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PR_kwDOACgets486S6q
| 2,614
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Class to handle Thermal displacements matrices
|
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[
"\n[](https://coveralls.io/builds/51541115)\n\nCoverage increased (+0.05%) to 63.567% when pulling **fccd68f68f7f829601e61efec48745f2cc5d2e92 on JaGeo:thermal_displacements** into **5ec1c1e40607bc52112308ee02dbca769e883ade on materialsproject:master**.\n",
"I don't think the failures come from my code. If there are any suggestions with regard to the structure, I am very happy to adapt it."
] | 2022-08-09T19:49:32
| 2022-08-09T21:34:20
|
2022-08-09T21:34:20Z
|
MEMBER
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## Summary
I have added a class and a function to handle and convert thermal displacement matrices from phonopy and potentially other codes.
This is a partial re-implementation of this matlab code from my PhD https://github.com/JaGeo/MolecularToolbox/
Tests and documentation have been added.
|
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PR_kwDOACgets48-tta
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Fix misleading doc string for `get_entry_by_material_id` `inc_structure` kwarg
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"\n[](https://coveralls.io/builds/51719492)\n\nCoverage increased (+0.03%) to 63.269% when pulling **84b15743d7743c290d2a9dff2ca3642c3422984c on janosh:fix-mprester-inc_structure-doc-str** into **dda4cd31af37e1488d3c4f280d96bcda4aeabc97 on materialsproject:master**.\n"
] | 2022-08-10T18:52:56
| 2022-08-17T17:38:01
|
2022-08-17T17:31:31Z
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MEMBER
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The docs for [`MPRester.get_entries_in_chemsys()`](https://github.com/janosh/pymatgen/blob/cb7620d5488b41798791f3f8ed7229bed9b5071d/pymatgen/ext/matproj.py#L863) and `MPRester.get_entry_by_material_id()` seem to be incorrect:
https://github.com/janosh/pymatgen/blob/cb7620d5488b41798791f3f8ed7229bed9b5071d/pymatgen/ext/matproj.py#L887-L891
```txt
inc_structure (str): If None, entries returned are ComputedEntries. If inc_structure="final",
ComputedStructureEntries with final structures are returned. Otherwise, ComputedStructureEntries with initial structures are returned.
```
It's the other way around: if `inc_structure="initial"`, the initial structure is returned, else the relaxed one.
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[WIP] Update IEEE conversion routine for tetragonal systems
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[
"Hi @montoyjh,\r\n\r\nCan you expand on this point:\r\n\r\n> Fix an issue with precision on prior test data\r\n\r\nI don't mind adding an additional test here if necessary, but not sure what else required.",
"Bumping this because it seems like a serious bug. If there's no additional context for the precision issue, I'd like to go ahead and merge with a minimal test added for the problem system.",
"The tests need to be supplied first. ",
"Seems like there might be more issues with the tensor rotations, as per my #3059 "
] | 2022-08-10T23:07:59
| 2024-08-03T19:01:57
|
CONTRIBUTOR
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## Summary
Tentative fix for rotating tensorial properties for tetragonal systems.
## TODO (if any)
* Need to add data for testing tetragonal system that previously failed
* Fix an issue with precision on prior test data
|
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PR_kwDOACgets49CemU
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Small extension of Thermal displacement matrices
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[
"Messed something up with git. If the tests pass, everything should be fine from my side.",
"Not sure what is going on with the other tests at the moment. "
] | 2022-08-11T16:09:43
| 2022-08-11T17:27:45
|
2022-08-11T17:27:44Z
|
MEMBER
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## Summary
I have now also added an implementation of a quality criterion for computed thermal displacement matrices as defined in https://doi.org/10.1039/C9CE00794F
Once can now also initialize the class from thermal displacement matrices as defined in the cif only.
Very tiny fixes to the documentation have been added as well.
No further extensions are planned for now. Maybe in the upcoming months, some extensions will follow. I would especially be happy to have functionality to read thermal displacements from cif files and be able to connect this to this class.
|
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| 1,336,513,566
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I_kwDOACgets5PqZQe
| 2,618
|
Unexpected behavior in CrystalNN: very low coordination numbers when adsorbates are present
|
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[] | 2022-08-11T21:27:50
| 2022-08-11T21:29:50
|
MEMBER
|
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I have the following structure of CO on a Rh surface. When using `CrystalNN()` on a surface Rh atom without an adsorbate, I get a coordination number of 9. When getting the coordination number of the surface Rh with CO bound to it, I get a coordination number of 1. One would expect the coordination number of the Rh with CO on it to be 1 greater than its neighboring sites. I'm not sure that this is a bug, but it's definitely unexpected! I have to dig into the root cause. @mkhorton, you might be interested.
<img width="701" alt="image" src="https://user-images.githubusercontent.com/8674072/184244987-2be207eb-9621-4472-9d5d-b16fd1114c4c.png">
```python
from pymatgen.core import Structure
from pymatgen.analysis.local_env import CrystalNN
s = Structure.from_file('test.cif')
cnn = CrystalNN()
cn1 = cnn.get_cn(s,0) # Rh surface site with CO (returns 1)
cn2 = cnn.get_cn(s,1) # Rh surface site without CO (returns 9)
```
[test.cif.txt](https://github.com/materialsproject/pymatgen/files/9312227/test.cif.txt)
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PR_kwDOACgets49HM0_
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|
Fix ordering of args in DOS docstrings
|
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[
"\n[](https://coveralls.io/builds/51633221)\n\nCoverage decreased (-0.002%) to 63.232% when pulling **b9b934127f8f0e53fb6c92ce595850191630761b on arosen93:rosen-dbands** into **fd83fe16afe1cb864abf8e7ca1e9dbc2f0888da8 on materialsproject:master**.\n"
] | 2022-08-12T18:53:06
| 2022-08-12T20:00:58
|
2022-08-12T19:14:55Z
|
MEMBER
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The docstrings for various DOS properties had the args in the wrong order. I updated the docstrings to match the order in the function calls.
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PR_kwDOACgets49SIXf
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|
Added 'get_orbit_and_generators'-method to SpaceGroup to class.
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[
"\n[](https://coveralls.io/builds/51715669)\n\nCoverage decreased (-0.02%) to 63.222% when pulling **2fd2db7a0d9a3ae3b8e1949524d0d36e0df4e368 on nheinsdorf:master** into **dda4cd31af37e1488d3c4f280d96bcda4aeabc97 on materialsproject:master**.\n",
"Great. Thanks.",
"Missed this PR when it was opened, also thanks! Super useful\r\n\r\nOn a test note, there's a subtle point about whether tests should be fully deterministic or not. Having randomness in a test can be useful (e.g., see [hypothesis](https://hypothesis.readthedocs.io/) for a formalized version of this) but can also make the test failures difficult to re-produce if there is a bug.\r\n\r\nIf using this approach in a future PR, one useful thing to do would be to add additional info to the `assert` statement, e.g. here:\r\n\r\n`self.assertLessEqual(len(orbit), sg.order, f\"{p=}\")`\r\n\r\nThis way, if this `assert` fails, we still see the value of `p` so we can go back to reproduce the bug."
] | 2022-08-16T23:28:41
| 2022-08-26T20:42:38
|
2022-08-21T16:14:53Z
|
CONTRIBUTOR
|
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## SUMMARY
I added a method to the SpaceGroup class that returns both the orbit (like the 'get_orbit'-method does) as well as the symmetry operations that generate it. As opposed to 'get_orbit' the method makes sure that the first element of the orbit is the point that has been passed to the function. Therefore the first element in the list of generators that are returned is always the identity operation.
A test making sure that this is always true has been implemented.
The above functionality is useful if a physical property (e.g. angular momentum) that needs to obey the crystal symmetry is assigned to a given site. The user can then generate the corresponding properties of the other sites of the orbit by using the generators of the orbit.
## TODO
It would be probably nice to implement this for PointGroup as well
|
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PR_kwDOACgets49U-UB
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|
Lobsterin generation extension
|
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[
"\n[](https://coveralls.io/builds/51828534)\n\nCoverage increased (+0.09%) to 63.351% when pulling **6e9529df415c3305551b434e6971a8d578dabfb4 on naik-aakash:lobsterin_generation_extension** into **e1be8691d5efb0ea037b7edc964fd59dc41340ef on materialsproject:master**.\n",
"## Summary\r\n\r\n* renamed option `standard_with_comp_range` to `standard_with_energy_range_from_vasprun` (reason : method objective is more clearer)\r\n* updated unit_test corresponding to it.\r\n\r\n",
"Hi @shyuep, I think this is all I intended to implement for now. \r\n\r\nPlease look and let me know if you have some feedback on these changes. If not, then it could be merged. :)",
"Thanks."
] | 2022-08-17T14:19:47
| 2024-01-10T12:23:03
|
2022-08-23T12:54:39Z
|
CONTRIBUTOR
|
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## Summary
* Added new option `standard_with_comp_range` for generating lobsterin files using vasp
* Added simple unit_test corresponding this new changes
|
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Integrate `pymatgen-ext-matproj` addon package
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[
"Please do not merge until I personally review this PR. @mkhorton ",
"\n[](https://coveralls.io/builds/51755597)\n\nCoverage decreased (-0.06%) to 63.208% when pulling **9228209451e89f4eb76d33ad7fc6d6acce460319 on munrojm:master** into **beac8d5361d8f5332c7335be3ce31b41cb131e31 on materialsproject:master**.\n",
"@shyuep @mkhorton happy to make whatever changes you both feel are necessary. ",
"Many thanks @munrojm! I'll pull + test soon. Let me know if you'd like a TestPyPI release too, for extra verification.",
"Thanks @mkhorton . I think a TestPyPI release is probably a good idea.",
"Hi @munrojm, this looks good! Switching between new/legacy APIs works well.\r\n\r\nNot officially approving this yet, have a few comments first, then we can get a TestPyPI release out and do some extra testing.\r\n\r\nFor this PR:\r\n\r\n* I would add a mention of `pymatgen-ext-matproj` to [`addons.rst`](https://github.com/materialsproject/pymatgen/blob/master/docs_rst/addons.rst)\r\n\r\nFor `pymatgen-ext-matproj` package:\r\n\r\n* Perhaps put all the legacy code into a separate file (say, `legacy.py`), to make the `client.py` cleaner and easier to parse.\r\n* I have some suggestions for the docstrings:\r\n * Replace \"old and new\" with \"new and legacy\"\r\n * Replace \"At the current moment, full parity between old and new API MPRester has not been implemented. This will be resolved in the near future. Power users of the old API should not use the new API until all such issues are resolved.\" with \"Consult the Materials Project documentation at ... for advice on which API to use.\" since (1) I'm not expecting parity (does this mean full backwards compatibility, etc.?) and (2) it's easier to update the docs and better to have a single source-of-truth for this advice.\r\n * Slight edit to \"You are using the legacy MPRester, which is deprecated. If you are not a power user, ie., you do not have a lot of legacy code that uses many different MPRester methods, it is recommended you get a new API key from the new Materials Project front end. Once you use get your new API key, using the new API key will automatically route you to using the new MPRester.\", perhaps, \"You are using the legacy MPRester. This version of the MPRester will no longer be updated. To access the latest data with the new MPRester, obtain a new API key from ... and consult the docs at ... for more information.\"\r\n * I would remove \"It is not recommended, but if you would like to select the specific version of the MPRester, you can initialize either _MPResterNew or _MPResterLegacy directly.\" If you moved the legacy MPRester into a separate file, it wouldn't need the `_`, and people could import it from, say, `pymatgen.ext.matproj.legacy` as they see fit.\r\n* Consider using `__new__` instead of `__init__` to return the correct class depending on API key, e.g. the legacy or new API. This will ensure that `type(MPRester)` will give more useful information (e.g. `pymatgen.ext.matproj.legacy.MPRester` or `mp_api.client.MPRester` accordingly).\r\n\r\nWith these suggestions in mind, maybe something like this could work?\r\n\r\n```\r\nclass MPRester:\r\n \"\"\"\r\n A convenience class to switch between new and legacy API.\r\n \r\n The new API requires an API key from ... and will return an\r\n instance of mp_api.client.MPRester\r\n \r\n More information on the new API is available at: \r\n \r\n The legacy API requires an API key from ... and will return \r\n an instance of pymatgen.ext.matproj.legacy.MPRester\r\n \r\n More information on the legacy API is available at: ...\r\n \r\n For advice on which API to choose, consult ...\r\n \"\"\"\r\n \r\n def __new__(cls, api_key, *args, **kwargs):\r\n \r\n if not api_key:\r\n raise ValueError(\"Please supply an API key. You can retrieve an API key from...\")\r\n \r\n # new API\r\n if len(api_key) == 32:\r\n return MPResterNew(api_key, *args, **kwargs)\r\n # legacy API\r\n elif len(api_key) == 16:\r\n return MPResterLegacy(api_key, *args, **kwargs)\r\n \r\n raise ValueError(f\"API key {api_key} is in an unknown format. Please check your API key at ...\")\r\n```\r\n\r\nLet me know what you think!",
"Thanks @mkhorton! No disagreements on my end. I'll make the suggested changes.",
"I should add that once it's on TestPyPI I want to do a few rounds of installation testing via different installation methods, just to fully satisfy myself there's no strange dependency issues we haven't accounted for -- I think we should be fine.\r\n\r\nFrom a quick audit, `robocrys` is the only major dep formally outside of MP and requires `matminer` so this may actually be an issue (it has very permissive dependencies itself otherwise though, and nothing else exceptional). We might also want to un-pin specific versions of `pydantic` and `pybtex` from `emmet-core` (the former is in `monty` too, and the latter is in `pymatgen`) and specify minimum versions for these instead.\r\n\r\nI might suggest, in this PR, that we put \"pymatgen-ext-matproj>=0.0.2,<1\" in the `setup.py` too, just in case we need to break something in future.",
"A few critical issues:\r\n1. Why do we need pymatgen to depend on pymatgen-ext-matproj, which then depends on mp-api? This kind of structure is rather convoluted. Either mp-api is integrated into pymatgen-ext-matproj or pymatgen-ext-matproj is integrated into pymatgen itself. There shouldn't be three layers of dependencies, which in turn have more dependencies.\r\n2. Why is pymatgen-ext-matproj not a public repo?\r\n3. I don't seem to see mp-api package within the materialsproject org. So I have no way to review the dependencies.\r\n4. In general, I do not like too many hard dependencies. Only things that are absolutely critical for 80% functionality should be within the dependency tree. I am not sure how robocys/matminer fits into a API package. Again, I have no way of seeing how it is structured.",
"> Why do we need pymatgen to depend on pymatgen-ext-matproj, which then depends on mp-api? This kind of structure is rather convoluted. Either mp-api is integrated into pymatgen-ext-matproj or pymatgen-ext-matproj is integrated into pymatgen itself. There shouldn't be three layers of dependencies, which in turn have more dependencies.\r\n\r\nThe issue is that I don't think it makes sense for the MP API client to live as an addon package to pymatgen. If we don't want to have that kind of structure, then I would vote to integrate the legacy client code into mp-api and make it an explicit dependency of pymatgen. I recognize others may disagree with me here.\r\n\r\n> Why is pymatgen-ext-matproj not a public repo?\r\n\r\nMy intention was to keep it private while we work out integration details to avoid confusing people who might stumble upon it.\r\n\r\n> I don't seem to see mp-api package within the materialsproject org. So I have no way to review the dependencies.\r\n\r\nhttps://github.com/materialsproject/api\r\n\r\n> In general, I do not like too many hard dependencies. Only things that are absolutely critical for 80% functionality should be within the dependency tree. I am not sure how robocys/matminer fits into a API package. Again, I have no way of seeing how it is structured.\r\n\r\nAgreed, the problem dependencies are introduced via emmet-core (https://github.com/materialsproject/emmet/blob/main/emmet-core/setup.py). I vote we make robocrys and the pymatgen analysis addon packages optional there to address this.\r\n"
] | 2022-08-17T22:44:47
| 2022-09-01T19:13:32
|
2022-09-01T19:13:32Z
|
MEMBER
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## Summary
This PR removes the `MPRester` code contained in `pymatgen.ext.matproj` and replaces it with an updated client in the external `pymatgen-ext-matproj` addon package. This addon provides access to both the updated and legacy Materials Project API.
## Additional dependencies introduced (if any)
`pymatgen-ext-matproj` is added to the dependency list which itself is dependent on the new `mp-api` package. This introduces a few other dependencies: `emmet-core`, `pydantic`, `maggma`, `mpcontribs-client`. These additions do not cause any issues.
## 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:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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PR_kwDOACgets49ZsOe
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Structure Graphs from Lobster Data - Update
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[
"Automatic tests have't been triggered.",
"I think the precommit leads to these errors in pylint. It reformats the files in such a way that the lines are too long. I guess I have to go into the pre-commit config and see how to fix this.\r\n\r\nWill also try to fix the other issue.",
"\n[](https://coveralls.io/builds/51779192)\n\nCoverage increased (+0.1%) to 63.362% when pulling **4e6d649bc47fe7eda0e387eba2d3fbecb6e43fa0 on JaGeo:lobster_graph2.0** into **beac8d5361d8f5332c7335be3ce31b41cb131e31 on materialsproject:master**.\n",
"Fixed everything. Introduced a side effect that I hadn't anticipated. All tests are passing now.",
"This was the last change from my side.",
"Great. Thanks."
] | 2022-08-18T15:25:12
| 2022-08-21T16:13:22
|
2022-08-21T16:13:14Z
|
MEMBER
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## Summary
I have extended the structure graphs that can be derived by Lobster.
To do so, I have extended the method `with_local_env_strategy` to have the additional parameter edge_properties.
I am now also setting the node properties in get_bonded_structure to arrive at a networkx graph object that includes the information of the nodes as well. So far, this information is only present in the additional structure object but not in the graph itself. I hope this does not lead to side effects in another package.
I have added a test case as well and further documenation.
I hope this is okay. I would be happy about further feedback.
|
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I_kwDOACgets5QF2b0
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MPXANESSet: COREHOLE setting inconsistent with literature
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[
"Ah, I have just noticed that there is logic in `FEFFDictSet` that changes `COREHOLE` to `RPA` when a reciprocal space calculation is invoked. \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/2a88940b8a4a1eb84e0077dce934765caada9395/pymatgen/io/feff/sets.py#L202\r\n\r\nIn my opinion, there is still value in considering a change to the .yaml value to minimize confusion for other users. I know that I (and I would suspect many others) look at the .yaml files as a clear, quick synopsis of what calculation settings are used by different input sets, so if it's likely that `COREHOLE` would be overwritten in many cases of practical interest, I'd advocate changing the .yaml to reflect the more likely scenario.\r\n\r\nWe could always reverse the logic in `FEFFDictSet` if it is desired to default to FSR for real-space calculations (although from what I can tell it's not clear that FSR is superior to RPA in this case; rather that RPA is definitely preferred for k-space calcs).",
"@rkingsbury I agree with everything you're saying here. I think though what's most important is that the default settings and behavior be _clearly exposed_ in the documentation. They're currently not, as they're buried in the `MPXANESSet.yaml` files and related. As I mentioned in #2611 I think this really needs to change. I am happy to implement those PR's if I get approval, then it will be much easier to specify the default behaviors and clarify these confusions."
] | 2022-08-18T22:22:51
| 2022-09-28T18:09:47
|
CONTRIBUTOR
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Both studies (cited below) that describe the development of high-throughput XANES workflows state that the 'RPA' method was chosen for screening of the core-hole potential. However `MPXANESSet.yaml` uses the default 'FSR' setting.
The ML paper (Zhenget al. 2018) seems to indicate that RPA gave more accurate results, and according to the user guide this is the preferred method if using reciprocal-space calculations.
I personally do not have a strong opinion one way or another, but if `MPXANESSet` is going to deviate from what is in the publications, I think it would be good to document that somewhere. The other settings in the yaml file appear to be generally consistent with the benchmarking work described in the studies.
I propose that we either revise the .yaml to use the RPA method, or add something to the docstrings to explain when FSR is preferable.
https://www.nature.com/articles/sdata2018151#citeas
> COREHOLE: The COREHOLE card is used for specifying how the core is treated during XANES calculation. The default choice in FEFF treats the core-hole interaction based on the Final State Rule (FSR), which could overestimate the strength of the core-hole and excludes the core-hole mixing effect[24](https://www.nature.com/articles/sdata2018151#ref-CR24). To overcome these deficiencies and avoid possible break down of FSR for the L-shell metals[25](https://www.nature.com/articles/sdata2018151#ref-CR25), the random phase approximation (RPA) is used to approximate the core-hole interactions in our high-throughput K-edge XANES calculations.
https://www.nature.com/articles/s41524-018-0067-x#citeas
(in Supporting Information Fig 3B)
> We use RPA as the default core-hole treatment setting.
The [FEFF10 user guide](https://github.com/times-software/feff10/releases/download/v10.0.0/feff10_users_guide.pdf) states
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IO support for res files (AIRSS results)
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[
"Thanks for working on this @ScottNotFound, it'll be a nice addition.\r\n\r\nIt looks like the PR is basically complete, are you waiting on anything besides linting? I'm not sure if the capitalized `CELL` etc. dataclass attributes on `Res` are a PEP8 violation, but otherwise the PR looks great.\r\n\r\nBeing unfamiliar with both the AIRSS file format and shelx, I will trust this is appropriate :) Are there any AIRSS input parameters that might substantially change the output format; are there any additional test example files that should be added?",
"Ah, I see a test failure too: \r\n\r\n> E AttributeError: type object 'ResIO' has no attribute 'structure_to_txt'\r\n\r\nI know this is marked as a WIP, so assume this is already known!",
"The implementation is pretty much done. I was going to add some more tests for the module. After those I'll mark it ready for review. \r\n\r\nPEP8 says something to the effect of constants being all caps, but I just named them the way the tags appear in the res file. They are frozen dataclasses.. not sure if that counts as constant. Those are all internal though so they can be changed if you prefer a different style. \r\n\r\nI actually don't know anything about the shelx file format other than it exists. I considered supporting it, but it was hard to find information on it. Also not sure if anyone other that AIRSS still uses it. \r\n\r\nAs for AIRSS parameters changing the format, I'm not sure. I've only used CASTEP with AIRSS. I've assumed some things are common to all AIRSS runs, but it's possible that may not be the case. I be surprised if the parts that matter (like the structure and TITL entry) were different. ",
"> Ah, I see a test failure too:\r\n> \r\n> > E AttributeError: type object 'ResIO' has no attribute 'structure_to_txt'\r\n> \r\n> I know this is marked as a WIP, so assume this is already known!\r\n\r\nYeah I found that while writing a test after refactoring. VSCode is not as good as pycharm at refactoring method names. ",
"\n[](https://coveralls.io/builds/52044000)\n\nCoverage increased (+0.2%) to 63.505% when pulling **31b99390c0e0ec272282f3b6dca0c6606b85e709 on ScottNotFound:res** into **beac8d5361d8f5332c7335be3ce31b41cb131e31 on materialsproject:master**.\n",
"Looks like the linter failed because mypy doesn't have type info for dateutil. I installed the type stubs into my env, but the linter env doesn't have them. I guess I can either:\r\n1. keep the code around dateutil unchanged, and you all add the type stubs or put in a mypy ignore for dateutil\r\n2. throw some type: ignores on those lines\r\n3. not use dateutil",
"Very nice PR! Thanks @ScottNotFound.",
"Thanks both for lending AIRSS expertise :) \r\n\r\nNot relevant to this PR, but I did want to point out we have new-ish `InputFile` and `InputSet` [base classes](https://github.com/materialsproject/pymatgen/blob/8dc6a15f7914f2f3d2c6f9e88d1e5d155a5f3666/pymatgen/io/core.py#L4-L27). If you're looking at expanding AIRSS support for writing inputs via pymatgen in the future this would be the way to go.\r\n\r\nI also have my own stalled CASTEP PR @ #2048 which is actually almost ready to merge, but I wanted to update to use these base classes myself.",
"Looks like `Testing Linux / test (3.10) (pull_request)` may be related to #2515?\r\n\r\nNot sure why `Linting / build (3.9) (pull_request)` is failing but it looks unrelated. ",
"Thanks @ScottNotFound, I have no concerns about this PR -- I'll go ahead and merge, thanks again.\r\n\r\nThe unrelated failures I can look into separately."
] | 2022-08-18T23:05:28
| 2023-05-03T18:29:28
|
2022-08-31T21:47:19Z
|
CONTRIBUTOR
|
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## Summary
Include a summary of major changes in bullet points:
* Adds res file io to handle results from airss searches, #2560
* This isn't proper support for the shelx format (does anyone use that anymore?), but if all we care about is airss then that's fine.
## Additional dependencies introduced (if any)
* no new dependencies
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* It only provides functions to build Structure types. I think there is an Entry class somewhere that uses energy for phase diagrams and whatnot. The parser fills out a parse tree made of dataclasses, so the energy, pressure, volume, and other stuff airss sticks in the header is trivial to pull out. I can add that next time I have down time.
* Make all the docstrings in the proper format
## 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:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
- [x] Support for Entries.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
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I_kwDOACgets5QK7V9
| 2,626
|
Minor one line bug in Wulffshape.get_plotly()
|
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[] | 2022-08-20T03:23:53
| 2022-08-20T06:37:35
|
2022-08-20T06:37:35Z
|
CONTRIBUTOR
|
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Line 615 handles normalizing the surface energies on the wulff shape between 0 and 1 to get the corresponding color via the following:
` norm_e = (plane.e_surf - min(e_surf_on_wulff)) / (max(e_surf_on_wulff) - min(e_surf_on_wulff))`
This will cause a division by zero error if there is ever a Wulffshape that only has one facet (min surface energy and max surface energy are the same). Please change line 615 to the following:
```
if max(e_surf_on_wulff) == min(e_surf_on_wulff):
norm_e = 1
else:
norm_e = (plane.e_surf - min(e_surf_on_wulff)) / (max(e_surf_on_wulff) - min(e_surf_on_wulff))
```
in order to handle shapes with only one stable facet
|
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PR_kwDOACgets49g_G4
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|
Document kwarg `min_bond_distance` of `JmolNN`
|
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[
"\n[](https://coveralls.io/builds/51819547)\n\nCoverage increased (+0.0005%) to 63.267% when pulling **11e380c8d7452e25769317e5f670f0006dbabdc3 on janosh:doc-str-JmolNN-min_bond_distance** into **f87c9f502225d7d60d5c856fabb0a9d786fbc305 on materialsproject:master**.\n",
"thanks."
