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https://api.github.com/repos/materialsproject/pymatgen/issues/1801 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1801/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1801/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1801/events | https://github.com/materialsproject/pymatgen/issues/1801 | 580,692,526 | MDU6SXNzdWU1ODA2OTI1MjY= | 1,801 | SpaceGroup.from_int_number(hexagonal=False) ineffective | {
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"Thanks. Can you pls implement the fix and submit a PR? Pls include unittests catching the wrong behavior.",
"Do you have a preference on whether I add the fix via option 1 or option 2 that I show above? sg_symbol_from_int_number() is the lower-level function, so it might be better there. But it could also have t... | 2020-03-13T15:54:18 | 2020-03-16T21:15:13 | 2020-03-16T21:15:13Z | CONTRIBUTOR | {
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} | **Describe the bug**
When initiating a SpaceGroup class using the SpaceGroup.from_int_number(), the hexagonal option is ineffective for the following spacegroups: 146,148,155,160,161,166,167
NOTE: This is similar to issue #1203. The big difference is that here, it's claimed functionality that is ineffective. While ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1802 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1802/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1802/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1802/events | https://github.com/materialsproject/pymatgen/issues/1802 | 580,759,791 | MDU6SXNzdWU1ODA3NTk3OTE= | 1,802 | Structure.from_spacegroup() inaccurate for trigonal crystal systems | {
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"@blondegeek would you be willing to comment here, since this would re-open your #454 issue and possibly break some existing code/tests?",
"I might have had the conventional assignment of spacegroups backwards. This would make the original code correct...\r\nWhen looking at the AFlow library ([here](http://aflowl... | 2020-03-13T18:02:25 | 2020-03-16T17:10:35 | 2020-03-16T17:10:35Z | CONTRIBUTOR | {
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} | I apologize in advance for the long post, but I think this is a confusing topic. I wanted to give a full justification for the changes I'm suggesting!
**Summary:**
Structure.from_spacegroup() will inaccurately produce structures for the following spacegroups:
143, 144, 145, 147, 149, 150, 151, 152,153, 154, 156, 1... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1803 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1803/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1803/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1803/events | https://github.com/materialsproject/pymatgen/pull/1803 | 580,779,764 | MDExOlB1bGxSZXF1ZXN0Mzg3OTI1MzUz | 1,803 | Fixing up where #1799 (Fix Q-Chem API) left off | {
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"Thanks @espottesmith ",
"Test failures: TestQCOutput.test_structural_change",
"I see it. As usual, it's an OpenBabel problem."
] | 2020-03-13T18:46:14 | 2022-01-31T21:04:28 | 2020-03-13T20:25:03Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1804 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1804/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1804/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1804/events | https://github.com/materialsproject/pymatgen/pull/1804 | 581,361,275 | MDExOlB1bGxSZXF1ZXN0Mzg4NDMwMDAz | 1,804 | [WIP] CP2K Module | {
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"Hi @nwinner, this looks great.\r\n\r\nRegarding the Bader analysis, could you explore the idea of merging implementations -- I'd prefer not to have two separate classes each for Gaussian Cube / VASP Chgcar given that they're basically equivalent. This might also be good time to add `user_bader_settings` as an opti... | 2020-03-14T20:33:15 | 2020-03-17T23:13:09 | 2020-03-17T23:13:09Z | CONTRIBUTOR | {
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} | Work in progress for integration of CP2K in pymatgen. Currently in working condition, but outputs.py and sets.py need to be fleshed out with more features. Also some small changes to existing files have been made that could be useful for this integration.
**Features**
1. Creation of pymatgen.io.cp2k module with the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1805 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1805/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1805/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1805/events | https://github.com/materialsproject/pymatgen/pull/1805 | 582,411,989 | MDExOlB1bGxSZXF1ZXN0Mzg5MzM1NTEx | 1,805 | Hexagonal Sym Issues | {
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"I limited the merge request to only fix #1801, as I found a mistake in my post for #1802.",
"Thanks"
] | 2020-03-16T15:59:25 | 2020-03-16T21:14:22 | 2020-03-16T21:14:16Z | CONTRIBUTOR | {
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} | This merge request addresses issues #1801 and #1802. I decided to add the #1801 fix to the SpaceGroup.from_int_number() method, which is not the lowest function with the hexagonal=True input. The respective unittests for each fix were also added.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1806 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1806/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1806/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1806/events | https://github.com/materialsproject/pymatgen/pull/1806 | 582,667,619 | MDExOlB1bGxSZXF1ZXN0Mzg5NTUyOTIx | 1,806 | [WIP] Add xTB IO to pymatgen | {
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"@espottesmith do you have an update on this PR?",
"I unfortunately have not been able to work towards this recently. However, I know that @arepstein (Alex Epstein) has been working towards this goal, as well as potentially adding xTB/CREST workflows for atomate. I can check in with him about the status there. It... | 2020-03-17T00:05:50 | 2022-09-28T16:12:17 | 2020-12-01T17:07:48Z | CONTRIBUTOR | {
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} | ## Summary
This PR will eventually add support in pymatgen for parsing input and output files for Grimme's Extended Tight-Binding (xTB) code (DOI: 10.1021/acs.jctc.7b00118, DOI: 10.1021/acs.jctc.8b01176, DOI: 10.26434/chemrxiv.8326202.v1).
