% when pulling **b7542b69cef567c539e1742d3ad44eea958b2bf5 on janosh:actions-checkout-v3** into **3d40b31b076aa10d49dbba59a712348c40ee98d3 on materialsproject:master**.\n"
... | 2022-03-02T11:03:03 | 2022-03-02T14:45:09 | 2022-03-02T14:43:00Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2450 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2450/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2450/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2450/events | https://github.com/materialsproject/pymatgen/pull/2450 | 1,157,834,002 | PR_kwDOACgets4z3KqF | 2,450 | Add monty `cached_class` to other compatibility schemes | {
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"Thanks @munrojm!\r\n\r\nFor the record, in private communication @munrojm noted that the decoding changes from ~7s to ~0.3s in our benchmark case of a set of entries in the `Fe-O` system, so a huge improvement.",
"\n[](https://coveralls.io/builds/4703... | 2022-03-03T00:28:45 | 2024-07-01T12:53:36 | 2022-03-03T00:41:24Z | MEMBER | {
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} | ## Summary
This PR adds the `@cached_class` decorator from monty to the `MaterialsProject2020Compatibility` and `MaterialsProjectAqueousCompatibility` classes. This fixes slow decoding of large lists of entry object which greatly impacts the new `MPRester` client.
## Additional dependencies introduced (if any)
... | {
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"\n[](https://coveralls.io/builds/47100065)\n\nCoverage decreased (-0.8%) to 83.37% when pulling **7dcb5287dc50a75a7792d8c197159912b1233209 on janosh:type-hints** into **3376f27a9c5a4cac1590169f2212361ab6c94388 on materialsproject:master**.\n",
"@janos... | 2022-03-05T09:25:23 | 2022-03-10T00:00:34 | 2022-03-10T00:00:31Z | MEMBER | {
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} | Add some more type hints in `electronic_structure/plotter.py`, `bandstructure.py`, `io/vasp/outputs.py`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2452 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2452/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2452/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2452/events | https://github.com/materialsproject/pymatgen/pull/2452 | 1,160,326,557 | PR_kwDOACgets4z_VxQ | 2,452 | Future annotations | {
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"\n[](https://coveralls.io/builds/47217777)\n\nCoverage decreased (-0.9%) to 83.24% when pulling **4d44b489c98a3c5ff36c4b73a987c217bf907c36 on janosh:future-annotations** into **eaa2b6287520f6e59730d9a0697e2d8f841f8bfb on materialsproject:master**.\n",
... | 2022-03-05T11:53:26 | 2022-03-11T06:42:32 | 2022-03-11T03:00:02Z | MEMBER | {
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} | Convert annotations to future syntax available through import in Python 3.7 upwards. [See PEP 563](https://www.python.org/dev/peps/pep-0563/#id6). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2453 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2453/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2453/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2453/events | https://github.com/materialsproject/pymatgen/issues/2453 | 1,160,536,246 | I_kwDOACgets5FLGC2 | 2,453 | Feature Suggestion: DOS-related descriptors (e.g. d-band center, upper d-band edge) | {
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} | Given that we already have tools to parse DOS data in Pymatgen, it would be great to add some DOS-related descriptors. Some ideas include:
- d-band center
- Plotting the Hilbert transform of the local, projected DOS
- Upper d-band edge (i.e. highest peak position of the Hilbert transform of the projected DOS)
Oth... | {
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"Hi @cedenoruel, I have not had chance to investigate this yet, but is it the case that this still happens even if you do not add oxidation states and skip that `add_oxidation_state_by_element` line? I'm wondering if the bond logic is oxidation-state dependent or not. e.g. is `(\"P\", \"O\"): 3` different to `(\"P5... | 2022-03-06T21:15:48 | 2022-03-08T12:57:16 | 2022-03-08T12:57:16Z | NONE | {
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} | Hi pymatgen developers.
I am generating slab structures for an inorganic crystal containing a phosphate ion (KH2PO4).
I would like to have no broken P--O bonds so I used the `bonds={("P", "O"): 3}`
```
from pymatgen.core.structure import Structure
KDP = Structure.from_file("input.cif")
KDP.add_oxidation_s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2455 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2455/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2455/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2455/events | https://github.com/materialsproject/pymatgen/pull/2455 | 1,160,784,241 | PR_kwDOACgets40ArtG | 2,455 | s-, p-, d-band properties: band filling, band center, band width, skewness, kurtosis, upper band edge | {
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"\n[](https://coveralls.io/builds/47217139)\n\nCoverage decreased (-0.7%) to 83.376% when pulling **b227fef96d359f4ffe5d2f2b5043703ed1125d19 on arosen93:rosen-dband** into **adafd2207e6c111560e3a98fc1353aa049c88076 on materialsproject:master**.\n",
"@m... | 2022-03-07T01:14:26 | 2022-03-10T10:01:31 | 2022-03-09T20:00:58Z | MEMBER | {
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} | ## Summary
This PR seeks to add additional features to `pymatgen.electronic_structure.dos` for various orbital-projected DOS properties used in catalysis, including:
- The orbital-projected band center, as defined by [Hammer and Norskov, _Surf. Sci._, 1995](https://www.sciencedirect.com/science/article/pii/0039602896... | {
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"Please visit matsci.org for questions of usage. Github Issues should be used for reporting Issues and Bugs only."