] | 2022-08-21T14:29:22
| 2022-08-21T16:12:20
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2022-08-21T16:12:17Z
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MEMBER
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PR_kwDOACgets49lWgz
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Handle disordered structures in `CrystalNN.get_bonded_structure()` and `get_cn()`
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[
"\n[](https://coveralls.io/builds/52044099)\n\nCoverage decreased (-0.002%) to 63.343% when pulling **56383d868c8925920a1aa2f7398ccee354fbc071 on janosh:gh-2070-disordered-nearneighbors** into **5a1f04aa43619f07d48348cf7606a5ae871bcc12 on materialsproject:master**.\n",
"Thanks for having a go at this @janosh \r\n\r\n> What should the default for on_disorder be? I chose 'take majority' to avoid new people encountering issues like https://github.com/materialsproject/pymatgen/issues/2070 but safer and less backward incompatible change would be 'error'.\r\n\r\nI think the default should be `take majority`; in terms of breaking backwards compatibility, I'm not sure anyone would have been relying upon the fact that CrystalNN raises when encountering a disordered structure, so it seems quite safe to add this new functionality.\r\n\r\nOne caution with bonding with disordered structures is sometimes, say, a light element like H might live on, say, four very near-by sites with 0.25 occupancy each. This kind of strategy will suggest the structure contains \"H-H\" bonds when they do not. In this sense, perhaps `take majority` should require that the occupancy really is the majority (i.e., > 0.5)?\r\n\r\nPR looks good otherwise, thank you! Unfortunate the easiest implementation requires making a copy of the structure, but a lot of the code in local_env.py is pretty slow anyway right now, so I'm not too concerned by this.",
"\r\n> I'm not sure anyone would have been relying upon the fact that CrystalNN raises when encountering a disordered structure, so it seems quite safe to add this new functionality.\r\n\r\nI am currently relying on the error being an `AttributeError` over at https://github.com/janosh/pymatviz/pull/50/commits/99bd2cd. Changing to `ValueError` is strictly speaking breaking. But yeah, probably not many cases of this.\r\n\r\n> One caution with bonding with disordered structures is sometimes, say, a light element like H might live on, say, four very near-by sites with 0.25 occupancy each. This kind of strategy will suggest the structure contains \"H-H\" bonds when they do not. In this sense, perhaps `take majority` should require that the occupancy really is the majority (i.e., > 0.5)?\r\n\r\nExcellent point. As I was submitting this, I realized maybe there should be 3rd option `'take max species'` which does what `'take majority'` currently does, and then `'take majority'` should raise `ValueError` on disordered sites that don't have a majority species. Happy to implement this if you think it's sensible.\r\n",
"> I am currently relying on the error being an AttributeError over at https://github.com/janosh/pymatviz/commit/99bd2cd.\r\n\r\nFair enough, I stand corrected :) Shows I should not make assumptions!\r\n\r\n> Excellent point. As I was submitting this, I realized maybe there should be 3rd option 'take max species' which does what 'take majority' currently does, and then 'take majority' should raise ValueError on disordered sites that don't have a majority species. Happy to implement this if you think it's sensible.\r\n\r\nThis would be great, thanks. One option here is instead of raising, that site could simply be omitted when you make the ordered copy. This would allow `take_majority` to still work fine for the rest of the structure, e.g. the case I mentioned with the disordered H sites, all the other sites could still be bonded.",
"> This would allow `take_majority` to still work fine for the rest of the structure, e.g. the case I mentioned with the disordered H sites, all the other sites could still be bonded.\r\n\r\nYou mean keep the existing behavior of `take_majority` as a 4th option, call it `take_majority_strict` which raises `ValueError` if no majority present, and make a new option `take_majority_drop` or whatever that drops all sites without majorities?\r\n\r\nBtw, do you prefer underscores over spaces? Happy to rename the options `take max species` $\\to$ `take_max_species`",
"> You mean keep the existing behavior of take_majority as a 4th option, call it take_majority_strict which raises ValueError if no majority present, and make a new option take_majority_drop or whatever that drops all sites without majorities?\r\n\r\nI was proposing that the behavior of `take_majority` is the latter, i.e., what you suggest as `take_majority_drop`. However, having both options, `take_majority_strict` and `take_majority_drop` would also work (and be better). It's difficult to imagine all the situations in which someone might want to use this.\r\n\r\n> Btw, do you prefer underscores over spaces? Happy to rename the options take max species → take_max_species\r\n\r\nNo strong feelings! I default to underscores since it makes it a valid identifier, but there's no reason spaces should be a problem. I'm not aware on any style guides for this sort of thing.",
"> However, having both options, `take_majority_strict` and `take_majority_drop` would also work (and be better).\r\n\r\nAlright, that's done.",
"@mkhorton The linter errors here are unrelated (also present [on `master`](https://github.com/materialsproject/pymatgen/runs/8079752678?check_suite_focus=true))\r\n\r\n```txt\r\npymatgen/analysis/nmr.py:59:19: E1121: Too many positional arguments for classmethod call (too-many-function-args)\r\npymatgen/analysis/nmr.py:61:19: E1121: Too many positional arguments for classmethod call (too-many-function-args)\r\npymatgen/analysis/nmr.py:155:19: E1121: Too many positional arguments for classmethod call (too-many-function-args)\r\npymatgen/analysis/nmr.py:157:19: E1121: Too many positional arguments for classmethod call (too-many-function-args)\r\n```\r\n\r\nI didn't touch `pymatgen/analysis/nmr.py`. The weird thing is I can't even reproduce locally:\r\n\r\n```sh\r\npylint pymatgen/analysis/nmr.py \r\n\r\n------------------------------------\r\nYour code has been rated at 10.00/10\r\n```",
"This linting problem suddently showed up in my PR. All tests were passing before on the master branch and I really only changed the documentation: https://github.com/materialsproject/pymatgen/pull/2639",
"Then maybe it's coming from a version change since stuff in `requirements-dev.txt` is unpinned? I just upgraded my local `pylint` but still can't reproduce. We should prob remove `--quiet` here to see what versions are being installed. Makes debugging easier.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/b1f8c168dedb0ff2381b7da2437eac8da2f48249/.github/workflows/lint.yml#L28",
"Thanks for the PR @janosh! Merged\r\n\r\nHave implemented the suggested change for the linter to see if we can track it down, but I won't discuss further in this specific PR just because it's unrelated to these changes."
] | 2022-08-22T18:29:23
| 2022-08-30T21:47:35
|
2022-08-30T21:21:29Z
|
MEMBER
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Closes #2070.
This PR fixes the `AttributeError` currently raised when passing disordered structures to methods like `get_cn()` and `get_bonded_structure()` of `CrystalNN` and other `NearNeighbors` subclasses.
Several open questions:
1. I added a helper function `_handle_disorder(structure: Structure, on_disorder: Literal["take majority", "error"])` that's reused in multiple places since there doesn't appear to be one central place where disordered structures can be ordered by taking majority species from each site for all downstream processing like @mkhorton [suggested](https://github.com/materialsproject/pymatgen/issues/2070#issuecomment-782239047).
2. What should the options for the `on_disorder` kwarg be? Is `"take majority"` and `"error"` ok?
3. Perhaps most important @shyuep @mkhorton: What should the default for `on_disorder` be? I chose `'take majority'` to avoid new people encountering issues like #2070 but safer and less backward incompatible change would be `'error'`.
I added tests that check both the error case and `'take majority'` case to make sure we no longer raise a generic `AttributeError` without a clear explanation of why it's not working.
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PR_kwDOACgets49lwAX
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|
Fix deprecation warning on scipy gaussian_filter1d function
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[] | null |
[
"\n[](https://coveralls.io/builds/51852857)\n\nCoverage decreased (-0.004%) to 63.342% when pulling **eb0de1300b78e9da30d1274d4ab500d9f475fe7d on arosen93:rosen-depre** into **5a1f04aa43619f07d48348cf7606a5ae871bcc12 on materialsproject:master**.\n"
] | 2022-08-22T20:23:52
| 2022-08-23T05:21:58
|
2022-08-23T05:21:57Z
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MEMBER
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I changed
```python
from scipy.ndimage.filters import gaussian_filter1d
```
to
```python
from scipy.ndimage import gaussian_filter1d
```
in `pymatgen.electronic_structure.dos` since the former is deprecated.
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I_kwDOACgets5QUj0M
| 2,632
|
Cannot import pbc_diff due to circular import
|
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[] | null |
[
"Hmm... I don't think any of this code has been changed in recent months/years..... But it seems to be a typing issue. This should be then jettisoned since typing is optinal."
] | 2022-08-23T08:42:45
| 2022-08-23T09:47:18
|
2022-08-23T09:47:18Z
|
MEMBER
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Using the latest pymatgen:
```python
from pymatgen.util.coord import pbc_diff
```
Gives
```python
from pymatgen.util.coord import pbc_diff
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-cfcfcb2ddde7> in <module>
----> 1 from pymatgen.util.coord import pbc_diff
~/dev/src/pymatgen/pymatgen/util/coord.py in <module>
16
17 from pymatgen.util import coord_cython as cuc
---> 18 from pymatgen.util.typing import ArrayLike
19
20 # array size threshold for looping instead of broadcasting
~/dev/src/pymatgen/pymatgen/util/typing.py in <module>
19 except ImportError:
20 ArrayLike = Union[Sequence[float], Sequence[Sequence[float]], Sequence[np.ndarray], np.ndarray] # type: ignore
---> 21 from pymatgen.core.composition import Composition
22 from pymatgen.core.periodic_table import DummySpecies, Element, Species
23
~/dev/src/pymatgen/pymatgen/core/__init__.py in <module>
13
14 from .composition import Composition
---> 15 from .lattice import Lattice
16 from .operations import SymmOp
17 from .periodic_table import DummySpecies, Element, Species
~/dev/src/pymatgen/pymatgen/core/lattice.py in <module>
22 from numpy.linalg import inv
23
---> 24 from pymatgen.util.coord import pbc_shortest_vectors
25 from pymatgen.util.num import abs_cap
26 from pymatgen.util.typing import ArrayLike
ImportError: cannot import name 'pbc_shortest_vectors' from partially initialized module 'pymatgen.util.coord' (most likely due to a circular import) (/Users/alexmganose/dev/src/pymatgen/pymatgen/util/coord.py)
```
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PR_kwDOACgets49n3wD
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Fix circular import
|
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[
"\n[](https://coveralls.io/builds/51867690)\n\nCoverage decreased (-0.003%) to 63.343% when pulling **8b2bb603f2135a74faaa0f5998e94cba7c955488 on utf:fix-circular-import** into **0abcca91396c22532322e901e54b52d5cf44767a on materialsproject:master**.\n"
] | 2022-08-23T08:54:05
| 2022-08-23T09:47:17
|
2022-08-23T09:47:17Z
|
MEMBER
|
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Fixes #2632
Importing pbc_diff directly fails due to a circular import. This doesn't seem to impact the code or tests since other modules are imported first. E.g. running the following works fine:
```python
from pymatgen.core import Composition
from pymatgen.util.coord import pbc_diff
```
The issue arrises because the `pymatgen.util.coord` module imports `ArrayLike` from `pymatgen.util.typing` for type hinting. This module in turn imports `Composition` which then tries to import `pbc_shortest_vectors` thus creating the circular import.
This PR avoids the issue by using postponed annotations and the `TYPE_CHECKING` constant. See: https://peps.python.org/pep-0563/
Unfortunately, I can't add a test as the bug is very specific to the order imports occur which is outside the control of a specific test.
|
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I_kwDOACgets5Qe2y5
| 2,634
|
Crash in Bader analysis due to missing file
|
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[
"@janosh: I'm guessing this can be closed as stale. It was likely addressed anyway in #3192. I've personally run thousands of Bader calcs and never got this error, for what it's worth.\r\n\r\n@pjf295: Let us know if you still get this error with newer versions of pymatgen.",
"Thanks Andrew. Closing as assumed fixed."
] | 2022-08-25T03:26:05
| 2023-09-03T19:42:07
|
2023-09-03T19:42:07Z
|
NONE
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**Describe the bug**
A clear and concise description of what the bug is.
Bader seems to run normally, but fails stating a file does not exist. The details are below.
**To Reproduce**
Steps to reproduce the behavior:
The files necessary to reproduce the bug are too large to post here (800 MB CHGCAR), but the CHGCAR was created for a 114 atom system. The detailed error message is below. I followed the progress of the bader program while the calculation was continuing and could see a temporary directory was created (see below) and indeed the file referenced in the error is missing, but no errors were given up to the point of the crash. The temporary directory was deleted upon the error.
```
-rw-r--r-- 1 9484 Aug 25 11:28 ACF.dat
-rw-r--r-- 1 2326 Aug 25 11:28 AVF.dat
-rw-r--r-- 1 15767 Aug 25 11:28 BCF.dat
-rw-r--r-- 1 407590595 Aug 25 11:28 BvAt0001.dat
-rw-r--r-- 1 407590595 Aug 25 11:29 BvAt0002.dat
-rw-r--r-- 1 407590595 Aug 25 11:29 BvAt0003.dat
-rw-r--r-- 1 407590595 Aug 25 11:29 BvAt0004.dat
-rw-r--r-- 1 407590595 Aug 25 11:29 BvAt0005.dat
-rw-r--r-- 1 407590595 Aug 25 11:30 BvAt0006.dat
-rw-r--r-- 1 407590595 Aug 25 11:30 BvAt0007.dat
-rw-r--r-- 1 407590595 Aug 25 11:30 BvAt0008.dat
-rw-r--r-- 1 407590595 Aug 25 11:30 BvAt0009.dat
-rw-r--r-- 1 407590595 Aug 25 11:31 BvAt0010.dat
-rw-r--r-- 1 407590595 Aug 25 11:31 BvAt0011.dat
-rw-r--r-- 1 407590595 Aug 25 11:31 BvAt0012.dat
-rw-r--r-- 1 407590595 Aug 25 11:31 BvAt0013.dat
-rw-r--r-- 1 407590595 Aug 25 11:32 BvAt0014.dat
-rw-r--r-- 1 407590595 Aug 25 11:32 BvAt0015.dat
-rw-r--r-- 1 407590595 Aug 25 11:32 BvAt0016.dat
-rw-r--r-- 1 407590595 Aug 25 11:32 BvAt0017.dat
-rw-r--r-- 1 407590595 Aug 25 11:33 BvAt0018.dat
-rw-r--r-- 1 407590595 Aug 25 11:33 BvAt0019.dat
-rw-r--r-- 1 407590595 Aug 25 11:33 BvAt0020.dat
-rw-r--r-- 1 407590595 Aug 25 11:34 BvAt0021.dat
-rw-r--r-- 1 407590595 Aug 25 11:34 BvAt0022.dat
-rw-r--r-- 1 407590595 Aug 25 11:34 BvAt0023.dat
-rw-r--r-- 1 407590595 Aug 25 11:34 BvAt0024.dat
-rw-r--r-- 1 407590595 Aug 25 11:35 BvAt0025.dat
-rw-r--r-- 1 407590595 Aug 25 11:35 BvAt0026.dat
-rw-r--r-- 1 407590595 Aug 25 11:35 BvAt0027.dat
-rw-r--r-- 1 407590595 Aug 25 11:35 BvAt0028.dat
-rw-r--r-- 1 407590595 Aug 25 11:36 BvAt0029.dat
-rw-r--r-- 1 407590595 Aug 25 11:36 BvAt0030.dat
-rw-r--r-- 1 407590595 Aug 25 11:36 BvAt0031.dat
-rw-r--r-- 1 407590595 Aug 25 11:36 BvAt0032.dat
-rw-r--r-- 1 407590595 Aug 25 11:37 BvAt0033.dat
-rw-r--r-- 1 407590595 Aug 25 11:37 BvAt0034.dat
-rw-r--r-- 1 407590595 Aug 25 11:37 BvAt0035.dat
-rw-r--r-- 1 407590595 Aug 25 11:37 BvAt0036.dat
-rw-r--r-- 1 407590595 Aug 25 11:38 BvAt0037.dat
-rw-r--r-- 1 407590595 Aug 25 11:38 BvAt0038.dat
-rw-r--r-- 1 407590595 Aug 25 11:38 BvAt0039.dat
-rw-r--r-- 1 407590595 Aug 25 11:38 BvAt0040.dat
-rw-r--r-- 1 407590595 Aug 25 11:39 BvAt0041.dat
-rw-r--r-- 1 407590595 Aug 25 11:39 BvAt0042.dat
-rw-r--r-- 1 407590595 Aug 25 11:39 BvAt0043.dat
-rw-r--r-- 1 407590595 Aug 25 11:40 BvAt0044.dat
-rw-r--r-- 1 407590595 Aug 25 11:40 BvAt0045.dat
-rw-r--r-- 1 407590595 Aug 25 11:40 BvAt0092.dat
-rw-r--r-- 1 407590595 Aug 25 11:40 BvAt0093.dat
-rw-r--r-- 1 407590595 Aug 25 11:41 BvAt0094.dat
-rw-r--r-- 1 407590595 Aug 25 11:41 BvAt0095.dat
-rw-r--r-- 1 407590595 Aug 25 11:41 BvAt0096.dat
-rw-r--r-- 1 407590595 Aug 25 11:41 BvAt0097.dat
-rw-r--r-- 1 407590595 Aug 25 11:42 BvAt0098.dat
-rw-r--r-- 1 69705047 Aug 25 11:42 BvAt0099.dat
-rw-r--r-- 1 815356319 Aug 25 11:27 CHGCAR
```
```
In [1]: from pymatgen.command_line.bader_caller import BaderAnalysis
In [2]: bader = BaderAnalysis()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [2], in <cell line: 1>()
----> 1 bader = BaderAnalysis()
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/monty/dev.py:97, in requires.__call__.<locals>.decorated(*args, **kwargs)
95 if not self.condition:
96 raise RuntimeError(self.message)
---> 97 return _callable(*args, **kwargs)
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/pymatgen/command_line/bader_caller.py:128, in BaderAnalysis.__init__(self, chgcar_filename, potcar_filename, chgref_filename, parse_atomic_densities, cube_filename)
121 raise RuntimeError(
122 "BaderAnalysis requires the executable bader to be in the path."
123 " Please download the library at http://theory.cm.utexas"
124 ".edu/vasp/bader/ and compile the executable."
125 )
127 if not (cube_filename or chgcar_filename):
--> 128 raise ValueError("You must provide either a cube file or a CHGCAR")
129 if cube_filename and chgcar_filename:
130 raise ValueError("You cannot parse a cube and a CHGCAR at the same time.")
ValueError: You must provide either a cube file or a CHGCAR
In [3]: bader = BaderAnalysis(chgcar_filename="CHGCAR",potcar_filename="POTCAR",parse_atomic_densities=True))
Input In [3]
bader = BaderAnalysis(chgcar_filename="CHGCAR",potcar_filename="POTCAR",parse_atomic_densities=True))
^
SyntaxError: unmatched ')'
In [4]: bader = BaderAnalysis(chgcar_filename="CHGCAR",potcar_filename="POTCAR",parse_atomic_densities=True)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Input In [4], in <cell line: 1>()
----> 1 bader = BaderAnalysis(chgcar_filename="CHGCAR",potcar_filename="POTCAR",parse_atomic_densities=True)
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/monty/dev.py:97, in requires.__call__.<locals>.decorated(*args, **kwargs)
95 if not self.condition:
96 raise RuntimeError(self.message)
---> 97 return _callable(*args, **kwargs)
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/pymatgen/command_line/bader_caller.py:214, in BaderAnalysis.__init__(self, chgcar_filename, potcar_filename, chgref_filename, parse_atomic_densities, cube_filename)
210 self.data = data
212 if self.parse_atomic_densities:
213 # convert the charge density for each atom spit out by Bader into Chgcar objects for easy parsing
--> 214 atom_chgcars = [
215 Chgcar.from_file(f"BvAt{str(i).zfill(4)}.dat") for i in range(1, len(self.chgcar.structure) + 1)
216 ]
218 atomic_densities = []
219 # For each atom in the structure
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/pymatgen/command_line/bader_caller.py:215, in <listcomp>(.0)
210 self.data = data
212 if self.parse_atomic_densities:
213 # convert the charge density for each atom spit out by Bader into Chgcar objects for easy parsing
214 atom_chgcars = [
--> 215 Chgcar.from_file(f"BvAt{str(i).zfill(4)}.dat") for i in range(1, len(self.chgcar.structure) + 1)
216 ]
218 atomic_densities = []
219 # For each atom in the structure
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/pymatgen/io/vasp/outputs.py:4002, in Chgcar.from_file(filename)
3994 @staticmethod
3995 def from_file(filename):
3996 """
3997 Reads a CHGCAR file.
3998
3999 :param filename: Filename
4000 :return: Chgcar
4001 """
-> 4002 (poscar, data, data_aug) = VolumetricData.parse_file(filename)
4003 return Chgcar(poscar, data, data_aug=data_aug)
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/pymatgen/io/vasp/outputs.py:3625, in VolumetricData.parse_file(filename)
3623 data_count = 0
3624 poscar = None
-> 3625 with zopen(filename, "rt") as f:
3626 for line in f:
3627 original_line = line
File /data/miniconda/envs/pymatgen/lib/python3.10/site-packages/monty/io.py:45, in zopen(filename, *args, **kwargs)
43 if ext in (".XZ", ".LZMA"):
44 return lzma.open(filename, *args, **kwargs)
---> 45 return open(filename, *args, **kwargs)
FileNotFoundError: [Errno 2] No such file or directory: 'BvAt0046.dat'
```
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
The bader charges should have been returned.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: Linux CentOS 7
- Version [e.g. 2019.9.16]
**Additional context**
Add any other context about the problem here.
|
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| 1,350,696,836
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PR_kwDOACgets49yPQR
| 2,635
|
store bond keys of ICOHP in graph edge prop
|
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[
"\n[](https://coveralls.io/builds/51973826)\n\nCoverage increased (+0.002%) to 63.353% when pulling **42293d5897ba71257226fb9b74a49f31374828be on naik-aakash:Lobster_structure_graph_update** into **2a88940b8a4a1eb84e0077dce934765caada9395 on materialsproject:master**.\n",
"This PR is ready to be merged @shyuep ",
"Pls add a unittest to check the bond keys are properly added. Thanks.",
"Great. Thanks.",
"> Great. Thanks.\r\n\r\nWelcome "
] | 2022-08-25T10:42:17
| 2022-08-26T10:45:35
|
2022-08-26T10:43:34Z
|
CONTRIBUTOR
|
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## Summary
Minor addition to Lobster graph edge properties
* Store ICOHPlist bond key in graph edge properties. Helps in getting further information from 'Lobsterpy' package
|
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PR_kwDOACgets490yoW
| 2,636
|
[WIP] Fix InsertionElectrode.get_summary_dict()
|
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[
"Thanks for this PR! Noting we're having some offline discussion about this.",
"It was decided that this issue would be resolved through a change in emmet which is being addressed in a separate PR (https://github.com/materialsproject/emmet/pull/520) so that `.get_summary_dict()` method would not need to be changed in pymatgen."
] | 2022-08-25T21:02:49
| 2022-08-30T22:12:23
|
2022-08-30T22:12:23Z
|
CONTRIBUTOR
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Update InsertionElectrode.get_summary_dict() to replace entry.entry_id with entry.data["material_id"] to correctly pull the material_id given changes in the entry
|
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PR_kwDOACgets495Nhv
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|
Fix descriptions in external tools
|
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[
"Not exactly sure how the linting is now failing in an nmr module. In any case, I only changed the documentation.",
"\n[](https://coveralls.io/builds/51994022)\n\nCoverage increased (+0.002%) to 63.352% when pulling **cbcc1e5f110413ce083bcc3f17aa9a5d6d6e0551 on JaGeo:patch-1** into **c0fc908d76f0c7ec2150c3536ea9835365e4aa80 on materialsproject:master**.\n",
"Thanks @JaGeo! No idea how that got mixed up",
"Oops, that was my mistake. 😓 \r\n\r\nAlready mixed up in the [original commit](https://github.com/JaGeo/pymatgen/commit/078479d67967ef6af4cd22edb8362ffa635d9e23#diff-de00fc0ed9e189502523ecc5869b9ecd0497e21ea9e227098662a063dde0576fR31).",
"Don't worry 😅. It happens. 🙂 You fixed so many other and much more servere mistakes in the code base! "
] | 2022-08-26T22:06:26
| 2022-08-30T05:13:25
|
2022-08-26T22:59:20Z
|
MEMBER
|
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## Summary
Descriptions of the external tools got mixed up. Switched the LobsterPy and the QuAcc description.
|
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Better docs for WSWQ
|
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[
"\n[](https://coveralls.io/builds/52009989)\n\nCoverage increased (+0.0001%) to 63.35% when pulling **df5d6392f40ec20d91b71afacdd038b7cb7ec98f on jmmshn:get_elphon** into **555ddeb5c62dbc1c44b463b7932cc5f31dc98b39 on materialsproject:master**.\n",
"Looks like Linting is failing due to something unrelated.\r\n\r\n\r\n",
"Thanks @jmmshn. I noticed the NMR linter issue in another PR, no idea where that crept in."
] | 2022-08-27T18:12:58
| 2022-08-29T20:54:30
|
2022-08-29T20:54:28Z
|
CONTRIBUTOR
|
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I noticed some errors in the documentation of WSWQ.
Also added a `data` field to make combining the real/imag parts easier.
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I_kwDOACgets5Qz-HB
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SpacegroupAnalyzer: Segmentation fault
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[
"The likely reason is that you have to change the tolerance. Given that I don't have matbench installed, I can't verify the error.",
"It seems the segmentation fault is caused by magmom and high symprec(~=1e-2) from spglib.\r\nI've opened the corresponding issue page linked above.\r\nFor now, dropping magmom entries from `Structure` will suppress the error.",
"Now, I believe this issue will be solved with spglib==2.0.1.",
"Related issues: https://github.com/spglib/spglib/issues/194 and https://github.com/spglib/spglib/issues/197. Not sure about 2.0.1 but definitely fixed in `spglib` 2.0.2 so closing."
