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https://api.github.com/repos/materialsproject/pymatgen/issues/2302 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2302/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2302/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2302/events | https://github.com/materialsproject/pymatgen/issues/2302 | 1,059,256,987 | I_kwDOACgets4_Ivqb | 2,302 | QCInput doesn't support multi-fragment molecule sections | {
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} | **Describe the bug**
Calculation inputs that represent any kind of fragment job (`fragmo` guess, BSSE, SCFMI/EDA, freezing string (FSM)) can't be read by the Q-Chem input parser. For this to work properly would probably require a fundamental rework of the parser and assumptions about what constitutes a molecule.
*... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2303 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2303/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2303/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2303/events | https://github.com/materialsproject/pymatgen/pull/2303 | 1,060,468,105 | PR_kwDOACgets4u3jb4 | 2,303 | More robust smart fermi method | {
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"Thanks @utf, this is very helpful. I followed up with the VASP folks on this, see [here](https://www.vasp.at/forum/viewtopic.php?p=20686). It sounds hopeful that this might be addressed in a future version."
] | 2021-11-22T18:26:43 | 2021-11-22T19:48:48 | 2021-11-22T19:48:48Z | MEMBER | {
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} | ## Summary
VASP 6.1+ sometimes puts the Fermi level just inside a valence or conduction band. This is related to a change in VASP tetrahedron which is described here: https://www.vasp.at/forum/viewtopic.php?f=4&t=17981
There is already logic inside pymatgen to try and catch this bug, unfortunately it is not relia... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2304 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2304/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2304/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2304/events | https://github.com/materialsproject/pymatgen/pull/2304 | 1,060,638,619 | PR_kwDOACgets4u4GuF | 2,304 | Fix to `get_continuous_path` method for line-mode band structures | {
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"\n[](https://coveralls.io/builds/47029579)\n\nCoverage decreased (-0.8%) to 83.372% when pulling **4b66ebc908cf8cb0322152d64f7491ccb2a84213 on munrojm:master** into **4b66ebc908cf8cb0322152d64f7491ccb2a84213 on materialsproject:master**.\n",
"Thanks f... | 2021-11-22T22:08:30 | 2022-03-02T22:45:42 | 2022-03-02T22:22:58Z | MEMBER | {
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} | ## Summary
This PR fixes a bug where band structure segments were missing in some cases due to an indexing issue with `0`.
## 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 must be checked:
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2305 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2305/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2305/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2305/events | https://github.com/materialsproject/pymatgen/issues/2305 | 1,061,186,071 | I_kwDOACgets4_QGoX | 2,305 | matplotlib 3.5 BSPlotterProjectedTest test error in electronic_structure test_plotter.py: ValueError: Number of rows must be a positive integer, not 5.5 | {
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"Was fixed in a1e223a."
] | 2021-11-23T12:00:50 | 2021-12-14T09:44:49 | CONTRIBUTOR | {
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} | **Describe the bug**
The BSPlotterProjectedTest test triggered by electronic_structure/tests/test_plotter.py has started failing with matplotlib 3.5. It was previously working with matplot 3.3 (I haven't tested matplotlib 3.4)
**To Reproduce**
Steps to reproduce the behavior:
1. Go to source dir
2. Run `PMG_TE... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2306 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2306/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2306/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2306/events | https://github.com/materialsproject/pymatgen/issues/2306 | 1,062,581,062 | I_kwDOACgets4_VbNG | 2,306 | Mistakes of argument type on the documentation | {
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"@mkhorton -- I think this can be closed.",
"Thanks for reporting @marinebox, this was fixed in https://github.com/materialsproject/pymatgen/commit/e1cbe781be6651fe9df08190e3620f97adadf22a",
"Also thanks @arosen93 for the reminder"
] | 2021-11-24T15:41:59 | 2022-03-29T20:55:59 | 2022-03-29T20:54:42Z | NONE | {
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} | The example of the argument of `gamma_automatic`([here](https://pymatgen.org/pymatgen.io.vasp.inputs.html#pymatgen.io.vasp.inputs.Kpoints.gamma_automatic)) is strange.
According to the source code, the type of `kpts` and `shift` should be tuple, but these are not tuple in the documentation.
In the other function([h... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2307 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2307/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2307/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2307/events | https://github.com/materialsproject/pymatgen/issues/2307 | 1,063,196,902 | I_kwDOACgets4_Xxjm | 2,307 | VASP 6.2.1 OUTCAR not properly parsed for run stats | {
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} | **Describe the bug**
When parsing the attached OUTCAR (from VASP 6.2.1) with the current version of Pymatgen, the number of cores is not output correctly because instead of the OUTCAR reading `running on 64` it reads `running 64`. (The average memory used here is `N/A` by VASP, so `None` is appropriate.)
```
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"\n[](https://coveralls.io/builds/44547772)\n\nCoverage decreased (-0.6%) to 83.121% when pulling **c5614ad9b04d0fbd090bb43ef36ce71a8c7e57c4 on arosen93:rosen-runstats** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
... | 2021-11-25T06:49:34 | 2021-12-17T18:21:46 | 2021-12-16T23:32:31Z | MEMBER | {
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} | Addresses #2307 wherein the number of cores was not being parsed properly for a VASP 6.2.1 OUTCAR file. I have added a test for this new VASP file.
## Summary
- Correctly parses number of cores from VASP 6.2.0+ files
- Stores the number of cores as an `int` instead of `str` | {
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"Many thanks @benedictsaunders ",
"HI @benedictsaunders, I saw you were a first-time contributor. So that we can acknowledge your contribution in [our documentation](https://pymatgen.org/team.html) please fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) if you have not already."
] | 2021-11-25T12:04:49 | 2022-01-06T22:49:20 | 2022-01-06T22:47:42Z | CONTRIBUTOR | {
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} | The double slashes were being misinterpreted in the current version of the documentation.
## Summary
* Replaced double backslases with ` \` as the `\\` was escaping and leading to no character bring printed in the rst math docstring.
## Checklist
Work-in-progress pull requests are encouraged, but please p... | {
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"\n[](https://coveralls.io/builds/44546398)\n\nCoverage decreased (-0.6%) to 83.124% when pulling **9b8995fdd168ea277308e6c0978b447beafdc951 on gpetretto:bugfix** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n",
"Many t... | 2021-11-25T15:05:02 | 2021-11-29T20:54:15 | 2021-11-29T20:54:11Z | CONTRIBUTOR | {
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} | ## Summary
In the current implementation of the write_Xdatcar in Trajectory the lattice is either written only once if `constan_lattice==True` or never if `constan_lattice==False`. Fix to write it multiple times if the lattice is not constant.
Added a specific check in the tests.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2311 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2311/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2311/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2311/events | https://github.com/materialsproject/pymatgen/issues/2311 | 1,064,895,527 | I_kwDOACgets4_eQQn | 2,311 | Cannot import name 'SpeciesLike' from 'pymatgen.util.typing' | {
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"It is an issue with your install.",
"Hello @shyuep \r\nI tried to reinstall my pymatgen, but the above error message still appears, thank you for your time and help!"
] | 2021-11-27T03:53:15 | 2021-11-27T12:34:27 | 2021-11-27T03:58:53Z | CONTRIBUTOR | {
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} | When I use PyCharm to run lattice.py in core package, I got the following error message.
Is this because of a problem with my Installation process or I did not install other dependent libraries yet?
What should I do to solve my problem. thank!
~~~sh
raceback (most recent call last):
File "D:/Gitdownload/pymatge... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2312 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2312/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2312/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2312/events | https://github.com/materialsproject/pymatgen/pull/2312 | 1,065,172,912 | PR_kwDOACgets4vFsY3 | 2,312 | Clearer handling of magmom flag | {
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"\n[](https://coveralls.io/builds/44615262)\n\nCoverage decreased (-0.6%) to 83.13% when pulling **e6ba47bd4236e6cded188f1bc688e94ed55d03c1 on arosen93:rosen-clarifications** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:master**.\n... | 2021-11-28T03:01:24 | 2021-12-20T19:57:56 | 2021-12-20T19:45:52Z | MEMBER | {
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} | ## Summary
### Clearer Handling of Magnetic Moments
I have made a few additional clarifications to `pymatgen.io.vasp.sets`, primarily with regards to the handling of magnetic moments as a follow-up to #2301:
1. Clearer docstrings. This is rather self-explanatory.
2. Only print the warning about low magnetic moments... | {
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"I just tried the query you specified and for me it works.\r\nI ran it from the [binder page](https://mybinder.org/v2/gh/Materials-Consortia/optimade-tutorial-exercises/HEAD?filepath=notebooks%2Fdemonstration-pymatgen-for-optimade-queries.ipynb) of the Optimade tutorial. The pymatgen version I used is 2022.0.16\r\n... | 2021-11-29T08:34:26 | 2021-11-30T08:22:54 | NONE | {
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} | I am trying to use the OPTIMADE Rester. But when running the following lines
`from pymatgen.ext.optimade import OptimadeRester
opt = OptimadeRester('mp')
data = opt.get_structures(elements=['Li','Mn','O'], nelements=[1,3])`
I get the following error messages
> Failed to extract required information from ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2314 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2314/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2314/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2314/events | https://github.com/materialsproject/pymatgen/issues/2314 | 1,066,112,227 | I_kwDOACgets4_i5Tj | 2,314 | `OptimadeRester`: Add ability to request additional response fields | {
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} | We have just run into an issue (https://github.com/Materials-Consortia/optimade-tutorial-exercises/issues/8) where the pymatgen OPTIMADE tutorial fails to pull custom provider fields since #2244 was merged, as this PR (correctly) enforced the response fields required to create pymatgen structures from OPTIMADE response... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2315 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2315/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2315/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2315/events | https://github.com/materialsproject/pymatgen/pull/2315 | 1,066,208,692 | PR_kwDOACgets4vIwXX | 2,315 | Add ability to request additional OPTIMADE fields | {
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"\n[](https://coveralls.io/builds/44604585)\n\nCoverage decreased (-0.6%) to 83.127% when pulling **642431eba9b5d5ca99d2f757cf533036eb0798dc on ml-evs:ml-evs/optimade_response_fields** into **dd3737011e76520da1347d5db75db3a3f87e520f on materialsproject:m... | 2021-11-29T15:59:14 | 2021-11-29T20:07:14 | 2021-11-29T20:07:14Z | CONTRIBUTOR | {
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} | ## Summary
Closes #2314 by adding the `additional_response_fields` argument when generating SNLs from OPTIMADE requests.