This is not at all finished or tested, and additional work will be needed ... | {
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"Thanks!"
] | 2020-03-17T08:18:04 | 2020-03-17T12:20:24 | 2020-03-17T12:01:54Z | CONTRIBUTOR | {
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} | ## Summary
* Reorder logic in BSPlotter, such that check for metal is only executed when needed.
* The current implementation causes trouble in my downstream usage of pymatgen, so I'd appreciate a merge. | {
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"Many thanks @Nokimann, this will need tests too.",
"Hi @Nokimann, I was wondering if you had any updates on this PR? I'm happy to merge this if it has a test added.",
"@mkhorton Can I request this PR in the newest version of pymatgen? \r\nFirst, I will close this PR section, and then request it again.\r\nI did... | 2020-03-18T12:56:47 | 2020-12-24T08:31:49 | 2020-12-24T08:24:02Z | NONE | {
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} | ## Summary
Three methods: `get_orbital_dos`, `get_element_orbital_dos`, `get_bundle_pdos` in `class CompleteDos` are added
`get_orbital_dos` gives projected DOS of s, px, py, pz, dxy, dyz, dz2, dxz, dx2, ...
`get_element_orbital_dos` gives projected DOS of s, px, py, pz, dxy, dyz, dz2, dxz, dx2, ... at a particu... | {
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"I think the tests are a bit too rudimentary. Diamond, NaCl and CsCl are hardly difficult structures. Can we include at least one more difficult structure?",
"I added LiFePO4 and tidied the tests a little.\r\n\r\nI didn't add the LiFePO4 test for MinimumVIRENN as it is very slow. ",
"> I didn't add the LiFePO4 ... | 2020-03-26T05:57:09 | 2020-03-27T02:25:46 | 2020-03-27T02:25:46Z | MEMBER | {
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} | ## Summary
The EconNN class was rewritten to properly reproduce the algorithm outlined in:
https://www.degruyter.com/view/j/zkri.1979.150.issue-1-4/zkri.1979.150.14.23/zkri.1979.150.14.23.xml
This improves the performance of the method, particularly when only considering bonding between sites of opposing charg... | {
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"Thanks @rwoodsrobinson, will merge once tests pass\r\n\r\n@dongsenfo be aware that the keyword args for `run_mcsqs` have changed here to merge `supercell` and `numatoms` options into a single `scaling` option (since both cannot be used simultaneously); I think the improvement is worthwhile to make the change, but ... | 2020-03-26T20:25:23 | 2020-03-27T02:25:58 | 2020-03-27T02:25:58Z | NONE | {
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} | ## Summary
* Improved tests
* Return objective function
* Simplified method signature
* Improved docs
* Fixed issue with `run_mcsqs` output
## TODO (if any)
* Further improvements in a future pull request (e.g. include MC temperature)
## Checklist
- [x] Code is in the [standard Python style](http... | {
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"This is not a bug. We have to define bonds for _periodic_ solids and this means each bond does not just have a `from_atom` and a `to_atom` but also a `to_image` which encodes which periodic image the bond is pointing towards.\r\n\r\nConsider an example of a simple cubic structure with a single atom whose single at... | 2020-03-26T22:59:39 | 2020-03-26T23:17:28 | 2020-03-26T23:16:12Z | CONTRIBUTOR | {
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} | **Describe the bug**
Not sure if this is a bug or something that's undocumented, but `StructureGraph.with_local_env_strategy(struct, CrystalNN())` produces a MultiDiGraph. This doesn't make much sense to me, since bonds do not inherently have directionality. This also inhibits intuitive use of the underlying `networkx... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1812 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1812/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1812/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1812/events | https://github.com/materialsproject/pymatgen/issues/1812 | 589,613,063 | MDU6SXNzdWU1ODk2MTMwNjM= | 1,812 | Unexpected structure.get_sorted_structure in structure to lammps data | {
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"Similar issues are with \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/561b4cfed1f74ede87074fae3903885b9d5c7868/pymatgen/io/lammps/data.py#L806-L807\r\n\r\nHere the structures are rotated without the end users knowing.. This causes unexpected mismatch between force vectors calculated with lammps and the... | 2020-03-28T16:42:43 | 2020-03-30T13:47:23 | 2020-03-30T13:47:23Z | CONTRIBUTOR | {
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} | https://github.com/materialsproject/pymatgen/blob/47c8223dfe2ef4af6ebc273c950a72ccf038c5c6/pymatgen/io/lammps/data.py#L805
I found this behavior unexpected for some applications.