] | 2022-03-08T11:01:07 | 2022-03-08T12:57:05 | 2022-03-08T12:57:04Z | NONE | {
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I want to add H atoms to the systems randomly, and maintain the distance between H and O , the steps are shown in the figure,
and which function can help me to realize this proc... | {
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} | **Describe the bug**
I noticed that some of the lattice matches I was getting with MPInterfaces' matching algorithm were missing in pymatgen's implementation with the same matching parameters. After a closer look, I narrowed the issue down to the transformation indices generated in `ZSLGenerator.generate_sl_transforma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2458 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2458/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2458/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2458/events | https://github.com/materialsproject/pymatgen/pull/2458 | 1,165,462,516 | PR_kwDOACgets40QBbj | 2,458 | Alchemy type hints | {
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"`actions/checkout@v3` (now with default `fetch-depth: 1`) run time went from 38s to 21s.",
"\n[](https://coveralls.io/builds/47249066)\n\nCoverage decreased (-0.8%) to 83.38% when pulling **696ecd20d24cf4753f747fcf624be5a1914cee69 on janosh:alchemy-ty... | 2022-03-10T16:39:53 | 2022-03-11T06:36:13 | 2022-03-11T03:00:31Z | MEMBER | {
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} | 945d8daabe type annotations for pymatgen/alchemy/materials.py
3c3e9417fb type annotations for pymatgen/transformations/transformation_abc.py
696ecd20d2 remove `fetch-depth: 0` from lint actions/checkout
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2459 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2459/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2459/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2459/events | https://github.com/materialsproject/pymatgen/issues/2459 | 1,165,820,609 | I_kwDOACgets5FfQLB | 2,459 | bug report on macOS with python3.7 | {
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"Pls delete your .pmgrc file and try again.",
"it works like a charm. Thanks. Dr. Ong. \r\nIt bothered me for 2 weeks..."
] | 2022-03-10T23:10:21 | 2022-03-11T00:02:53 | 2022-03-10T23:11:21Z | NONE | {
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} | **Describe the bug**
I have an issue to. import the Composition module when installing latest pymatgen on a macOS using conda with python3.7
it takes long time to import and finally failed and get this error :
Successfully installed future-0.18.2 plotly-5.6.0 pymatgen-2022.0.17 ruamel.yaml-0.17.21 tenacity-8.0.1 u... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2460 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2460/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2460/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2460/events | https://github.com/materialsproject/pymatgen/issues/2460 | 1,169,906,881 | I_kwDOACgets5Fu1zB | 2,460 | Add option to disable the progress bar for MPRester query | {
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"I just pushed an option called `show_progress_bar` to allow you to disable it.",
"@shyuep: excellent, thank you. Btw, there's an even easier way to do it: I think you can just change `tqdm(...)` to `tqdm(..., disable=not show_progress_bar)`. Up to you, what you've done should fix the issue.",
"Hmmm thanks. I w... | 2022-03-15T16:28:06 | 2022-03-19T00:32:56 | 2022-03-15T16:56:29Z | CONTRIBUTOR | {
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There seems to be no way to disable the progress bar for these queries. This breaks the progress bar/output stream depending on Jupyter and other things. It's a simple improvement and should ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2461 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2461/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2461/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2461/events | https://github.com/materialsproject/pymatgen/issues/2461 | 1,170,313,234 | I_kwDOACgets5FwZAS | 2,461 | Broken `MagneticSpaceGroupTest.test_symmetry_ops()`? | {
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"Hi @janosh, I wrote that test, not intentional, I imagine it was an omission. Thanks for flagging it."
] | 2022-03-15T22:07:04 | 2022-03-22T17:11:03 | 2022-03-22T17:11:03Z | MEMBER | {
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} | `msg_1` isn't being tested unlike `msg_(2|3|4)`. Is this intentional?
https://github.com/materialsproject/pymatgen/blob/a740053063c8d0864f23d697a45bcafef3aaadf4/pymatgen/symmetry/tests/test_maggroups.py#L78-L85 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2462 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2462/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2462/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2462/events | https://github.com/materialsproject/pymatgen/pull/2462 | 1,172,976,417 | PR_kwDOACgets40oInA | 2,462 | Allow for passing of Structure/Molecule kwargs in ASEAtomsAdaptor and add new charge_spin_check kwarg to Molecule/IMolecule | {
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"\n[](https://coveralls.io/builds/47479449)\n\nCoverage decreased (-0.7%) to 83.387% when pulling **285c41b582fb63c60af80153f2762d21b553a85f on arosen93:rosen-aseio** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n"
] | 2022-03-17T22:16:39 | 2022-03-24T23:00:52 | 2022-03-22T18:43:51Z | MEMBER | {
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} | ## Summary
This PR serves three purposes:
1. When using the `ASEAtomsAdaptor.get_structure()` or `.get_molecule()` commands, optional kwargs to the `Structure()` and `Molecule()` classes can now be passed, such as the `validate_proximity` kwarg.