## 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 must be checked:
-... | {
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"Since these are all additions not changes, they have my blessing!\r\n\r\nOpen to changes too but would be more discussion required.",
"As long as it doesn't change the workflow I have no objections either. Thanks for the docstring cleanup, too @arosen93 !",
"Great, thanks! I updated the hash accordingly, and i... | 2021-12-03T01:03:23 | 2021-12-21T07:08:17 | 2021-12-03T17:10:00Z | MEMBER | {
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} | @rkingsbury and @mkhorton: Some elements that are currently in the VASP PAW .54 PBE library have defined pseudopotentials but aren't in the `MPScanRelaxSet.yaml` file because they never existed in the original PAW PBE set used in the GGA calculations on MP. This change won't influence anything in your R2SCAN workflow b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2317 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2317/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2317/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2317/events | https://github.com/materialsproject/pymatgen/issues/2317 | 1,070,935,153 | I_kwDOACgets4_1Sxx | 2,317 | divide by zero encountered in true_divide error | {
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"Let me check this but I think it's just a warning that happens for some values of mu in the gap.\r\nDoes the final plot look reasonable?",
"You are right. It's just a warning and the plots are looking reasonable. Thanks :)"
] | 2021-12-03T20:17:46 | 2021-12-07T07:24:22 | NONE | {
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} | I'm trying to use boltztrap2 module to plot conductivity, seeback etc but I get following error
```
---/lib/python3.6/site-packages/pymatgen/electronic_structure/boltztrap2.py:810: RuntimeWarning:
divide by zero encountered in true_divide
```
Could you help me to solve this issue?
script I use:
```
from p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2318 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2318/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2318/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2318/events | https://github.com/materialsproject/pymatgen/pull/2318 | 1,071,259,645 | PR_kwDOACgets4vZNlJ | 2,318 | Use f-string automatic string coercion: f"{str(x)}" -> f"{x}" | {
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"@shyuep The workflow \r\n\r\n```sh\r\npytest pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line\r\n```\r\n\r\ntimed out on Windows and macOS. There is no error, just that the operation was cancelled. Does this require fixing or is it a flaky test?",
"@shyuep Just resolved the merg... | 2021-12-04T17:45:18 | 2022-01-15T15:40:12 | 2022-01-12T19:20:28Z | MEMBER | {
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} | Related #2294. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2319 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2319/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2319/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2319/events | https://github.com/materialsproject/pymatgen/issues/2319 | 1,073,015,557 | I_kwDOACgets4_9OsF | 2,319 | Boltztrap2 module for 2D systems | {
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"I never used it for 2D systems. I think some changes are needed.\r\nPlease, have a look at BoltzTraP forum, this topic has been discussed multiple times in depth:\r\nhttps://groups.google.com/forum/#!forum/boltztrap"
] | 2021-12-07T07:34:14 | 2021-12-07T17:00:45 | NONE | {
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} | Hi,
I'm using bolztrap2 module to compute thermoelectric coefficients of the 2D systems. Can I use straightforwardly this module for 2D systems if not what kind of changes do I need to make? For example, I generated the following plot for the WSe2 monolayer. Do I just need to change the unit (cm^-3 to cm^-2) here or... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2320 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2320/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2320/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2320/events | https://github.com/materialsproject/pymatgen/pull/2320 | 1,074,005,229 | PR_kwDOACgets4viKB9 | 2,320 | Absorption | {
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"Thanks for opening this PR @yang-ruoxi!\r\n\r\nSince you're a new contributor, I have to manually approve the automatic tests. These should now be running.",
"Overall this looks good!\r\n\r\nThe main thing this is lacking right now is tests. You may be able to copy a test from the existing input sets (see `test_... | 2021-12-08T04:42:11 | 2022-07-01T23:44:50 | 2022-07-01T23:44:40Z | MEMBER | {
"total": 0,
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} | ## Summary
* Added optical absorption input set for independent-particle approximation (IPA) and random-phase approximation (RPA), expected to be used with AbsorptionFW in atomate
* Added the AbsorptionSet.yaml for the default input set (IPA)
* Two modes are possible to choose from: IPA or RPA
* If IPA is c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2321 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2321/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2321/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2321/events | https://github.com/materialsproject/pymatgen/issues/2321 | 1,074,165,909 | I_kwDOACgets5ABniV | 2,321 | Pourbaix diagram is missing compounds | {
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"https://matsci.org/t/materials-project-database-release-log/1609/18\r\n\r\nUpgrading the pymatgen version from 2020.1.10 to 2022.0.16 worked.\r\n\r\n\r\n",
"Thanks for sharing your resolution @CFRP-07 !"
] | 2021-12-08T08:59:39 | 2021-12-08T19:28:25 | 2021-12-08T09:59:11Z | NONE | {
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} | Hello,
I am new to pymatgen and am trying to reproduce the Pourbaix diagram from the website in python. However, the plot seems to be missing some compounds and I can not figure out why.
Is it possible to resolve this?
Thanks!
My code:
`# Import necessary tools from pymatgen`
`from pymatgen import MPRe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2322 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2322/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2322/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2322/events | https://github.com/materialsproject/pymatgen/issues/2322 | 1,074,997,696 | I_kwDOACgets5AEynA | 2,322 | Finish Wyckoff functionality in cif parsing/writing | {
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"You can use the SpaceGroupAnalyzer.get_symmetrized_structure to get the Wyckoff symbols.",
"I think this issue is more about propagating metadata already existing in the CIF, i.e. for Wyckoff symbols that have already been annotated, these could be parsed as site properties.",
"Yes, indeed the get_symmetrized ... | 2021-12-09T01:13:57 | 2022-01-12T22:32:37 | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
I would like to use Pymatgen's wonderful structure manipulation functionality but cif parsing/manipulating/rewriting pipeline in Pymatgen doesn't preserve the wyckoff letters and multiplicities. I see in the code that it's planned for implementation in... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2323 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2323/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2323/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2323/events | https://github.com/materialsproject/pymatgen/pull/2323 | 1,083,489,197 | PR_kwDOACgets4wA_cl | 2,323 | Add new automatic kpoint scheme that normalizes by lattice lengths | {
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"This one is good to go. It's just that broken Mac Windows test holding it up.",
"Many thanks for this @arosen93! Will be investigating failing tests shortly"
] | 2021-12-17T17:54:37 | 2022-01-07T00:58:16 | 2022-01-06T22:45:36Z | MEMBER | {
"total": 0,
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} | ## Summary
This PR creates a new automatic k-point generation scheme, `automatic_density_by_lengths`, which allows the user to specify a density of k-points in each dimension (rather than just for the entire volume). This is particularly important for slab calculations, because you almost always want 1 k-point in the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2324 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2324/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2324/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2324/events | https://github.com/materialsproject/pymatgen/pull/2324 | 1,083,959,772 | PR_kwDOACgets4wCdv0 | 2,324 | Pass magmoms and selective dynamics between ASE Atoms and Pymatgen Structure in ASEAtomsAdaptor | {
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"This one is good to go. It's just that broken Mac Windows test holding it up (although somehow one of the commits passed magically!).\r\n\r\nEdit: Made some improvements but still good to go now!",
"Thanks!"
] | 2021-12-18T22:40:52 | 2022-01-07T00:58:13 | 2022-01-06T22:47:07Z | MEMBER | {
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} | Currently, the `pymatgen.io.ase.ASEAtomsAdaptor` does not pass the magnetic moments or selective dynamics tags between the ASE `Atoms` and Pymatgen `Structure` objects (in either direction). As an example of where this came up for me recently, I was using the `mp_api` to fetch `Structure` objects from MP. When I conver... | {
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"Notifying @rkingsbury too as likely relevant for SCAN input sets.",
"Just to clarify for my own notes too: This is really only relevant if `LAPSH = True`.",
"Thanks @mkhorton ; if you change the SCAN sets just please make sure to check if any validation rules in the validation builder need to change (I don't t... | 2021-12-20T21:55:48 | 2023-09-03T19:42:38 | 2023-09-03T19:42:38Z | MEMBER | {
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} | Thanks @arosen93:
> If the PAW one-center expansion of the density has component up to L, then the one-center expansion of the kinetic energy density has components up to L+2. This means that as a rule of thumb, for s-elements: LMAXTAU=2, for p: LMAXTAU=4, and for d: LMAXTAU=6. If you are willing to live with the co... | {
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"Closing because of the discussion in #2330. "
] | 2021-12-26T18:28:14 | 2022-01-07T22:33:56 | 2022-01-07T22:33:56Z | MEMBER | {
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} | When using `pymatgen.symmetry.analyzer.SpacegroupAnalyzer`'s `get_conventional_standard_structure()`, all site properties in the pymatgen structure object (e.g. magnetic moments) are stripped.