If I want to calculate the site descriptors for a given site index in a structure using lammps, I can get wrong results since this lin... | {
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} | On a new machine (a Macintosh in this case), following the instructions from the pymatgen homepage (using omg config -p <expanded> <pymatgen_potcar> results in a setup that does leads to errors in POTCAR file generation.
**To Reproduce**
I have encountered some problems with the use of pymatgen and the generation o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1814 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1814/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1814/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1814/events | https://github.com/materialsproject/pymatgen/pull/1814 | 589,837,352 | MDExOlB1bGxSZXF1ZXN0Mzk1Mjg0OTc3 | 1,814 | Lammpsdata fix | {
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"Pls add a test to ensure this does not occur again. I would also add a new kwarg to allow people to sort if they want.",
"@shyuep Sure. ",
"Thanks."
] | 2020-03-29T17:07:50 | 2020-03-30T13:47:24 | 2020-03-30T13:47:24Z | CONTRIBUTOR | {
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} | ## Summary
This PR fixes #1812
Previously Structure is reordered before writing to lammps data file. This could result in unexpected site index mismatch between structure and the final outcome from lammps. | {
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"Let me check that.\r\nI have a couple of edits done but not pushed yet.\r\nThank for reporting. Do not hesitate if you find something else.",
"It is great to hear that. Looking forward to your edits. Thanks.",
"I pushed a new version. \r\nPlease have a look.\r\nAny suggestion is welcome.\r\n"
] | 2020-03-30T08:46:35 | 2023-08-13T16:33:40 | 2023-08-13T16:33:40Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1816 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1816/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1816/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1816/events | https://github.com/materialsproject/pymatgen/issues/1816 | 590,708,848 | MDU6SXNzdWU1OTA3MDg4NDg= | 1,816 | import error in pymatgen | {
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"Hi @srajpand87, I don't think this is a pymatgen issue -- it's likely you're trying to use an old script.",
"Thanks for the reply.\r\nActually i was trying whole day to sort out the issue but I couldn’t.\r\nI am afraid to say do you mean old script is the pymatgen from the above link and I need to use the latest... | 2020-03-31T01:13:40 | 2020-04-01T22:27:23 | 2020-04-01T19:43:55Z | NONE | {
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} | Hi,
I installed pymatgen from github (https://github.com/materialsproject/pymatgen.git) .
When i was trying to run some python file name GaAs.py i got an error which is as follows
File "/global/homes/s/srajpand/.conda/envs/myenv/lib/python3.8/site-packages/OPTpy-4.2.2-py3.8.egg/OPTpy/utils/response.py", line 2... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1817 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1817/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1817/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1817/events | https://github.com/materialsproject/pymatgen/pull/1817 | 592,168,100 | MDExOlB1bGxSZXF1ZXN0Mzk3MjAyNTkw | 1,817 | Tem Calculator | {
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"Thanks for the quick turnaround on this :-)\r\n\r\nBefore merging, have you also tested a few random structures with random directions? I'm wondering what the test coverage is like here -- I only tested myself along some high symmetry directions with some common structures.",
"> Thanks for the quick turnaround o... | 2020-04-01T19:58:39 | 2020-04-02T18:52:48 | 2020-04-02T18:52:48Z | CONTRIBUTOR | {
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} | Include a summary of major changes in bullet points:
Edits made to Frank Wan's previous TEM calculator, a project under Shyam's direction:
- Changed method get_interplanar_spacing to call lattice.d_hkl rather than separately calculating for different crystal systems.