] | 2022-08-30T13:46:31
| 2023-05-22T17:51:14
|
2023-05-22T17:51:14Z
|
NONE
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```python
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from matbench.bench import MatbenchBenchmark
## ----------------------------------------------------------------------------
def get_matbench_task(name):
mb = MatbenchBenchmark(autoload=False)
task = mb.tasks_map[f'matbench_{name}']
task.load()
return task
## ----------------------------------------------------------------------------
df = get_matbench_task('log_gvrh').df
s = df['structure'][1117]
print(s)
## ----------------------------------------------------------------------------
sga = SpacegroupAnalyzer(s)
sga._get_symmetry()
```
Returns the following error:
```shell
> python debug.py
Full Formula (Cu1 Br2)
Reduced Formula: CuBr2
abc : 3.492558 4.223779 6.451834
angles: 87.282014 74.296218 65.578883
pbc : True True True
Sites (3)
# SP a b c magmom
--- ---- -------- -------- -------- --------
0 Cu 0 0 0 0.005
1 Br 0.267375 0.223251 0.241999 0.002
2 Br 0.732625 0.776749 0.758001 0.002
Segmentation fault
```
Versions:
```
pymatgen 2022.8.23
spglib 2.0.0
matbench 0.6
python 3.10.4
```
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PR_kwDOACgets4-LFSJ
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Add `as_dict()` method to `AirssProvider`
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[
"Hmm, I don't know the situations where `as_dict` methods are currently used, but I assume the use case is typically for databases? I wonder if it might be worth having `ResProvider` inherit from `MSONable` like a lot of other classes do. Otherwise I think the TITL entry, REM entries, and structure are enough to recreate the object.",
"> I wonder if it might be worth having `ResProvider` inherit from `MSONable` like a lot of other classes do.\r\n\r\nI was thinking about that as well.\r\n\r\n\r\n\r\n> Otherwise I think the TITL entry, REM entries, and structure are enough to recreate the object.\r\n\r\nThanks. 👍 ",
"As a general principle, inheriting from MSONAble should be the default unless there is good reason to implement a separate as_dict. If you implement as_dict, you generally have to implement from_dict as well.",
"@shyuep Would the MSONable API work in this case? `AirssProvider` currently is not meant to be created through `__init__`:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/9407e8dcf8fbc51ac6af1148c280e4975fa74530/pymatgen/io/res.py#L395-L397",
"The MSONAble API does not rely on what method you use to init it. As long as res and parse_rems are part of the attributes, it will work. E.g., you rarely use the Poscar init method and mostly uses from_file. But Poscar still works with the MSONable api. All the API is meant to do is for serialization.",
"Looking at the way MSONable works, if you make ResProvider inherit from it, then you get the as_dict and from_dict methods without having to do any implementation. They are just access wrappers so _res is all you need. Then you can override and stick any extra keys like structure in there after calling from super.",
"@ScottNotFound Thanks for pointing that out! We should probably make both `ResProvider` and `Res` inherit from `MSONable`? Else `AirssProvider.from_file(res_file).as_dict()` would have key `'res'` be an instance of `Res`, meaning not serializable.",
"Res is a dataclass meaning it has a `__init__` that includes all its attributes so it just works with MSONable apparently.\r\n\r\nEdit: Oh I see the problem. I guess the class isn't smart enough to serialize a dataclass. You would have to have all of them inherit or you can do something with `__repr__`. I'll play with it.",
"Hmmm... I assumed the output from `as_dict()` is meant to be dicts all the way down? Seems weird to return a dict containing classes like `Res` and `AirssTITL`.",
"> Edit: Oh I see the problem. I guess the class isn't smart enough to serialize a dataclass. You would have to have all of them inherit or you can do something with `__repr__`. I'll play with it.\r\n\r\nYeah, I think all the classes in `pymatgen/io/res.py` would have to be children of `MSONable` in order for the `AirssProvider.as_dict()` to be a dict of dicts.\r\n",
"Alternatively, you can modify the MSONAble protocol to handle dataclass? That would be better for future usability rather than just fixing the problem for this one case. MSONable was written at a time when dataclasses were not a thing....",
"At this point, the `as_dict()` method won't be useful for my original purpose where I just want the pymatgen `Structure` and top level fields like title, volume, energy, etc. spread into columns of a dataframe:\r\n\r\n```py\r\n\r\ndf_res = pd.DataFrame(\r\n [AirssProvider.from_file(file).as_dict() for file in res_files]\r\n).set_index(\"seed\")\r\n```\r\n\r\nShould we have another function, say `AirssProvider.summary()` for that in `pymatgen`? If not, I'll just keep it in my AIRSS project.\r\n\r\n\r\n",
"> Alternatively, you can modify the MSONAble protocol to handle dataclass? That would be better for future usability rather than just fixing the problem for this one case. MSONable was written at a time when dataclasses were not a thing....\r\n\r\nI like this idea.",
"How about I suggest this:\r\n1. Someone can look into whether it is easy to add support for dataclasses in MSONable.\r\n2. You can still implement an as_dict method. I would suggest you make AirssRes MSONable in any case and override as_dict. You can have a kwarg called verbosity and default it to full verbosity and it will just delegate to super().as_dict. You then implement a lower verbosity level for your purpose. Note that the Structure.as_dict method has a similar thing - there are different verbosities. This is because the default Site objects carry the Lattice object, and for the purposes of serializing a crystal structure, it is extremely wasteful to repeat the same Lattice object on all sites.",
"> At this point, the as_dict() method won't be useful for my original purpose where I just want the pymatgen Structure and top level fields like title, volume, energy, etc. spread into columns of a dataframe:\r\n\r\nIs there any other functionality in pymatgen that takes calculation results and supplies it in a form suitable for a dataframe? It would be nice to keep a consistent interface. I see that `IStructure` provides `as_dataframe`, perhaps an `as_datarow` would suffice if there is no existing similar function elsewhere?\r\n",
"@ScottNotFound I don't think there is a need for that functionality. The reason is because dataframes can take a dict. \r\n\r\nE.g., one of the most common ways I construct a dataframe is simply:\r\n\r\n`pd.DataFrame([o.as_dict() for o in objects])`\r\n\r\nThe MPRester.query method returns a list of dicts. If you simply do `pd.DataFrame(MPRester().query(....whatever arguments))`, you get a DataFrame. I do this often.\r\n\r\nIn essence, the as_dataframe method is rather redundant because you are replacing a single line of code.\r\n\r\n",
"@janosh I just added support for dataclasses in the MSONAble protocol. It should now work without having to mess with the subclasses.",
"@shyuep Great. I did what you suggested. `as_dict()` now has a verbose flag that delegates to `super().as_dict()` if `True` (the default) and has the previous behavior useful for dataframe if `verbose=False`. I only made `ResProvider(MSONable)` inherit from `MSONable` since it's not a `dataclass`. All the data classes were left as is.",
"\n[](https://coveralls.io/builds/52293147)\n\nCoverage increased (+0.005%) to 63.517% when pulling **5faa3f9fb04d9d93aa9fc160879be814c9f32cb6 on janosh:AirssProvider-as_dict** into **7500268b4b8b3089207bf0495a074a4109d7c0eb on materialsproject:master**.\n"
] | 2022-09-01T01:25:31
| 2022-09-08T01:46:14
|
2022-09-08T01:44:35Z
|
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@mkhorton This is a small follow-up to #2625. I think a convenience method to turn the most important attributes of an `AirssProvider` into a dict would be nice to have.
```py
from pymatgen.io.res import AirssProvider
res_file = "/good_castep/NaLiTa2O6-28290-4142-1.res"
AirssProvider.from_file(res_file).as_dict()
```
<details>
<summary>sample output</summary>
```py
{'structure': {'@module': 'pymatgen.core.structure',
'@class': 'Structure',
'charge': 0,
'lattice': {'matrix': [[5.35841, 0.0, 3.2810798275095844e-16],
[-3.420358136599889e-16, 5.585868740246209, -0.0037514850704228257],
[0.0, 0.0, 7.70098]],
'pbc': (True, True, True),
'a': 5.35841,
'b': 5.58587,
'c': 7.70098,
'alpha': 90.03848,
'beta': 90.0,
'gamma': 90.0,
'volume': 230.5009196038728},
'sites': [{'species': [{'element': 'Li', 'occu': 1}],
'abc': [-0.4570528716928, 0.1473363079843, -0.2499276126345],
'xyz': [-2.4490766782074167, 0.8230012770727893, -1.9252402763057663],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.0429471283072, -0.1473363079843, 0.2499276126345],
'xyz': [0.23012832179258363, -0.8230012770727893, 1.9252402763057663],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'O', 'occu': 1}],
...
'energy': -42060.247,
'integrated_spin_density': 0.0,
'integrated_absolute_spin_density': 0.0,
'spacegroup_label': 'Pmn21',
'appearances': 1}
```
</details>
@ScottNotFound Feel free to jump in if I missed any important attributes.
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GitHub Workflows security hardening
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"Thanks "
] | 2022-09-01T15:01:56
| 2022-09-01T15:06:19
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2022-09-01T15:06:10Z
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CONTRIBUTOR
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This PR adds explicit [permissions section](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#permissions) to workflows. This is a security best practice because by default workflows run with [extended set of permissions](https://docs.github.com/en/actions/security-guides/automatic-token-authentication#permissions-for-the-github_token) (except from `on: pull_request` [from external forks](https://securitylab.github.com/research/github-actions-preventing-pwn-requests/)). By specifying any permission explicitly all others are set to none. By using the principle of least privilege the damage a compromised workflow can do (because of an [injection](https://securitylab.github.com/research/github-actions-untrusted-input/) or compromised third party tool or action) is restricted.
It is recommended to have [most strict permissions on the top level](https://github.com/ossf/scorecard/blob/main/docs/checks.md#token-permissions) and grant write permissions on [job level](https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs) case by case.
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Integrate `mp-api.client.MPRester` into `pymatgen.ext.matproj`
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[
"@mkhorton @shyuep I have realized that `msgpack` is required as an install to properly pull BS and DOS data. It only depends on cython (which is already required through scipy), and is therefore lightweight. Let me know your thoughts and if this is okay.",
"\n[](https://coveralls.io/builds/52356133)\n\nCoverage decreased (-0.2%) to 63.357% when pulling **a51389c080e84974c1abf49e052d8eae4e1d05b5 on munrojm:new_mprester** into **d26d374dabe01686950162132f24c66baaf298fe on materialsproject:master**.\n",
"Interesting, I have no objections (given that it's lightweight, as you say). It could be added to the `mp-api` requirements.",
"> Interesting, I have no objections (given that it's lightweight, as you say). It could be added to the `mp-api` requirements.\r\n\r\nIndeed, that is where I have added it. I believe it used to get automatically installed with maggma, which was removed as a required dependency. ",
"msgpack is fine. Monty has it as an optional dependency too\r\n",
"Many thanks @munrojm! This looks good. Noting here that I'd like to make a test (TestPyPI) release prior to the next real release to double-check nothing unexpected happens."
] | 2022-09-02T20:18:31
| 2022-09-12T20:31:47
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2022-09-12T20:31:46Z
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## Summary
- `mp-api` made an explicit dependency
- `MPRester` now detects the API key type (new or legacy) and instantiates the appropriate version of `MPRester`
## Additional dependencies introduced (if any)
`msgpack` is the only additional dependency added to enable BS and DOS data retrieval with the new API.
## TODO (if any)
Finalize clean up of `mp-api` dependencies and client code (https://github.com/materialsproject/api/pull/666) before merging.
## 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:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
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"\n[](https://coveralls.io/builds/52970829)\n\nCoverage remained the same at 63.38% when pulling **128f64d3eca7abc0851dfbc92d788784cf55487b on pre-commit-ci-update-config** into **6345c201d1973afddb813342bd62e481daeee26a on master**.\n",
"Outdated."
] | 2022-09-05T20:47:20
| 2022-10-10T16:54:29
|
2022-10-10T16:54:25Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/PyCQA/autoflake: v1.4 → v1.6.1](https://github.com/PyCQA/autoflake/compare/v1.4...v1.6.1)
- [github.com/asottile/pyupgrade: v2.37.3 → v2.38.2](https://github.com/asottile/pyupgrade/compare/v2.37.3...v2.38.2)
- [github.com/psf/black: 22.6.0 → 22.8.0](https://github.com/psf/black/compare/22.6.0...22.8.0)
- [github.com/PyCQA/flake8: 5.0.2 → 5.0.4](https://github.com/PyCQA/flake8/compare/5.0.2...5.0.4)
- [github.com/pre-commit/mirrors-mypy: v0.971 → v0.981](https://github.com/pre-commit/mirrors-mypy/compare/v0.971...v0.981)
<!--pre-commit.ci end-->
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PR_kwDOACgets4-d3Mv
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improve outcar parsing
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[
"Please add tests for the new functionality...",
"\n[](https://coveralls.io/builds/52258489)\n\nCoverage increased (+0.009%) to 63.513% when pulling **1911784599024f43c75ee89f871c92f52e4b3f8f on gpetretto:bugfix** into **fcc81a59c204c0d3046e1312889725ac685ee353 on materialsproject:master**.\n",
"thanks.\r\n"
] | 2022-09-06T20:55:06
| 2022-09-07T14:27:32
|
2022-09-07T14:27:29Z
|
CONTRIBUTOR
|
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## Summary
While parsing a large OUTCAR file coming from an MD simulation I realized that a lot of time was taken by the `read_table_pattern` to extract the number of plane waves for kpoints. The quantitiy appears early in the file, but for very long simulations the execution of the regex on the rest of the file can be very slow and pointless.
I added the option to stop the parsing of the table patterns at the first occurence and used it for the case of the plane waves.
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I_kwDOACgets5RXP2G
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Compatibility with older code
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[
"Pls upgrade to Python 3.9 and reinstall pymatgen. ",
"Updating Python worked perfectly! Thank you :)\r\nSorry for the inconvenience."
] | 2022-09-07T18:34:49
| 2022-11-17T22:59:56
|
2022-11-17T22:59:56Z
|
NONE
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Hi,
I've used pymatgen almost 2 years ago and especially the dopant suggestion feature from pymatgen, but pymatgen has been updated some times and my code is not running anymore. I have used this code example (https://matgenb.materialsvirtuallab.org/2018/11/06/Dopant-suggestions-using-Pymatgen.html) and I would like to update it but I had many issues doing so (API errors especially). Could you help me update this code so I can run it ?
Example of error code I encountered : pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403. Content: b'{"valid_response": false, "error": "API_KEY is not supplied.", "version": {"db": "2020_09_08", "pymatgen": "2022.0.8", "rest": "2.0"}, "created_at": "2022-09-07T11:14:04.038449"}'
Note : I did set "API_KEY = "my api key"" as a variable.
I'm using Python 3.7.12 on Windows 10. I hope my issue is clear enough.
Thank you in advance !
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PR_kwDOACgets4-jb5j
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|
Add extra info extraction from .xsf file
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[
"\n[](https://coveralls.io/builds/52297180)\n\nCoverage decreased (-0.003%) to 63.516% when pulling **21d60b9964a352e121e032fc35b2b40404d9e30d on VvVLzy:master** into **00df8be39cd18e898a3c98ff9e944b831f9c62dc on materialsproject:master**.\n",
"Many thanks. Can you add a few tests into the pymatgen/io/tests/test_xsf.py file to confirm the code is implemented correctly."
] | 2022-09-08T03:48:33
| 2024-08-03T19:01:57
|
NONE
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I have been working with some `.xsf` files that contain not only structures, but also forces and energies of the structure. I add code that can read in such information and store it in the XSF object for later access.
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Tweak .github/workflows/release.yml
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[
"\n[](https://coveralls.io/builds/52401783)\n\nCoverage increased (+0.0001%) to 63.517% when pulling **598c872a48325aaa97ef61e78cfefae6e72b4ebd on janosh:release-ci** into **d26d374dabe01686950162132f24c66baaf298fe on materialsproject:master**.\n",
"You **can** release to pypi more than once. Different wheels for different python versions and OSes. ",
"Is that actually happening here? The only thing that looks platform dependent in `setup.py` are the `numpy` header files (which should be wrapped in a list btw, i.e. `include_dirs=[numpy.get_include()]`). Is this the reason for OS -specific releases?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/d26d374dabe01686950162132f24c66baaf298fe/setup.py#L192-L193\r\n\r\nAnd also, which files actually compile against `numpy` headers? This `.pyx` file maybe (which is old enough to contain py2 compat code 😄)?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/d26d374dabe01686950162132f24c66baaf298fe/pymatgen/optimization/neighbors.pyx#L10",
"Yes. The cython based modules are compiled against specific numpy. ",
"@shyuep Good to know! I restored the release job's matrix strategy in \r\nf6aaae0 but removed the dependency installation step since running `python setup.py` [will do that anyway](https://stackoverflow.com/a/53069528).",
"I noticed the [PyPI description](https://pypi.org/project/pymatgen) is incorrectly parsed:\r\n\r\n\r\n\r\nFixed in this PR.",
"Merging (thanks!), but adding a note that I've been meaning to switch over to use this action for a while: https://cibuildwheel.readthedocs.io/en/stable/\r\n\r\nI've used this in another project and it works very well for producing cross-platform wheels.",
"@mkhorton I assume cross-platform wheels containing compiled code would be larger than platform-specific? Presumably they would need to bundle the `numpy` header files for Windows, Linux _and_ macOS arm64?\r\n\r\nI guess the pymatgen wheel is already quite large so adding that wouldn't make much difference?",
"The wheels are uploaded separately to PyPI, you only download the one you need on the platform you're installing on, so that's not a big concern.\r\n\r\nFor an example, contrast the `numpy` wheels available for the latest version here:\r\n\r\nhttps://pypi.org/project/numpy/#files\r\n\r\nto the `pymatgen` wheels here:\r\n\r\nhttps://pypi.org/project/pymatgen/#files",
"We do occasionally have user support requests from people with difficulty installing on one system or another (typically, if they install outside `conda`), and that's the main reason this is useful. It also slightly speeds up the install time too which is a nice side benefit."
] | 2022-09-10T19:46:41
| 2022-09-12T20:40:02
|
2022-09-12T20:26:33Z
|
MEMBER
|
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I just noticed the `release` job GitHub action runs on a matrix strategy. That seems very odd since you can't release a package version to PyPI more than once. I might be missing sth?
I also changed the trigger to
```diff
on:
release:
- types: [created]
+ types: [published]
```
based on [this SO heuristic](https://stackoverflow.com/a/61066906).
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PR_kwDOACgets4-3Yx8
| 2,650
|
Fix some bugs for tem.py
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[
"\n[](https://coveralls.io/builds/52428361)\n\nCoverage increased (+0.002%) to 63.353% when pulling **2cf0e57a501ee80de4efa2548c18269c8db4ea7d on chunweizhu:fix-1** into **de1614a1e68f9d5fc5be896f2f88fa95276ee086 on materialsproject:master**.\n",
"Thanks."
] | 2022-09-13T13:27:25
| 2022-09-13T16:29:41
|
2022-09-13T16:29:36Z
|
CONTRIBUTOR
|
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Signed-off-by: chunweizhu <c_w_zhu@163.com>
## Summary
Include a summary of major changes in bullet points:
* fix the bugs when runing `TEMCalculator`
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports A, but not B.
## 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:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
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PR_kwDOACgets4-6Jhu
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|
Fix GitHub language calculation
|
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[
"\n[](https://coveralls.io/builds/52450778)\n\nCoverage decreased (-0.002%) to 63.348% when pulling **d8271c414e1c7cacb449f731938f091e0a3ec8f6 on janosh:fix-gh-languages** into **deea7d2fc470a04b0394a1f6eb309c8f98cd6580 on materialsproject:master**.\n"
] | 2022-09-14T03:50:27
| 2022-09-14T04:11:11
|
2022-09-14T03:52:33Z
|
MEMBER
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The paths in `.gitattributes` work the same as in `.gitignore`. So to exclude HTML, rST and test files from the GitHub language calculation, were currently missing a few wildcards to include more deeply nested files.
This change should turn the language composition bar into almost pure Python (once GH had time to recompute).
<img src="https://user-images.githubusercontent.com/30958850/190055014-63ba1975-dbc3-4391-b5bb-3d724ee956cc.png" alt="Screen Shot 2022-09-13 at 20 44 39" width=300 >
Related https://github.com/materialsproject/atomate2/pull/148.
|
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I_kwDOACgets5R4YbP
| 2,652
|
Old API key raises unknown format error
|
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[
"I would just change it to else rather than elif. "
] | 2022-09-15T00:23:55
| 2022-09-15T16:55:57
|
2022-09-15T16:55:57Z
|
MEMBER
|
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```py
from pymatgen.ext.matproj import MPRester
elemental_reference_energies = MPRester().query(
{"nelements": 1}, ["material_id", "pretty_formula", "energy_per_atom"]
)
```
raises
```py
ValueError: API key ****************** is in an unknown format. Please check your API key at https://materialsproject.org/api
```
My key has length 17 and hence doesn't trigger either of these cases
https://github.com/materialsproject/pymatgen/blob/8670716641bd643545874aca972d79afd654e711/pymatgen/ext/matproj.py#L1779-L1786
Maybe we should change to this @munrojm?
```py
elif len(api_key) in (16, 17):
```
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PR_kwDOACgets4_CgHw
| 2,653
|
Fix GitHub language statistics - take 2
|
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[
"\n[](https://coveralls.io/builds/52509637)\n\nCoverage remained the same at 63.351% when pulling **ea3dbca703b4fb9c398328eb3291e0775c80cbcd on janosh:fix-gh-languages-2** into **8670716641bd643545874aca972d79afd654e711 on materialsproject:master**.\n",
"Cool, this time I got everything.\r\n\r\n<img src=\"https://user-images.githubusercontent.com/30958850/190464553-0de9a6b6-3c55-4e2d-bb1a-aa69adfa1a98.png\" width=400 alt=\"Screen Shot 2022-09-15 at 09 59 39\">"
] | 2022-09-15T16:15:15
| 2022-09-15T17:00:50
|
2022-09-15T16:40:36Z
|
MEMBER
|
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I missed a few large HTML and test files in #2651:
```txt
dev_scripts/NIST Atomic Ionization Energies Output.html
test_files/cohp/bandOverlaps.lobster.1
test_files/cohp/bandOverlaps.lobster.2
test_files/cohp/bandOverlaps.lobster.new.1
test_files/cohp/bandOverlaps.lobster.new.2
test_files/cohp/lobsterin.1
test_files/cohp/lobsterin.2
test_files/cohp/lobsterin.3
```
Yet more wildcards in `.gitattributes` to the rescue.
One interesting thing I learned is that linguist overrides do not change how files are treated when performing a repo search for a specific language. E.g. using language qualifier `l=roff` will still return those files in the search results, even when treated as vendored by linguist.
|
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https://github.com/materialsproject/pymatgen/pull/2654
| 1,374,819,882
|
PR_kwDOACgets4_CoiK
| 2,654
|
Always use _MPResterLegacy if len(api_key) != 32
|
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[] | null |
[
"\n[](https://coveralls.io/builds/52510673)\n\nCoverage increased (+0.002%) to 63.355% when pulling **9a88b79ba68c2fa28605a09d5f182027615700a7 on janosh:gh-2652** into **e37284de4777ecb41e4c2b7f672e425e7dca5c71 on materialsproject:master**.\n"
] | 2022-09-15T16:50:14
| 2022-09-15T17:16:29
|
2022-09-15T16:55:56Z
|
MEMBER
|
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Closes #2652.
|
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| 1,375,363,060
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I_kwDOACgets5R-l_0
| 2,655
|
PatchedPhaseDiagram raises on keep_all_spaces=True
|
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[] | 2022-09-16T03:43:40
| 2022-09-20T18:30:07
|
2022-09-20T18:30:07Z
|
MEMBER
|
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@CompRhys
```py
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram
from pymatgen.ext.matproj import MPRester
entries = MPRester().get_entries("Li O".split())
PatchedPhaseDiagram(entries, keep_all_spaces=True)
```
raises
```py
AttributeError: 'set' object has no attribute 'sort'
```
<details>
<summary>stack trace</summary>
```py
----> 175 PatchedPhaseDiagram(entries, keep_all_spaces=True)
File ~/dev/pmg/pymatgen/analysis/phase_diagram.py:1544, in PatchedPhaseDiagram.__init__(self, entries, elements, keep_all_spaces, verbose)
1541 spaces = systems
1543 # Calculate pds for smaller dimension spaces first
-> 1544 spaces.sort(key=len, reverse=False)
1546 pds = [self._get_pd_patch_for_space(s) for s in tqdm(spaces, disable=(not verbose))]
1547 pds = dict(pds)
AttributeError: 'set' object has no attribute 'sort'
```
</details>
|
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| 1,375,365,487
|
PR_kwDOACgets4_Eciw
| 2,656
|
Fix AttributeError: 'set' object has no attribute 'sort' from PatchedPhaseDiagram(keep_all_spaces=True)
|
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[] | null |
[
"\n[](https://coveralls.io/builds/52549822)\n\nCoverage decreased (-0.002%) to 63.352% when pulling **34460ced6b7446f8122faf2d360c3569fb036817 on janosh:gh-2655** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n",
"Thanks,"
] | 2022-09-16T03:47:38
| 2022-09-20T18:36:31
|
2022-09-20T18:30:07Z
|
MEMBER
|
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Closes #2655.
|
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I_kwDOACgets5R-ncW
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|
PatchedPhaseDiagram raises on keep_all_spaces=False
|
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[] | null |
[
"This one is actually still broken. Will submit another PR for this."
] | 2022-09-16T03:54:01
| 2022-09-20T18:37:45
|
2022-09-20T18:34:01Z
|
MEMBER
|
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|
@CompRhys Similar example to #2655 but leaving the default `keep_all_spaces=False`:
```py
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram
from pymatgen.ext.matproj import MPRester
entries = MPRester().get_entries("Li O".split())
PatchedPhaseDiagram(entries, keep_all_spaces=False)
```
also raises
```py
ValueError: max() arg is an empty sequence
```
<details>
<summary>stack trace</summary>
```py
----> 174 PatchedPhaseDiagram(entries)
File ~/dev/pmg/pymatgen/analysis/phase_diagram.py:1532, in PatchedPhaseDiagram.__init__(self, entries, elements, keep_all_spaces, verbose)
1530 # Remove redundant chemical spaces
1531 if not keep_all_spaces:
-> 1532 max_size = max(len(s) for s in spaces)
1534 systems = []
1535 # NOTE reduce the number of comparisons by only comparing to larger sets
ValueError: max() arg is an empty sequence
```
</details>
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| 1,376,471,523
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PR_kwDOACgets4_IH9K
| 2,658
|
write charge if set
|
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[
"\n[](https://coveralls.io/builds/52547566)\n\nCoverage increased (+0.0004%) to 63.355% when pulling **4b9c1981cc9b3acc063237d11d2eb62b4cd3470c on jmmshn:patch-vasprun-chg** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n"
] | 2022-09-16T21:05:13
| 2022-09-23T19:06:22
|
2022-09-23T16:31:55Z
|
CONTRIBUTOR
|
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## Set the structure_charge while parsing Potcar
Currently while creating the `Vasprun` object, the `_structure._charge` is `None` if the charge was determined to be 0. If we ensure that the `_charge` parameter is always set, then we can use the check
```
_structure._charge is None
```
To figure out if the charge was properly read from the POTCAR files.
This allows some downstream logic for parsing charged defect outputs to be much easier.
|
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PR_kwDOACgets4_IqI6
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|
Fix ThermalDisplacementMatrices.compute_directionality_quality_criterion()
|
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"\n[](https://coveralls.io/builds/52634277)\n\nCoverage decreased (-0.006%) to 63.349% when pulling **5345eccb88a36ffa696974e09f3b13da946158ba on janosh:fix-ThermalDisplacementMatrices-compute_directionality_quality_criterion** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n",
"I will work on an additional test so that this error is fixed for the long term."
] | 2022-09-17T03:24:35
| 2022-09-23T17:51:41
|
2022-09-23T16:31:23Z
|
MEMBER
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https://github.com/materialsproject/pymatgen/blob/722ea4648bbcd9e792991e51365fed5b78eba3f4/pymatgen/phonon/thermal_displacements.py#L264-L270
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PR_kwDOACgets4_Nqqb
| 2,660
|
Patch the cube spherical mask
|
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[
"\n[](https://coveralls.io/builds/52585233)\n\nCoverage remained the same at 63.355% when pulling **9fb6457c58c67a0bd7839dee0acc5669f9ab52e9 on nwinner:cube-patch** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n",
"@nwinner since we already have an internal pymatgen definition of `VolumentricData` it might be helpful to have some of the methods here moved to VolumetricData and that way the VASP folks and get access to them too.\r\nThen we just need a `from_cube_file` class method for `Volumetric data`. This also avoids the problem discussed here for similar large objects that might need to be serialized at some point down the line:\r\nhttps://github.com/materialsproject/pymatgen/issues/2661\r\n\r\nSome of the masking logic here can also merge with or replace the masking logic here:\r\n\r\nhttps://github.com/materialsproject/pymatgen-analysis-defects/blob/a56874d8b3ed8a411669805be0339d5b65d76e3e/pymatgen/analysis/defects/utils.py#L360-L395\r\n\r\nSo if they were made available in VolumetricData I would be able to just use them in the defect package directly.\r\n\r\n",
"Seems sensible. Wouldn't that require moving VolumetricData to a code agnostic location? If we do what you suggest right now, anyone wanting to parse cube data, which is used by people outside that vasp community, would have to go into the vasp module to find it.",
"I don't have a problem with moving VolumetricaData. ",
"Agreed! moving VolumetricData makes sense. \r\n\r\nPS: on a semi related note I have this package as well that's meant to deal with representation of periodic data:\r\nhttps://github.com/materialsproject/pyrho\r\n\r\nIf we rip volumetric data out into a code agnostic place that leaves the possibility of intergrating pyrho in the future and you can get some regridding and compression and interpolation features for free.\r\n\r\n",
"On a semi-semi-related note. Any possibility to move some of the k-point logic from the VASP module into something code agnostic? Generating k-point grids does not need to be specific to VASP.",
"So I took a look at the `Kpoints` code and I think that'll be difficult.\r\nSince the object is already `MSONable` with heavy design influences from VASP I think it might be difficult to strip it out.\r\nEspecially with all the tetrahedron stuff.\r\n\r\nI think we shelve the idea of stripping out the `Kpoints` until another program needs it and think about a redesign (inheritance pattern) at a later time.",
"Sure. I'm going to push k-points and bandstructure support for cp2k by next week, and it uses the vasp kpoints module, but its not *crucial* to modify that at the moment since not many people use the code. Something to keep in mind for later though.",
"Anyway where should the VolumetricData be moved to that would make the most structural sense? A new place in io module?",
"I think something like `io.periodic.py` would be goodc then you can put any future common classes for Kpoints and band structure in there.",
"I would just call it io.common or something.\r\n",
"I've made a new PR for this `io.common` idea and it can be found here:\r\n\r\nhttps://github.com/materialsproject/pymatgen/pull/2667#issue-1386968182"
] | 2022-09-19T16:36:19
| 2022-09-29T20:26:14
|
2022-09-27T02:13:21Z
|
CONTRIBUTOR
|
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Simple patch for cube parsers spherical mask. It now functions properly and is cleaner.