Importantly, this also means that when using the MP API, doing `mpr.get_structure_by_material_id(mp_id, conventional_unit_ce... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2327 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2327/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2327/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2327/events | https://github.com/materialsproject/pymatgen/issues/2327 | 1,089,615,088 | I_kwDOACgets5A8jTw | 2,327 | Group numbers for the lanthanides and actinides are strange | {
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"Thanks. Feel free to propose a conventional and implement a change. For me, group numbers don't really make any kind of sense of the TM and rare earth series. If you are planning to use it for ML purposes, I would say group number is probably one of the worst choices you can use. I for one don't believe the large ... | 2021-12-28T05:06:01 | 2022-02-02T05:18:01 | 2022-02-02T05:18:00Z | MEMBER | {
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} | When accessing the `.group` property of a `specie` that is a lanthanide or actinide, the returned group number is quite unconventional. For instance, the group number for Yb is 16. For Lu it's 17. While there is certainly debate to be had around the group numbers for the lanthanides and actinides, I don't believe this ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2328 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2328/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2328/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2328/events | https://github.com/materialsproject/pymatgen/issues/2328 | 1,090,783,337 | I_kwDOACgets5BBAhp | 2,328 | Battery Analyzer for Anion Batteries | {
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"This sounds great."
] | 2021-12-29T22:48:11 | 2022-01-31T22:05:01 | 2022-01-31T22:05:01Z | CONTRIBUTOR | {
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Currently, the pymatgen.apps.battery.analyzer module only can handle cation batteries, but there are several emerging battery chemistries with a negatively charged working ion, such as fluoride or chloride. I have some spare time in the next week, so I'll try to update the module to work for anion batteries in ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2329 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2329/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2329/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2329/events | https://github.com/materialsproject/pymatgen/pull/2329 | 1,092,126,433 | PR_kwDOACgets4wco51 | 2,329 | Battery analysis for anion batteries [WIP] | {
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"@sthartman, I'm having the same issue with the test suite via GitHub Actions. I don't think it's due to any changes you introduced. (cc @mkhorton, this is a different one than before).",
"Hi @sthartman , I recently made sure all the tests are properly passing. Can you merge the latest master into your PR first? ... | 2022-01-02T23:36:39 | 2022-01-13T16:56:18 | 2022-01-13T16:56:18Z | CONTRIBUTOR | {
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} | ## Summary
#2328
* Battery analysis now handles working ion with negative charge
* Added appropriate tests
## TODO (if any)
Pytest run from the command line finds no errors in the pymatgen/apps directory, where I made the changes, but I still need to figure out why the build as a whole is failing.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2330 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2330/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2330/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2330/events | https://github.com/materialsproject/pymatgen/pull/2330 | 1,092,946,648 | PR_kwDOACgets4wfUHw | 2,330 | Keep site properties after calling spglib in get_refined_structure() and find_primitive() | {
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"How does this work with magnetically ordered structures @arosen93? e.g. the primitive structure may not be large enough to retain the magnetic ordering from the input structure",
"@mkhorton:\r\n\r\nIn this PR, the site properties are carried over to any symmetrically equivalent site in the refined or primitive s... | 2022-01-04T02:01:41 | 2022-01-14T21:56:16 | 2022-01-07T18:24:35Z | MEMBER | {
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} | In `pymatgen.symmetry.analyzer.SpacegroupAnalyzer`, the `get_refined_structure()` and `find_primitive()` functions both strip Pymatgen structure objects of all their site properties, including magnetic moments. This PR carries over the site properties after calling `spglib`. Test have been added.
Addresses #2326.
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"Pls provide the actual text POSCAR in the issue report. Giving an image is very difficult for me to try to reproduce the error.",
"> Pls provide the actual text POSCAR in the issue report. Giving an image is very difficult for me to try to reproduce the error.\r\n\r\nHere is my POSCAR file.\r\n\"\r\nCs1 Pb1 Br3\... | 2022-01-07T06:06:35 | 2022-01-09T11:25:09 | 2022-01-08T16:32:37Z | NONE | {
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I wanted to convert my POSCAR file to structure object in pymatgen.
but there's something wrong in the library or my code.
Here is my situation
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"@chc273 Can you look into this?",
"@shyuep on it.",
"@shyuep This is mostly a Cython version issue. The older Cython generated the C code that does not work with python 3.10. It should have been fixed by your commits yesterday 40c1ff014908a08f11af05f58b252f8764df5bf7 \r\n\r\nI have tested on Ubuntu 20.04.3 LT... | 2022-01-07T12:23:29 | 2022-01-08T22:53:47 | 2022-01-08T22:53:47Z | NONE | {
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} | **Describe the bug**
Building fails for Python 3.10 because the `pymatgen/optimization/neighbors.c` uses an undocumented struct member `use_tracing` that was removed. See this issue for reference: https://bugs.python.org/issue43760
I know that the package does not officially state support for Python 3.10, but wanted ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2333 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2333/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2333/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2333/events | https://github.com/materialsproject/pymatgen/issues/2333 | 1,096,311,713 | I_kwDOACgets5BWGOh | 2,333 | Build broken on Python 3.8 | {
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"Thanks. Indeed there are some really annoying crap happening with numpy binary compatibility between versions. For now, I have followed your recommendation to increment the numpy version.",
"Quick update that a new version of pymatgen was released which should fix these problems for now.",
"Thanks for the rel... | 2022-01-07T13:20:22 | 2022-01-12T11:16:30 | 2022-01-07T17:34:44Z | NONE | {
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} | Building `pymatgen` on Python 3.8 currently seems broken, see for example [this recent action](https://github.com/materialsproject/pymatgen/runs/4733023541?check_suite_focus=true) on the `master` branch. The problem seems to be the well-known incompatibility of the `numpy` package used for building and the one used whe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2334 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2334/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2334/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2334/events | https://github.com/materialsproject/pymatgen/issues/2334 | 1,096,719,827 | I_kwDOACgets5BXp3T | 2,334 | Invalid documentation in generate_all_slabs() for tol parameters | {
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} | **Describe the bug**
In the documentation below for `pymatgen.core.surface.generate_all_slabs()`, the description for the `tol` kwarg is incorrect. That description should be associated with the `ftol` kwarg. The `tol` kwarg is related to the symmetry (e.g. primitive cell search) tolerance. There is no docstring for t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2335 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2335/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2335/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2335/events | https://github.com/materialsproject/pymatgen/pull/2335 | 1,097,946,347 | PR_kwDOACgets4wvIL8 | 2,335 | Corrected and Extended IO for Quantum Espresso Input Files | {
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"\n[](https://coveralls.io/builds/45494507)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **2a0ec0e09641ac6c10bdc241f0279913cf1ab7ae on vorwerkc:qe-io** into **fb7706ce15913fd480daeb802b62ff73a408cefc on materialsproject:master**.\n",
"Great. M... | 2022-01-10T14:10:17 | 2022-01-10T15:10:57 | 2022-01-10T14:51:01Z | CONTRIBUTOR | {
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} | ## Summary
This merge request fixes the parsing of QE input files. The previous code was based on an outdated QE code format, expecting curly brackets in the definition of CELL_PARAMETERS and ATOMIC_POSITIONS. The merge request adds a new test for the pymatgen.io.pwscf.PWInput.from_string function.
Additionally, ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2336 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2336/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2336/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2336/events | https://github.com/materialsproject/pymatgen/pull/2336 | 1,098,277,939 | PR_kwDOACgets4wwNn_ | 2,336 | Mixing Scheme | {
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"@mkhorton could you please re-trigger the tests? It appears the only failure is coming from XAS and if I understood you correctly, that should be fixed now?\r\n\r\n```\r\n___________________________ XASTest.test_stitch_l23 ____________________________\r\n\r\nself = <xas.tests.test_spectrum.XASTest testMethod=test_... | 2022-01-10T19:17:37 | 2022-01-14T22:48:05 | 2022-01-14T22:45:12Z | CONTRIBUTOR | {
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} | ## Summary
Implementation of the SCAN / GGA(+U) mixing scheme. Mixing scheme code lives in the new file `mixing_scheme.py` and is implemented as a `Compatibility` class.
In addition to the core mixing scheme, this PR contains the following minor supporting changes:
* Changes to `MateraialsProjectAqueousCompati... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2337 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2337/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2337/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2337/events | https://github.com/materialsproject/pymatgen/issues/2337 | 1,098,430,960 | I_kwDOACgets5BeLnw | 2,337 | Drift correction and framework ions in DiffusionAnalyzer | {
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"1. Yes unless you believe the framework is not moving much.\r\n2. Again, this really depends. If the ions are randomly moving and the average motion is close to 0, then it doesn't make a difference whether you include or not.\r\n3. I would definitely choose all ions other than the moving ions to be the famework. I... | 2022-01-10T22:01:04 | 2022-01-13T15:00:56 | 2022-01-13T15:00:56Z | NONE | {
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} | The drift correction in `DiffusionAnalyzer` is automatically applied when calculating ionic diffusivity.