3. When instantiating a `Molecule()` or `IMolecule()` object, a new o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2463 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2463/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2463/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2463/events | https://github.com/materialsproject/pymatgen/pull/2463 | 1,174,101,471 | PR_kwDOACgets40rob2 | 2,463 | Fix ValueError when cations, anions are not detected (LobsterEnv) | {
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"\n[](https://coveralls.io/builds/47509279)\n\nCoverage decreased (-0.7%) to 83.387% when pulling **806629043b85562b592b4a9e3ea5f7abceae8431 on JaGeo:master** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n",
"Thanks.",
... | 2022-03-18T23:14:04 | 2022-03-22T15:44:33 | 2022-03-22T15:42:40Z | MEMBER | {
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} | ## Summary
This fixes a problem in the tool to determine coordination environments based on a Lobster analysis. In case, there are no cations, anions in the compound, a more useful error message is raised. In such a case, cation-anion bonds cannot be used to determine coordination environments. I have also added tes... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2464 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2464/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2464/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2464/events | https://github.com/materialsproject/pymatgen/issues/2464 | 1,174,116,467 | I_kwDOACgets5F-5hz | 2,464 | [Not an issue actually] Counterintuitive behavior with assign_site_properties in AdsorbateSiteFinder | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2465 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2465/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2465/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2465/events | https://github.com/materialsproject/pymatgen/issues/2465 | 1,174,209,911 | I_kwDOACgets5F_QV3 | 2,465 | PDplotter plotly backend ternary diagram default colors are terrible | {
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"Hi @Youjin1985, please try the matplotlib backend. The 3D ternary plot is intended primarily for _interactive_ use, where the plot can be rotated to allow it to be read more easily, rather than for publication figures.\r\n\r\nI am working personally on a 2D version of this plot with the plotly backend, but not sur... | 2022-03-19T08:29:52 | 2023-06-03T00:55:14 | 2023-06-03T00:55:14Z | NONE | {
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Black font on black markers, completely invisible!
It's nowhere near publication quality plot, please change default look or allow customisation by arguments of PDPlotter. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2466 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2466/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2466/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2466/events | https://github.com/materialsproject/pymatgen/pull/2466 | 1,174,509,210 | PR_kwDOACgets40swk3 | 2,466 | Types for `pymatgen/symmetry/groups.py` | {
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"Just for the record, seems a bit odd that `class SymmetryGroup` implements `__getitem__`. `__iter__` to loop through all sym-ops would make more sense to me but that's absent. What's the meaning of an index into a group of symmetry operations that are implemented as a `set()`, i.e. have no inherent order anyway?",... | 2022-03-20T11:05:23 | 2022-03-22T17:56:50 | 2022-03-22T17:11:03Z | MEMBER | {
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} | 2a0ed0e2df add type hints to `pymatgen/symmetry/groups.py`
3b7b6ab3ae `yesqa **/*.py`
e876dc99b9 fix `MagneticSpaceGroupTest.test_symmetry_ops()` unused 1st test case (closes #2461)
91f7942549 improve doc strings for `fractional_composition` + `reduced_composition`
21d5183b57 delete dead code
872da47137 fix ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2467 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2467/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2467/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2467/events | https://github.com/materialsproject/pymatgen/pull/2467 | 1,176,181,216 | PR_kwDOACgets40yBEb | 2,467 | Allow for nearest neighbor algorithms other than VoronoiNN in get_surface_sites | {
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"Ah, I see this is using the weight VN polyhedra. This is a bit too much work for me to want to mess around with it. Abandoning for now."
] | 2022-03-22T02:22:20 | 2022-03-22T02:41:04 | 2022-03-22T02:41:04Z | MEMBER | {
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} | The `get_surface_sites()` function when dealing with surfaces is hard-coded to use `VoronoiNN`. However, this is no particular reason to do so, and in fact it would be nice to let the user choose their own preferred method (e.g. `CrystalNN`). This PR gives the user that option with a new kwarg called `local_env`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2468 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2468/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2468/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2468/events | https://github.com/materialsproject/pymatgen/pull/2468 | 1,176,646,717 | PR_kwDOACgets40zjZ7 | 2,468 | Import ABC from collections.abc for Python 3.10 compatibility | {
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"\n[](https://coveralls.io/builds/47575501)\n\nCoverage decreased (-0.7%) to 83.381% when pulling **46d1ee36c7237c25ee5bb757420366e342e3bf26 on tirkarthi:fix-collections** into **a740053063c8d0864f23d697a45bcafef3aaadf4 on materialsproject:master**.\n"
] | 2022-03-22T11:28:08 | 2022-03-22T11:57:32 | 2022-03-22T11:41:39Z | CONTRIBUTOR | {
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} | ## Summary
Import ABC from `collections` was deprecated and removed in Python 3.10. Use `collections.abc` .
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2469 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2469/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2469/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2469/events | https://github.com/materialsproject/pymatgen/pull/2469 | 1,177,157,432 | PR_kwDOACgets401RKh | 2,469 | Fix bad `ValueError` message in `SimpleVaspToComputedEntryDrone.assimilate()` | {
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"@shyuep Wait, I need to appease the linter first. 😆 ",
"Also, I'm always wary when changing strings f-strings about potential errors. So tests passing is important here.",
"I will fix it. Don't worry. I will issue a new release shortly."