- Vectorized method generate_points to be using... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1818 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1818/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1818/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1818/events | https://github.com/materialsproject/pymatgen/pull/1818 | 592,171,052 | MDExOlB1bGxSZXF1ZXN0Mzk3MjA1MDAz | 1,818 | Optimize CubicSupercellTransformation for diagonal transformations | {
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"Thanks @utf.\r\n\r\nOut of interest, is there an easy way to modify Cubic to give you a square slab instead? e.g. square in x, y but a small z -- this would be useful for some folks doing (S)TEM image simulation, square slabs are useful as multi slice inputs",
"I think that should be possible. I wonder if @rees-... | 2020-04-01T20:04:17 | 2020-04-21T04:26:54 | 2020-04-15T19:31:57Z | MEMBER | {
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} | ## Summary
`CubicSupercellTransformation` had some unnecessary complexity for diagonal only transformations. This PR implements a more optimised method. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1819 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1819/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1819/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1819/events | https://github.com/materialsproject/pymatgen/pull/1819 | 592,173,942 | MDExOlB1bGxSZXF1ZXN0Mzk3MjA3NDAx | 1,819 | Fix BrunnerNN methods | {
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"Thanks @utf!"
] | 2020-04-01T20:09:54 | 2020-04-02T18:52:05 | 2020-04-02T18:51:55Z | MEMBER | {
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} | ## Summary
Two of the BrunnerNN methods were implemented incorrectly leading to poor performance. This PR fixes their implementation to be in line with: https://scripts.iucr.org/cgi-bin/paper?S0567739477000461 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1820 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1820/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1820/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1820/events | https://github.com/materialsproject/pymatgen/pull/1820 | 593,064,148 | MDExOlB1bGxSZXF1ZXN0Mzk3OTI2MDAz | 1,820 | VolumetricData speedup | {
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"This is great, thanks @mturiansky! Optimizations always very welcome :-)\r\n\r\nNow there's the question of why large arrays of floats are stored in ascii to start with ... perhaps time to kindly ask the VASP devs for a native hdf5 output.",
"> Now there's the question of why large arrays of floats are stored in... | 2020-04-03T04:16:13 | 2020-04-03T23:17:36 | 2020-04-03T05:23:53Z | CONTRIBUTOR | {
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} | ## Summary
Got frustrated while reading a 1.5 GB file, so I tried to speed it up. Changed a couple lines in VolumetricData.parse_file, and here's what I got on my computer:
* test_files/CHGCAR.Fe3O4: 655 ms -> 368 ms (1.78x speedup)
* test_files/CHGCAR.NiO_SOC.gz: 779 ms -> 495 ms (1.57x)
* test_files/LOCPOT: 2... | {
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"The likelihood is that the Materials PRoject is down. You will need to contact the Materials Project people.",
"Yes, an error like that is usually a connection issue, not a pymatgen issue.\r\n\r\nWe haven't registered any connection issues with Materials Project since March 6th (35 minutes), though I would not b... | 2020-04-03T06:32:10 | 2020-04-03T20:05:45 | 2020-04-03T13:02:21Z | NONE | {
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MPRestError: ('Connection aborted.', OSError("(10051, 'WSAENETUNREACH')")) | {
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"It seems there is an error because of a whitespace after an open `[` .\r\nLet me know if you want me to fix this.",
"Yes pls. All linting has to pass as well as the tests.",
"Many thanks."
] | 2020-04-08T15:24:12 | 2020-04-08T21:33:55 | 2020-04-08T21:33:50Z | CONTRIBUTOR | {
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} | ## Summary
Improve parsing of structures if multiple optimization, for example in the case of relaxed scan.
* In case of scan the attribute `opt_structures` store optimized structure contrary to the old `structures` attribute who store all structures
* Fix a bug in read_scan() function linked to a change betwee... | {
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"@JosephMontoya-TRI do you see any problem with just setting `compatible_only=True` as a temporary fix?",
"@JosephMontoya-TRI as part of the longer-term solution, we are thinking of moving the `AqueousCompatibility` scheme to a standalone `Compatibility` class that doesn't require an underlying `Correction` class... | 2020-04-09T23:17:48 | 2020-05-05T22:45:43 | 2020-05-05T22:45:43Z | CONTRIBUTOR | {
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} | **Describe the bug**
@JosephMontoya-TRI and I recently discovered a bug in the `AqueousCorrection` class (used by `MaterialsProjectAqueousCompatibility` and `MITProjectAqueousCompatibility`) that causes unexpected behavior when correcting the energy of aqueous H2. As a result, the hydrogen energy may vary depending on... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1824 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1824/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1824/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1824/events | https://github.com/materialsproject/pymatgen/issues/1824 | 598,370,384 | MDU6SXNzdWU1OTgzNzAzODQ= | 1,824 | Pip installation error help! | {