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I_kwDOACgets5SPUsN
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|
Proposed change to waveder
|
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[
"I support this proposal. Pls implement and submit a PR. Thanks."
] | 2022-09-20T17:18:30
| 2023-03-18T04:26:11
|
2023-03-18T04:26:11Z
|
CONTRIBUTOR
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https://github.com/materialsproject/pymatgen/blob/722ea4648bbcd9e792991e51365fed5b78eba3f4/pymatgen/io/vasp/outputs.py#L5509
Currently, there are two Waveder objects basically accomplish the same thing be just have two different constructor methods.
They also cannot be serialized since their `__init__` requires the filename.
Proposed change:
- Combine the two objects into one `Waveder` dataclass object with the `cder` data.
- Change the two different constructors `from_waveder` and `from_wavederf`.
Let me know if this messes with anyone's stuff (especially the original author @migueldiascosta) and I will PR.
Best
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PR_kwDOACgets4_TM6I
| 2,662
|
Fix PatchedPhaseDiagram raises ValueError on empty spaces set
|
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"\n[](https://coveralls.io/builds/52627172)\n\nCoverage decreased (-0.007%) to 63.348% when pulling **2d3b25f113079d91ee913dc1fcc6f2bb0d3f403f on janosh:gh-2657** into **a9a1d483957afde9465d70eefc1c25992983660f on materialsproject:master**.\n"
] | 2022-09-20T19:35:15
| 2022-09-20T19:53:32
|
2022-09-20T19:36:10Z
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MEMBER
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Closes #2657.
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PR_kwDOACgets4_adkk
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Additional test for thermal displacement matrices
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[
"Will fix the test. Sorry.",
"\n[](https://coveralls.io/builds/52682539)\n\nCoverage increased (+0.004%) to 63.349% when pulling **384b647490fb12515d425302a16beca1795cc2c7 on JaGeo:fix_displacements** into **6c23d744efbd892ec48346297d61b4f3f86b1478 on materialsproject:master**.\n",
"Fixed.",
"Thanks."
] | 2022-09-22T09:32:07
| 2022-09-23T16:31:24
|
2022-09-23T16:31:18Z
|
MEMBER
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## Summary
I have added an additional test to make sure that the error fixed in https://github.com/materialsproject/pymatgen/pull/2659 does not show up again. I have started from @janosh 's branch.
JG
|
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I_kwDOACgets5ScK94
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BVS Analyzer
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[] | 2022-09-22T23:17:41
| 2022-09-26T16:33:08
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2022-09-26T16:30:58Z
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NONE
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I'm trying to use BVSAnalyzer module. My structure is periodic, and I'm doing:
```
Fh = Structure.from_file("Fh_Ehm_2007.cif")
Fh.add_oxidation_state_by_element({"Fe":3, "O":-2})
Fh_bvs = bond_valence.BVAnalyzer()
Fh_valences =Fh_bvs.get_valences(Fh)
Fh_valences
```
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PR_kwDOACgets4_dyCd
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change equality comparison operation to `as_dict`
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"\n[](https://coveralls.io/builds/52701226)\n\nCoverage increased (+0.002%) to 63.347% when pulling **7b350d1ed26eee7da2e4f09bc35185c14ed8d197 on orionarcher:fix_input_set_equality** into **6c23d744efbd892ec48346297d61b4f3f86b1478 on materialsproject:master**.\n",
"> ## Summary\r\n> \r\n> The current equality operation for InputSet's will fail if `InputSet.inputs` has mutable values. This happens often because InputSet is designed to support `InputFile`s as `inputs`. I have changed the equality operation to use `as_dict` which will coerce all nested elements to immutable types, enabling easier comparison. Would love a final look from @rkingsbury to make sure this makes sense.\r\n> \r\n> This follows up on a previous issue I raised where the equality operation was failing entirely.\r\n\r\nThanks for identifying @orionarcher . This looks find to me and appears innocuous as far as compatibility goes. Could you add a test that compares `InputSet` with mutable types?\r\n\r\nFor others reading this - see #2575 for previous work on this issue. ",
"I don't think InputSets are meant to be compared?",
"> I don't think InputSets are meant to be compared?\r\n\r\nIt may be somewhat unusual , but since `InputSet` are dict-like mappings it makes sense to me that it should be possible to compare them.",
"@rkingsbury No no.... the question is whether they are *meant* to be compared. The default answer for most objects should be no. In the case of input sets, it is an algorithm to generate a set of input files for a given structure. You can compare structures. But something like MPStaticSet == MPRelaxSet makes zero sense. ",
"> @rkingsbury No no.... the question is whether they are _meant_ to be compared. The default answer for most objects should be no. In the case of input sets, it is an algorithm to generate a set of input files for a given structure. You can compare structures. But something like MPStaticSet == MPRelaxSet makes zero sense.\r\n\r\nI agree that MPStaticSet == MPRelaxSet makes no sense. But in the new IO paradigm, remember that MPStaticSet and MPRelaxSet would be _input generators_ which lack structure information. What Orion is referring to is comparing a specific `InputSet` created by the generator, for a specific structure. You might want to do this if you have a large number of calculations prepared, and you need to deduplicate them. If all the settings are the same (i.e., all the `InputSet` attributes), and the structure is the same, then the two `InputSet` define identical calculations, and it makes sense to consider them \"equal\".",
"I guess I really don't understand the use case. If InputSet contains structure, then the structure comparison will tell you whether it is equal. If the InputSet is merely a generator that does not contain structure, then you should initialize only one InputSet for each distinct type of calculation you do. I don't see a scenario where I initialize multiple InputSets and end up having to deduplicate them. Deduplication should take place at the level of the structure, not at the InputSet level. ",
"> I guess I really don't understand the use case. If InputSet contains structure, then the structure comparison will tell you whether it is equal. If the InputSet is merely a generator that does not contain structure, then you should initialize only one InputSet for each distinct type of calculation you do. I don't see a scenario where I initialize multiple InputSets and end up having to deduplicate them. Deduplication should take place at the level of the structure, not at the InputSet level.\r\n\r\nI hear what you're saying. I think there is confusion here because of terminology - when we developed the Abstract IO interface we decided to retain the name `InputSet` even though its meaning changed slightly compared to the legacy approach. The potential for confusion is compounded by the fact that the VASP `InputSet` in pymatgen still use the legacy paradigm. (Much progress has been made porting VASP workflows to the new paradigm over in `atomate2`, and I think that work will be moved to pymatgen soon.)\r\n\r\nLet me try to clarify. In the new paradigm, `InputGenerator` do exactly what you describe here:\r\n> you should initialize only one InputSet for each distinct type of calculation you do\r\n\r\nYou initialize one `InputGenerator` e.g. a `MPRelaxSetGen()` for each calculation type. This contains all settings but no structure. Then you call `InputGenerator().get_input_set(structure)` to create an `InputSet` that is a concrete calculation (settings + structure). This object is similar to `VaspInput`. _That_ is the object that we want to compare.\r\n\r\n> Deduplication should take place at the level of the structure, not at the InputSet level.\r\n\r\nI would say you want to deduplicate on the level of structure+settings, hence the value of having `InputSet` equality.",
"I disagree on the deduplication strategy. Let me phrase it differently. Say you have a MPStaticGenerator and a MPRelaxGenerator (using the old terminology for convenience here). Why would I want to bother checking the *settings* as well as the structure? I would deduplicate the structures first. That guarantees that the inputs generated would be unique. You will need to provide me with a scenario where equal structures can have equal input settings for different generators, or equal structures can have different input settings for the same generator. ",
"> Say you have a MPStaticGenerator and a MPRelaxGenerator (using the old terminology for convenience here). Why would I want to bother checking the settings as well as the structure?\r\n\r\n_Provided that all `InputSet` have been created by the same `InputGenerator`_, then you would not need to bother checking settings. However, one of the goals in the new IO paradigm was to standardize the behavior of `InputSet`, regardless of how it was generated. That means I could have a collection of `InputSet` that are created from different generators.\r\n\r\nConsider this pseudo-code example:\r\n```\r\ns = Structure(...)\r\nMPRelaxGenerator(<relaxation settings>).get_input_set(s) -> InputSet1\r\n\r\nMPStaticGenerator(<static settings>).get_input_set(s) -> InputSet2\r\n```\r\n`InputSet1` and `InputSet2` behave the same way by design - they have the same class methods and attributes, etc. But one defines a static calc and the other a relax. If we only compared based on the structure, we would conclude `InputSet1 == InputSet2`. But that's not the case. They define different sets of calculation inputs.",
"Yes, what I mean is when would you be in no control of InputGen1 InputGen2 such that you have to ex-post check for equality of InputSets? My conceptualization is that you will decide you only want to use InputGen1 and InputGen2, and you supply unique structures to Gen1 and Gen2. By definition, the four InputSets will all be unique. There is no reason to check it at the end. In fact, checking at the end of InputSet guarantees that instead of checking only n structures for equality, you will have to check n*k InputSets. Given that checking is O(N^2), that scales extremely poorly.\r\n\r\nIf you insist on checking InputSets rather than ensuring uniqueness, then I would suggest you simply have a metadata that says this InputSet was created using InputGen1. In that case, you can do checks in two separate n and k checks rather than one giant n*k check.",
"> Yes, what I mean is when would you be in no control of InputGen1 InputGen2 such that you have to ex-post check for equality of InputSets? My conceptualization is that you will decide you only want to use InputGen1 and InputGen2, and you supply unique structures to Gen1 and Gen2. By definition, the four InputSets will all be unique. There is no reason to check it at the end. In fact, checking at the end of InputSet guarantees that instead of checking only n structures for equality, you will have to check n*k InputSets. Given that checking is O(N^2), that scales extremely poorly.\r\n> \r\n> If you insist on checking InputSets rather than ensuring uniqueness, then I would suggest you simply have a metadata that says this InputSet was created using InputGen1. In that case, you can do checks in two separate n and k checks rather than one giant n*k check.\r\n\r\nFair enough. Regardless of whether this is an efficient workflow or not though, I don't see any harm in having an equality operation in place for `InputSet`. It inherits from `MutableMapping`, behaves similar to a dictionary, and therefore I think it's reasonable that users might expect to be able test equality.\r\n\r\nan equality check is also useful for unit testing, where you might want to do\r\n```\r\nis1 = SomeInputSet.from_directory(<test_dir>)\r\nis2 = SomeInputGenerator().get_input_set(s)\r\nassert is1==is2\r\n```\r\nI think this is how @orionarcher discovered the problem documented here and in the linked issue.",
"I'd like to offer another perspective to the one above. I've never used VASP and I have never used the Pymatgen `Structure`. I have been using the new pymatgen IO while developing the `pymatgen.io.openmm` [add-on package](https://github.com/orionarcher/pymatgen-io-openmm). There, as @rkingsbury said, I test equality in the unit tests to make sure that writing objects to and from MSON does not alter them. Since I am mixing together code from the `openmm` and `pymatgen` pacakges, this was not straightforward.\r\n\r\nTesting equality has already been useful for me and I think it's worth keeping in mind use cases beyond our immediate development workflows, especially in light of the new `pymatgen.addon` infrastructure.",
"I think we need to distinguish between unittest checking - an esoteric thing that just checks if something works as intended, vs an actual functionality that is encouraged for users. E.g., when we do unittest checking, we can do really blunt stuff like comparing strings of input files. Terrible for efficiency and very prone to numerical issues, but nonetheless, a good enough thing for a lot of purposes.\r\n\r\nRe the openmm, I am somewhat confused by the statement that pymatgen Structure is not used. I would think the whole idea of pymatgen.io.xxx is to go from a pymatgen Molecule/Structure to a set of input files? ",
"> Re the openmm, I am somewhat confused by the statement that pymatgen Structure is not used. I would think the whole idea of pymatgen.io.xxx is to go from a pymatgen Molecule/Structure to a set of input files?\r\n\r\nIt uses `Molecule` to generate a set of input files\r\n\r\nI feel our discussion is getting off track. As you often remind me @shyuep , we can't put so many guardrails in pymatgen that we guarantee users won't do silly things. If someone wants to put a single MPRester query in a `for` loop and run it a million times (and thrash our API), we can't prevent that. `InputSet` equality checking may not always be the most efficient way to accomplish a task, but it is clearly useful (as demonstrated for unit testing and as evidenced by the fact that @orionarcher , who has developed a very nice pymatgen addon package, needs it for further work). Moreover, we _already_ have equality checking in place, this PR is just a bugfix.\r\n\r\nI'd like to refocus on our choices here, which are 1) to move forward with the bugfix or 2) to remove `InputSet` equality checking altogether, which will put a significant amount of extra work on @orionarcher to create good quality tests for the new OpenMM IO. Moreover as you point out @shyuep , doing so might require \"blunt stuff like comparing strings of input files.\" that are \"Terrible for efficiency and very prone to numerical issues\". Resorting to approaches like that inherently reduces the quality of the tests in my opinion, because it's much easier to make a subtle mistake.\r\n\r\nIn the particular case of openmm, the input files are .xml based due to the way the code is constructed, so the effort to get tests working would be even more involved.\r\n\r\nNeedless to say, I favor option 1. Do you see any technical problems with using `as_dict` as the basis for the equality check?",
"I'm not sure I'd agree that checking if something works as intended is esoteric, but I do see your point RE efficiency. In this case, perhaps prioritizing developer time over computational cost might be the right move, as the cost of IO will be dwarfed by the cost of simulations. In short, I'd support option 1.\r\n\r\nIn classical MD simulations we need to specify bonding ahead of time, so Molecule and Structure are not very convenient representations. The IO heavily uses the new `pymatgen` IO paradigm and `Molecule`s do enter the code in several places.",
"I favor not checking InputSets for equality. In the end, what you are saying is that instead of:\r\n\r\n```python\r\nself.assertEqual(inputset1, inputset2)\r\n```\r\n\r\nthe developer has to write\r\n\r\n```python\r\nself.assertEqual(inputset1.as_dict(), inputset2.as_dict())\r\n```\r\n\r\nThe latter doesn't seem like a lot of effort to me and is in fact used in many places for tests (other than strings).\r\n\r\nMy view is that the commitment to an `__eq__` implementation is highly significant and requires rigorous definition. That is why Python objects by default do not implement `__eq__` and only checks for equality of ids. Let me present a scenario - let's say someone supplies methane to an input set and say that person is not particularly careful and supplies a second methane that is rotated by 15 degrees to the first. For all intents and purposes, the two InputSets are equal for most computational codes - Gaussian, VASP, whatever you can think of. But using as_dict would result in the two InputSets as unequal. \r\n\r\nThe collorary I can give is `Structure.__eq__` vs `Structure.matches`. Here, we have a definition that `__eq__ `is meant to compare based on numerical closeness while `matches` (a far more expensive method) actually handles site mappings. The latter is the \"correct\" way of doing everything. There are almost no instances where structure1 == structure2 is the correct method to call by a user. But there is an important use case in that we need Structure to be usable as a key in a dictionary that is being updated and that's where the `__eq__` comes in. That \"important to be usable as a key in a dict\" is just about the only situation where I think it is useful to have a non-rigorous `__eq__` definition. This applies to things like ComputedEntry as well.\r\n\r\nCertainly I agree we do not need to put too many guardrails on users. But here, we are actively implementing a feature that encourages bad use with very limited good use case (unittest is certainly one good use case, but like I pointed out, it is not a `user` use-case and it can be dealt with using minimal additional code). In essence, we are giving users a way to do an O((Nk)^2) comparison instead of an O(N^2) comparison with zero difference in outcomes. I also don't see InputSets being used as keys in a dict. In fact, usage as a key would violate the general concept that \"sets\" are usually non-hashable.",
"> My view is that the commitment to an `__eq__` implementation is highly significant and requires rigorous definition. That is why Python objects by default do not implement `__eq__` and only checks for equality of ids.\r\n\r\nI see; I didn't realize that there was a more general architectural decision to not implement `__eq__` methods. You make a good point that we can just use `InputSet1.as_dict() == InputSet2.as_dict()` in tests. That's an equally good technical solution that doesn't impose extra overhead on developers.\r\n\r\nMaybe the best course of action then is to remove the `__eq__` method. @orionarcher , if you agree, would you mind updating your PR accordingly?",
"I've opened a PR to remove __eq__ so I think we can close this one. Hopefully this will not cause too much disruption to ongoing development of inherited classes.",
"I'll close this as completed by #2671."
] | 2022-09-23T00:32:04
| 2023-05-08T19:50:14
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2023-05-08T19:50:13Z
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CONTRIBUTOR
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## Summary
The current equality operation for InputSet's will fail if `InputSet.inputs` has mutable values. This happens often because InputSet is designed to support `InputFile`s as `inputs`. I have changed the equality operation to use `as_dict` which will coerce all nested elements to immutable types, enabling easier comparison. Would love a final look from @rkingsbury to make sure this makes sense.
This follows up on a previous issue I raised where the equality operation was failing entirely.
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PR_kwDOACgets4_iEA8
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fixed waveder serialization
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[
"\n[](https://coveralls.io/builds/52819268)\n\nCoverage increased (+0.02%) to 63.368% when pulling **0116ad5ae528948f75923c1b9872077fa9695381 on jmmshn:patch_waveder** into **d7e9b7a7986f06601136190398d2dc2ecb7ca85d on materialsproject:master**.\n",
"Thanks @jmmshn. Since this is a breaking change, can you add a note to https://github.com/materialsproject/pymatgen/blob/master/docs_rst/compatibility.rst, and then I can merge?",
"Ok, added the comment about the breaking change.",
"There are some unrelated `mypy` errors in linting, also present on the other PRs.",
"Thanks @jmmshn"
] | 2022-09-24T00:44:38
| 2022-09-29T16:25:44
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2022-09-28T14:06:43Z
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CONTRIBUTOR
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# Merge Waverder and Wavederf
Originally discussed in #2661
- Merge the two classes into one object with two constructors
- Allow the object to be serializable
- Modified to test files with `LVEL=.TRUE.` in INCAR
- Added comment about running with `LVEL=.TRUE`
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Move VolumetricData to io/common and merge cube support
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[
"@shyuep what do you think about this solution?\r\n\r\n`VolumetricData` is now defined in common, but in the `vasp.outputs` module we import it as `BaseVolumetricData` and define a new child class called `VolumetricData`. Its not especially elegant, but this way legacy code will import `VolumetricData` from the `vasp.outputs` module and get the expected behavior, but we have a common object for cube and hdf5.\r\n\r\nAlso it looks like linting fails on parts of the PR unrelated to my code. I guess the main branch doesn't pass all checks?",
"\n[](https://coveralls.io/builds/54483355)\n\nCoverage decreased (-63.6%) to 0.0% when pulling **e3c1d93bcbb7dba2cd0c4a9eee0e82196ce022ef on nwinner:volumetric-data-patch** into **e01d044986d6b321ee0254a6c9c89a5edd693935 on materialsproject:master**.\n",
"Just a note that master is failing the tests, not this new feature.",
"I think this PR can be better handled if you just do the refactor to `io.common` and then add the CPMD stuff later.",
"But the issue is in the average along axis method, so wouldn’t it still be\nthere? That method comes from the current VASP implementation.\n\n(Sent from iPhone)\n\nOn Tue, Nov 22, 2022 at 9:53 AM Jimmy Shen ***@***.***> wrote:\n\n> I think this PR can be better handled if you just do the refactor to\n> io.common and then add the CPMD stuff later.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/2667#issuecomment-1324044556>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/ACDKYLJFXUYJQSL3CL4NJC3WJUCA7ANCNFSM6AAAAAAQWKVQ7Q>\n> .\n> You are receiving this because you were mentioned.Message ID:\n> ***@***.***>\n>\n",
"> But the issue is in the average along axis method, so wouldn’t it still be there? That method comes from the current VASP implementation. (Sent from iPhone)\r\n\r\nI thought the function was for generating a sphere.",
"Oh i see. My mistake @jmmshn . The quoted code included the bottom of the get_average_along axis function and I thought that's what you were referring to. I agree that the sphere stuff can be removed until a later date.",
"@shyuep It looks like all conversations have been resolved for this. The two checks that failed are failing on \r\n\r\n`pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py:81`\r\n\r\nwhich is not related to this PR. "
] | 2022-09-27T02:12:08
| 2022-12-13T18:08:55
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2022-12-13T18:08:55Z
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CONTRIBUTOR
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## Summary
Migrate VolumetricData to a new `io.common` module, which can be used by other file formats such as hdf5 and cubes.
Update the vasp output module to use the new class in common.
Only "inelegance" is that a new `VaspVolumetricData` method had to be defined in `io.vasp.outputs` because from_file and write_file in the original `VolumetricData` used logic from `io.vasp.inputs.Poscar` which creates circular imports if ported to `io.common`. An elegant solution to this would be a good improvement.
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Extension ThermalDisplacementMatrices class
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[
"\n[](https://coveralls.io/builds/53115513)\n\nCoverage increased (+0.08%) to 63.433% when pulling **ad7b8d09fec69a36da5cbc79d01d8c910950a2ba on JaGeo:fix_displacements** into **d7e9b7a7986f06601136190398d2dc2ecb7ca85d on materialsproject:master**.\n",
"Currently mypy is failing but I don't see a direct connection to my pull request. I would be very happy about any hint how to potentially solve this issue.",
"All linting errors are fixed now.",
"Thanks!",
"Thanks for merging and fixing the docu and comments, @janosh !\r\nJG",
"We should probably automate doc style checking with `pre-commit` at some point."
] | 2022-09-27T10:16:28
| 2022-10-08T15:35:29
|
2022-10-08T14:58:24Z
|
MEMBER
|
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## Summary
I have extended the ThermalDisplacementMatrices class. It can now also read cif files in P1 format, produce structures including Ucif as site_property (handy for sorting structures and thermal displacement properties, for example), and print VESTA files in P1 space group including vectors indicating the directionality of two different sets of computed displacement parameters.
While doing so, I have refactored the classes parsing the cif files a tiny bit. In general, I found it very hard to reuse any of the code in there as this warning state of the class would require me to make instances of classes. While I understand the purpose of saving the warnings like this, it has this drawback. Otherwise, most of the methods in there could be static methods.
|
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I_kwDOACgets5Sx7Cb
| 2,669
|
SlotPickleMixin removed in the latest version
|
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[] | 2022-09-28T06:43:37
| 2022-09-28T06:43:37
|
NONE
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With the latest version 2022.9.21, the following:
```
from pymatgen.util.serialization import SlotPickleMixin
```
leads to the error `ImportError: cannot import name 'SlotPickleMixin' from 'pymatgen.util.serialization'`. I obtained this while I was trying to use [USPEX](https://uspex-team.org/). Reverting to a previous version using `pip install pymatgen==2022.9.8` fixed the issue.
I'm not sure if this is considered breaking. This was removed in #2649.
|
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PR_kwDOACgets4_31B7
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|
Optical analysis VASP
|
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[
"\n[](https://coveralls.io/builds/53192707)\n\nCoverage increased (+0.07%) to 63.451% when pulling **bf6996c6d38b40616ac30ab12e6ee29b727bbd2d on jmmshn:optics** into **6345c201d1973afddb813342bd62e481daeee26a on materialsproject:master**.\n",
"This is a fantastic PR, thanks @jmmshn!\r\n\r\nPushed a small fix a test in another module due to the addition of the extra vasprun.xml, and some typos, otherwise looks good.\r\n\r\nRegarding printing the symmetry operators in the vasprun.xml, I could ask the VASP devs if this would be helpful? Would this be a straightforward add for them?",
"> Regarding printing the symmetry operators in the vasprun.xml, I could ask the VASP devs if this would be helpful? Would this be a straightforward add for them?\r\n\r\nThat would be super useful and should be an easy add for them since it is already stored in memory and used in various places in VASP. Can you also CC me on that email?",
"Also if you are able to turn on ISYM there are other subtle things when the data is printed in VASP that might need to change like one of the indices of the WAVEDER only runs over occupied bands with ISYM != 0 but runs over all bands with ISYM=0. And there are sum weird interactions with a hidden VASP LVEL flag there were basically all brushed under the rug with ISYM=0."
] | 2022-09-29T16:40:44
| 2022-10-12T01:02:56
|
2022-10-11T23:16:31Z
|
CONTRIBUTOR
|
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## More Flexible reproduction of VASP's optical code
Added `DielectricFunctionCalculator` class which will allow you to:
- Have full control of the matrix elements before and after Fermi's golden rule and before and after Kramers-Kronig transformation.
- This allows you to obtain the band-decomposed and kpoint-decomposed versions of the optical properties: Free-carrier absorption + defect absorption.
|
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PR_kwDOACgets4_4NhP
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InputSet: remove __eq__ method
|
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[
"\n[](https://coveralls.io/builds/52883088)\n\nCoverage decreased (-0.003%) to 63.378% when pulling **86b12b2c1eea95953ea0ae6fa640718457a4c1f9 on rkingsbury:noeq** into **02873b378ab7540b6858744fdf0c6b9b5d2b0c21 on materialsproject:master**.\n"
] | 2022-09-29T18:08:40
| 2024-10-10T01:54:48
|
2022-09-30T13:50:02Z
|
CONTRIBUTOR
|
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## Summary
Remove the `__eq__` method from `InputSet`, per discussion in #2665 (and will replace that PR).
Flagging @utf in case this change will affect development of VASP `InputSet` in `atomate2`.
|
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PR_kwDOACgets4_41IO
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Cp2k 2.0
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[
"\n[](https://coveralls.io/builds/55610575)\n\nCoverage: 19.367% (-7.9%) from 27.266% when pulling **52a75003529245a8e82abd2b2f59d0acff44c304 on nwinner:cp2k-2.0** into **d0ab147a6bc7b9bb8bae91432fdd85cca00c13a3 on materialsproject:master**.\n",
"Thanks. based on the changes, it seems only the test_inputs was changed in one line. Should there be more tests for all the new functionality in outputs, sets, etc.?",
"I can add a few basic tests and some new test data for it. I'll @ you afterwards.",
"@shyuep I did a minor update to the tests and the test files to reflect changes. ",
"Sorry for the premature @, @shyuep . Those simple tests were bugged. Now it should be ready for merge if you agree.",
"Just as a note, I merged master when I fixed @janosh 's comment and a test is failing there.",
"@shyuep @janosh (anybody else who should get @ for this?)\r\n\r\nAfter a very long time, I finally finished this PR. Could I get a review?\r\n\r\nTwo tests failing on split 1 are related to chemenv tests, which are not part of this PR and are an issue elsewhere in pymatgen.",
"Sorry, currently traveling and not in front of a large enough screen to review such a significant PR. But looks like a lot of great work! 🥇",
"Thanks @nwinner! This looks like a ton of work! 👍 \r\n\r\n@shyuep @mkhorton Merging this as test and lint errors appear unrelated."
] | 2022-09-29T20:39:04
| 2023-01-03T19:56:40
|
2023-01-03T19:39:03Z
|
CONTRIBUTOR
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## Summary
PR for major updates to CP2K functionality in pmg, plus a minor edit to `compatibility.py`. PR has been geared towards simplifying certain features, while making others more compatible with the new `atomate2` package, which will use this version.