(1) Is it always required to include the drift correction for a trajectory?
(2) It makes sense to include it if all the ions moving in the same direction, but what if the ions are randomly moving around?
(3) If... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2338 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2338/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2338/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2338/events | https://github.com/materialsproject/pymatgen/issues/2338 | 1,098,680,251 | I_kwDOACgets5BfIe7 | 2,338 | ValueError: zero-size array to reduction operation maximum which has no identity | {
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"I think the reason is that you only have one species in your trajectory, therefore, your `framework_indices` is empty. A quick fix could be the following:\r\n```python:\r\nif len(framework_indices) == 0:\r\n dc = displacements\r\nelse:\r\n framework_disp = displacements[framework_indices]\r\n drift = np.a... | 2022-01-11T05:50:56 | 2022-01-19T09:04:41 | NONE | {
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I am trying to calculate the diffusivity of Li ions on a Li metal surface from the VASP AIMD output files (XDATCAR, vasprun.xml) by using the pymatgen. I have used the following code:
--------------------------------------------------------------------------------------------------
%matplotlib inline
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2339 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2339/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2339/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2339/events | https://github.com/materialsproject/pymatgen/issues/2339 | 1,099,501,324 | I_kwDOACgets5BiQ8M | 2,339 | Structure.get_sorted_structure does not preserve magmom site property | {
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"Hi @bocklund,\r\n\r\nI think this can be resolved by using the `Structure.add_site_property()` function, which is the preferred method of adding magnetic moments (and other site properties, like selective dynamics). I personally would recommend against trying to \"manually\" specify site properties, as they get st... | 2022-01-11T18:39:05 | 2022-03-29T20:58:39 | CONTRIBUTOR | {
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} | **Describe the bug**
The `Structure.get_sorted_structure` method seems to clobber `magmom` attributes. As a consequence, all `DictSet` subclasses don't allow setting magnetic moments using site properties by default, since the default keyword argument `sort_structure=True` calls this method.
**To Reproduce**
`... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2340 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2340/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2340/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2340/events | https://github.com/materialsproject/pymatgen/issues/2340 | 1,099,624,596 | I_kwDOACgets5BivCU | 2,340 | Pip cache not used in GitHub CI | {
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"Yes that would be helpful. I recently disabled the cache for debugging purposes. But I think we can re-enable them now."
] | 2022-01-11T21:17:46 | 2022-01-12T16:06:45 | 2022-01-12T16:06:45Z | MEMBER | {
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} | The GitHub test workflows for Linux, Mac and Windows all cache installed pip dependencies but then never check if there's a cache hit from previous runs. Would be great for saving time and energy to fix this soon.
https://github.com/materialsproject/pymatgen/blob/81e96a4a5739e383f921b7272db7ebf8b1710cb9/.github/work... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2341 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2341/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2341/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2341/events | https://github.com/materialsproject/pymatgen/issues/2341 | 1,099,626,000 | I_kwDOACgets5BivYQ | 2,341 | Incorrect Oxidation States with add_charges_from_oxi_state_guesses Method | {
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} | **Describe the bug**
I’ve noticed that the add_charges_from_oxi_state_guesses method in the pymatgen.core.composition module provides incorrect oxidation state numbers for materials which only contain one atom of an element in a material that can undergo charge disproportionation, such as BiO2.
**To Reproduce**
Th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2342 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2342/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2342/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2342/events | https://github.com/materialsproject/pymatgen/pull/2342 | 1,099,869,221 | PR_kwDOACgets4w1Yy2 | 2,342 | Clarify docstring for core.surface.generate_all_slabs() and structure.add_site_property() | {
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"\n[](https://coveralls.io/builds/45554453)\n\nCoverage decreased (-0.6%) to 83.184% when pulling **a71c84fbc9b9056f3e7cde13b0a34cbdad468f4b on arosen93:rosen-docs** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Tha... | 2022-01-12T04:34:02 | 2022-01-13T15:01:46 | 2022-01-13T15:01:42Z | MEMBER | {
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} | Addresses #2334 and #2339.
- The docstring for `generate_all_slabs()` was missing the description for the `ftol` kwarg and had the wrong description for the `tol` kwarg.
- I added examples on how to use `structure.add_site_property()` for adding magnetic moments and selective dynamics because, when I was a new user... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2343 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2343/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2343/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2343/events | https://github.com/materialsproject/pymatgen/pull/2343 | 1,099,870,904 | PR_kwDOACgets4w1ZIh | 2,343 | Update row and group number for lanthanoids/actinoids | {
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"\n[](https://coveralls.io/builds/46097286)\n\nCoverage decreased (-0.4%) to 83.434% when pulling **433e7d8819cb9a40a98b18e81d434ef85fd4c5a9 on arosen93:rosen-group** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Be... | 2022-01-12T04:37:32 | 2022-01-31T22:02:12 | 2022-01-31T22:02:08Z | MEMBER | {
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} | ## Purpose
This PR addresses #2327 wherein the group number for lanthanoids and actinoids was set to unconventional values of 3-17 depending on the element. The row was also set to the fictional values of 8 and 9, which is equally unconventional (although convenient for plotting).
## Changes
- The group number for... | {
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"\n[](https://coveralls.io/builds/45570143)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **568ca1c08dec9dd4c5149a4ac49e54a53b0586dd on janosh:gh-ci-caching** into **81e96a4a5739e383f921b7272db7ebf8b1710cb9 on materialsproject:master**.\n",
"Th... | 2022-01-12T09:31:47 | 2022-01-12T16:08:02 | 2022-01-12T16:06:46Z | MEMBER | {
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} | Closes #2340. | {
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"I think it is useful to keep it for forks. The tests help inform the developer whether his code is working or not.",
"> The tests help inform the developer whether his code is working or not.\r\n\r\nThis is already taken care of by the emails everyone gets from the workflows running on this repo. The fork runs a... | 2022-01-12T18:37:09 | 2022-02-22T11:43:17 | 2022-01-12T19:20:02Z | MEMBER | {
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```yaml
jobs:
test:
if: github.repository_owner == 'materialsproject'
# ...
```
Would save compute and it's annoying to keep getting emails about failed runs on my fork when submitting PRs:
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"\n[](https://coveralls.io/builds/45579054)\n\nCoverage decreased (-0.6%) to 83.183% when pulling **531561d8d1dd55b3104d923c585861340c2223f0 on janosh:no-ci-on-forks** into **e04bf536e0245805f0f42860ca81ed1582e62314 on materialsproject:master**.\n",
"T... | 2022-01-12T20:36:11 | 2022-01-13T15:10:49 | 2022-01-13T15:01:17Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2348 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2348/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2348/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2348/events | https://github.com/materialsproject/pymatgen/issues/2348 | 1,101,950,392 | I_kwDOACgets5Brm24 | 2,348 | Rename master to main | {
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"It has always been master. It is the other repos that rename themselves to main to serve some woke bullshit. I am not bowing to this kind of crap. You can ask the ones which are called main to go back to master. ",
"I agree that dropping the name `master` doesn't actually help with any entrenched societal proble... | 2022-01-13T15:39:01 | 2022-01-19T08:26:33 | 2022-01-13T15:43:56Z | MEMBER | {
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} | Bit annoying that the primary branch is inconsistently named across MP repos. Many still use `master` ([pymatgen](https://github.com/materialsproject/pymatgen), [custodian](https://github.com/materialsproject/custodian), [mapidoc](https://github.com/materialsproject/mapidoc), ...) while some have adopted GitHub's new d... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2349 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2349/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2349/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2349/events | https://github.com/materialsproject/pymatgen/pull/2349 | 1,104,175,647 | PR_kwDOACgets4xEBsI | 2,349 | Provide an option to keep site properties when calling spglib | {
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"\n[](https://coveralls.io/builds/45652538)\n\nCoverage decreased (-0.6%) to 83.315% when pulling **ab6cfd13de4371eaacbf543b924aaeff91525bd9 on arosen93:rosen-siteprops** into **ef6a4b09940531083bab1b587b3d80445163cfae on materialsproject:master**.\n",
... | 2022-01-14T22:26:23 | 2022-01-18T03:12:22 | 2022-01-15T14:55:42Z | MEMBER | {
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} | As discussed in greater detail in #2330, this PR provides a new keyword option (`keep_site_properties`) in various `structure.symmetry.analyzer` functions to keep the site properties on the sites after a transformation. The docstring makes it clear that this may lead to undesirable side-effects as a result of the trans... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2350 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2350/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2350/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2350/events | https://github.com/materialsproject/pymatgen/pull/2350 | 1,104,246,316 | PR_kwDOACgets4xEQyZ | 2,350 | Correction of small bugs in Lobster module | {
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"\n[](https://coveralls.io/builds/45649985)\n\nCoverage decreased (-0.6%) to 83.306% when pulling **adf3368150ae6bb49098c6bcbad26c4e155df18e on JaGeo:master** into **0604210825c8bb2e38d5e0e8cce32a5fc265c3e6 on materialsproject:master**.\n",
"All tests ... | 2022-01-15T00:54:37 | 2022-01-15T14:55:08 | 2022-01-15T14:55:04Z | MEMBER | {
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} | ## Summary
This is a pull request to correct small bugs in the Lobster module (set and environment classes). I have added tests to ensure they will not show up again.