] | 2022-03-22T18:37:52 | 2022-03-22T19:35:18 | 2022-03-22T18:42:49Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2470 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2470/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2470/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2470/events | https://github.com/materialsproject/pymatgen/issues/2470 | 1,178,121,783 | I_kwDOACgets5GOLY3 | 2,470 | Circular import when importing SpaceGroup | {
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"Glad to learn about `typing.TYPE_CHECKING` though, that was new to me! Seems useful",
"Damn it, that fix over in #2471 is not going well. 😄 \r\nI should prob stop doing other stuff and focus on it. And run tests locally instead of waiting for CI emails to come back."
] | 2022-03-23T13:25:55 | 2022-03-25T02:15:10 | 2022-03-25T02:15:10Z | CONTRIBUTOR | {
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} | **Describe the bug**
The most recent release (2022.3.22) introduced a circular import error the SpaceGroup class
**To Reproduce**
Running the line...
``` python
from pymatgen.symmetry.groups import SpaceGroup
```
...produces the following error...
``` python
Traceback (most recent call last):
File "<stdi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2471 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2471/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2471/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2471/events | https://github.com/materialsproject/pymatgen/pull/2471 | 1,178,134,508 | PR_kwDOACgets404gIT | 2,471 | Fix circular import in `pymatgen.symmetry.groups` | {
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"No worries! Thanks for the quick response and fix. 😄 ",
"It is odd that this was not caught in any of the tests earlier? All the tests passed.",
"@shyuep Yes, I'm trying to figure out why not.",
"@shyuep I had the same thought... but I'm able to successfully reproduce this error in a clean conda env using t... | 2022-03-23T13:36:40 | 2022-03-25T02:15:10 | 2022-03-25T02:15:10Z | MEMBER | {
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@jacksund Sorry about that. But thanks for the detailed error report! | {
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} | I have a POSCAR file of Na3Zr2Si2PO12 (mp-532695).
I'd like to substitute Zr2 -> HfZr at POSCAR file and get a minimum Ewald sum structure by using pymatgen.
So I tried to use Ewald minimizer, but I can't understand about the parameter of Ewald minimizer especially m_list.
Can I get a example of Ewald minimize... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2473 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2473/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2473/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2473/events | https://github.com/materialsproject/pymatgen/pull/2473 | 1,179,414,713 | PR_kwDOACgets408i3L | 2,473 | Dead code | {
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"\n[](https://coveralls.io/builds/47655395)\n\nCoverage decreased (-0.7%) to 83.389% when pulling **bb7b4c165f17f2b485e29e18c6220cb9350e77f8 on janosh:dead-code** into **ff4d66cc237734a7abec8cb8e14e8901626b36c2 on materialsproject:master**.\n"
] | 2022-03-24T11:57:06 | 2022-03-25T07:59:26 | 2022-03-25T02:14:57Z | MEMBER | {
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} | Restoring/deleting some dead code.
Test cases that pass were restored. Code that seemed outdated was deleted. | {
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"While I agree some stateless stuff can be non-objects (e.g., pymatgen.util are mostly methods based), I should outline the basic principles. OOP can be used as either a state tool or an organizational tool. MPRester actually does have states - the session, API key and the url. Similarly, SpacegroupAnalyzer wraps a... | 2022-03-27T16:15:57 | 2022-06-22T16:04:00 | 2022-06-22T15:43:25Z | MEMBER | {
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} | Let me preface by saying I understand `pymatgen` is a mature code base with a large user base (for a research code), hence any breaking changes to the interface will be a slow and painful process. So feel free to close this issue if it's an unwelcome discussion.
---
The point I would like to raise is that many pa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2475 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2475/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2475/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2475/events | https://github.com/materialsproject/pymatgen/pull/2475 | 1,183,898,209 | PR_kwDOACgets41Lgi1 | 2,475 | Cp2k 1.0 | {
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"Linting says that X | Y syntax requires python 3.10. This syntax was added in by Shyue, so I think that it should be alright. Please let me know if I should revert.",
"I think this problem can be solved by using `from __future__ import annotations`?",
"Oh you're right I didn't realize I'd removed that. Added i... | 2022-03-28T19:37:13 | 2022-09-29T20:26:04 | 2022-03-28T22:44:44Z | CONTRIBUTOR | {
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} | ## Summary
First major update to the CP2K IO module. Unless some changes are desired by devs. I think I'll title this v1.0 for the module.
inputs.py:
* Feature 1: New SectionList allows for repeated section names. Analogous to KeywordList
* Feature 2: New strict set action for less error prone custodian modific... | {
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"This PR is getting larger than expected.\r\n\r\nAnyway, for potential reviewers: the only interesting changes are in \r\n\r\n- abdafc7\r\n- 82b225b\r\n- 8e4a7eb\r\n- 7579245",
"[1 failing test left](https://github.com/materialsproject/pymatgen/runs/5740699569?check_suite_focus=true#step:6:52).\r\n\r\nJust had a ... | 2022-03-29T12:33:06 | 2022-04-04T19:18:51 | 2022-04-04T19:15:32Z | MEMBER | {
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} | Follow up to https://github.com/materialsproject/pymatgen/pull/2291#discussion_r746839280.