`inputs.py`
- New Kpoints section objects
- New bandstructure objects
- dataclass representations of basis sets and pseudopotentials
`sets.py`
- Simplified number of sets
- DftSet now supports new basis/potential scheme
- DftSet now handles more printing/features
- DftSet now includes a simple validator for non-compatible features
`outputs.py`:
- Now supports parsing some of the CP2K properties, such as the hyperfine_coupling tensor. Support for all properties not available
- New Dos parsing
`utils.py`
- Now supports fewer functions. Some of the messy basis utility functions are now handled using the new objects in `inputs.py`
`pmg_config.py`
- In order to make code similar to VASP module, and to allow for improved handling of pseudopotentials, a config option has been added to pmg_config that is similar to the potcar configuration for VASP. This will now replace the settings.yaml file, which is a large file to move through github.
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I_kwDOACgets5TBESS
| 2,673
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Structure.charge and as_dict() bug in recent versions of pmg
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[
"I just noticed that @arosen93 changed that line `2208 \"charge\": self.charge`.\r\nCould you comment on this?",
"Hi @fraricci --- thanks for the ping and apologies about any issues. It looks like the change was made in [this PR](https://github.com/materialsproject/pymatgen/pull/2388) based on [this issue](https://github.com/materialsproject/pymatgen/issues/2384). I will look into this in more detail tomorrow --- I'm away from my computer at the moment. Hopefully that provides some insight though.",
"I went down the rabbit hole a little more and I think the issue is in the MagOrderingTransformation at this line:\r\nhttps://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/transformations/advanced_transformations.py#L791\r\n\r\nWhen it removes the dummy species, it explicitly define the oxi_state attr and set it to zero.\r\nThis returns a structure where some sites have no oxi_state and some with it, making the charge func failing.\r\n\r\n@mkhorton what you think?",
"I proposed a fix here #2791, changing the Structure.charge().\r\nI think it's the best way, since setting a Species.oxi_state to None seems something quite used, \r\nespecially when dealing with spins. Also, Species.oxi_state can be None by its definition https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/core/periodic_table.py#L1051",
"Fixed in #2791."
] | 2022-09-30T18:10:12
| 2023-05-20T17:39:54
|
2023-05-20T17:39:54Z
|
CONTRIBUTOR
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Here what happens when I try to get a dict of a structure after applying a MagOrderingTransformation.
```
enumerator.transformations['afm'].apply_transformation(st).as_dict()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-4-3d3739281aeb> in <module>
----> 1 enumerator.transformations['afm'].apply_transformation(st_p).as_dict()
~/python-venvs/main/lib64/python3.9/site-packages/pymatgen/core/structure.py in as_dict(self, verbosity, fmt, **kwargs)
2206 "@module": self.__class__.__module__,
2207 "@class": self.__class__.__name__,
-> 2208 "charge": self.charge,
2209 "lattice": latt_dict,
2210 "sites": [],
~/python-venvs/main/lib64/python3.9/site-packages/pymatgen/core/structure.py in charge(self)
966 """
967 if self._charge is None:
--> 968 return super().charge
969 return self._charge
970
~/python-venvs/main/lib64/python3.9/site-packages/pymatgen/core/structure.py in charge(self)
344 for site in self:
345 for specie, amt in site.species.items():
--> 346 charge += getattr(specie, "oxi_state", 0) * amt
347 return charge
348
TypeError: unsupported operand type(s) for *: 'NoneType' and 'int'
```
I investigated where this comes from and found that, while the input structure has a `_charge` set to `0`, the output structure has a `_charge` set to `None'. This lead to call the charge function in the as_dict(). And,
as specie.oxi_state are None (I think this is general), the charge function is failing.
To note that in previous versions of pmg (at least 2022.0.4) the Structure.as_dict() had this line instead:
"charge": self._charge
This allows to avoid calling the charge function and not to crash for any values of _charge (int or None).
I see different problems here and I do not know what's the best approach:
1. simply go back to self._charge. I noticed that in the structure.py _charge is mostly used to get the charge
2. make MagOrderingTransformation set the `_charge=0` as in the input structure. I haven't check if other transformers have the same issue
3. the function to compute the charge could be improved to handle oxi_state=None
Let me know what you think.
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Changes to Q-Chem IO to allow CDFT and coupling calculations
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[
"\n[](https://coveralls.io/builds/56598875)\n\nCoverage: 78.186% (-0.7%) from 78.875% when pulling **1fa997b2862421216d1b50ddabd137cc19b39236 on espottesmith:charge_transfer** into **cf4ab40036ec48f0248a55ce37051c947b594364 on materialsproject:master**.\n",
"Hey @janosh @mkhorton @shyuep, I believe this is ready to be merged."
] | 2022-10-01T21:24:42
| 2023-02-03T21:09:18
|
2023-02-03T21:04:44Z
|
CONTRIBUTOR
|
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## Summary
This PR adds to the Q-Chem IO module in pymatgen, allowing for the following types of calculations:
- Calculations where the input is not well defined by a single molecule (e.g. fragment calculations)
- Charge- or spin-constrained DFT calculations (CDFT)
- Direct coupling (DC) calculations, which rely on CDFT
- Calculations involving diabatization of multiple states and the calculation of electronic coupling parameters, using the absolutely localized molecular orbitals (ALMO), projection operator diabatization (POD), and fragment orbital DFT (FODFT) methods
These additions
## TODO (if any)
QCInput allows for CDFT-CI (configuration interaction) multistate calculations (this required only small modifications to the CDFT input section). However, an output parser for CDFT-CI outputs has not been written.
## 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:
- [X] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence*- on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [X] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [X] Type annotations are **highly*- encouraged. Run [mypy](https://github.com/python/mypy) to type check your code.
- [X] Tests have been added for any new functionality or bug fixes.
- [X] All linting and tests pass.
(As usual, I've only checked tests related to files that I've changed)
|
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I_kwDOACgets5TJ6RO
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DOS plotting issue
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[
"Without the vasprun. I can't tell what really is happening. But this suggests that you don't really have a PDOS calculated or parsed. ",
"Hello,\n\nAttached please find my vasprun and doscar files as well as INCAR and\nPOSCAR.\n\nThanks,\n\nOn Mon, Oct 3, 2022 at 11:44 AM Shyue Ping Ong ***@***.***>\nwrote:\n\n> Without the vasprun. I can't tell what really is happening. But this\n> suggests that you don't really have a PDOS calculated or parsed.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/2675#issuecomment-1265880076>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/A3M7FAQ3D5IWXLHRMHZSRSDWBMSPXANCNFSM6AAAAAAQ32GE4U>\n> .\n> You are receiving this because you authored the thread.Message ID:\n> ***@***.***>\n>\n",
"Is there a way to plot the total dos if the calculations are not including the flag for the pdos (i.e., no LORBIT = 11 in the INCAR)?",
"This might look trivial, but I need to parse the eigenvalues from either\r\nthe eigenval file or the vasprun.xml file generated by vasp. Where can I\r\nfind an example for that? I assume that it will be 'easier' to extract from\r\nan eigenval file. Calculations are spin-unpolarized. I need the eigenvalues\r\nto be parsed out as a dictionary or a list. Thanks for your help.",
"Is there a way to plot the total dos if the calculations are not including\r\nthe flag for the pdos (i.e., no LORBIT = 11 in the INCAR)?",
"You can always plot the total dos. "
] | 2022-10-03T17:53:36
| 2022-11-17T23:01:45
|
NONE
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**Describe the bug**
I am trying to plot dos calculations using my own DFT-calculated doscar and vasprun. Pymatgen comes back with an error saying: KeyError: PeriodicSite. A screengrab of the error traceback attached. Please let me know how to resolve this issue.
Thanks.
*Expected behavior**
DOS should be plotted.
**Screenshots**
Attached.
**Desktop (please complete the following information):**
- OS: Windows
-
**Additional context**
<img width="512" alt="Error" src="https://user-images.githubusercontent.com/114946690/193648772-fbcfb52e-b901-4b2c-81f6-5e078d3c1a09.png">
N/A
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I_kwDOACgets5TLWRL
| 2,676
|
Weird `NbSetWeight.__eq__()` implementation
|
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[] | 2022-10-04T00:02:43
| 2022-10-21T22:46:59
|
MEMBER
|
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Doesn't this code mean all subclasses of `NbSetWeight` (like `DistanceNbSetWeight`) are always equal? What's the point of that?
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L2285-L2286
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L2348-L2349
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L2425-L2426
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L2505-L2506
Going by `__author__` and `__credits__` in that file, @davidwaroquiers @hautierg are you the right people to ask?
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L41-L43
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PR_kwDOACgets5AKZly
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`mypy` type narrowing with `isinstance` in `__eq__` methods
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[
"\n[](https://coveralls.io/builds/53115949)\n\nCoverage increased (+0.03%) to 63.413% when pulling **5c8284843f66331828fc2bf6a2c94b3a2f58162b on janosh:mypy-isinstance-__eq__** into **6345c201d1973afddb813342bd62e481daeee26a on materialsproject:master**.\n"
] | 2022-10-04T20:18:51
| 2022-10-08T16:43:35
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2022-10-08T16:40:57Z
|
MEMBER
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Fixes a lot of `mypy` errors. Also, we now return `NotImplemented` if type check fails.
|
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PR_kwDOACgets5AXLep
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Sortation of FEFF input
|
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[
"\n[](https://coveralls.io/builds/53122802)\n\nCoverage decreased (-0.0004%) to 63.412% when pulling **8b4e41dd359ae86989422266aef1a4b122976d1e on Ameyanagi:master** into **9026d4acc0cbcd785fb1f9ce5561f20991c7bdc9 on materialsproject:master**.\n",
"Thanks for the nice summary! Could you add a test to `pymatgen/io/feff/tests/test_inputs.py` that verifies the new behavior, i.e. that fails with the old code and passes with your change?",
"Thank you for the comment, I modified test_inputs.py to test the new behavior. I changed the `test_files/ATOMS` files as well because they did not contain atoms with a distance above 10 Å. This also changed the chemical formula, but the test will pass. Let me know if I need to make separate ATOMS files just for this test.\r\n\r\nThe old code will fail as following:\r\nE AssertionError:\r\nE Not equal to tolerance rtol=1e-05, atol=0\r\nE\r\nE Mismatched elements: 584 / 585 (99.8%)\r\nE Max absolute difference: 8.08273\r\nE Max relative difference: 4.03232605\r\nE x: array([ 0. , 10.071798, 10.071798, 10.071798, 10.09169 , 10.09169 ,\r\nE 10.09169 , 10.09169 , 10.09169 , 10.09169 , 10.093188, 10.093188,\r\nE 10.093188, 10.093188, 10.093188, 10.093188, 10.165263, 10.165263,...\r\nE y: array([ 0. , 2.00142, 2.00142, 2.00142, 2.00896, 3.24426,\r\nE 3.24426, 3.24426, 3.24427, 3.24427, 3.24427, 3.24525,\r\nE 3.29708, 3.29708, 3.29708, 3.29708, 3.29708, 3.29708,...\r\n\r\n",
"Thanks!",
"@Ameyanagi Btw if you'd like to be added to the pymatgen dev team, please submit [this form](https://docs.google.com/forms/d/e/1FAIpQLSccv6R3vXKQdl_m2aMbhyepK18DEjDBWXywbpuViGH6Xn_ZLg/viewform). You'll be listed here https://pymatgen.org/team.",
"@janosh Thank you very much!! I will submit the form."
] | 2022-10-07T02:54:59
| 2022-10-10T22:20:13
|
2022-10-09T19:29:59Z
|
CONTRIBUTOR
|
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## Summary
- This PR fixes the sortation of the FEFF IO module to create ATOMS input.
- Main change is to sort the distance by `float` instead of `string`. This will prevent the sorting issue with atom distance above 10 angstroms.
- For example, an atom with a distance of "10 angstroms" was listed before an atom with a distance of "2 angstroms" previously, but it is fixed to be listed in numerical order.
## 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:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence*- on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly*- encouraged. Run [mypy](https://github.com/python/mypy) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the `pre-commit` hooks specified in the pymatgen
repo. Simply `pip install -U pre-commit && pre-commit install` and linters will run prior to every commit.
|
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PR_kwDOACgets5AXWcS
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|
Added get_proj_plot() method in phonon.plotter.PhononBSPlotter class
|
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[
"\n[](https://coveralls.io/builds/53257442)\n\nCoverage increased (+0.1%) to 63.556% when pulling **1e4869797ba3c2cac2419479ecc963f7afe18f39 on cnncnnzh:phonon_plot_proj** into **76bea1b34816f8f436d79522d782fccc72a8c198 on materialsproject:master**.\n",
"Here's the plot output from `test_proj_plot()` for later reference/discussion.\r\n\r\nIs the text extending beyond the legend boundary easy to fix?\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n",
"I changed the default legends to \"0\", \"1\" and \"2\" so that they fit in the box. But now the rgb_label variable can be passed to the method to change the legend. How does that sound?\r\n\r\n\r\n",
"I think you force-pushed over the commit 709cda1 I added after 702b5bd to fix `mypy` errors. Would be better if you could `git pull` remote changes to your branch first before you force push in the future.\r\n\r\nSame thing with the commits pushed by the `pre-commit.ci` bot. Simply pull them in with `git pull`.\r\n\r\n> I changed the default legends to \"0\", \"1\" and \"2\" so that they fit in the box. But now the rgb_label variable can be passed to the method to change the legend. How does that sound?\r\n\r\nSounds good. 👍 "
] | 2022-10-07T04:30:35
| 2022-10-13T19:27:36
|
2022-10-13T19:27:36Z
|
CONTRIBUTOR
|
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## Summary
A method that allows users to plot the atom-resolved phonon band structures. The contribution from each type (or group) of atoms is calculated based on the magnitude of the eigendisplacements. Support 2 (rb), 3 (rgb) and 4 (cmyk) unique groups of atoms.
So far I just used the existing NaCl example for testing, let me know if more cases are needed!
## Additional dependencies introduced (if any)
matplotlib.pyplot.plt —> essential for the colored plot
matplotlib.collections.LineCollection —> essential for the colored plot
pymatgen.electronic_structure.plotter.BSDOSPlotter —> For creating the color line and color triangle
## TODO (if any)
1. Make a color legend for the 4-color case.
2. Allow projecting band based on eigenvectors instead of eigendisplacement?
I would appreciate any suggestions from you! Thanks.
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I_kwDOACgets5TlU1s
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Problems of new MPRester
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[
"@munrojm @mkhorton I will let you answer these. For inc_structure, all new MPRester entries by default includes structure. The only problem is just that the inc_structure kwarg was dropped. The mp-api code just needs to add it back in. As for legacy, it should be up until end of this year at least.\r\n\r\nNote that I do have feedback from other users as well that the new MPRester is not as convenient as the old one. I think it is mainly because some of the feature parity is not there yet. Once those are done, I think the users should be ok with it.",
"@shyuep @Jeff-oakley The argument is now added back for compatibility, but does not affect the data returned as `ComputedStructureEntry` objects are always provided by the API.\r\n\r\nCould you provide me the query that gave you the threading issue @Jeff-oakley? Also, what sort of machine are you running on? ",
"You can reproduce that with the following code:\r\n```\r\nUSER_API_KEY='apikey'\r\nmpr = MPRester(USER_API_KEY)\r\nmp_entries = mpr.get_entries_in_chemsys(['Li','Mn','O'])\r\n```\r\nCan you also take a look at my second question? \"Cannot start new thread issue\" raises up as it seems that the MPRester limits the amounts of query. I was querying about 1000 compositional systems, in the 935th query it shows error message in the contents above.\r\n\r\n",
"Yes, I am looking into the threading issue. What machine did you run the query on? ",
"I am running this in FSU computing cluster https://rcc.fsu.edu/",
"Okay, can you test again with the latest client release and tell me if you are having the same issue @Jeff-oakley?\r\n\r\nAlso, you might want to edit the comment above to remove your API key.",
"It seems that this is not resolved. I was parsing 1000 compositional spaces up until the 933rd. It gives me the following:\r\n\r\n`Traceback (most recent call last):\r\n File \"/gpfs/research/ouyanggroup/shared_by_group/Bin_test/query_entries_for_echem_win.py\", line 31, in <module>\r\n mp_entries = mpr.get_entries_in_chemsys(ele_lst)\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/mprester.py\", line 833, in get_entries_in_chemsys\r\n entries.extend(self.get_entries(all_chemsyses))\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/mprester.py\", line 479, in get_entries\r\n for doc in self.thermo.search(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/routes/thermo.py\", line 136, in search\r\n return super()._search(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py\", line 920, in _search\r\n return self._get_all_documents(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py\", line 969, in _get_all_documents\r\n results = self._query_resource(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py\", line 294, in _query_resource\r\n data = self._submit_requests(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py\", line 404, in _submit_requests\r\n initial_data_tuples = self._multi_thread(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py\", line 609, in _multi_thread\r\n future = executor.submit(\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/concurrent/futures/thread.py\", line 176, in submit\r\n self._adjust_thread_count()\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/concurrent/futures/thread.py\", line 199, in _adjust_thread_count\r\n t.start()\r\n File \"/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/threading.py\", line 935, in start\r\n _start_new_thread(self._bootstrap, ())\r\nRuntimeError: can't start new thread`",
"So, a single client instance shouldn't be producing a lot of active threads. In fact, I have it wait for threads to finish before starting new ones to avoid issues like this. The max number of threads is set either to the value of `multiprocessing.cpu_count()`, or 8 if that cannot be determined. Both of these are very modest values.\r\n\r\nThe one query you provide does not cause any issues for me. In order for me to diagnose this, it may be helpful to have the full script you are using to query the 1000 compositional systems.",
"I guess one easy test is to do the following\r\n\r\n```\r\nUSER_API_KEY='[redacted]'\r\n\r\nmpr = MPRester(USER_API_KEY)\r\n\r\nfor i in range(10000):\r\n\r\n mp_entries = mpr.get_entries_in_chemsys(['Li','Mn','O'])\r\n```\r\n",
"I am not able to recreate this issue.",
"@Jeff-oakley I think the correct way is to do is not to create 10000 get_entries call, but rather just to use MPRester().get_entries([\"Li-Fe-O\", \"Li-O\", \"Fe-O\", ....]). In other words, do a single query.\r\n\r\nI am not sure what the threading issue is, but it might be just your OS running out of memory.",
"Thanks for the suggestion. I agree it could be due to memory issues. I will run that in a different cluster with more memories.",
"Just to follow up on this. I realize it is a systematic error message that happens in many supercomputers. It generally works well on a PC with regular university internet. However, whenever I run the following code in super computers, e.g. RCC at FSU and PSC at Pittsburg (Bridge2 allocation from ACCESS). It will consistently give an error message:\r\n`\"mp_api.client.core.client.MPRestError: HTTPSConnectionPool(host='api.materialsproject.org', port=443): Max retries exceeded with url: /thermo/?is_stable=True&_fields=entries&chemsys=Br-Cl-F-I-Mn&_limit=7 (Caused by ResponseError('too many 429 error responses'))\"`\r\n\r\nI suppose such query method is blocked or limited in many supercomputers?\r\n\r\nHere is the code I used:\r\n\r\n```\r\nfrom mp_api.client import MPRester\r\nmpr = MPRester('[redacted]')\r\nele_lst = ['Li','Mn','O','F','Cl','Br','I']\r\nentries = mpr.get_entries_in_chemsys(ele_lst, additional_criteria={'is_stable': True})\r\n```\r\n\r\n\r\n",
"@Jeff-oakley Be aware the snippet you posted includes your API key.",
"> I suppose such query method is blocked or limited in many supercomputers?\r\n\r\nThere is no intentional blocking or limiting of supercomputers. We would definitely like people to use the API, including on supercomputers. It's unclear why you're getting the 429 response without additional context."
] | 2022-10-09T14:34:49
| 2023-05-20T14:26:40
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2023-05-20T14:26:40Z
|
NONE
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The old MPRester is disabled (I guess because the legacy MP is offline) so I have to use the new MPRester (mp_api.client.MPRester). However, it seems that it is not as convenient as the old one. There are two major issues I have so far:
1. There is no "inc_structure=True" option for get_entries_in_chemsys. I checked the source code in mp_api. It seems that querying entry with structures are well unstraightforward. Can you let me know if there is any function I can use to do the same thing as get_entries_in_chemsys(['A','B','C'],inc_structure=True)
2. "Cannot start new thread issue" raises up as it limits the amounts of query. I was querying about 1000 compositional systems, in the 935th query it shows:
<details>
<summary>stack trace</summary>
```
File "/gpfs/research/ouyanggroup/shared_by_group/Bin_test/query_entries_for_echem_win.py", line 31, in <module>
mp_entries = mpr.get_entries_in_chemsys(ele_lst)
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/mprester.py", line 833, in get_entries_in_chemsys
entries.extend(self.get_entries(all_chemsyses))
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/mprester.py", line 479, in get_entries
for doc in self.thermo.search(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/routes/thermo.py", line 136, in search
return super()._search(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py", line 920, in _search
return self._get_all_documents(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py", line 969, in _get_all_documents
results = self._query_resource(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py", line 294, in _query_resource
data = self._submit_requests(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py", line 404, in _submit_requests
initial_data_tuples = self._multi_thread(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/site-packages/mp_api/client/core/client.py", line 609, in _multi_thread
future = executor.submit(
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/concurrent/futures/thread.py", line 176, in submit
self._adjust_thread_count()
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/concurrent/futures/thread.py", line 199, in _adjust_thread_count
t.start()
File "/gpfs/home/bo22b/miniconda3/envs/work/lib/python3.10/threading.py", line 935, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can't start new thread
```
</details>
Can you give some suggestions on these two issues? Meanwhile, do we lose MP legacy forever or just temporarily?
|
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PR_kwDOACgets5Ac4n9
| 2,681
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Add `on_error` kwarg to `PhaseDiagram.get_decomp_and_e_above_hull()`
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[
"\n[](https://coveralls.io/builds/53158321)\n\nCoverage decreased (-0.006%) to 63.406% when pulling **50f3cdca41bc1b7db7f79d85d124471a58ab2865 on pd-on-no-decomp-error** into **9026d4acc0cbcd785fb1f9ce5561f20991c7bdc9 on master**.\n"
] | 2022-10-09T16:48:03
| 2022-10-11T22:20:45
|
2022-10-11T22:20:43Z
|
MEMBER
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Including new test case in cda8604.
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PR_kwDOACgets5AguOE
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Fix `TqdmExperimentalWarning`: Using `tqdm.autonotebook.tqdm` in notebook mode
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"\n[](https://coveralls.io/builds/53146363)\n\nCoverage increased (+0.002%) to 63.415% when pulling **959fbc47229e9d21ec503b297cefb63dd36754ba on fix-tqdm-exp-warning** into **fdd7c746e970bc1d4470b9933efba211bf6f04db on master**.\n"
] | 2022-10-10T17:23:27
| 2022-10-10T17:40:52
|
2022-10-10T17:29:55Z
|
MEMBER
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Occurs when importing `from pymatgen.ext.matproj import MPRester` in Jupyter.
Rest of warning: `pymatgen/analysis/phase_diagram.py:26`: Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console).
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PR_kwDOACgets5AmiYG
| 2,683
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Run CI in lowest supported Python version
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"\n[](https://coveralls.io/builds/53190207)\n\nCoverage remained the same at 63.412% when pulling **b4ab6acc6aacbef4ee2d0b506d65177e2ee30c69 on ci-py-version** into **356084c51f66aa3f742d674105da853e8d1cbc9e on master**.\n",
"Remaining error\r\n\r\n```py\r\npymatgen/ext/tests/test_matproj.py:45: \r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \r\npymatgen/ext/matproj.py:210: in __init__\r\n db_version = self.get_database_version()\r\npymatgen/ext/matproj.py:307: in get_database_version\r\n d = self._make_request(\"/api_check\")\r\n```\r\n\r\nis due to https://matsci.org/t/44750"
] | 2022-10-11T21:19:32
| 2022-10-12T04:14:02
|
2022-10-11T22:05:57Z
|
MEMBER
|
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|
The most important Python version to run CI is the lowest supported (currently 3.8). Running in higher versions means we won't catch some SyntaxErrors e.g. from modern type annotations like `lst: list[int] = [1, 2, 3]` (which [I think was the reason](https://github.com/materialsproject/pymatgen/runs/8157637404?check_suite_focus=true) for bumping to 3.10?). Such errors would now pop up at runtime for people below Python 3.10.
If we want to test later Python versions too (e.g. due to upcoming 3.11 release), we should setup a matrix strategy.
|
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| 1,405,469,416
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PR_kwDOACgets5AnRw5
| 2,684
|
~2x number of PatchedPhaseDiagrams tests
|
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"\n[](https://coveralls.io/builds/53196460)\n\nCoverage increased (+0.004%) to 63.455% when pulling **589bdfc2ed88c682f8c2d9055f2c72a230b54649 on more-ppd-tests** into **8ae54c760db5c5f5bf49b30adba29c86a705eefc on master**.\n"
] | 2022-10-12T02:43:05
| 2022-10-12T04:21:37
|
2022-10-12T04:04:57Z
|
MEMBER
|
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Refactor existing ones to `pytest`.
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|
Lint dev scripts
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"The dev scripts are of course rarely used. But they are used from time to time. E.g., when I need to regenerate the periodic_table.json file when certain properties are added.",
"\n[](https://coveralls.io/builds/53217636)\n\nCoverage decreased (-0.005%) to 63.453% when pulling **b32def6a8833fccf091f4235d2600f28c19d387e on lint-dev-scripts** into **db8ad7a5838137ee13d5fbfedacfbe96b619f8cc on master**.\n"
] | 2022-10-12T16:11:57
| 2022-10-12T17:26:41
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2022-10-12T17:15:48Z
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MEMBER
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@shyuep Are the files under `dev_scripts/` still used?
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Typos
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[
"Why would we bother to lint cmd_line? These are not our files. Other people are responsible for them. ",
"@shyuep My bad, didn't really look at those files. Reverting.",
"\n[](https://coveralls.io/builds/53230757)\n\nCoverage remained the same at 63.455% when pulling **ee74ed62c936e0f27af0ff19fdcf80dc7c9c6692 on lint-cmd-line** into **76bea1b34816f8f436d79522d782fccc72a8c198 on master**.\n"
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| 2022-10-13T04:28:57
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2022-10-13T04:20:54Z
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| 1,407,146,169
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PR_kwDOACgets5As6V5
| 2,687
|
PatchedPhaseDiagram magic methods
|
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[
"\n[](https://coveralls.io/builds/53231442)\n\nCoverage decreased (-0.002%) to 63.455% when pulling **12ceeb284a50fda7e174a9facca43d6ed03c1317 on ppd-magic-methods** into **bba5a44de6a16fba32a91845032831175ca9e3c3 on master**.\n"
] | 2022-10-13T04:58:54
| 2022-10-13T05:23:21
|
2022-10-13T05:23:20Z
|
MEMBER
|
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- `__len__`
- `__getitem__`
- `__setitem__`
- `__delitem__`
- `__iter__`
- `__contains__`
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PR_kwDOACgets5AxNA7
| 2,688
|
Split CDER to real and imag parts
|
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[
"\n[](https://coveralls.io/builds/53381720)\n\nCoverage increased (+0.03%) to 63.59% when pulling **0948f42784cc84efc74ffaea1e3ccbd5a74dc05a on jmmshn:patch-optics-cder** into **db28d097bd291ac20c3c730ccb1c3769f59f0a31 on materialsproject:master**.\n",
"Maybe `monty` could be made to support serializing complex arrays? [People seem to have managed](https://stackoverflow.com/a/27948073) though not sure if using `base64` is space and time efficient.",
"> Maybe `monty` could be made to support serializing complex arrays? [People seem to have managed](https://stackoverflow.com/a/27948073) though not sure if using `base64` is space and time efficient.\r\n\r\nYeah I might come back to this after I finish speeding this up. There are quite a few places that need to serialize complex stuff.",
"The [test failure in `CoordinationGeometryFinderTest.test_abstract_geometry()`](https://github.com/materialsproject/pymatgen/actions/runs/3275161416/jobs/5390727457#step:5:17) seems unrelated."