Test files were zipped which led to more changes.
Let me know if there are suggestions. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2351 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2351/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2351/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2351/events | https://github.com/materialsproject/pymatgen/pull/2351 | 1,104,556,174 | PR_kwDOACgets4xFY8n | 2,351 | Fix CI status badge | {
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"Closed because, actually, I'm not 100% sure about this. Will just open an issue.",
"\n[](https://coveralls.io/builds/45687645)\n\nCoverage decreased (-0.6%) to 83.316% when pulling **8313f18c5cad747699bbb0f4dcc46cb1105e513e on arosen93:rosen-ci** into... | 2022-01-15T06:51:44 | 2022-01-17T22:36:56 | 2022-01-17T15:52:18Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2352 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2352/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2352/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2352/events | https://github.com/materialsproject/pymatgen/pull/2352 | 1,105,558,689 | PR_kwDOACgets4xIkc5 | 2,352 | Format + typo fixes | {
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"\n[](https://coveralls.io/builds/45679059)\n\nCoverage decreased (-0.6%) to 83.317% when pulling **6517cef8726ab009c42626fadcc2455ac161c974 on janosh:fixes** into **8128f3062a334a2edd240e4062b5b9bdd1ae6f58 on materialsproject:master**.\n",
"@shyuep Re... | 2022-01-17T09:04:44 | 2022-01-31T21:06:41 | 2022-01-17T15:25:06Z | MEMBER | {
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} | 3rd time's the charm (#2294, #2318). | {
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"\n[](https://coveralls.io/builds/45710406)\n\nCoverage decreased (-0.6%) to 83.323% when pulling **c38e7f33f3d290cf0d7da8a77468ab6f5685c808 on arosen93:rosen-ase** into **d72686269bd513c2edd8fb219de9011334fbdf7d on materialsproject:master**.\n",
"Than... | 2022-01-17T20:16:38 | 2022-01-18T22:04:31 | 2022-01-18T21:31:22Z | MEMBER | {
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} | - When creating a Pymatgen `molecule` object from an ASE `Atoms` object using `pymatgen.io.ase.AseAtomsAdaptor.get_molecule()`, the `molecule.charge` and `molecule.spin_multiplicity` are now appropriately set. Before, they would always be set to their default values of 0 and 1, respectively.
- Now, _all_ Pymatgen site... | {
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} | **Describe the bug**
When I use the [get_pattern()](https://github.com/materialsproject/pymatgen/blob/905fa8592423f51784b9e83e02c53bb0c6ea0aa3/pymatgen/analysis/diffraction/tem.py#L278) method for [TEM diffraction](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/diffraction/tem.py) to create... | {
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"This was an issue with ComputedEntry entries having the same entry_id. Not sure where this id was generated."
] | 2022-01-19T09:58:55 | 2022-01-19T13:24:25 | 2022-01-19T13:23:30Z | NONE | {
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} | Between v2022.0.9 and v2022.0.10 calculating the phase diagram breaks. For a simple phase field (Mn, Fe, O) the energies above the hull are all 0 meV atom-1 in v2022.0.10 with entry in stable_entries and no entries in unstable_entries.
All entries should either be in stable_entries or unstable_entries
Working wi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2356 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2356/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2356/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2356/events | https://github.com/materialsproject/pymatgen/pull/2356 | 1,108,466,645 | PR_kwDOACgets4xSE3Z | 2,356 | Minor cleanup of bader_caller.py + new get_partial_charge() convenience function | {
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"\n[](https://coveralls.io/builds/45782579)\n\nCoverage decreased (-0.6%) to 83.33% when pulling **671fd7f6a15261715c594694e4e3aad5e4b47d6f on arosen93:rosen-bader** into **fd553a8e80935d77df285fed1a14d7bf63669c14 on materialsproject:master**.\n",
"Tha... | 2022-01-19T19:17:20 | 2022-01-25T18:25:49 | 2022-01-25T14:49:36Z | MEMBER | {
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} | I'll be adding a `chargemol_caller.py` soon, so this is a PR that does some minor cleanup of things I've found in `bader_caller.py` in the process.
- Add a new convenience function `get_partial_charge()`, which is just the negative of the `get_charge_transfer()`. This is to parallel the forthcoming `chargemol_caller... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2357 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2357/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2357/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2357/events | https://github.com/materialsproject/pymatgen/pull/2357 | 1,108,474,543 | PR_kwDOACgets4xSGiT | 2,357 | Create a ChargemolAnalysis command line caller (for DDEC6, CM5 analysis) | {
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"\n[](https://coveralls.io/builds/45815529)\n\nCoverage decreased (-0.7%) to 83.306% when pulling **c6d38b11dadf4ed5ada3f98cb7bf58a34960eb62 on arosen93:rosen-ddec** into **6753761b1f332b70507b8e019114ac65c45b5c75 on materialsproject:master**.\n",
"@ox... | 2022-01-19T19:26:21 | 2022-01-31T16:41:02 | 2022-01-31T16:39:31Z | MEMBER | {
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} | # Purpose
This PR introduces `pymatgen.command_line.chargemol_caller` with a `ChargemolAnalysis` class that functions in an analogous way as `BaderAnalysis` but for DDEC6/CM5 population analyses. It analyzes the output files from [Chargemol](https://sourceforge.net/projects/ddec/files/) and can also execute Chargemol ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2358 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2358/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2358/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2358/events | https://github.com/materialsproject/pymatgen/pull/2358 | 1,108,490,990 | PR_kwDOACgets4xSJ6s | 2,358 | Don't perform dict type-check on the MAGMOM flag in io.vasp.sets (fixes downstream Atomate issue) | {
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"\n[](https://coveralls.io/builds/45807775)\n\nCoverage decreased (-0.6%) to 83.328% when pulling **5792dcb1a66814c4390ad64b73dd2f899fa32cdd on arosen93:rosen-mags** into **d5370df167e92aa4293a1bd15cc49c327be46cbd on materialsproject:master**.\n",
"Tha... | 2022-01-19T19:46:06 | 2022-01-20T22:08:07 | 2022-01-20T22:08:06Z | MEMBER | {
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} | - Addresses https://github.com/materialsproject/pymatgen/commit/9cfef441c16fd4c68290b80bb0383d52a0a8c0fe#r64164646 by reverting the type-check on the MAGMOM key-value pair. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2359 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2359/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2359/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2359/events | https://github.com/materialsproject/pymatgen/issues/2359 | 1,108,506,427 | I_kwDOACgets5CEnc7 | 2,359 | Fix yaml.safe_load() deprecation warnings | {
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"Btw, `pyyaml` [also exports a `load()` function](https://pyyaml.org/wiki/PyYAMLDocumentation) so it wouldn't throw an error to use `pyyaml.load()` for people who don't have `ruamel.yaml` but it would no longer be \"safe\". Not sure if that's an issue? I guess we could monkey-patch it:\r\n\r\n```py\r\ntry:\r\n f... | 2022-01-19T20:05:24 | 2022-01-19T21:41:23 | 2022-01-19T21:41:23Z | MEMBER | {
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} | My `pytest` and `fireworks` logs are full of `yaml.safe_load()` deprecation warnings originating in `pymatgen` and `monty`.
```py
site-packages/monty/serialization.py:85: PendingDeprecationWarning:
load will be removed, use
yaml=YAML(typ='unsafe', pure=True)
yaml.load(...)
instead
ret... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2360 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2360/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2360/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2360/events | https://github.com/materialsproject/pymatgen/pull/2360 | 1,108,515,479 | PR_kwDOACgets4xSPDc | 2,360 | flake8 add per-file-ignores = __init__.py: F401 | {
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"This has become quite the opinionated PR with more monkey patching than expected.\r\n\r\nSince the `safe_load` method will be removed soon, something like the mess I'm creating here will become necessary unless `pymatgen` decides to be more opinionated about the YAML parser it requires users to have. I.e. by sayin... | 2022-01-19T20:16:10 | 2022-01-19T21:45:08 | 2022-01-19T21:44:05Z | MEMBER | {
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} | ~Closes #2359.~ Closes nothing.