Quoting the docs:
> [NotImplemented](https://docs.python.org/3.6/library/constants.html#NotImplemented) should be returned by the binary special methods (e.g. __eq__(), __lt__(), __add__(), __rsub__(), etc.) to indicate tha... | {
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"\n[](https://coveralls.io/builds/47797396)\n\nCoverage decreased (-0.0002%) to 84.008% when pulling **38be5b65af40b76a85fe2dbdea7843265960da78 on mkhorton-patch-1** into **8650675d098997edbdca5e2839f1a78c5fe2987f on master**.\n",
"Without knowing exac... | 2022-03-29T18:18:07 | 2022-10-10T17:53:53 | 2022-03-29T20:09:10Z | MEMBER | {
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} | Suspect some interaction with `dataclasses` and `pydantic` but root cause of bug is still unclear.
Notifying @munrojm (can you add some context to this PR in case it helps others?) and also notifying @janosh since it relates to whether we should have these imports everywhere by default or not. | {
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"\n[](https://coveralls.io/builds/47815160)\n\nCoverage decreased (-0.8%) to 83.258% when pulling **acadab7ebd9bd82a8fe701291d5f18bb8f696a1d on nwinner:patch-2** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:master**.\n",
"Hmmm...... | 2022-03-30T05:04:38 | 2023-05-08T19:56:59 | 2023-05-08T19:56:59Z | CONTRIBUTOR | {
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} | Sometimes, we have calculations with continue from a previous calculation. For example, you run a coarse relaxation followed by a fine relaxation in separate fireworks. In that case, it would be convenient to have a Transformation which represents that relaxation that can be part of the second calculation's transformat... | {
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"Pls provide an actual series of code that I can use to reproduce the error.",
"**To Reproduce**\r\nfrom pymatgen.alchemy.transmuters import CifTransmuter\r\nfrom pymatgen.transformations.standard_transformations import SubstitutionTransformation, RemoveSpeciesTransformation\r\ntrans = []\r\ntrans.append(Substitu... | 2022-03-30T05:07:52 | 2022-04-06T14:18:48 | 2022-04-06T14:17:28Z | NONE | {
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} | **Describe the bug**
I made some transformations on a structure, output **final_structure** and **structures**. But I found these two properties are the same. It means **structures** property didn't work. And I view its source code. I found it's due to the **input_structure** key within **hdict** is removed by no reas... | {
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"Thanks for raising this issue @pjf295 and for sharing an example `vasprun.xml`. I have not had chance to try this functionality myself yet but agree the MLFF output should also be available. It seems reasonable a user may want to access the MLFF steps separately from the AIMD steps? If both were available via a co... | 2022-03-30T12:58:56 | 2022-10-11T10:42:55 | 2022-05-18T19:28:17Z | NONE | {
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} | **Describe the bug**
Vasp 6.3.0 includes the ability to use machine learning (ML) to generate force fields (FF) based upon ab-initio results. Ths results is a large speed up in calculation speeds. The ML process mixes both ab-initio MD with ML FF results based upon a Bayesian approach. This results in the vasprun.xml ... | {
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"\n[](https://coveralls.io/builds/47842442)\n\nCoverage decreased (-0.7%) to 83.264% when pulling **fe6db1cd1574c5c1890fab78a00eaf0bb9b4df58 on fraricci:bugfix_bsplotter_bztinterp** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:mast... | 2022-03-30T18:06:09 | 2022-04-04T19:14:55 | 2022-04-04T19:14:55Z | CONTRIBUTOR | {
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} | I fix two bugs:
- the units of vbm and cbm in the BztInterpolator were wrong and leading to a wrong energy range.
- BSPlotter in case of metallic bands and zero_to_efermi=False was broken. | {
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"\n[](https://coveralls.io/builds/47886499)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **497f0e5054e7db4d2520a4d14fd636ad8fe49bc3 on janosh:fix-sort-struct-graph** into **02ac6df9b8f70d13ccd23040818afb86d8b17f36 on materialsproject:master**.\n... | 2022-03-31T16:25:14 | 2022-03-31T18:42:50 | 2022-03-31T18:40:13Z | MEMBER | {
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"\n[](https://coveralls.io/builds/48335796)\n\nCoverage decreased (-0.7%) to 83.277% when pulling **6b068a4d149395ad07e1d4e032de9ae265a549cb on peikai:master** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n",
"Pls add a... | 2022-04-02T08:18:36 | 2022-04-18T01:23:15 | 2022-04-18T01:23:10Z | CONTRIBUTOR | {
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} | The results that entries_discharge and entries_discharge attributes returned in _pymatgen/apps/battery/conversion_battery.py_ were confused. I fixed this problem that entries in charge/discharged state should be the entries from step1/step2, respectively.
We can find evidence in similar attribute, vol_discharge, tha... | {
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updates:
- [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](https://github.com/asottile/pyupgrade/compare/v2.31.0...v2.31.1)
- [github.com/psf/black: 22.1.0 → 22.3.0](https://github.com/psf/black/compare/22.1.0...22.3.0)
- [github.com/pre-commit/mirrors-mypy: v0.930 → v0.942](https://github... | {
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"Thanks for catching this! Concerning to have such a big change that wasn't in the release notes / change log."