] | 2022-10-13T20:59:51
| 2022-10-18T19:21:13
|
2022-10-18T19:21:13Z
|
CONTRIBUTOR
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## Split CDER into real and imag parts
Serialization of complex ndarray is not supported by MSONable.
So any large object with complex numbers that need to be serialized should have the real and imaginary part split into two different arrays.
|
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I_kwDOACgets5T93SM
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|
Problem with MPRester in pymatgen 2022.9.21
|
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[
"`mpr.query` has been replaced with `mpr.summary.search`. You can use that new method and pass all of your wildcard formulas to the `formula` argument."
] | 2022-10-14T04:01:50
| 2023-05-20T14:24:33
|
2023-05-20T14:24:33Z
|
NONE
|
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I have installed `pymatgen` v. 2022.9.21 on my Linux system and I have the MP API key. However, when I tried to use the MPRester to get data from the Materials Project, it provides several 'AttributeError:'s. For instance for a simple script as below, only the `m.get_structure_by_material_id` works.
```python
from pymatgen.ext.matproj import MPRester
with MPRester("apikey") as m:
# Structure for material id
structure = m.get_structure_by_material_id("mp-1234")
print(structure)
data = m.get_data("Fe2O3")
print(data)
# Dos for material id
dos = m.get_dos_by_material_id("mp-1234")
# Bandstructure for material id
bandstructure = m.get_bandstructure_by_material_id("mp-1234")
# Get all energies of materials with formula "*2O".
results = m.query("*2O", ['energy'])
# Get the formulas and energies of materials with materials_id mp-1234
# or with formula FeO.
results = m.query("FeO mp-1234", ['pretty_formula', 'energy'])
# Get all compounds of the form ABO3
results = m.query("**O3", ['pretty_formula', 'energy'])
```
For other results, pymatgen gives the 'AttributeError:'s. For example, AttributeError: '_MPResterNew' object has no attribute 'query'.
Can you please suggest the possible reasons for these errors and how to solve them?
|
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I_kwDOACgets5T_7Ib
| 2,690
|
MpRester.query() is replaced with MpRester.summary.search()
|
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[
"See https://matsci.org/t/how-do-you-access-the-cif-data-in-the-new-api/44850",
"@munrojm Thank you for reply. This will help me definitely. Do I able to access all the elements of periodic table in single query instead of accessing the single element ?\r\n",
"If you would like to query structures containing any element, simply remove the `elements` argument and only pass `fields` to `search`. It will default to querying structure data for every material in the database.",
"Thank you @munrojm . It's working.",
"@munrojm I have another doubt . How do I get the band gap value for the each element from the structured data of material",
"I have used the below query to access the all elements with structure and band_gap fields.\r\n\r\nresults = mpr.summary.search(fields= ['structure',\"band_gap\"]) and converted into CIF file. After converting into the CIF file I have resued the cif file and trying to access the structure and bandgap. But I'm only able to access the structure but I'm not able to access the bandgap\r\n\r\nand I used the function to get structure . struct1 = struct.get_structures()[0]\r\n\r\ncan anyone help me out in getting the bandgap from the structured data ?\r\n",
"To clarify, you want the element projected band gap for each material?",
"Yes @munrojm . I figured it out. Thank you for your time and help."
] | 2022-10-14T12:19:06
| 2023-05-20T14:22:53
|
2023-05-20T14:22:53Z
|
NONE
|
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**Describe the bug**
Before I used the MpRester.query() to download and access the all elements in the Material project but it changed to MpRester.summary.search() so I could pass the mongoDB query to download and access all the elements with properties = ['cif]
Can someone suggest a command or query to download and access the all elements in the periodic table as cif file (using python /pymatgen).
Thanks in advance
|
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PR_kwDOACgets5A2Pkd
| 2,691
|
Test methods downstream from `PD.get_decomp_and_e_above_hull_on_error()` can also ignore errors
|
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"@shyuep I removed `pydocstyle` in 7699c98 from `lint` CI as it was raising a lot of errors with the new config from cf8e0af. I think before it wasn't doing anything. At least I don't remember ever getting an error from it.",
"\n[](https://coveralls.io/builds/53299266)\n\nCoverage decreased (-0.006%) to 63.549% when pulling **80ec79b085fa92c94818da320b3a277d885d7029 on test-downstream-methods-can-ignore** into **db28d097bd291ac20c3c730ccb1c3769f59f0a31 on master**.\n"
] | 2022-10-14T22:29:05
| 2022-10-15T04:33:15
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2022-10-15T04:31:26Z
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MEMBER
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Related #2681.
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Updating Lammps inputs and inputsets/generators to facilitate integration into atomate2
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"\n[](https://coveralls.io/builds/53522456)\n\nCoverage increased (+0.1%) to 63.647% when pulling **8a771252f9a252c1ee5e9af1bc9820a0be936928 on gbrunin:htmd** into **a429629ed543ec1d8ceb4f02300cb5c95328e6d4 on materialsproject:master**.\n",
"Thanks @gbrunin for this. I just looked through the code and commented on the documentation. I hope this might help.",
"Hey @gbrunin , I am currently on holiday. It might take a bit until I have time review in detail. I am adding @QuantumChemist to the pull request as well.",
"Hi @gbrunin, \r\nI had a chance to shortly have a look the classes. Thanks for your work!\r\n\r\nI have one question: \r\nhow would one generate an md run with a new structure with the help of these classes? Would I need to start from LAMMPsData? To me, this is not immediately obvious.\r\n\r\n",
"Hi @JaGeo,\r\n\r\nThanks for your comments.\r\nIn the end, we decided to have sets and generators in a separate repository (https://github.com/Matgenix/atomate2-lammps) in the same spirit as atomate2. So, this stuff in pymatgen is there to be used as an input analyzer/builder/modifier but not necessarily automatically, while the input generation from a structure will be handled in atomate2-lammps (it is already, through https://github.com/Matgenix/atomate2-lammps/blob/main/src/atomate2/lammps/sets/base.py). I hope this makes sense !\r\n",
"Thanks, @gbrunin ! It does make sense but I would still recommend a method/function that allows to easily create inputs for LAMMPS with different structures in pymatgen. After all, this is what I would expect from an IO module for LAMMPS. I would recommend moving the LammpsInputSet back to pymatgen. \r\n**EDIT:**\r\nThe more I think about it, I think it should all go into pymatgen. I would not expect to look for this in an atomate2 add-on.",
"Thanks a lot @rkingsbury ! This is very helpful. I have made a few changes according to your comments. Just a few points left open for discussion.",
"> Thanks a lot @rkingsbury ! This is very helpful. I have made a few changes according to your comments. Just a few points left open for discussion.\r\n\r\nI'm glad they were helpful! Let me think more about the two comments that are still open and I'll reply later today.",
"Hi @JaGeo, @QuantumChemist, @ml-evs and @rkingsbury, thanks again to all of you for your suggestions. This is just to let you know that I think this PR can drop its WIP status now. Let me know if you still want to review it before that. \r\nCheers !",
"Hi @janosh and @shyuep, this PR is now ready to be reviewed. Thanks in advance!"
] | 2022-10-17T12:15:12
| 2023-03-10T17:42:30
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2023-03-10T17:42:30Z
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CONTRIBUTOR
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## Summary
Based on previous work from @manaslkht and @rkingsbury, I create this PR to integrate the LammpsInputFile object in pymatgen. Basic InputSet and InputGenerator are added as well, based on templates. For more advanced automatic tools and usage, the user is suggested to use atomate2's addon atomate2-lammps (see https://github.com/Matgenix/atomate2-lammps).
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AttributeError: 'NoneType' object has no attribute 'contributions'
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"Can't repro. Worked for me with both with new and old API key.\r\n\r\n@munrojm What's worrying though, I get different numbers of entries depending on which key I use:\r\n\r\n```py\r\nfrom pymatgen.ext.matproj import MPRester\r\n\r\nfor key in (old_api_key, new_api_key):\r\n mpr = MPRester(key)\r\n \r\n # Get all pourbaix entries corresponding to the Cu-O-H chemical system.\r\n entries = mpr.get_pourbaix_entries([\"Cu\"])\r\n \r\n print(f'{len(entries)=}')\r\n print(f'{len(api_key)=}')\r\n\r\n>>> len(entries)=57\r\nlen(api_key)=17\r\n\r\n>>> len(entries)=102\r\nlen(api_key)=32\r\n```\r\n\r\n\r\n@MGriot What's your `len(key)`?",
"I don't know why this only happens to me.\r\nIt counts that I started from a new env and I installed the library via conda or pip, I don't think it makes big difference.\r\n\r\nTo answer your question is `len(key)=32`",
"@janosh you are right. Looks like there are duplicate entries coming out of the new pourbaix method. I can take a closer look at this. @rkingsbury, do you have any sense of what might be going on here?",
"@munrojm Thanks!\r\n\r\n@MGriot Can you post the full track trace?",
"Yes, of course, I just put the key in the form of a variable since it is personal.\r\nCode:\r\n```Python\r\nfrom pymatgen.ext.matproj import MPRester\r\n\r\nmpr = MPRester(key)\r\n\r\n# Get all pourbaix entries corresponding to the Cu-O-H chemical system.\r\nentries = mpr.get_pourbaix_entries([\"Cu\"])\r\n\r\nprint(f'{len(entries)=}')\r\n```\r\nOutput:\r\n```\r\nd:\\Documenti_personali\\Programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\\pymatgen\\analysis\\phase_diagram.py:26: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\r\n from tqdm.autonotebook import tqdm\r\nd:\\Documenti_personali\\Programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\\mp_api\\client\\mprester.py:147: builtins.UserWarning: Problem loading MPContribs client: SSL support unavailable\r\nOutput exceeds the [size limit](command:workbench.action.openSettings?[). Open the full output data [in a text editor](command:workbench.action.openLargeOutput?2c696f5e-2e8d-42b8-baaf-30a09db943ee)\r\n---------------------------------------------------------------------------\r\nAttributeError Traceback (most recent call last)\r\nCell In [2], line 6\r\n 3 mpr = MPRester(key)\r\n 5 # Get all pourbaix entries corresponding to the Cu-O-H chemical system.\r\n----> 6 entries = mpr.get_pourbaix_entries([\"Cu\"])\r\n 8 print(f'{len(entries)=}')\r\n\r\nFile d:\\Documenti_personali\\Programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\\mp_api\\client\\mprester.py:626, in MPRester.get_pourbaix_entries(self, chemsys, solid_compat, use_gibbs)\r\n 620 chemsys = sorted(e.capitalize() for e in chemsys)\r\n 622 # Get ion entries first, because certain ions have reference\r\n 623 # solids that aren't necessarily in the chemsys (Na2SO4)\r\n 624 \r\n 625 # download the ion reference data from MPContribs\r\n--> 626 ion_data = self.get_ion_reference_data_for_chemsys(chemsys)\r\n 628 # build the PhaseDiagram for get_ion_entries\r\n 629 ion_ref_comps = [\r\n 630 Ion.from_formula(d[\"data\"][\"RefSolid\"]).composition for d in ion_data\r\n 631 ]\r\n\r\nFile d:\\Documenti_personali\\Programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\\mp_api\\client\\mprester.py:773, in MPRester.get_ion_reference_data_for_chemsys(self, chemsys)\r\n 736 def get_ion_reference_data_for_chemsys(\r\n 737 self, chemsys: Union[str, List]\r\n 738 ) -> List[Dict]:\r\n 739 \"\"\"\r\n...\r\n 731 ).result()[\"data\"]\r\n 732 ]\r\n 734 return ion_data\r\n\r\nAttributeError: 'NoneType' object has no attribute 'contributions\r\n```",
"Would be good to see the place where the code tries to access `something.contributions` where `something` is `None`.\r\n\r\nWhat's the version output of pip`pip show pymatgen mp-api`? Have you tried `pip install -U pymatgen mp-api`?",
"> @janosh you are right. Looks like there are duplicate entries coming out of the new pourbaix method. I can take a closer look at this. @rkingsbury, do you have any sense of what might be going on here?\r\n\r\nI can investigate next week. All the work on the new Pourbaix methods has been in the new client though; I have a feeling this issue is related to the recent change that brought the new method into pymatgen.ext.matptoj. I'm not up to speed on how that was done.\r\n\r\nDo the duplicate entries still occur when just using the new client?",
"For the first question I honestly have no idea what you are asking me, sorry.\r\n\r\nI have executed the two commands, as far as the first is successful, and the second brings out an error that I have never seen and I do not know how to correct.\r\nFor the first:\r\n`pip show pymatgen mp-api`\r\nOutput:\r\n```\r\nName: pymatgen\r\nVersion: 2022.9.21\r\nSummary: Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://materialsproject.org).\r\nHome-page: https://pymatgen.org\r\nAuthor: Pymatgen Development Team\r\nAuthor-email: ongsp@eng.ucsd.edu\r\nLicense: MIT\r\nLocation: d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\r\nRequires: matplotlib, monty, mp-api, networkx, numpy, palettable, pandas, plotly, pybtex, requests, ruamel.yaml, scipy, spglib, sympy, tabulate, tqdm, uncertainties\r\nRequired-by: emmet-core, mp-api, mpcontribs-client\r\n---\r\nName: mp-api\r\nVersion: 0.29.1\r\nSummary: API Server for the Materials Project\r\nHome-page: https://github.com/materialsproject/api\r\nAuthor: The Materials Project\r\nAuthor-email: feedback@materialsproject.org\r\nLicense: modified BSD\r\nLocation: d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages\r\nRequires: emmet-core, monty, msgpack, pymatgen, requests, setuptools, typing-extensions\r\nRequired-by: pymatgen\r\nNote: you may need to restart the kernel to use updated packages.\r\n```\r\n\r\nFor the second:\r\n`pip install -U pymatgen mp-api`\r\nOutput:\r\n```\r\nRequirement already satisfied: pymatgen in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (2022.9.21)\r\nCollecting pymatgen\r\n Downloading pymatgen-2022.10.22.tar.gz (2.6 MB)\r\n ---------------------------------------- 2.6/2.6 MB 4.9 MB/s eta 0:00:00\r\n Installing build dependencies: started\r\n Installing build dependencies: finished with status 'done'\r\n Getting requirements to build wheel: started\r\n Getting requirements to build wheel: finished with status 'done'\r\n Installing backend dependencies: started\r\n Installing backend dependencies: finished with status 'done'\r\n Preparing metadata (pyproject.toml): started\r\n Preparing metadata (pyproject.toml): finished with status 'done'\r\nRequirement already satisfied: mp-api in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (0.29.1)\r\nCollecting mp-api\r\n Downloading mp_api-0.29.3-py3-none-any.whl (69 kB)\r\n ---------------------------------------- 69.3/69.3 kB 3.9 MB/s eta 0:00:00\r\nRequirement already satisfied: palettable>=3.1.1 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (3.3.0)\r\nRequirement already satisfied: requests in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (2.28.1)\r\nRequirement already satisfied: ruamel.yaml>=0.17.0 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (0.17.21)\r\nRequirement already satisfied: pybtex in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (0.24.0)\r\nRequirement already satisfied: pandas in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (1.5.0)\r\nRequirement already satisfied: matplotlib>=1.5 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (3.6.1)\r\nRequirement already satisfied: networkx>=2.2 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (2.8.7)\r\nRequirement already satisfied: scipy>=1.5.0 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (1.9.1)\r\nRequirement already satisfied: sympy in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (1.11.1)\r\nRequirement already satisfied: uncertainties>=3.1.4 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pymatgen) (3.1.7)\r\nRequirement already satisfied: 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d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from ruamel.yaml>=0.17.0->pymatgen) (0.2.6)\r\nRequirement already satisfied: future in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from uncertainties>=3.1.4->pymatgen) (0.18.2)\r\nRequirement already satisfied: pytz>=2020.1 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from pandas->pymatgen) (2022.4)\r\nRequirement already satisfied: mpmath>=0.19 in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from sympy->pymatgen) (1.2.1)\r\nRequirement already satisfied: colorama in d:\\documenti_personali\\programming\\miniconda3\\envs\\pourbaix_diagrams\\lib\\site-packages (from tqdm->pymatgen) (0.4.5)\r\nBuilding wheels for collected packages: pymatgen\r\n Building wheel for pymatgen (pyproject.toml): started\r\n Building wheel for pymatgen (pyproject.toml): finished with status 'error'\r\nFailed to build pymatgen\r\nNote: you may need to restart the kernel to use updated packages.\r\n```\r\n",
"> For the first question I honestly have no idea what you are asking me, sorry.\r\n\r\nYour stack trace looks incomplete. At least it's not showing the most interesting line: the one on which the error actually occurs. Some variable is `None` and yet Python tries to access the `contributions` attribute on it. Would be good to see which variable that is.\r\n\r\nRe `pip show pymatgen mp-api`: You're running the same package versions as me. Very strange that I can't reproduce your error.",
"There is the same problem like mine [here](https://stackoverflow.com/questions/73637567/cant-install-pymatgen-could-not-build-wheels-for-pymatgen)",
"I tried to update the library via conda:\r\n```\r\n(base) C:\\Users\\Admin>activate pourbaix_diagrams\r\n\r\n(pourbaix_diagrams) C:\\Users\\Admin>python v\r\npython: can't open file 'C:\\\\Users\\\\Admin\\\\v': [Errno 2] No such file or directory\r\n\r\n(pourbaix_diagrams) C:\\Users\\Admin> python -V\r\nPython 3.10.6\r\n\r\n(pourbaix_diagrams) C:\\Users\\Admin>pymatgen==2022.10.22\r\n\"pymatgen\" non è riconosciuto come comando interno o esterno,\r\n un programma eseguibile o un file batch.\r\n\r\n(pourbaix_diagrams) C:\\Users\\Admin>conda install pymatgen==2022.10.22\r\nCollecting package metadata (current_repodata.json): done\r\nSolving environment: done\r\n\r\n\r\n==> WARNING: A newer version of conda exists. <==\r\n current version: 4.12.0\r\n latest version: 22.9.0\r\n\r\nPlease update conda by running\r\n\r\n $ conda update -n base -c defaults conda\r\n\r\n\r\n\r\n## Package Plan ##\r\n\r\n environment location: D:\\Documenti_personali\\Programming\\miniconda3\\envs\\pourbaix_diagrams\r\n\r\n added / updated specs:\r\n - pymatgen==2022.10.22\r\n\r\n\r\nThe following packages will be downloaded:\r\n\r\n package | build\r\n ---------------------------|-----------------\r\n numpy-1.23.4 | py310h4a8f9c9_0 6.3 MB conda-forge\r\n pymatgen-2022.10.22 | py310h232114e_0 3.7 MB conda-forge\r\n ------------------------------------------------------------\r\n Total: 10.0 MB\r\n\r\nThe following packages will be UPDATED:\r\n\r\n numpy 1.23.3-py310h4a8f9c9_0 --> 1.23.4-py310h4a8f9c9_0\r\n pymatgen 2022.9.21-py310h232114e_2 --> 2022.10.22-py310h232114e_0\r\n\r\n\r\nProceed ([y]/n)? y\r\n\r\n\r\nDownloading and Extracting Packages\r\npymatgen-2022.10.22 | 3.7 MB | ############################################################################ | 100%\r\nnumpy-1.23.4 | 6.3 MB | ############################################################################ | 100%\r\nPreparing transaction: done\r\nVerifying transaction: done\r\nExecuting transaction: done\r\n```\r\n\r\nAnd re-launching the initial codes the result does not improve:\r\n\r\n```\r\n{\r\n\t\"name\": \"AttributeError\",\r\n\t\"message\": \"'NoneType' object has no attribute 'contributions'\",\r\n\t\"stack\": \"\\u001b[1;31m---------------------------------------------------------------------------\\u001b[0m\\n\\u001b[1;31mAttributeError\\u001b[0m Traceback (most recent call last)\\nCell \\u001b[1;32mIn [2], line 4\\u001b[0m\\n\\u001b[0;32m 1\\u001b[0m \\u001b[39mfrom\\u001b[39;00m \\u001b[39mmp_api\\u001b[39;00m\\u001b[39m.\\u001b[39;00m\\u001b[39mclient\\u001b[39;00m \\u001b[39mimport\\u001b[39;00m MPRester\\n\\u001b[0;32m 3\\u001b[0m \\u001b[39mwith\\u001b[39;00m MPRester(\\u001b[39m\\\"\\u001b[39m\\u001b[39myF5Fsyp9TtVLVH3LmODfdSwhgmEhzLw8\\u001b[39m\\u001b[39m\\\"\\u001b[39m) \\u001b[39mas\\u001b[39;00m mpr:\\n\\u001b[1;32m----> 4\\u001b[0m entries \\u001b[39m=\\u001b[39m mpr\\u001b[39m.\\u001b[39;49mget_pourbaix_entries([\\u001b[39m\\\"\\u001b[39;49m\\u001b[39mCr\\u001b[39;49m\\u001b[39m\\\"\\u001b[39;49m])\\n\\nFile \\u001b[1;32md:\\\\Documenti_personali\\\\Programming\\\\miniconda3\\\\envs\\\\pourbaix_diagrams\\\\lib\\\\site-packages\\\\mp_api\\\\client\\\\mprester.py:626\\u001b[0m, in \\u001b[0;36mMPRester.get_pourbaix_entries\\u001b[1;34m(self, chemsys, solid_compat, use_gibbs)\\u001b[0m\\n\\u001b[0;32m 620\\u001b[0m chemsys \\u001b[39m=\\u001b[39m \\u001b[39msorted\\u001b[39m(e\\u001b[39m.\\u001b[39mcapitalize() \\u001b[39mfor\\u001b[39;00m e \\u001b[39min\\u001b[39;00m chemsys)\\n\\u001b[0;32m 622\\u001b[0m \\u001b[39m# Get ion entries first, because certain ions have reference\\u001b[39;00m\\n\\u001b[0;32m 623\\u001b[0m \\u001b[39m# solids that aren't necessarily in the chemsys (Na2SO4)\\u001b[39;00m\\n\\u001b[0;32m 624\\u001b[0m \\n\\u001b[0;32m 625\\u001b[0m \\u001b[39m# download the ion reference data from MPContribs\\u001b[39;00m\\n\\u001b[1;32m--> 626\\u001b[0m ion_data \\u001b[39m=\\u001b[39m \\u001b[39mself\\u001b[39;49m\\u001b[39m.\\u001b[39;49mget_ion_reference_data_for_chemsys(chemsys)\\n\\u001b[0;32m 628\\u001b[0m \\u001b[39m# build the PhaseDiagram for get_ion_entries\\u001b[39;00m\\n\\u001b[0;32m 629\\u001b[0m ion_ref_comps \\u001b[39m=\\u001b[39m [\\n\\u001b[0;32m 630\\u001b[0m Ion\\u001b[39m.\\u001b[39mfrom_formula(d[\\u001b[39m\\\"\\u001b[39m\\u001b[39mdata\\u001b[39m\\u001b[39m\\\"\\u001b[39m][\\u001b[39m\\\"\\u001b[39m\\u001b[39mRefSolid\\u001b[39m\\u001b[39m\\\"\\u001b[39m])\\u001b[39m.\\u001b[39mcomposition \\u001b[39mfor\\u001b[39;00m d \\u001b[39min\\u001b[39;00m ion_data\\n\\u001b[0;32m 631\\u001b[0m ]\\n\\nFile \\u001b[1;32md:\\\\Documenti_personali\\\\Programming\\\\miniconda3\\\\envs\\\\pourbaix_diagrams\\\\lib\\\\site-packages\\\\mp_api\\\\client\\\\mprester.py:773\\u001b[0m, in \\u001b[0;36mMPRester.get_ion_reference_data_for_chemsys\\u001b[1;34m(self, chemsys)\\u001b[0m\\n\\u001b[0;32m 736\\u001b[0m \\u001b[39mdef\\u001b[39;00m \\u001b[39mget_ion_reference_data_for_chemsys\\u001b[39m(\\n\\u001b[0;32m 737\\u001b[0m \\u001b[39mself\\u001b[39m, chemsys: Union[\\u001b[39mstr\\u001b[39m, List]\\n\\u001b[0;32m 738\\u001b[0m ) \\u001b[39m-\\u001b[39m\\u001b[39m>\\u001b[39m List[Dict]:\\n\\u001b[0;32m 739\\u001b[0m \\u001b[39m\\\"\\\"\\\"\\u001b[39;00m\\n\\u001b[0;32m 740\\u001b[0m \\u001b[39m Download aqueous ion reference data used in the construction of Pourbaix diagrams.\\u001b[39;00m\\n\\u001b[0;32m 741\\u001b[0m \\n\\u001b[1;32m (...)\\u001b[0m\\n\\u001b[0;32m 770\\u001b[0m \\u001b[39m compounds and aqueous species, Wiley, New York (1978)'}}\\u001b[39;00m\\n\\u001b[0;32m 771\\u001b[0m \\u001b[39m \\\"\\\"\\\"\\u001b[39;00m\\n\\u001b[1;32m--> 773\\u001b[0m ion_data \\u001b[39m=\\u001b[39m \\u001b[39mself\\u001b[39;49m\\u001b[39m.\\u001b[39;49mget_ion_reference_data()\\n\\u001b[0;32m 775\\u001b[0m \\u001b[39mreturn\\u001b[39;00m [d \\u001b[39mfor\\u001b[39;00m d \\u001b[39min\\u001b[39;00m ion_data \\u001b[39mif\\u001b[39;00m d[\\u001b[39m\\\"\\u001b[39m\\u001b[39mdata\\u001b[39m\\u001b[39m\\\"\\u001b[39m][\\u001b[39m\\\"\\u001b[39m\\u001b[39mMajElements\\u001b[39m\\u001b[39m\\\"\\u001b[39m] \\u001b[39min\\u001b[39;00m chemsys]\\n\\nFile \\u001b[1;32md:\\\\Documenti_personali\\\\Programming\\\\miniconda3\\\\envs\\\\pourbaix_diagrams\\\\lib\\\\site-packages\\\\mp_api\\\\client\\\\mprester.py:727\\u001b[0m, in \\u001b[0;36mMPRester.get_ion_reference_data\\u001b[1;34m(self)\\u001b[0m\\n\\u001b[0;32m 694\\u001b[0m \\u001b[39m@lru_cache\\u001b[39m\\n\\u001b[0;32m 695\\u001b[0m \\u001b[39mdef\\u001b[39;00m \\u001b[39mget_ion_reference_data\\u001b[39m(\\u001b[39mself\\u001b[39m) \\u001b[39m-\\u001b[39m\\u001b[39m>\\u001b[39m List[Dict]:\\n\\u001b[0;32m 696\\u001b[0m \\u001b[39m\\\"\\\"\\\"\\u001b[39;00m\\n\\u001b[0;32m 697\\u001b[0m \\u001b[39m Download aqueous ion reference data used in the construction of Pourbaix diagrams.\\u001b[39;00m\\n\\u001b[0;32m 698\\u001b[0m \\n\\u001b[1;32m (...)\\u001b[0m\\n\\u001b[0;32m 722\\u001b[0m \\u001b[39m compounds and aqueous species, Wiley, New York (1978)'}}\\u001b[39;00m\\n\\u001b[0;32m 723\\u001b[0m \\u001b[39m \\\"\\\"\\\"\\u001b[39;00m\\n\\u001b[0;32m 725\\u001b[0m ion_data \\u001b[39m=\\u001b[39m [\\n\\u001b[0;32m 726\\u001b[0m d\\n\\u001b[1;32m--> 727\\u001b[0m \\u001b[39mfor\\u001b[39;00m d \\u001b[39min\\u001b[39;00m \\u001b[39mself\\u001b[39;49m\\u001b[39m.\\u001b[39;49mcontribs\\u001b[39m.\\u001b[39;49mcontributions\\u001b[39m.\\u001b[39mget_entries(\\n\\u001b[0;32m 728\\u001b[0m project\\u001b[39m=\\u001b[39m\\u001b[39m\\\"\\u001b[39m\\u001b[39mion_ref_data\\u001b[39m\\u001b[39m\\\"\\u001b[39m,\\n\\u001b[0;32m 729\\u001b[0m fields\\u001b[39m=\\u001b[39m[\\u001b[39m\\\"\\u001b[39m\\u001b[39midentifier\\u001b[39m\\u001b[39m\\\"\\u001b[39m, \\u001b[39m\\\"\\u001b[39m\\u001b[39mformula\\u001b[39m\\u001b[39m\\\"\\u001b[39m, \\u001b[39m\\\"\\u001b[39m\\u001b[39mdata\\u001b[39m\\u001b[39m\\\"\\u001b[39m],\\n\\u001b[0;32m 730\\u001b[0m per_page\\u001b[39m=\\u001b[39m\\u001b[39m500\\u001b[39m,\\n\\u001b[0;32m 731\\u001b[0m )\\u001b[39m.\\u001b[39mresult()[\\u001b[39m\\\"\\u001b[39m\\u001b[39mdata\\u001b[39m\\u001b[39m\\\"\\u001b[39m]\\n\\u001b[0;32m 732\\u001b[0m ]\\n\\u001b[0;32m 734\\u001b[0m \\u001b[39mreturn\\u001b[39;00m ion_data\\n\\n\\u001b[1;31mAttributeError\\u001b[0m: 'NoneType' object has no attribute 'contributions'\"\r\n}\r\n```",
"@MGriot Did you install the [mpcontribs-client](https://pypi.org/project/mpcontribs-client/)? It's needed to retrieve the ion ref data and you should see a warning on import if it isn't installed. HTH",
"@tschaume okay, now everything works after installing mpcontribs-client, unfortunately I have not seen it in the documentation or if there was I have not looked carefully.\r\nThank you, now the code works.",
"@tschaume @munrojm Would be great to raise a more informative error here. If someone tries to use mpcontribs functionality without it installed, the import warning should probably be an import error."