#2359 was closed in d7cfd8a4a6a00fce1860f1a4d2ed0a3830520dbc. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2361 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2361/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2361/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2361/events | https://github.com/materialsproject/pymatgen/issues/2361 | 1,108,862,374 | I_kwDOACgets5CF-Wm | 2,361 | Incorrect Gvec generation in Wavecar class of pymatgen.io.vasp.outputs module | {
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"@RyanNKHall: Just a head's up, the line you want is probably\r\n\r\n```python\r\nself.encut = np.fromfile(f, dtype=np.float64, count=1)[0]\r\n```\r\nWithout the `[0]` indexing, `self.encut` is returned as a length-one array instead of a float.",
"Thanks @arosen93. I actually spotted this the other day too. It do... | 2022-01-20T04:56:22 | 2022-03-07T08:20:42 | 2022-03-07T08:19:27Z | NONE | {
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} | **Describe the bug**
Within the `pymatgen.io.vasp.outputs` module's `Wavecar` class is a function called `_generate_G_points` (line 5012) that generates the G vectors for the plane wave expansion of the wavefunction using the cutoff energy from the Wavecar file and the kpoints. This function fails to generate the corr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2362 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2362/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2362/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2362/events | https://github.com/materialsproject/pymatgen/pull/2362 | 1,109,165,041 | PR_kwDOACgets4xUVjd | 2,362 | Clean up conditional typing.Literal imports | {
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"@shyuep There's one error here that says to contact you about changes to an input set. In this case just a whitespace change.\r\n\r\n```py\r\n=================================== FAILURES ===================================\r\n_____________________ SetChangeCheckTest.test_sets_changed _____________________\r\n\r\ns... | 2022-01-20T11:08:20 | 2022-01-31T21:41:58 | 2022-01-25T14:47:47Z | MEMBER | {
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Also, brings `.pre-commit-config.yaml` up to date and adds `pyupgrade` commit hook. | {
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"Will have a look at it as soon as I am back from my vacation ... (On Monday)\r\n\r\nIt's just there to warn users if they use the POTCARs including these keywords. If you know how to fix it, please go ahead. Errors seem to be new, though...\r\n\r\nAnd, thanks for putting all the work into this. 🙂",
"I guess one... | 2022-01-20T15:34:00 | 2022-01-20T20:19:57 | 2022-01-20T20:19:57Z | MEMBER | {
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} | `class Lobsterin()._get_potcar_symbols()` causes [CI errors in `atomate`](https://github.com/hackingmaterials/atomate/runs/4871532128?check_suite_focus=true#step:8:115)
https://github.com/materialsproject/pymatgen/blob/fd553a8e80935d77df285fed1a14d7bf63669c14/pymatgen/io/lobster/inputs.py#L612-L633
```sh
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"This is definitely desired. I would be happy to discuss.",
"Thanks for the interest. Here are some considerations that I hope will be useful as a starting point.\r\n\r\nThe distinction between the `Molecule` and `Structure` objects always worked well for me in general. Other codes (e.g. ASE, aiida) handle all ca... | 2022-01-20T17:13:54 | 2022-05-26T18:15:13 | 2022-05-26T18:15:13Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
We (I and @davidwaroquiers) were thinking about what would be the best option to handle objects with partial periodic boundary conditions.
In particular this would be helpful for defining the inputs of codes that support calculations with this option... | {
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"\n[](https://coveralls.io/builds/45803835)\n\nCoverage decreased (-0.6%) to 83.33% when pulling **e181a7fb800d7dff1a1074bc0be25f10e8558034 on janosh:fix_get_potcar_symbols** into **fd553a8e80935d77df285fed1a14d7bf63669c14 on materialsproject:master**.\n... | 2022-01-20T19:18:55 | 2022-01-20T20:40:02 | 2022-01-20T20:19:58Z | MEMBER | {
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} | Closes #2363. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2366 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2366/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2366/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2366/events | https://github.com/materialsproject/pymatgen/issues/2366 | 1,111,687,357 | I_kwDOACgets5CQwC9 | 2,366 | np.bool/np.int deprecation warnings | {
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"Great, thanks for taking care of this! "
] | 2022-01-22T21:04:20 | 2022-01-23T00:08:05 | 2022-01-23T00:05:40Z | MEMBER | {
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} | Currently, Pymatgen has several areas where there are `np.bool` and `np.int` deprecation warnings. Similar to #2359, it would be nice to address this in part so `pytest` (here and in other downstream projects) isn't cluttered.
> c:\users\asros\github\pymatgen\pymatgen\analysis\structure_matcher.py:556: DeprecationWa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2367 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2367/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2367/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2367/events | https://github.com/materialsproject/pymatgen/issues/2367 | 1,111,696,009 | I_kwDOACgets5CQyKJ | 2,367 | Vasprun().final_energy does not report energy(sigma->0) for VASP 6 & Vasprun and Outcar final energies are inconsistent | {
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"I think the reason is mostly historical. And I am fine with changing everything to default to e_0_energy unless @mkhorton has any concerns.",
"Good to know. Based on the details below, I think it is actually **a VASP 6+ bug for `Vasprun`** but a historical decision for `Outcar`.\r\n\r\nI did some digging into th... | 2022-01-22T21:43:55 | 2022-01-25T02:32:46 | 2022-01-25T02:32:45Z | MEMBER | {
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} | @shyuep, @mkhorton: There is a bug with the `final_energy` property in `Vasprun` for VASP 6+, and the `final_energy` property in `Outcar` is somewhat unintuitive.
## Background
For the attached VASP 6 files below, there are the three types of energies in the output for the final step.
Vasprun.xml:
```
<i na... | {
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} | For wurtzite MnO, the description given by ICSD is as follows:
```
$ cat ICSD_CollCode262928.cif
#(C) 2021 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure. All rights reserved.
data_262928-ICSD
_database_code_ICSD 262928
_audit_creation_date 2012-08-01
_chemical_name_common 'Manganese oxi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2369 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2369/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2369/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2369/events | https://github.com/materialsproject/pymatgen/pull/2369 | 1,111,749,464 | PR_kwDOACgets4xc44S | 2,369 | Return the correct Vasprun().final_energy for VASP 6+ and change the default Outcar().final_energy to be energy(sigma->0) | {
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"@mkhorton -- this is ready for your review at your next convenience.",
"\n[](https://coveralls.io/builds/45904732)\n\nCoverage decreased (-0.6%) to 83.338% when pulling **c5b8d495e400e49a66aad90ddbb2ca31c91ee8f9 on arosen93:rosen-energy** into **48137... | 2022-01-23T02:17:49 | 2022-01-25T01:48:41 | 2022-01-25T01:28:34Z | MEMBER | {
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} | ## The Problem
This is to address #2367. In short, there are two issues:
1. `Vasprun().final_energy` does not report `e_0_energy` (the desired energy quantity) for VASP 6+. In an attempt to address the VASP 5.x.x bug documented [here](https://www.vasp.at/forum/viewtopic.php?f=3&t=16942) where `e_wo_entrp` and `e_0_en... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2370 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2370/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2370/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2370/events | https://github.com/materialsproject/pymatgen/issues/2370 | 1,111,769,561 | I_kwDOACgets5CREHZ | 2,370 | [Not actually a problem] Ionic step energies in Vasprun() w/ vdW interactions are missing the vdW component | {
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"Closed because of a misunderstanding on my part. Apologies. I missed the first three keys of the `vasprun.ionic_steps[-1]` dict, which show the expected values. The values I reported above were in the `electronic_steps` part of the dict. It's been a long day of debugging..."
] | 2022-01-23T04:24:06 | 2022-01-23T05:19:53 | 2022-01-23T05:15:06Z | MEMBER | {
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} | In troubleshooting my PR for #2369, I stumbled upon a different but related error involving `Vasprun` and vdW calculations (not sure if this is VASP6-specific or not, but it probably is).
For the attached `vasprun.xml.gz` file, doing
```python
from pymatgen.io.vasp.outputs import Vasprun
Vasprun('vasprun.xml.gz'... | {
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"\n[](https://coveralls.io/builds/45866319)\n\nCoverage decreased (-0.6%) to 83.344% when pulling **31f9f33cd3ea19aec9196163b285f8fbe512aace on arosen93:rosen-ase-props** into **4813709cbccd35543e192cef6b7cf78153624cd6 on materialsproject:master**.\n",
... | 2022-01-24T04:41:44 | 2022-01-25T18:06:15 | 2022-01-25T14:47:27Z | MEMBER | {
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} | This hopefully should be my last update in my quest to enhance the `AseAtomsAdaptor`.
In this PR:
1. Oxidation states are now passed from Pymatgen structure/molecule objects to ASE atoms objects. Since these aren't `site_properties`, they never got transferred. This is the main change.
2. Charges passed from Pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2372 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2372/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2372/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2372/events | https://github.com/materialsproject/pymatgen/pull/2372 | 1,112,677,141 | PR_kwDOACgets4xf1IV | 2,372 | Added file_path parameter to ComputedEntry and fixed entry_id in Vasprun.get_computed_entry | {
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"Sorry about the delay in reviewing this PR. However, I don't think file path is a key parameter that needs an attribute by itself. The entry object already has a \"data\" attribute that allows you to store variables in there. Can you rewrite this to just store the file path in the data attribute? Thanks.",
"@shy... | 2022-01-24T13:52:19 | 2023-01-17T16:03:10 | 2023-01-17T15:53:03Z | NONE | {
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} | ## Summary
Include a summary of major changes in bullet points:
* file_path parameter added to ComputedEntry
* fixed problem with generating entry_id in get_computed_entry method of Vasprun
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* Nothing else needs done. [WIP] added... | {
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"Thanks for reporting this. This is due to a recent change in the way yaml files are handled in ruamel.yaml. \r\nI just fixed it in the code."
] | 2022-01-24T14:16:49 | 2022-01-24T14:21:35 | 2022-01-24T14:20:58Z | NONE | {
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} | **Describe the bug**
Cannot configure POTCAR setup as "pmg config" fails to add keywords to .pmgrc.yaml
**To Reproduce**
Fresh install with conda:
$ conda create --name my_pmg python=3.8
$ conda activate my_pmg
$ conda install -c conda-forge pymatgen
run "pmg config --add", for example:
pmg config --add P... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2374 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2374/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2374/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2374/events | https://github.com/materialsproject/pymatgen/pull/2374 | 1,112,921,211 | PR_kwDOACgets4xgotM | 2,374 | Added property symbol_list to class SiteCollection. | {
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"Thanks for the suggested contribution. But since this is a method that is a one-liner and not that frequently used, I am not in favor of adding it to the already long list of Structure properties/methods.",
"Thanks for your comment @shyuep. I agree that there are already plenty of methods / properties in `Struct... | 2022-01-24T17:12:45 | 2022-01-24T18:17:21 | 2022-01-24T17:18:32Z | CONTRIBUTOR | {
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} | ## Summary
* Added a new property, symbol_list, within the class SiteCollection in core/structure.py. This property returns the list of chemical symbols of all atoms in the collection. This property may be useful for postprocessing purposes, as the "species" property does not return a list of strings.