] | 2022-04-05T16:45:44 | 2022-04-26T21:51:49 | 2022-04-26T21:51:49Z | CONTRIBUTOR | {
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} | I noticed that (at least) version 6.3 of VASP has changed the units for the dipole (LCALC=True) from, i.e.:
Ionic dipole moment: p[ion]=( 0.00000 0.00000 19.70306 ) **electrons** Angst
to
Ionic dipole moment: p[ion]=( 0.00000 0.00000 -19.70306 ) **|e|** Angst
This means that these vectors ne... | {
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"Could you add a quick test to this @fraricci? Then will merge ASAP",
"Thanks @fraricci! Looks like test failures are unrelated (CrystalAIResterTest.test_query) so will go ahead and merge"
] | 2022-04-05T16:50:37 | 2022-04-20T18:16:14 | 2022-04-20T18:16:14Z | CONTRIBUTOR | {
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} | Fix for the new units in recent vasp versions (at least 6.3, maybe even before).
Discussed in #2485 | {
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"If we believe bader doesn't modify anything, we can do the analysis without copying to scratch. Feel free to make the modifications to pymatgen and submit a PR.",
"I'm also fine with these changes, but interested:\r\n\r\n> Use chgsum.pl AECCAR0 AECCAR2.pl directly. Don't read in the AECCARs via Pymatgen. This wo... | 2022-04-05T23:31:14 | 2023-08-08T19:14:54 | 2023-08-08T19:14:54Z | MEMBER | {
"total": 0,
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} | **Describe the bug**
When using the `bader_caller` in Pymatgen (specifically `bader_analysis_from_path`), it can take many times longer to run a Bader analysis than just using the standalone scripts provided by the Henkelman group. I suspect this is related to excessive file I/O related to reading in the CHGCAR, AECCA... | {
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"\n[](https://coveralls.io/builds/48070886)\n\nCoverage decreased (-0.7%) to 83.275% when pulling **6349dfac44a058e1954613090d19e14ad53dc3f3 on arosen93:rosen-band** into **040c45a68f7c787e062078aca28c3532c7c817e9 on materialsproject:master**.\n"
] | 2022-04-07T03:43:00 | 2022-04-07T11:34:27 | 2022-04-07T11:34:26Z | MEMBER | {
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} | Removed a redundant mathematical operation in the `CompleteDos` properties. The line `energies = dos.energies - dos.efermi` was included in two places. I deleted the second instance.
https://github.com/materialsproject/pymatgen/blob/040c45a68f7c787e062078aca28c3532c7c817e9/pymatgen/electronic_structure/dos.py#L860-L86... | {
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"\n[](https://coveralls.io/builds/48213263)\n\nCoverage decreased (-0.7%) to 83.276% when pulling **e65f680502b70dfd7117222cc0dae730592c4036 on lan496:speedup-group-structures** into **a82f60db3e4af40e2f21ed2cb968ffc398cf3a75 on materialsproject:master**... | 2022-04-12T13:34:12 | 2022-04-12T23:32:19 | 2022-04-12T16:16:57Z | CONTRIBUTOR | {
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} | ## Summary
- Speed up `StructureMatcher.group_structures` by skipping redundant transformations on given structures.
`group_structures` calls `fit` or `fit_anonymous` to compare two structures in a given list. Every time `fit` or `fit_anonymous` are called, the structures are reduced by searching their primitive ... | {
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"\n[](https://coveralls.io/builds/48225994)\n\nCoverage decreased (-0.7%) to 83.277% when pulling **f3c8c2c53cbcdf348c6b2c3531235ae3bf3a0e22 on kavanase:master** into **834dc9c507f0ceb735887be2db358be37c52a4d7 on materialsproject:master**.\n"
] | 2022-04-12T19:38:21 | 2022-04-19T14:35:02 | 2022-04-19T14:35:02Z | CONTRIBUTOR | {
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} | Specify `dtype` in numpy array generation
## Summary
Due to the new `VisibleDeprecationWarning` in `numpy` for creating arrays from ragged nested sequences, the `dtype` must be specified when generating the arrays, otherwise the following three warnings are printed for each defect correction calculated:
```
/ho... | {
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"\n[](https://coveralls.io/builds/48233648)\n\nCoverage decreased (-0.7%) to 83.276% when pulling **cc0a69945317307853844d153a0cc180ca72f330 on lan496:pylint-hook** into **834dc9c507f0ceb735887be2db358be37c52a4d7 on materialsproject:master**.\n",
"Than... | 2022-04-13T01:33:08 | 2022-04-16T14:20:19 | 2022-04-13T17:04:54Z | CONTRIBUTOR | {
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} | ## Summary
[The linter workflow](https://github.com/materialsproject/pymatgen/blob/master/.github/workflows/lint.yml) in GitHub actions uses `pylint`, but `.pre-commit-config.yaml` did not call it. This PR adds `pylint` in `.pre-commit-config.yaml`.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2493 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2493/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2493/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2493/events | https://github.com/materialsproject/pymatgen/issues/2493 | 1,202,657,935 | I_kwDOACgets5HrxqP | 2,493 | analysis/adsorption.py add_adsorbate is not working | {
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"Hi @zuhalcakir not sure if this is still an issue (the original issue seems more like a bug from the ASE side).\r\n\r\n```\r\nase==3.23.0\r\nnumpy==2.1.3\r\npymatgen==2024.10.29\r\n```\r\n\r\nWith the following code snippet I seem to get the correct structure ([POSCAR_with_ads](https://github.com/user-attachments/... | 2022-04-13T02:05:54 | 2024-11-09T06:31:23 | NONE | {
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} | **Describe the bug**
add_adsorbate function is not working properly.