] | 2022-10-17T13:21:18
| 2022-11-05T15:26:38
|
2022-11-05T08:17:00Z
|
NONE
|
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**Describe the bug**
When I try to replicate the tutorial on how to generate Pourbaix diagrams I run into a code error: `AttributeError: 'NoneType' object has no attribute 'contributions'`.
**Code**
```
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
%matplotlib inline
mpr = MPRester(key)
# Get all pourbaix entries corresponding to the Cu-O-H chemical system.
entries = mpr.get_pourbaix_entries(["Cu"])
>AttributeError: 'NoneType' object has no attribute 'contributions'
```
**Desktop:**
- OS: Windows 10
- Version 21H2
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PR_kwDOACgets5BIbFg
| 2,694
|
VASP Optics Masking, and plotting
|
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[
"\n[](https://coveralls.io/builds/53498078)\n\nCoverage increased (+0.03%) to 63.617% when pulling **a485734b043945e6bfdc5635b26a9b06dd121aaa on jmmshn:patch-optics-cder** into **221603977924450e6282f85432c0d914e8a20b6c on materialsproject:master**.\n",
"@janosh, ready to merge this is failing due to something unrelated.\r\n",
"> @janosh, ready to merge this is failing due to something unrelated.\r\n\r\nNot sure where the error on master crept in. I was just investigating and working on a fix in #2695. It seems to be related to the pinned version of `spglib`:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/e01d044986d6b321ee0254a6c9c89a5edd693935/requirements.txt#L10",
"OK, so due to the fact that VASP can be compiled with different dtypes I'm just gonna set `data_type=\"complex64\"` and let the users pick when they are running for the `Waverder` object, `gamma_only` is just not enough information.\r\n\r\nIn the optics module, I'm trying to read the larger dtypes first to force a value error during reshaping. then trying smaller dtypes.",
"Thanks @jmmshn! 👍"
] | 2022-10-19T18:26:07
| 2022-10-21T18:11:08
|
2022-10-21T18:10:41Z
|
CONTRIBUTOR
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## Vasp optics masking and plotting features
Summary:
- Allow masking of matrix elements without recreating the object
- Allow users to access a filtered version of the matrix element data for analysis
You can now pass a `mask` kwarg in the calculation and get the portion of the dielectric function contributed by the transitions that you selected.
|
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PR_kwDOACgets5BNZ9W
| 2,695
|
Fix CI `TypeError` from `spglib`
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[
"@shyuep Updating `spglib` to v2 fixes the error on `master` CI reported by @nwinner in #2672 and @jmmshn in #2694. Not sure why this is necessary (i.e. why the error started occurring) but I don't think there are any implications for older pythons from upgrading `spglib` and maybe was overdue anyway.\r\n\r\nHowever, the upgrade [introduces a new CI error](https://github.com/materialsproject/pymatgen/actions/runs/3291097155/jobs/5424812318#step:5:77):\r\n\r\n```\r\nFe Fe0 4 0.21872822 0.75000000 0.47486711 1\r\n P P1 4 0.09461309 0.25000000 0.41824327 1\r\n O O2 8 0.165[70](https://github.com/materialsproject/pymatgen/actions/runs/3291097155/jobs/5424812318#step:5:71)974 0.04607233 0.28538394 1\r\n O O3 4 0.04337231 0.75000000 0.70[71](https://github.com/materialsproject/pymatgen/actions/runs/3291097155/jobs/5424812318#step:5:72)3767 1\r\n O O4 4 0.09664244 0.25000000 0.74132035 1\"\"\"\r\n for l1, l2 in zip(str(writer).split(\"\\n\"), answer.split(\"\\n\")):\r\n> self.assertEqual(l1.strip(), l2.strip())\r\nE AssertionError: \"2 'x, y, z'\" != \"2 '-x, -y, -z'\"\r\nE - 2 'x, y, z'\r\nE + 2 '-x, -y, -z'\r\nE ? + + +\r\n\r\npymatgen/io/tests/test_cif.py:518: AssertionError\r\n```",
"I think you can just fix the CI error. This is probably some notational/ordering issue. E.g., they swapped the x, y, z and the inversion -x, -y, -z operations. It has no effect on the accuracy.",
"\n[](https://coveralls.io/builds/53464844)\n\nCoverage decreased (-0.001%) to 63.591% when pulling **6af4cd173afe7a0e039e8a447ee431b7b03151ce on fix-ci-typeerror-from-spglib** into **e01d044986d6b321ee0254a6c9c89a5edd693935 on master**.\n"
] | 2022-10-20T15:58:31
| 2022-10-20T18:30:19
|
2022-10-20T18:28:41Z
|
MEMBER
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An attempt to fix [CI failing even on `master`](https://github.com/materialsproject/pymatgen/actions/runs/3284341401/jobs/5410182347#step:5:17) noted e.g. here: https://github.com/materialsproject/pymatgen/pull/2672#issuecomment-1284403537 by updating `spglib` to v2+.
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PR_kwDOACgets5BOL8p
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No double CI runs
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[
"@munrojm Not sure how busy you are. If you have time, could you take a look at [this MPResterLegacy error in pymatgen's CI](https://github.com/materialsproject/pymatgen/actions/runs/3292206613/jobs/5427297154#step:5:61):\r\n\r\n```py\r\npymatgen\\ext\\tests\\test_matproj.py:426: \r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\r\npymatgen\\ext\\matproj.py:1600: in get_download_info\r\n for doc in self.query({\"task_id\": {\"$in\": material_ids}}, [\"task_id\", \"blessed_tasks\"]):\r\npymatgen\\ext\\matproj.py:1039: in query\r\n num_results = self._make_request(\"/query\", payload=count_payload, method=\"POST\")\r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\r\n\r\nself = <pymatgen.ext.matproj._MPResterLegacy object at 0x000001CF9C39F040>\r\nsub_url = '/query'\r\npayload = {'criteria': '{\"task_id\": {\"$in\": [\"mvc-2970\"]}}', 'options': '{\"count_only\": true}', 'properties': '[\"task_id\", \"blessed_tasks\"]'}\r\nmethod = 'POST', mp_decode = True\r\n\r\n def _make_request(self, sub_url, payload=None, method=\"GET\", mp_decode=True):\r\n response = None\r\n url = self.preamble + sub_url\r\n try:\r\n if method == \"POST\":\r\n response = self.session.post(url, data=payload, verify=True)\r\n else:\r\n response = self.session.get(url, params=payload, verify=True)\r\n if response.status_code in [200, 400]:\r\n if mp_decode:\r\n data = json.loads(response.text, cls=MontyDecoder)\r\n else:\r\n data = json.loads(response.text)\r\n if data[\"valid_response\"]:\r\n if data.get(\"warning\"):\r\n warnings.warn(data[\"warning\"])\r\n return data[\"response\"]\r\n raise MPRestError(data[\"error\"])\r\n \r\n raise MPRestError(f\"REST query returned with error status code {response.status_code}\")\r\n \r\n except Exception as ex:\r\n msg = f\"{ex}. Content: {response.content}\" if hasattr(response, \"content\") else str(ex)\r\n> raise MPRestError(msg)\r\nE pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403. Content: b'{\"valid_response\": false, \"error\": \"API_KEY is not a valid key.\", \"version\": {\"db\": \"2020_09_08\", \"pymatgen\": \"2022.0.8\", \"rest\": \"2.0\"}, \"created_at\": \"2022-10-20T12:12:45.904394\"}'\r\n\r\npymatgen\\ext\\matproj.py:291: MPRestError\r\n```",
"\n[](https://coveralls.io/builds/53467246)\n\nCoverage increased (+0.004%) to 63.592% when pulling **5197a382d91890be2c10ed7d053c78fb259fa505 on no-double-ci-runs** into **ebe9ca2f8e2f259b4d5ae3df66949e9ce4bdb8e3 on master**.\n"
] | 2022-10-20T19:01:14
| 2022-10-20T19:45:16
|
2022-10-20T19:41:56Z
|
MEMBER
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The `text-linux` and `lint` CI workflows currently run twice for every PR due to being triggered both by push and PR to _any_ branch:
```yml
name: Testing Linux
on: [push, pull_request]
```
We can run only once, thereby saving time, CI budget and energy (esp. with `test-linux` which takes long), by triggering only on push/PR to `master`:
```yml
on:
push:
branches: [master]
pull_request:
branches: [master]
```
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PR_kwDOACgets5BPyrr
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Define `EntryLike` in `pymatgen/util/typing.py`
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"> Following is outdated, see next comment.\r\n\r\nThis isn't super useful atm since `EntryLike` can only be imported like this:\r\n\r\n```py\r\nif TYPE_CHECKING:\r\n from pymatgen.util.typing import EntryLike\r\n```\r\n\r\ndue to `if TYPE_CHECKING` guard. A bare import\r\n\r\n```py\r\nfrom pymatgen.util.typing import EntryLike\r\n```\r\n\r\nwill raise\r\n\r\n```py\r\nE ImportError: cannot import name 'EntryLike' from 'pymatgen.util.typing' (/Users/janosh/dev/pmg/pymatgen/util/typing.py)\r\n```\r\n\r\nNeed to check how to work around this without changing pmg pkg structure.\r\n",
"\n[](https://coveralls.io/builds/53477565)\n\nCoverage increased (+0.007%) to 63.599% when pulling **4b165998dbb09e1d9497d2ec0225b26445f5945b on EntryLike** into **221603977924450e6282f85432c0d914e8a20b6c on master**.\n",
"Oh cool, just realized wrapping everything in quotes works. Makes `EntryLike` importable at run time and `mypy` still understands this.\r\n\r\n```py\r\nif TYPE_CHECKING: # needed to avoid circular imports\r\n from pymatgen.analysis.phase_diagram import PDEntry\r\n from pymatgen.entries import Entry\r\n from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry\r\n\r\n# Entry or any of its subclasses or dicts that can be unpacked into any of them\r\nEntryLike = Union[Dict[str, Any], \"Entry\", \"PDEntry\", \"ComputedEntry\", \"ComputedStructureEntry\"]\r\n```\r\n\r\nAfter\r\n\r\n```diff\r\n# pymatgen/analysis/phase_diagram.py\r\nclass PhaseDiagram:\r\n- def unstable_entries(self) -> set[Entry]:\r\n+ def unstable_entries(self) -> set[EntryLike]:\r\n\r\nreveal_type(PhaseDiagram().unstable_entries)\r\n```\r\n\r\n`mypy pymatgen/analysis/phase_diagram.py` prints\r\n\r\n\r\n> pymatgen/analysis/phase_diagram.py:3485: note: Revealed type is \"builtins.set[Union[builtins.dict[builtins.str, Any], pymatgen.entries.Entry, pymatgen.analysis.phase_diagram.PDEntry, pymatgen.entries.computed_entries.ComputedEntry, pymatgen.entries.computed_entries.ComputedStructureEntry]]\"\r\n"
] | 2022-10-21T01:52:56
| 2022-10-21T05:02:39
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2022-10-21T05:00:52Z
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MEMBER
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```py
if TYPE_CHECKING: # needed to avoid circular imports
from pymatgen.analysis.phase_diagram import PDEntry
from pymatgen.entries import Entry
from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
# Entry or any of its subclasses or dicts that can be unpacked into any of them
EntryLike = Union[Dict[str, Any], Entry, PDEntry, ComputedEntry, ComputedStructureEntry]
```
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PR_kwDOACgets5BQR8H
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Let env vars override `.pmgrc.yaml` in `_load_pmg_settings()` and make `~/.config` new default location for `.pmgrc.yaml`
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[
"\n[](https://coveralls.io/builds/53501797)\n\nCoverage increased (+0.006%) to 63.621% when pulling **564671f0f44de20ca350c45e9c29b4705be86664 on env-vars-override-pmgrc** into **fe42ce1fa2f471e256debb240e57e08415b6dd79 on master**.\n",
"If we're going to mess around with `.pmgrc.yaml` I would prefer more comprehensive changes:\r\n\r\n1. `pydantic` is now a dependency via `monty`, and has excellent features for [settings management](https://pydantic-docs.helpmanual.io/usage/settings/) -- we use this in other projects, why not here?\r\n2. Rather than drop `.pmgrc.yaml` in $HOME, we could be better citizens and adopt the [XDG specification](https://maex.me/2019/12/the-power-of-the-xdg-base-directory-specification/) and put it in `$HOME/.config` instead.\r\n\r\nTo the specific point here, I think letting env vars override the settings is absolutely ok. But I would prefer we just use it as an opportunity to adopt a better solution.\r\n\r\n[Edit: apologies, hit enter too soon]",
"I think pydantic is overcomplicated. We are talking about a few settings here. Unless we want to move a lot of pymatgen settings to the config file (e.g., default potentials, etc.), I think the current format is fine.\r\n\r\nI am also fine if we want to generate the file in .config by default henceforth, but keep backward compatibility by checking $HOME/.config, followed by $HOME.",
"What makes the pydantic `Settings` option over-complicated?\r\n\r\nWhat I like:\r\n\r\n1. It implements logic (like deciding between env variables and config files) for us, we don't have to write our own\r\n2. It makes it very obvious what settings are possible and what their types and defaults are (-> it makes it easier to add new settings too), this I think is the main benefit\r\n3. It's already dependency, and seeing increased adoption in community, so I don't see specific downside\r\n4. Other MP codes are using it, so we make it easier for developers to contribute to multiple codes, since we're adopting a common pattern\r\n5. It has additional features, like support for `.env` files, secrets, etc. that we may not wish to implement ourselves, but could be useful to others\r\n\r\n",
"@mkhorton I am not saying pydantic does not have benefits. All the benefits you listed are valid. I am saying right now, pymatgen has just the API key and a few config settings like VASP PSP directory. It is not like we have a list of 50 settings to manage. I think the pydantic use case is a lot more useful for something like FireWorks or atomate where you need to specify server settings, and a whole host of config variables. Some of the other benefits are not that useful in pymatgen's case, e.g., knowing what are valid values for certain settings. \r\n\r\nFeel free to implement pydantic if you really feel strongly about it. I don't mind one way or the other. My one and only condition is that whatever implemented must work with existing pymatgen installations.",
"Big fan of option 2 (moving `.pmgrc.yaml` to `$HOME/.config`)! Been thinking of suggesting that as well.\r\n\r\n> I am also fine if we want to generate the file in .config by default henceforth, but keep backward compatibility by checking $HOME/.config, followed by $HOME.\r\n\r\nWe could even move it to `$HOME/.config` ourselves when detecting a `.pmgrc.yaml` in the home directory and print a message to the user about it. Would speed up the transition but might create edge cases that break existing pymatgen installations.\r\n\r\n---\r\n\r\nRe `pydantic`: haven't used it yet so don't have an opinion on it (yet). One very minor downside is that it's incompatable with certain future type annotations (as I discovered in https://github.com/materialsproject/atomate2/pull/165#issuecomment-1238620700) which pmg makes widespread use of now. But should be fine as long as we stick to old annotations in files parsed by `pydantic`. Just something that contributors will have to be aware of.",
"I don't think we should automatically move files to .config. That is executing a specific write operation on a user's computer. It is not too much trouble to just support $HOME/.config and $HOME.\r\n\r\nI didn't know about the type annotation issue. If that is the case, let's just table the pydantic move for now. I recognize the benefits but at the time, there is no pressing need.",
"I believe that issue was fixed: https://github.com/pydantic/pydantic/pull/2761 ",
"@mkhorton That was a partial fix. Some future annotations syntax like the pipe `|` for type unions can't be supported unless the codebase is py3.10+ (pmg is 3.8+) where `|` between types becomes valid syntax outside of annotation contexts. See https://github.com/pydantic/pydantic/issues/3300#issuecomment-1034007897.",
"To be specific, at what point would this bug be triggered? Would it only be if we use the `futures` import in the specific file that holds the settings, i.e. as long as we don't use the pipe operator inside settings it would be ok?",
"> Would it only be if we use the futures import in the specific file that holds the settings, i.e. as long as we don't use the pipe operator inside settings it would be ok?\r\n\r\nThat's correct. Which is why I called it a small downside. I think it's only worth mentioning since someone not knowing this limitation might trip over it (like I did).",
"Ok -- this is something I do feel strongly about. I think a clear list of allowed settings (with types) is beneficial. However, I don't have time to implement this minute, so in this sense I abdicate my opinion for the moment :) ",
"> However, I don't have time to implement this minute, so in this sense I abdicate my opinion for the moment :)\r\n\r\nI'll go ahead and implement support for `.pmgrc.yaml` under `~/.config` in this PR then and then merge it since prioritizing env vars is independent of using `pydantic`.",
"Thanks for the suggestions @janosh . I am in favor of moving `.pmgrc.yaml` to `$HOME/.config` and of reversing the order such that ENV variables override the .yaml file; I think that behavior will reduce the potential for confusion. I don't know enough about pydantic settings to offer a well-informed opinion."
] | 2022-10-21T04:37:05
| 2022-10-27T14:27:46
|
2022-10-21T20:15:45Z
|
MEMBER
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@shyuep @mkhorton `_load_pmg_settings()` currently reads env vars first and then overrides them with `.pmgrc.yaml`. It's usually the other way around.
This gives users no way to override on a case by case basis. E.g.
```sh
PMG_MAPI_KEY=xxxxxxxxxxxxxxxx python -c 'from pymatgen.ext.matproj import MPRester; MPRester().query("mp-1234", ["formula"])'
```
will be identical to
```py
python -c 'from pymatgen.ext.matproj import MPRester; MPRester().query("mp-1234", ["formula"])'
```
Following [POLA](https://en.wikipedia.org/wiki/Principle_of_least_astonishment), I think we should swap this around and let env vars override `.pmgrc.yaml`.
|
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I_kwDOACgets5UgPa7
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Add PMG_LEGACY_API_KEY to `.pmgrc.yaml`
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[
"Tagging @munrojm here. The new MPRester adaptor should choose either the legacy or new API based on the length of the API key. Is this not working?",
"> The new MPRester adaptor should choose either the legacy or new API based on the length of the API key. Is this not working?\r\n\r\n@mkhorton It is working for pymatgen users but doesn't help with the tests (unless I'm missing sth). There, we explicitly import the old Rester since that's the one we want to test.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/41abff0b5f8eceb99af2d4d8492694f701096d12/pymatgen/ext/tests/test_matproj.py#L26\r\n\r\nAnd it's trying to use a new API key since that's the only one we pass to the GH action as a secret:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/fe42ce1fa2f471e256debb240e57e08415b6dd79/.github/workflows/test-linux.yml#L37\r\n\r\nThis assumes the answer to my above question is yes, i.e. the GH secret is a new API key which I suspect is true since it was updated on Sep 13.",
"Hm, well the new MPRester tests are inside the [api repo](https://github.com/materialsproject/api) anyway; perhaps it's better we only test legacy inside pymatgen itself? It could keep the pymatgen tests cleaner since when the legacy API is removed, we could remove the API tests from pymatgen altogether, and remove a common failure mode (ideally, pymatgen tests do not fail because of a server outage). In this case, we just change the secrets API key back to the legacy API key.",
"That sounds sensible. I set my own old API key as PMG_LEGACY_API_KEY secret on this repo to test this. Will remove it again. Will you set `PMG_MAPI_KEY` to an old one?",
"> Will you set PMG_MAPI_KEY to an old one?\r\n\r\nDone!",
"I'm super late to this party, but I found current handling of MP API keys very confusing as env var in, and I'm happy to open a separate issue/PR if you think it's worth detailed discussion.\r\n\r\nAlso I'm pretty new to the entire software stack so don't know much about the history around naming of MP API key, but as far as I'm aware, at least the `mp-api`'s side uses https://github.com/materialsproject/api/issues/949:\r\n- `PMG_MAPI_KEY` for the new length 32 key\r\n- `MP_API_KEY` for the legacy key (15 <= length <= 17)\r\n\r\nHowever `pymatgen` seems to reuse the same `PMG_MAPI_KEY` for both legacy and new API keys, but determine its type by checking its length: https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/ext/matproj.py#L416-L426\r\n\r\nI'm having some issue for this design in https://github.com/materialsvirtuallab/matgenb/pull/61 where the CI workflow tests both legacy and new `MPRester`. As only one `PMG_MAPI_KEY` is possible, it would either test the legacy or new API, but not both (passing it as a plain-text arg would be a terrible idea I guess).\r\n\r\nWhat about we make `pymatgen` read another `MP_API_KEY` env var (similar to `PMG_LEGACY_API_KEY` but consistent with `mp-api` naming), as make this takes higher priority when both legacy and new keys are set, as the `MPRester` from `pymatgen` is mostly designed for the legacy API if I understand correctly?\r\n",
"@DanielYang59 Just to clarify here. The `mp_api` client only uses new-style API keys and only connects to the new/next-gen API (i.e. https://api.materialsproject.org vs https://legacy.materialsproject.org/rest/v2). This issue from 2022 was around the time when the new API and its python client `mp-api` became production-ready. `pymatgen` was/is trying to maintain some backward-compatibility with our legacy API and ease the transition for users as long as it's still available. Generally, our recommendation is not to develop any tools against the legacy API and to move existing tools away from the legacy API. The underlying data is years outdated and the code behind it is not maintained. It will soon be retired / taken down entirely. HTH",
"> Generally, our recommendation is not to develop any tools against the legacy API and to move existing tools away from the legacy API. The underlying data is years outdated and the code behind it is not maintained. It will soon be retired / taken down entirely. HTH\r\n\r\nThat absolutely makes sense, I personally don't have a use case for the legacy API, just some examples in `matgenb` explicitly require the legacy API https://github.com/materialsvirtuallab/matgenb/pull/61, I would see if I could migrate them to the new API, if not I guess the best thing to do is to skip the test for now (or remove it if the data is super outdated).\r\n\r\nThanks again and sorry for digging up the ancient thread"
] | 2022-10-21T04:55:20
| 2024-12-06T02:12:38
|
2022-10-21T20:49:25Z
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Is the `PMG_MAPI_KEY` used in [GH action](https://github.com/materialsproject/pymatgen/settings/secrets/actions) one of length 32 for the new API?
I think that's the reason we're getting [this error in CI](https://github.com/materialsproject/pymatgen/actions/runs/3294713178/jobs/5432504709#step:5:97):
> pymatgen.ext.matproj.MPRestError: REST query returned with error status code 403. Content: b'{"valid_response": false, "error": "API_KEY is not a valid key.", "version": {"db": "2020_09_08", "pymatgen": "2022.0.8", "rest": "2.0"}, "created_at": "2022-10-20T21:17:27.506782"}'
Would be nice to have the ability to co-operate old and new `MPRester` and would also allow us to fix CI. That would require adding a new key like `PMG_LEGACY_API_KEY` to `.pmgrc.yaml`. Old MPRester looks for that first and falls back on PMG_API_KEY else. Any thoughts?
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PR_kwDOACgets5BQXkH
| 2,700
|
Fix _MPResterLegacy tests in pymatgen/ext/tests/test_matproj.py failing due to new API key
|
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"\n[](https://coveralls.io/builds/53502622)\n\nCoverage increased (+0.003%) to 63.623% when pulling **51c96240cf2432b33c31564e20ef37a4addad52c on fix-mprester-legacy-ci** into **aad30d4706ebbafe40ad9977c0b6042e4fd33174 on master**.\n"
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| 2022-10-21T20:50:55
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2022-10-21T20:49:24Z
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Closes #2699.
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|
Regular release schedule and TestPyPI or PyPI option
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[
"I am unclear what a regular release schedule means. We release when there are a significant number of changes that warrant a release. For many people, they could be using 2019 versions of pymatgen and not notice a difference with the 2022 version.",
"> just a PyPI option for the current master branch\r\n\r\nMaybe this helps `pip install -U git+https://github.com/materialsproject/pymatgen`? This is basically what an automated release to PyPI after every commit to `master` would give you.",
"@shyuep I guess it's more important that the changes happen at predictable intervals so people can plan accordingly.\r\nIt's hard telling people that something will be fixed in the next release and have no timeline for when that will happen.",
"@janosh \r\n\r\npip install -U git+https://github.com/materialsproject/pymatgen\r\nThat doesn't fix the issue of extremely slow install from the GitHub in the CI. Also releasing any downstream code is not possible if any of the dependencies is from github\r\n",
"Changes do not happen at regular intervals. That is the reality of all software codes. If I deem a bug fix important enough, I usually issue a release immediately. If there are no changes between today and a month from now, I see no reason to do a release. Most changes in pymatgen are in the form of new functionality. ",
"So say I have feature A in `pymatgen` that fixes allow feature B in `pymatgen-analysis-diffusion` and is needed to merge a PR on atomate2. The problem can be completely fixed but before there is a `pymatgen` release all those other things are completely on hold.\r\n\r\nIf the releases are mostly meant to deal with bug fixes, then we should have some mechanism that allows people to use the newest master branch (that is not just downloading the GitHub repo because I have ran into situations where the user's internet and computer speed made that really difficult, in addition to the slow CI workflow problem stated above)",
"When such situations occur, by all means let us know and request to do a release. To date, I have never denied any such requests. There is a way to use master for the downstream codes that is stipulated by @janosh. For CI purposes, that is not a problem. ",
"OK, then can I get a release? 😄 ",
"@shyuep I fixed [a small bug](https://github.com/materialsproject/pymatgen/pull/2702/files#diff-9931b710fdada44a5468d08079cf19a3e8f1825cfd3eaff24ae2bf1ed3784cc0R43) in #2702. Maybe wait for that to merge.\r\n\r\n",
"@jmmshn done."