## Addition... | {
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"Thanks. Can you add a unittest for the non-Laue part of the code pls? The tests should be in pymatgen/core/tests/test_surface.py",
"Hello, I modified the function test_get_symmetric_sites in pymatgen/core/tests/test_surface.py to test the new version of the get_symmetric_site function.\r\n\r\n> Thanks. Can you a... | 2022-01-24T18:15:44 | 2022-05-31T16:36:46 | 2022-05-31T16:36:46Z | NONE | {
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} | ## Summary
* The current version of get_symmetric_site relies on slabs to have Laue symmetry. Treating a slab as a 3D object introduces symmetry operators that duplicate a site to a neighbouring cell in the z direction. This introduces two possible issues:
* some of the operators will duplicate the point to be ... | {
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"You should open an issue with pycdt. As noted [here](https://pymatgen.org/#major-announcement-v2022-0), `from pymatgen import Structure, Element` should now be `from pymatgen.core import Structure, Element`. You can refer to the aforementioned page for additional details.\r\n\r\npycdt will either need to update th... | 2022-01-25T02:28:01 | 2022-03-07T19:10:58 | 2022-03-07T19:10:58Z | NONE | {
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} | When I used pycdt, it give error as:
it did not happen in old version.
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/bin/pycdt", line 4, in <module>
__import__('pkg_resources').run_script('pycdt==2.0.5', 'pycdt')
File "/public1/home/sch1893/apps/miniconda3/envs/pycdt/lib/python3.9/site-packages/pk... | {
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"I already fixed it in the latest release. BUt if your pymatgen is 2022.0.17, that is the old version.",
"Hi,\r\nI have a similar problem:\r\nwhen enter: pmg config --add PMG_VASP_PSP_DIR /home/myname/PYMATGEN_POTCAR/POT_GGA_PAW_PBE/\r\nerror:\r\n**Existing /home/myname/.pmgrc.yaml backed up to /home/linwen/.pmgr... | 2022-01-25T05:09:52 | 2022-03-27T07:53:59 | 2022-01-25T15:54:36Z | NONE | {
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```python
Traceback (most recent call last):
File "/usr/local/bin/pmg", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.7/dist-packages/pymatgen/cli/pmg.py... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2378 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2378/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2378/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2378/events | https://github.com/materialsproject/pymatgen/issues/2378 | 1,113,528,470 | I_kwDOACgets5CXxiW | 2,378 | pmg command becomes not to work | {
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"You need to replace the `<MY_PSP>`, etc. with the actual variables relevant for your system. ",
"Dear shyuep, \r\n\r\nThank you for your comment.\r\nI reset the locations of potcar files like\r\n`pmg config -p ~/POT_GGA_PAW_PBE_52 ~/vasp_potentials`\r\n`pmg config --add PMG_VASP_PSP_DIR ~/vasp_potentials`\r\n\r\... | 2022-01-25T07:35:10 | 2022-01-26T02:30:48 | 2022-01-25T14:54:25Z | NONE | {
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} | Dear all,
I installed pymatgen through conda. Installation of pymatgen was OK.
However, after setting up the location of POTCAR files according to the instruction in the official web page, pmg command become not t work anymore. In the the setting up of the POTCAR files, I run these command.
> pmg config -p <EXTR... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2379 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2379/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2379/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2379/events | https://github.com/materialsproject/pymatgen/pull/2379 | 1,114,009,850 | PR_kwDOACgets4xkKXz | 2,379 | Flynt | {
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"\n[](https://coveralls.io/builds/45936403)\n\nCoverage decreased (-0.6%) to 83.373% when pulling **8b697ed4fa702bb2b7ddefb4d9fb9a60fa6a3657 on janosh:flynt** into **5a05f662d35ab3c0d93f252f1c73e813e87c75f6 on materialsproject:master**.\n"
] | 2022-01-25T15:11:19 | 2022-01-25T19:29:19 | 2022-01-25T19:01:30Z | MEMBER | {
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} | [`flynt`](https://github.com/ikamensh/flynt) auto-converts old string literal formatting to [faster](https://realpython.com/python-f-strings/#speed) and more concise f-strings. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2380 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2380/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2380/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2380/events | https://github.com/materialsproject/pymatgen/pull/2380 | 1,114,285,248 | PR_kwDOACgets4xlEiQ | 2,380 | flynt --aggressive | {
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"\n[](https://coveralls.io/builds/45955901)\n\nCoverage decreased (-0.6%) to 83.372% when pulling **04d7a99182cfea007e048b1e5700208bb4e721c3 on janosh:flynt-aggressive** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n"
] | 2022-01-25T19:35:03 | 2022-01-26T19:04:01 | 2022-01-26T18:28:34Z | MEMBER | {
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"\n[](https://coveralls.io/builds/46011293)\n\nCoverage decreased (-0.6%) to 83.39% when pulling **0d26db1b7167db6efa81b3192317609efa221bee on jmmshn:defect_finder** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Tha... | 2022-01-26T00:52:06 | 2022-02-21T03:16:06 | 2022-02-21T03:16:06Z | CONTRIBUTOR | {
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* Added function to find the weighted average of positions in a periodic lattice
* Added test
This is in preparation for a provenance agnostic defect position identification | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2384 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2384/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2384/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2384/events | https://github.com/materialsproject/pymatgen/issues/2384 | 1,114,745,156 | I_kwDOACgets5CcalE | 2,384 | structure.as_dict()["charge"] is None even though structure.charge == 0 | {
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"I agree. As for why it is self._charge, I think that stores the input charge given by the user. But in other cases, the charge of the structure is given by the sum of the oxidation states of the species where available. In general, charge on a structure is pretty arbitrarily defined. "
] | 2022-01-26T08:20:19 | 2022-01-26T18:36:32 | 2022-01-26T18:36:32Z | MEMBER | {
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from pymatgen.core import Structure
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
print(structure.charge) # prints 0
print(structure.as_dict()["charge"]) # prints None
assert structure.charg... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2385 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2385/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2385/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2385/events | https://github.com/materialsproject/pymatgen/pull/2385 | 1,114,750,679 | PR_kwDOACgets4xmkHR | 2,385 | Autoflake | {
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"\n[](https://coveralls.io/builds/45961062)\n\nCoverage decreased (-0.6%) to 83.371% when pulling **c3592de6d003fd0439af90d3ddf19bd5c0b81b4c on janosh:autoflake** into **6c31f7e38268986bd23110c2fbd4f14a09042a2a on materialsproject:master**.\n"
] | 2022-01-26T08:26:47 | 2022-01-26T19:04:00 | 2022-01-26T18:28:13Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2386 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2386/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2386/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2386/events | https://github.com/materialsproject/pymatgen/issues/2386 | 1,115,046,053 | I_kwDOACgets5CdkCl | 2,386 | crystal orientation of slab in all directions | {
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"Not quite sure what you mean. If you are referring to the lattice directions, that can be obtained from the Slab.lattice object.",
"Ok, maybe my question was not clear.\r\nSuppose that I created a slab that has the crystal direction say [1-100] (for HCP family as an example) of the slab surface. Now, I want to k... | 2022-01-26T13:55:47 | 2022-01-27T04:30:42 | 2022-01-26T14:36:24Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2387 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2387/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2387/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2387/events | https://github.com/materialsproject/pymatgen/pull/2387 | 1,115,108,792 | PR_kwDOACgets4xnvV7 | 2,387 | Fix readme badges | {
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"While we're at it, what do you think of converting the readme to Markdown? RST is a pain to write.",
"\n[](https://coveralls.io/builds/45969046)\n\nCoverage decreased (-0.6%) to 83.373% when pulling **dfd56f6706c44ef35716280786fe796b6fcbd025 on janosh... | 2022-01-26T14:51:41 | 2022-01-27T08:10:07 | 2022-01-26T18:26:48Z | MEMBER | {
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} | Follow-up to #2351.
- uniform shield.io readme badges
- brought onto 1 line
- fix GH CI badge
- add PyPI download badge
## Before
## After
![Screen Shot 2022-01-... | {
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"Pls add a test to make sure the new behavior is correct. Thanks.",
"\n[](https://coveralls.io/builds/45976139)\n\nCoverage decreased (-0.6%) to 83.375% when pulling **b706b6560ea94f1444bb48d0cdb960b255ec850d on arosen93:rosen-charge** into **6c31f7e38... | 2022-01-26T16:39:16 | 2022-01-26T18:36:43 | 2022-01-26T18:27:50Z | MEMBER | {
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"Thanks. I don't have a problem with this. The repr is purely for end user readability."
] | 2022-01-26T18:19:23 | 2022-01-26T19:03:11 | 2022-01-26T18:26:11Z | MEMBER | {
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} | Override `Entry.__repr__` in `PDEntry` to include the `name` if its not the fallback value of reduced composition.