**To Reproduce**
Steps to reproduce the behavior:
atoms = read(contcar)
pym_slab = pym_ase.get_structure(atoms)
mol = molecule('N2')
pym_mol = Molecule(species=[atom.symbol for atom in mol], coords=[atom.position for atom in m... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2494 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2494/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2494/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2494/events | https://github.com/materialsproject/pymatgen/pull/2494 | 1,205,982,769 | PR_kwDOACgets42T35s | 2,494 | Fix scipy deprecation warnings | {
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"\n[](https://coveralls.io/builds/48326618)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **3aa44fe7d9720f496a5a1c1ccd95088b7e8c1690 on arosen93:rosen-dep** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n"
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https://api.github.com/repos/materialsproject/pymatgen/issues/2495 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2495/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2495/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2495/events | https://github.com/materialsproject/pymatgen/pull/2495 | 1,206,071,542 | PR_kwDOACgets42UGol | 2,495 | Clean up tests | {
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"Hey, just say your comment for the lobster tests. I think I forgot to include one assertion... \r\n\r\nCould you add \"self.assertEqual(icooplist_bise, self.icoop_bise.icohplist)\" to line 621 of test_lobster.py? I think this should work. Otherwise, I will put this on my ToDo.\r\n",
"\n[![Coverage Status](https:... | 2022-04-16T09:53:40 | 2022-04-19T14:35:33 | 2022-04-19T14:35:32Z | MEMBER | {
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} | Boring part of this PR: Fix some flake8 violations.
Worth reviewing are changes to
- `PathFinderTest.test_image_num()`
- dulong-petit test case in `ElasticTensorExpansionTest.test_thermal_expansion_coeff()` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2496 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2496/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2496/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2496/events | https://github.com/materialsproject/pymatgen/pull/2496 | 1,206,140,080 | PR_kwDOACgets42US_Y | 2,496 | Improvement of pre-commit hook settings for `pylint` | {
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"\n[](https://coveralls.io/builds/48331133)\n\nCoverage decreased (-0.7%) to 83.272% when pulling **0aacddddb8e47b282ba151e5e4043bc97175f71d on lan496:pylint-hook** into **827ad4ee1e85bd723e0d29ef9ce8f708c44a1e61 on materialsproject:master**.\n",
"Oops... | 2022-04-16T15:26:03 | 2022-04-20T00:38:13 | 2022-04-19T14:34:36Z | CONTRIBUTOR | {
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} | Improvement of settings for `pylint` in `.pre-commit-config.yaml`, continuation of https://github.com/materialsproject/pymatgen/pull/2492 (@janosh, thank you for telling me the snippet!)
- I have confirmed `pylint` is now automatically installed when pre-commit hooks are called.
- Adding instructions to set up option... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2498 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2498/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2498/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2498/events | https://github.com/materialsproject/pymatgen/pull/2498 | 1,209,095,885 | PR_kwDOACgets42dl2Z | 2,498 | Fix link to Bader code in docstring | {
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"Might make sense to run a link checker on the docs to catch broken links automatically. Looks like there are some that cover all pymatgen-relevant markup languages, i.e. HTML, MD and rST: https://github.com/lycheeverse/lychee (can be run [as an action](https://github.com/lycheeverse/lychee-action))."
] | 2022-04-20T02:51:37 | 2022-04-20T19:53:39 | 2022-04-20T03:25:26Z | MEMBER | {
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} | Closes #1874. Fixes a broken URL in the docstring. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2499 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2499/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2499/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2499/events | https://github.com/materialsproject/pymatgen/issues/2499 | 1,209,418,486 | I_kwDOACgets5IFkL2 | 2,499 | Add a kwarg to avoid POTCAR checking in correction scheme | {
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"Closed in fad0576eb85af458cdc18daf4df9e861c75971ed"
] | 2022-04-20T09:26:30 | 2023-07-11T05:30:03 | 2023-07-11T05:30:02Z | MEMBER | {
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} | This mainly concerns the `MaterialsProject2020Compatibility` scheme, so I'm CC'ing @rkingsbury here.
https://github.com/materialsproject/pymatgen/blob/dcc4576fb8fb89b7adc2f31158654392348e6498/pymatgen/entries/compatibility.py#L941-L944
The above codeblock checks the POTCAR symbols when getting a correction. While... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2500 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2500/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2500/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2500/events | https://github.com/materialsproject/pymatgen/issues/2500 | 1,209,426,984 | I_kwDOACgets5IFmQo | 2,500 | Improve useability of the `MaterialsProject2020Compatibility` Scheme | {
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} | Another one for @rkingsbury regarding `MaterialsProject2020Compatibility`.