] | 2022-10-21T20:26:00
| 2022-10-22T13:44:37
|
2022-10-22T13:44:36Z
|
CONTRIBUTOR
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@shyuep @mkhorton @janosh I think it would be super helpful to have:
1. A regular (bi-weekly) release schedule, because downloading the repo from github is still too "technologically advanced" for some people.
2. A version of the code on TestPyPI (or just a PyPI option for the current master branch) that is always pointed to master so that CI and/or releases of downstream code is smoother, currently if I'm point a dependency at the github repo it really slows down the CI.
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PR_kwDOACgets5BUQDp
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Test `_load_pmg_settings()`
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"\n[](https://coveralls.io/builds/53505135)\n\nCoverage increased (+0.01%) to 63.633% when pulling **345534a41ef55f7125ad3a1fce43d4a9c46d203f on test-load-settings** into **3b160fce1a35202d6d498565858400c79e1db05f on master**.\n"
] | 2022-10-21T22:11:33
| 2022-10-21T23:02:42
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2022-10-21T23:00:45Z
|
MEMBER
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Add new test module `pymatgen/core/tests/test_settings.py` to cover `_load_pmg_settings()`.
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Pandas fix
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"\n[](https://coveralls.io/builds/53511594)\n\nCoverage remained the same at 63.628% when pulling **3ceb90f1c888c193eca18febcff19d5748abe5e5 on pandas-fix** into **929af6100884f38cb70307c0e13f701641d107b0 on master**.\n"
] | 2022-10-22T17:15:40
| 2022-10-22T17:43:02
|
2022-10-22T17:41:41Z
|
MEMBER
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Closes https://github.com/materialsproject/pymatgen/issues/2510. Update the deprecated `df.append` method to `pd.concat` in `pymatgen/io/lammps/data.py`.
Continuation of #2536.
|
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`pytest-split` in CI
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[
"Looks like this takes the runtime for the main `text-linux` workflow from [~18 min](https://github.com/materialsproject/pymatgen/actions/runs/3301921055/jobs/5448046731) down to [~9 min](https://github.com/materialsproject/pymatgen/actions/runs/3309228600/jobs/5462200922). The number of parallel jobs went from 4 to 10. Setting up the repo and installing deps is a ~3.5 min constant time for every job. So probably not that useful to crank the parallel job count much higher.\r\n\r\n@shyuep @mkhorton Wanted to get your opinion on this before merging since it's a bigger-than-usual change to the main CI workflow. We could add the same splitting to the `mac` and `windows` workflows. In fact, is there still a strong reason to not run the same test suite on all 3 platforms? Would make maintenance of the workflow files easier since we could get rid of `.github/workflows/test-{max,win}.yml` and simply add `os` to `matrix` strategy in `.github/workflows/test-linux.yml`.",
"Sure this is fine.",
"\n[](https://coveralls.io/builds/53566139)\n\nCoverage increased (+18.08%) to 81.711% when pulling **9af323a966e2206a8ce8f131335828f6aad59f70 on pytest-split-in-ci** into **302ca2c157c8e6f295fd2722c1af45775adf9d6f on master**.\n",
"> [](https://coveralls.io/builds/53566139)\r\n> \r\n> Coverage increased (+18.08%) to 81.711% when pulling **[9af323a](https://github.com/materialsproject/pymatgen/commit/9af323a966e2206a8ce8f131335828f6aad59f70) on pytest-split-in-ci** into **[302ca2c](https://github.com/materialsproject/pymatgen/commit/302ca2c157c8e6f295fd2722c1af45775adf9d6f) on master**.\r\n\r\nJust noticed the coverage increased by 18% in this PR. Is this because a fifth of the test suite wasn't running before with the old splitting setup?\r\n\r\n```yml\r\ninclude:\r\n - pkg: pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism\r\n pkg_id: 1\r\n - pkg: pymatgen/analysis --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism\r\n pkg_id: 2\r\n - pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext\r\n pkg_id: 3\r\n - pkg: pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line\r\n pkg_id: 4\r\n```\r\n"
] | 2022-10-24T00:31:24
| 2022-10-25T23:01:54
|
2022-10-25T03:08:44Z
|
MEMBER
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https://github.com/jerry-git/pytest-split is a `pytest` plugin that splits the test suite into equally sized splits based on test execution time.
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I_kwDOACgets5UrAfb
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Error when importing mp_api.client
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[
"Downgrading python, pymatgen, and mp-api to the following using conda worked. \r\n`python=3.9.13`\r\n`mp-api=0.29.1`\r\n`pymatgen=2022.9.21`\r\n\r\nI get the following error instead. (I know I need to set up that .yaml file 😅) \r\n\r\n```\r\n/my/dir/miniconda3/envs/venv/lib/python3.9/site-packages/pymatgen/core/__init__.py:51: UserWarning: Error loading .pmgrc.yaml: dictionary update sequence element #0 has length 1; 2 is required. You may need to reconfigure your yaml file.\r\n warnings.warn(f\"Error loading .pmgrc.yaml: {ex}. You may need to reconfigure your yaml file.\")\r\n/my/dir/miniconda3/envs/venv/lib/python3.9/site-packages/pymatgen/analysis/phase_diagram.py:26: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\r\n```\r\n",
"Could you try `pip install pymatgen==2022.10.22` and report if that also raises `ValueError` or just issues a warning?",
"> Could you try `pip install pymatgen==2022.10.22` and report if that also raises `ValueError` or just issues a warning?\r\n\r\nYeah the same problem happens..\r\n@janosh \r\n\r\n```\r\nPython 3.8.10 (default, Jun 22 2022, 20:18:18) \r\n[GCC 9.4.0] on linux\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> import mp_api.client\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/mp_api/client/__init__.py\", line 4, in <module>\r\n from .mprester import MPRester\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/mp_api/client/mprester.py\", line 9, in <module>\r\n from emmet.core.electronic_structure import BSPathType\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/emmet/core/electronic_structure.py\", line 11, in <module>\r\n from pymatgen.analysis.magnetism.analyzer import (\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/pymatgen/analysis/magnetism/__init__.py\", line 8, in <module>\r\n from pymatgen.analysis.magnetism.analyzer import (\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/pymatgen/analysis/magnetism/analyzer.py\", line 23, in <module>\r\n from pymatgen.core.structure import DummySpecies, Element, Species, Structure\r\n File \"/home/your/favorite/directory/lib/python3.8/site-packages/pymatgen/core/__init__.py\", line 66, in <module>\r\n locals().update(SETTINGS)\r\nValueError: dictionary update sequence element #0 has length 1; 2 is required\r\n>>> \r\n```",
"> I get the following error instead. (I know I need to set up that .yaml file 😅)\r\n\r\nI think that file must already be present on your machine but not in the expected format. If you had no `~/.config/.pmgrc.yaml` or `~/.pmgrc.yaml` file, there should be no error. Can you look for a file in both places and post the content here if you find one?",
"I had the same issue. I accidentally had \r\n\r\n`PMG_VASP_PSP_DIR = ~/Documents/my_psp`\r\n\r\ninstead of \r\n\r\n`PMG_VASP_PSP_DIR: ~/Documents/my_psp`\r\n\r\nin my ~/.pmgrc.yaml. Changing the syntax resolved my issue\r\n\r\nPython 3.10.7\r\npymatgen 2023.1.20\r\nmp-api 0.30.6",
"@wladerer Thanks for reporting. Closing this as syntax error requiring user fix.",
"> > I get the following error instead. (I know I need to set up that .yaml file 😅)\r\n> \r\n> I think that file must already be present on your machine but not in the expected format. If you had no `~/.config/.pmgrc.yaml` or `~/.pmgrc.yaml` file, there should be no error. Can you look for a file in both places and post the content here if you find one?\r\n\r\nJust commenting here for posterity. \r\n\r\nI had this issue again when i used `pip install mp-api` in a new conda environment so i came back to this issue and i found `~/.pmgrc.yaml` in that directory so i deleted it and `from mp_api.client import MPRester` worked. \r\n\r\nThank you. "
] | 2022-10-24T09:55:52
| 2023-08-07T00:22:21
|
2023-01-20T23:47:39Z
|
NONE
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**Describe the bug**
For some reason when I import `mp_api.client` I get the following error
**To Reproduce**
Steps to reproduce the behavior:
1. create new virtual environment and install mp-api the one that pip got was `mp_api-0.29.3-py3-none-any.whl (69 kB)`
2. run `python` the version I'm using is `Python 3.10.6`
3. `import mp_api.client`
```
Python 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:36:39) [GCC 10.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mp_api.client
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/my/local/dir/venv/lib/python3.10/site-packages/mp_api/client/__init__.py", line 4, in <module>
from .mprester import MPRester
File "/home/my/local/dir/venv/lib/python3.10/site-packages/mp_api/client/mprester.py", line 8, in <module>
from emmet.core.electronic_structure import BSPathType
File "/home/my/local/dir/venv/lib/python3.10/site-packages/emmet/core/electronic_structure.py", line 11, in <module>
from pymatgen.analysis.magnetism.analyzer import (
File "/home/my/local/dir/venv/lib/python3.10/site-packages/pymatgen/analysis/magnetism/__init__.py", line 8, in <module>
from pymatgen.analysis.magnetism.analyzer import (
File "/home/my/local/dir/venv/lib/python3.10/site-packages/pymatgen/analysis/magnetism/analyzer.py", line 23, in <module>
from pymatgen.core.structure import DummySpecies, Element, Species, Structure
File "/home/my/local/dir/venv/lib/python3.10/site-packages/pymatgen/core/__init__.py", line 66, in <module>
locals().update(SETTINGS)
ValueError: dictionary update sequence element #0 has length 1; 2 is required
>>>
```
The same exact thing happens when I try to use `from mp_api.client import MPRester` which is how I originally ran into this issue.
**Desktop :**
This is on WSL2 Ubuntu 20.04. I ran this over both VScode and terminal and got the same exact errors. Fresh installations.
|
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PR_kwDOACgets5BdE4_
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|
Fix parsing of "Atomic configuration" in POTCAR
|
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[
"\n[](https://coveralls.io/builds/53590171)\n\nCoverage increased (+17.3%) to 80.956% when pulling **ea3b7547940c9fd397e6e965821227e6930bcbeb on yuzie007:atomic_configuration** into **302ca2c157c8e6f295fd2722c1af45775adf9d6f on materialsproject:master**.\n",
"Thanks for the fix and the great summary! 👍 "
] | 2022-10-24T22:59:49
| 2022-10-25T16:01:18
|
2022-10-25T15:58:28Z
|
CONTRIBUTOR
|
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First of all, thank you so much for the development of pymatgen!
## Summary
Due to the missing regex option of `(?s)` (https://docs.python.org/3/library/re.html#re.S, which makes the `.` special character match any character at all, including a newline), "Atomic configuration" in POTCAR (52 and 54) was actually not parsed. I think this part is sometimes useful for, e.g., estimating a reasonable NBANDS value. My pull request fixes the issue above. In more detail:
- `re.search` for this is slightly simplified.
- The change above adds "nentries" and "Orbitals" to PSCTR. In `get_potcar_hash`, these two keys are excluded to keep the same hash values as before.
- A new test `test_psctr` is added to check if the parsing is done correctly.
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PR_kwDOACgets5Bd2yZ
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Merge `requirements{,-dev,-optional}.txt` into `setup.py`
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[
"\n[](https://coveralls.io/builds/53601073)\n\nCoverage increased (+0.0001%) to 81.723% when pulling **1bdd1b7c6f5b12079c48cc06a6e6443bec070ed3 on reqs-into-setup-py** into **523cfce173f4045878f503009e3e49909cd52a6f on master**.\n"
] | 2022-10-25T04:15:34
| 2022-10-25T21:37:24
|
2022-10-25T21:23:35Z
|
MEMBER
|
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Then replace `pip install -r requirements{,-dev,-optional}.txt` with editable `extras_require` installs in CI workflows.
E.g.
```diff
- pip install -r requirements.txt
- pip install -r requirements-optional.txt -r requirements-dev.txt
- pip install -e .
+ pip install -e '.[dev,optional]'
```
|
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PR_kwDOACgets5BiU8u
| 2,708
|
Run full test suite on Windows
|
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[
"Maybe we shouldn't run on `macos` actually since it's limited to 5 concurrent runners so would come with significant wait times ([docs on GH action usage limits](https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits)) and it's unlikely to surface errors that wouldn't also show up on `ubuntu`.",
"@shyuep These lines don't work on windows. Is there any point trying to fix that? `Linux_64bit` sounds like the binary wouldn't run anyway?\r\n\r\n```sh\r\nfor pkg in cmd_line/*;\r\n do echo \"$(pwd)/cmd_line/$pkg/Linux_64bit\" >> \"$GITHUB_PATH\";\r\ndone\r\n```\r\n\r\nNo tests fail without them (presumably because tests are skipped if CLI commands can't be found). So we could just skip those lines on Windows.",
"There is no need for full tests on windows or macOS. ",
"Why not on windows? From my experience, there's a large number of errors that only show up on Windows. I think we should try to catch and fix them early.",
"\n[](https://coveralls.io/builds/53777843)\n\nCoverage decreased (-70.2%) to 0.0% when pulling **f6b3b006447ca68a6c151539278b8b5e84a35a5b on single-ci-tests-file** into **455c17a637eaca7e4aa9963a4fe424b07c58728a on master**.\n",
"I'd be pro testing on more platforms too (Windows especially, since we have seen some odd errors in the past).\r\n\r\nI don't feel the need for this on every PR, although I am not against that either, but on the main branch sure.",
"Because some CLI tools are not available on windows. If you want to compile all the CLI tools for all platforms and keep them updated, sure. But I only care that those work on Linux at the minimum. ",
"> Because some CLI tools are not available on windows. If you want to compile all the CLI tools for all platforms and keep them updated, sure. But I only care that those work on Linux at the minimum.\r\n\r\nAgreed, I should have been clearer. My proposal was all the tests that can easily be run on Windows should be. For stuff that doesn't install, I agree we should skip it (like I did in f89b31b).",
"I was chatting with @janosh a bit. Our group has also had some issues with pymatgen on Windows in the past, I think that was mostly on the installation side when trying to install pymatgen via Anaconda (I generally prefer miniconda environments).",
"@sgbaird raises a good point too; in our test suite, we don't actually test our packaging at all. Packaging issues have actually caused several issues in the past (I'm thinking specifically of one issue we had with Linux wheels, another issue we've had a few times with missing files), none of which are caught by our current CI.",
"I am not sure how packaging can be tested. We already automate most of it and missing files happen rarely only when someone added some new config file but forgot to add it into META or setup.py. Those usually affect a very small number of people.",
"@shyuep Something like this maybe?\r\n\r\n```py\r\nfrom glob import glob\r\nfrom os.path import dirname, exists\r\n\r\nimport pytest\r\n\r\nROOT = dirname(dirname(__file__))\r\npackage_sources_path = f\"{ROOT}/pymatgen.egg-info/SOURCES.txt\"\r\n\r\n\r\n@pytest.mark.skipif(\r\n not exists(package_sources_path),\r\n reason=\"No pymatgen.egg-info/SOURCES.txt file, run pip install . to create\",\r\n)\r\ndef test_egg_sources():\r\n \"\"\"Check that all source and data files under pymatgen/**/* are listed in pymatgen.egg-info/SOURCES.txt.\"\"\"\r\n with open(package_sources_path) as file:\r\n sources = file.read()\r\n\r\n src_files = [x for x in glob(f\"{ROOT}/pymatgen/**/*\", recursive=True) if \"tests\" not in x]\r\n\r\n for filepath in src_files:\r\n rel_path = filepath.split(f\"{ROOT}/pymatgen/\")[1]\r\n assert rel_path in sources\r\n```\r\n\r\nI added a similar test in https://github.com/CompRhys/aviary/pull/46 after we repeatedly forgot to package some JSON data/embedding files.",
"I wouldn't do it as a unittest. That is a violation of what a unittest means. I would add it as a release check in the invoke tasks.py file. ",
"@shyuep Happy to add it to `tasks.py`.\r\n\r\n> That is a violation of what a unittest means.\r\n\r\nDo you mean we're not testing the code base itself but its deployment? I would say let's test whatever gives us peace of mind.",
"Can't one test the packaging also simply by having a workflow that does a `pip install` or similar of the latest version, and run tests against that?",
"@mkhorton We could do that too. Though considering we're at <80% coverage, there's no guarantee we would catch files missing from the package this way.",
"Fair. I was really thinking e.g. of the one issue we had with Linux installs a while back. It seems like installation issues are ones that can affect large numbers of people, but are also ones that have slipped through our CI without being noticed. With that said, we usually hear about it fairly quickly if it happens so can fix... ",
"@janosh I would say unittest are meant to test code functionality, not code packaging or deployment. Regardless of packaging, someone working from the Github fork will always have a working code if the unittests pass.\r\n\r\nMissing package files are a deployment/release issue. I am all for implementing checks on the *release* process to ensure that we do not have packaging issues. I don't think we need to put it in unittests because it is not a code functionality issue."
] | 2022-10-25T21:39:11
| 2022-11-01T03:39:36
|
2022-11-01T03:38:32Z
|
MEMBER
|
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Now that we auto-split tests onto 10 parallel runners using `pytest-split` (#2704), we could run all tests on all platforms (`ubuntu`, `mac`, `windows`).
Before, the largest test suite ([don't even think it was the full one](https://github.com/materialsproject/pymatgen/commit/5cb1270310cd25a3ba1f3bbb4584f84466592c31#diff-fb0daef94ea304514bcccf51bdd0e30a073788e28fce22a7303d91203c69db70L23-L32)) was run only on `ubuntu`.
Still a WIP. CI is expected to fail due to install errors from BoltzTrap2 on Windows and [due to commenting out](https://github.com/materialsproject/pymatgen/compare/single-ci-tests-file?expand=1#diff-faff1af3d8ff408964a57b2e475f69a6b7c7b71c9978cccc8f471798caac2c88R45-R48):
```sh
# for pkg in cmd_line/*;
# do echo "$(pwd)/cmd_line/$pkg/Linux_64bit" >> "$GITHUB_PATH";
# done
```
|
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I_kwDOACgets5U146S
| 2,709
|
Showing wrong coordinates
|
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[] | 2022-10-26T04:17:55
| 2022-10-26T09:32:31
|
2022-10-26T09:32:31Z
|
NONE
|
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When using Materials Project Crystal Toolkit to view file, the displayed coordinates are wrong, No oxygen atom found in the center of the unit cell.
```
data_fcc
_audit_creation_method generated by ABACUS
_cell_length_a 3.02611
_cell_length_b 3.02611
_cell_length_c 3.02611
_cell_angle_alpha 60
_cell_angle_beta 60
_cell_angle_gamma 60
_symmetry_space_group_name_H-M
_symmetry_Int_Tables_number
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Mg 0 0 0
O 0.5 0.5 0.5
```
<img width="881" alt="image" src="https://user-images.githubusercontent.com/29646077/197933269-241dff08-bd3c-4aaa-8379-343849387d9e.png">
|
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I_kwDOACgets5U6C7c
| 2,710
|
Python 3.11 support
|
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[] | 2022-10-26T18:12:51
| 2023-02-22T23:50:53
|
2023-02-22T23:50:52Z
|
MEMBER
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[Now that Python 3.11 is out](https://docs.python.org/3.11/whatsnew/3.11.html), we should make sure `pymatgen` supports it. Just tried it out on M1 Pro running macOS 10.13 and encountered no problems. We should leave this open until we've [run CI in 3.11](https://github.com/actions/python-versions/releases/tag/3.11.0-3328127706) though.
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PR_kwDOACgets5BtEnb
| 2,711
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Add `check_egg_sources_txt_for_completeness()` to `tasks.py`
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[
"You need `@task` only if it is a command that is invoked. E.g., `invoke release` means run the function called `release`. Since your new method is only used internally for checking the generated files, you do not need to add `@task`",
"> You need `@task` only if it is a command that is invoked. E.g., `invoke release` means run the function called `release`. Since your new method is only used internally for checking the generated files, you do not need to add `@task`\r\n\r\nOk, that's what I assumed.",
"\n[](https://coveralls.io/builds/53683325)\n\nCoverage decreased (-0.002%) to 81.723% when pulling **0d0232dae6f97899a9f1c649a89ee12e1593bab1 on release-task-check-egg-sources** into **c21242935e838d51cc08326f4483cfb2030a87d6 on master**.\n"
] | 2022-10-27T22:56:53
| 2022-10-27T23:24:40
|
2022-10-27T23:06:15Z
|
MEMBER
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Following discussion initiated by @sgbaird and @mkhorton in https://github.com/materialsproject/pymatgen/pull/2708#issuecomment-1292477362.
@shyuep I'm not familiar with `invoke`. The function I added `check_egg_sources_txt_for_completeness()` is not `@task` decorated. it's simply called by the `release` task. Every other function in `tasks.py` seems to be. Is that a requirement?
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PR_kwDOACgets5B7JKv
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Better error handling in `_load_pmg_settings()`
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"\n[](https://coveralls.io/builds/53773382)\n\nCoverage decreased (-11.5%) to 70.198% when pulling **7f70860f059a80918647186ed7ca3d8e5f463d46 on gh-2698-followup** into **25768faa7aa0a34ee4357a92bc92ae41ef21bc1d on master**.\n"
] | 2022-10-31T23:03:49
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2022-10-31T23:41:23Z
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Following on the heels of #2698.
This PR was triggered by taking another look at `_load_pmg_settings()` due to the error reported in #2705. Don't think the error there has anything to do with #2698 though.
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PR_kwDOACgets5B7O5U
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Breaking: swap `fmt` and `filename` in `Structure.to()`
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[
"My vote is no. In an ideal world, I would prefer these to be kw only args. I almost always write Structure.to(filename=\"hello.cif\"). We are already friendlier than pandas, which requires to_csv, to_excel etc to be specified. Matt can cast the deciding vote. I am fine if it changes. ",
"\n[](https://coveralls.io/builds/53777348)\n\nCoverage decreased (-0.004%) to 81.721% when pulling **c35bce59e8d9a2607ca841c7e773319dd13d3931 on structure-to** into **2865ed1a291e10d77cd7119234d230dc97a4ca09 on master**.\n",
"I agree, these should remain as keyword arguments regardless. But swapping the order of the keyword arguments as a usability benefit seems worthwhile and harmless enough. People who continue to use these as keyword arguments would be unaffected. I don't feel strongly about this either however!",
"I'm equivocating; I say go for it.",
"Roger! :shipit: "
] | 2022-10-31T23:39:52
| 2022-11-01T03:16:45
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2022-11-01T03:02:26Z
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MEMBER
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@shyuep @mkhorton It's a breaking change but was wondering if we could swap the order of kwargs `fmt` and `filename` in `Structure.to()`.
https://github.com/materialsproject/pymatgen/blob/25768faa7aa0a34ee4357a92bc92ae41ef21bc1d/pymatgen/core/structure.py#L2421-L2427
The annoying thing about having `fmt` first is that the most common use case (imo writing to file) of `to()` raises an error:
```py
from pymatgen.core import Lattice, Structure
structure = Structure(
lattice=Lattice.cubic(5),
species=("Fe", "O"),
coords=((0, 0, 0), (0.5, 0.5, 0.5)),
)
struct.to("struct.json")
>>> ValueError: Invalid format: `struct.json`
```
I did a quick look through the code base and didn't find any cases where `fmt` was passed as positional arg so don't think this would break much.
```py
struct.to("json") # this would break
struct.to(fmt="json") # this still works
```
|
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PR_kwDOACgets5B72wE
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Add `python-version` 3.11 to GH action matrix strategy
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[
"\n[](https://coveralls.io/builds/56199303)\n\nCoverage: 78.846%. Remained the same when pulling **046782479d7d0324450c1c4bfb1b144ba5f2173a on test-py311** into **dcbbe002cc46dba726b6a84bb0c7533ce9c2941b on master**.\n",
"From the py3.11 test logs here, the error comes from trying to build fdint. As far as I can tell, pymatgen itself works fine with python 3.11. Debian for instance has pymatgen 2022.11.7 built with python 3.11, see https://buildd.debian.org/status/package.php?p=pymatgen\r\n\r\nOne workaround could be setting up a test workflow in .github/workflows/test.yml which does not include the installation of optionals, to test basic py3.11 compatibility. cf. https://github.com/materialsproject/pymatgen/blob/046782479d7d0324450c1c4bfb1b144ba5f2173a/.github/workflows/test.yml#L67",
"@drew-parsons Yeah I've been using pymatgen on python 3.11 without problem for several months now. Like you said, `fdint` is the only remaining blocker. And it's only used in `pymatgen/electronic_structure/boltztrap.py`.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/13a860aab7cbf914c1aaedfa5b06a703211de202/pymatgen/electronic_structure/boltztrap.py#L2381\r\n\r\nI'd be happy to move it from `extras_require.optional` deps to a new `extras_require.electronic_structure` block which would allow us to make a py3.11 compatible release. Any objections or alternate suggestions @shyuep?",
"@shyuep I received no reply on my issue from 3 weeks ago (https://github.com/scott-maddox/fdint/issues/22) asking if `fdint` is looking for maintainers. Which suggests the project is abandoned, meaning we should probably drop it from our deps altogether at some point."
] | 2022-11-01T03:50:24
| 2023-02-22T23:50:52
|
2023-02-22T23:50:51Z
|
MEMBER
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Closes #2710.
We don't actually need to merge into `master` as that would double CI budget consumption but should be run at least once to check `pymatgen` is Python 3.11 compatible.
|
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PR_kwDOACgets5B76u2
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Fix pydocstyle D202
|
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[
"\n[](https://coveralls.io/builds/53778991)\n\nCoverage remained the same at 0.0% when pulling **4e91df7b51cb5dd367cad89f6cb38603590a150d on pydocstyle-D202** into **c1f1e95d93a1fab758610aeb9a68d5711e1fce82 on master**.\n"
] | 2022-11-01T04:13:04
| 2022-11-01T04:32:16
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2022-11-01T04:30:55Z
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MEMBER
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Across all files.
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AttributeError: 'ChargeInsertionAnalyzer' object has no attribute 'get_local_extrema'
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[] | 2022-11-01T06:25:57
| 2022-11-02T10:02:41
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2022-11-02T10:02:41Z
|
NONE
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Dear Sir
I am using pymatgen v. 2022.9.21 on my Linux. I am working on an interstitial point defect. When I tried to use the 'ChargeInsertionAnalyzer' object from the pymatgen.analysis.defects.utils, pymatgen imports the object without any problem. However, when I used the 'ChargeInsertionAnalyzer' object to obtain the 'get_local_extrema' then it gives the attribute error as follows:
AttributeError: 'ChargeInsertionAnalyzer' object has no attribute 'get_local_extrema'
Can you please help to resolve this issue? Thank you very much.
Best regards
Arindam Sannyal
|
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PR_kwDOACgets5B-xb-
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Fix release workflow
|
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[
"Also fixes the readme CI status badge:\r\n\r\n\r\n\r\nNoticed that coverage was at 0% last night and 36% this morning. Not sure if that will auto-fix. We might want to transition to GH-only coverage tracking anyway and remove 3rd party [Coveralls](https://coveralls.io/github/materialsproject/pymatgen?branch=master).",
"\n[](https://coveralls.io/builds/53805430)\n\nCoverage remained the same at 0.0% when pulling **e14e8d9dee7caee1bbad026b2bd05b5acc923ce3 on fix-release-wf** into **5baba8d10d32525f5bff433f8e36a11137677fed on master**.\n"
] | 2022-11-01T16:11:51
| 2022-11-01T16:35:13
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2022-11-01T16:17:44Z
|
MEMBER
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The changes in c2124293 broke `.github/workflows/release.yml` causing
> Error: No file in /Users/runner/work/pymatgen/pymatgen matched to [**/requirements.txt], make sure you have checked out the target repository
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