**Before**
```py
PDEntry("LiFeO2", 53, name="mp-757614")
>>> PDEntry : Li1 Fe1 O2 with energy = 53.0000
```
**After**
```py
PDEntry("LiFeO2", 53, name="mp-757614")
>>> PDEntry : Li1 Fe1 O2... | {
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"I already fixed it."
] | 2022-01-26T18:46:46 | 2022-01-26T20:09:17 | 2022-01-26T20:09:16Z | MEMBER | {
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"\n[](https://coveralls.io/builds/45980918)\n\nCoverage decreased (-0.6%) to 83.375% when pulling **4f87d606bc831e3294ffa2fd0c0c0a93f80e3d35 on janosh:compat.process_entry** into **a13843919e6fe57fad7e1056b2af260462bb76cb on materialsproject:master**.\n"... | 2022-01-26T20:33:32 | 2022-01-27T16:05:58 | 2022-01-27T16:05:58Z | MEMBER | {
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"@shyuep There are some YAML related `mypy` errors. Not sure if that's related to the recent YAML changes:\r\n\r\n```\r\nmypy pymatgen/entries/correction_calculator.py\r\n\r\npymatgen/entries/correction_calculator.py:480: error: \"YAML\" has no attribute \"YAML\"\r\npymatgen/entries/correction_calculator.py:488: er... | 2022-01-27T11:26:33 | 2022-01-28T06:43:57 | 2022-01-27T16:05:21Z | MEMBER | {
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} | Python 3.6 is [EOL since 23 Dec 2021](https://endoflife.date/python) and regular `dict`s are insertion-ordered since Python 3.7 so safe to replace `OrderedDict`. | {
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"\n[](https://coveralls.io/builds/46004527)\n\nCoverage decreased (-0.6%) to 83.38% when pulling **7fd109a7143350b5dba492dfb4aa755b5a602d8a on vorwerkc:qe_kpoints_output** into **a13843919e6fe57fad7e1056b2af260462bb76cb on materialsproject:master**.\n",
... | 2022-01-27T14:57:47 | 2022-01-27T16:04:49 | 2022-01-27T16:04:49Z | CONTRIBUTOR | {
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Additionally, the pull request adds a news test for the output of k-grids in Quantum Espresso input files. | {
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"\n[](https://coveralls.io/builds/46012333)\n\nCoverage decreased (-0.6%) to 83.385% when pulling **08ff11c436018a2ffd8c8a81fdfd5d0865d83edc on JaGeo:master** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-27T18:13:22 | 2022-01-27T20:17:34 | 2022-01-27T20:17:27Z | MEMBER | {
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} | ## Summary
This pull request fixes an issue with gzipped DOSCAR files in the Lobster module.
I also included a test. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2395 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2395/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2395/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2395/events | https://github.com/materialsproject/pymatgen/pull/2395 | 1,116,660,198 | PR_kwDOACgets4xsv-P | 2,395 | Q-Chem Updates | {
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"\n[](https://coveralls.io/builds/46014173)\n\nCoverage decreased (-0.6%) to 83.39% when pulling **9c3b416d6dd77b94189a8cb4e3a3510375877a34 on samblau:qchem** into **72849371a03ffda519e1f590776001b9076c9cd8 on materialsproject:master**.\n",
"Thanks."
] | 2022-01-27T19:31:20 | 2022-01-27T20:17:11 | 2022-01-27T20:17:06Z | CONTRIBUTOR | {
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} | ## Summary
All minor points, though important:
* Fixed SCF parsing in the presence of a specific warning
* Parsing new errors associated with failing CPSCF in analytic frequencies to enable Custodian handling
* Multiple NBO7 parsing fixes + new tests
| {
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"\n[](https://coveralls.io/builds/46044516)\n\nCoverage decreased (-0.6%) to 83.392% when pulling **b83b8031d324e387c02c6deb1b2f9deebf8cb9ac on adam-kerrigan:masked_sphere_correction** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:m... | 2022-01-28T17:30:03 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* The mask_sphere function returned a mask of distance values that doesn't vary with site
* Changed this use the get_points_in_sphere from Lattice
## TODO (if any)
* A discussion about what this returns:
* I think just returning the indices ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2397 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2397/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2397/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2397/events | https://github.com/materialsproject/pymatgen/pull/2397 | 1,118,289,397 | PR_kwDOACgets4xx994 | 2,397 | Delete overdue deprecations | {
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"\n[](https://coveralls.io/builds/46060118)\n\nCoverage decreased (-0.6%) to 83.451% when pulling **ce3615803666b28726e56f1a1fd11c3676b06c60 on janosh:drop-deprecated** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"... | 2022-01-29T18:07:58 | 2022-01-31T16:39:10 | 2022-01-31T16:37:44Z | MEMBER | {
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} | Noticed that a bunch of stuff has deprecation messages saying it would be removed in pmg `2020.*`. This PR removes those functions and methods since we're already at v2022.1.24. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2398 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2398/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2398/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2398/events | https://github.com/materialsproject/pymatgen/issues/2398 | 1,118,298,501 | I_kwDOACgets5Cp-GF | 2,398 | Is MaterialsProjectCompatibility deprecated? | {
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} | MaterialsProjectCompatibility does not issue a deprecation warning. @rkingsbury said it used to. Was this removed intentionally? Should it be reinstated?
```py
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
mpc = MaterialsProjectCompatibility()
processed_entries = mpc.process_entries(u... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2399 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2399/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2399/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2399/events | https://github.com/materialsproject/pymatgen/pull/2399 | 1,118,461,970 | PR_kwDOACgets4xyePf | 2,399 | ASEAtomsAdaptor: magmom/charge site properties in Structure/Molecule become initial (rather than final) magmoms/charges in Atoms object | {
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"\n[](https://coveralls.io/builds/46075357)\n\nCoverage decreased (-0.6%) to 83.391% when pulling **e578fca0d451231cf18cf92c9a17e0353b8b18ce on arosen93:rosen-asemags** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n"
] | 2022-01-30T08:49:20 | 2022-01-31T16:38:43 | 2022-01-31T16:38:43Z | MEMBER | {
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} | **Summary**:
In this PR, the naming convention for the magnetic moments (and charges) are modified such that "magmom" in the pymatgen `Structure`/`Molecule` object is set as the _initial_ magnetic moment in ASE rather than the _final_ when using the `ASEAtomsAdaptor`. Looks like I still had a bit of refinement left to... | {
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"\n[](https://coveralls.io/builds/46095020)\n\nCoverage decreased (-0.6%) to 83.425% when pulling **d60d53273b721b5d09580552c78bcbae293755be on arosen93:rosen-zeo** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
"Can ... | 2022-01-30T08:59:52 | 2023-06-03T02:25:23 | 2022-01-31T20:45:24Z | MEMBER | {
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} | Closes #2255.
The Zeo++ installation steps in `pymatgen.io.zeopp` are extremely out of date. I've modernized them and added the reference that should be cited when using Zeo++. | {
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"\n[](https://coveralls.io/builds/46064662)\n\nCoverage decreased (-0.6%) to 83.394% when pulling **76088c3f1e8512f50f792b753a0ed65c237ac625 on janosh:gha-auto-pip-cache** into **07794afb624f7613b3dbcebdf0034cab4c9ee7ea on materialsproject:master**.\n",
... | 2022-01-30T10:10:21 | 2022-01-31T16:37:13 | 2022-01-31T16:36:11Z | MEMBER | {
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https://github.blog/changelog/2021-11-23-github-actions-setup-python-now-supports-dependency-caching
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https://api.github.com/repos/materialsproject/pymatgen/issues/2402 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2402/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2402/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2402/events | https://github.com/materialsproject/pymatgen/issues/2402 | 1,118,675,902 | I_kwDOACgets5CraO- | 2,402 | Highlight selected points in plotly PDPlotter | {
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"Would also be nice to be able to pass in additional information for the hover labels i.e. a DOI for the entry etc ",
"Additionally if using `PDEntry` `entry_id = getattr(entry, \"entry_id\", \"no ID\")` doesn't grab the name as `PDEntry` calls the identifier `name`",
"> Sometimes I want to plot a phase diagram... | 2022-01-30T19:04:52 | 2023-06-03T00:55:13 | 2023-06-03T00:55:13Z | CONTRIBUTOR | {
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} | Sometimes I want to plot a phase diagram and highlight points that are not on the convex hull. It would be nice to be able to give a list of entry names that would then be highlighted in a separate list to "stable" and "above hull".
@mattmcdermott Is this something that seems reasonable to be able to add? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2403 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2403/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2403/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2403/events | https://github.com/materialsproject/pymatgen/issues/2403 | 1,118,703,913 | I_kwDOACgets5CrhEp | 2,403 | The Vasprun parser does not store site_properties in the ionic_steps structure objects | {
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"Closed because, to my surprise, the total magnetization doesn't appear to be in the `vasprun.xml` file. I guess that can only be parsed from OUTCAR."
] | 2022-01-30T21:04:05 | 2022-01-30T23:07:16 | 2022-01-30T23:07:15Z | MEMBER | {
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} | Example:
```python
from pymatgen.io.vasp.outputs import Vasprun
v = Vasprun('vasprun.xml.gz')
v.ionic_steps[-1]["structure"].site_properties
```
The above example does not return "magmom" site properties in the returned structure object.
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/796691... | {
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