# Issue 1: Oxide Type
If the `.data` field is empty in a `ComputedEntry`, the compatibility scheme fails because of the bottom line. We should copy the section from the sulfide correction and call `oxide_type()` if a `structure` object is at... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2501 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2501/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2501/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2501/events | https://github.com/materialsproject/pymatgen/pull/2501 | 1,209,902,433 | PR_kwDOACgets42gLBb | 2,501 | No complex | {
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"Thanks @jmmshn! More descriptive PR titles would be appreciated though :) \r\n\r\nWas this because of issues with serialization when leaving them as complex?",
"> Was this because of issues with serialization when leaving them as complex?\r\n\r\nSorry for the short title. Yes, I'm trying to make this more JSON ... | 2022-04-20T16:08:39 | 2022-04-20T18:16:11 | 2022-04-20T18:14:12Z | CONTRIBUTOR | {
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} | # Removed complex numbers from the definition of WSWQ
- split the complex numbers into a real and imaginary parts
- added test for proper orthonormality of WSWQ | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2502 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2502/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2502/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2502/events | https://github.com/materialsproject/pymatgen/issues/2502 | 1,210,331,020 | I_kwDOACgets5IJC-M | 2,502 | Can't import pymatgen.core "No module named 'pymatgen.core'" | {
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"I have no idea what pymatgen.py is. I suspect it is because you named your script pymatgen and by default, python uses the package in the current directory. Rename the code to some other name.",
"of course! thanks."
] | 2022-04-20T23:48:31 | 2022-04-21T23:51:26 | 2022-04-21T02:05:00Z | NONE | {
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I've used pip install pymatgen with Python 3.9.1 on Windows 10 to install pymatgen, but I'm getting the following error:
Traceback (most recent call last):
File "D:\code\pymatgen\pymatgen.py", line 1, in <module>
import pymatgen.core as mg
File "D:\code\pymatgen\pymatgen.py", line 1, in <mod... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2505 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2505/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2505/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2505/events | https://github.com/materialsproject/pymatgen/pull/2505 | 1,215,089,168 | PR_kwDOACgets42wcSG | 2,505 | FEFF: support Molecule as input | {
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"This is ready for review. Note that there is one non-deterministic test failure that sometimes occurs and sometimes passes:\r\n\r\n```\r\nE AssertionError: 'PATH[72 chars]6884 1 Fe\\n-5.133990 -0.916498 -5.379918 1 Fe\\[188 chars]0 Fe' != 'PATH[72 chars]6884 2 Fe\\n-5.133990 -0.916498 -5.379918 2 Fe\\[188 ch... | 2022-04-25T21:58:31 | 2022-09-29T18:04:18 | 2022-09-28T17:32:15Z | CONTRIBUTOR | {
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} | ## Summary
This PR includes minimal changes to FEFF I/O to support the use of non-periodic input structures (e.g., `Molecule` rather than `Structure` objects). Tested with `MPXANESSet`. This also includes a fix for an edge case in which there is only a single absorbing atom present. When that occurs, some changes we... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2506 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2506/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2506/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2506/events | https://github.com/materialsproject/pymatgen/issues/2506 | 1,215,751,965 | I_kwDOACgets5Iducd | 2,506 | Corruption of `.pmgrc.yaml` still happening | {
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"No idea. I don't even know why MPRester needs to write to the pmgrc file. @mkhorton should look into this and make sure it is proper json and/or put it in another file. rc files are for configuration variables. The current ones that I see are not.",
"Maybe it's not `MPRester()` after all. At least I couldn't rep... | 2022-04-26T10:33:41 | 2022-04-26T21:36:22 | 2022-04-26T21:36:22Z | MEMBER | {
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} | Pinging @shyuep as I think this was supposed to be fixed in https://github.com/materialsproject/pymatgen/issues/2421.
Using `MPRester` still corrupts `.pmgrc.yaml`:
```yaml
dictitems:
MAPI_DB_VERSION:
LAST_ACCESSED: '2020_09_08'
LOG: {'2020_09_08': 1}
PMG_DEFAULT_FUNCTIONAL: PBE_54
PMG_MAPI_KE... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2507 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2507/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2507/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2507/events | https://github.com/materialsproject/pymatgen/pull/2507 | 1,216,132,073 | PR_kwDOACgets42z5uk | 2,507 | Report exceptions in `MPRester.__init__()` when trying to read/write `SETTINGS_FILE` | {
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"\n[](https://coveralls.io/builds/48585235)\n\nCoverage decreased (-0.7%) to 83.278% when pulling **74ee108dd1d7db531bbf4be575814eca8ad7b535 on janosh:mprester-init-exception-handling** into **da8d0a996584b716e2f9a6f2e3fdf9a94d80454a on materialsproject:... | 2022-04-26T15:29:59 | 2022-04-28T20:59:56 | 2022-04-26T21:45:08Z | MEMBER | {
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} | Relates to #2506.
Changes `MPRester.__init__()` to print exceptions when trying to read/write `SETTINGS_FILE` instead of swallowing them silently. This might help identify the underlying issue leading to `.pmgrc.yaml` corruption. | {
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