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"Hi @LaboratoryofDexter, the error is this:\r\n\r\n```\r\n error: Microsoft Visual C++ 14.0 is required. Get it with \"Build Tools for Visual Studio\": https://visualstudio.microsoft.com/downloads/\r\n```\r\n\r\nMany Python codes (including pymatgen) have C extensions as an optimization to make certain code perf... | 2020-04-11T23:15:21 | 2020-04-22T21:22:44 | 2020-04-11T23:39:34Z | NONE | {
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} | **Describe the bug**
I just installed the Python 3.7.7 version and when I used "pip install pymatgen" to install pymatgen, but the terminal gave out error information as:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Collecting pymatgen
Using cached pymatgen-2020.4.2.tar.gz (2.7 MB)
Requirement already satisfied: numpy>=1.1... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1825 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1825/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1825/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1825/events | https://github.com/materialsproject/pymatgen/issues/1825 | 598,489,554 | MDU6SXNzdWU1OTg0ODk1NTQ= | 1,825 | VoronoiNN._extract_nn_info() ValueError when calculating max_weight | {
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"Hi @CompRhys , `VoronoiNN` takes a `cutoff` parameter as an optimization, but it does need to be increased with some structures. Try `VoronoiNN(cutoff=15)` and you should find it works.\r\n\r\nI'm not ruling out an underlying improvement that could be made here, if you're inclined you could take a look at the beha... | 2020-04-12T13:51:47 | 2023-08-13T16:33:41 | 2023-08-13T16:33:41Z | CONTRIBUTOR | {
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} | **Describe the bug**
Trying to generate a Structure Graph from the Voronoi Neighbours gives `ValueError: max() arg is an empty sequence` for some structures when trying to calculate max_weight in `VoronoiNN._extract_nn_info()` .
**To Reproduce**
Minimal Code:
```
from pymatgen.core.structure import Structure
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1826 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1826/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1826/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1826/events | https://github.com/materialsproject/pymatgen/pull/1826 | 599,245,055 | MDExOlB1bGxSZXF1ZXN0NDAyOTI5NDE3 | 1,826 | Abstract Compatibility interface + self-contained Aqueous Compatibility class | {
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"Hi @rkingsbury, can you talk a little bit about the logic here?\r\n\r\nThe current Compatability (now named MITMPCompatibility in this PR) class is almost an abstract base class itself, it just takes a list of `corrections` to apply, e.g. its `process_entry`, `get_explanation_dict` etc. methods are pretty general.... | 2020-04-14T02:08:50 | 2020-07-27T16:58:52 | 2020-05-05T22:45:44Z | CONTRIBUTOR | {
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} | ## Abstract `Compatibility` interface
This pull request refactors `Compatibility` to define a common interface for pymatgen energy correction and referencing schemes. The goal of doing this is to enable more flexible correction schemes that do not necessarily require a list of `Correction` classes, and also to incre... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1827 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1827/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1827/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1827/events | https://github.com/materialsproject/pymatgen/pull/1827 | 599,401,787 | MDExOlB1bGxSZXF1ZXN0NDAzMDUyMDc4 | 1,827 | [WIP] Edge Case of VoronoiNN() not finding neighbours when called by StructureGraph.with_local_env_strategy() | {
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"### Fails\r\n```\r\nStructureGraph.with_local_env_strategy(crystal, local_env.VoronoiNN(cutoff=8.0778))\r\nprint(\"baz - finds all polyhedra from StructureGraph\")\r\n```\r\n\r\n### \"Works\"\r\n```\r\nStructureGraph.with_local_env_strategy(crystal, local_env.VoronoiNN(cutoff=8.0777))\r\nprint(\"baz - finds all po... | 2020-04-14T08:47:48 | 2020-04-15T17:15:55 | 2020-04-15T16:35:36Z | CONTRIBUTOR | {
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} | ## Summary
This PR is related to #1825 and aims to track down the source of the bug.
## Minimal Test for Edge Case
### Code
```
from pymatgen.core.structure import Structure
from pymatgen.analysis import local_env
from pymatgen.analysis.graphs import StructureGraph
with open("breaking-oqmd-4866.txt", 'r') a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1828 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1828/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1828/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1828/events | https://github.com/materialsproject/pymatgen/pull/1828 | 600,535,545 | MDExOlB1bGxSZXF1ZXN0NDAzOTQ2NTQ0 | 1,828 | Units k cal | {
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"Thanks @mamachra, could you add a test to https://github.com/materialsproject/pymatgen/blob/master/pymatgen/core/tests/test_units.py?",
"Thanks!"
] | 2020-04-15T19:28:11 | 2020-04-27T20:42:01 | 2020-04-21T21:09:13Z | NONE | {
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} | ## Summary
kCal units added to units.py
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https://api.github.com/repos/materialsproject/pymatgen/issues/1829 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1829/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1829/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1829/events | https://github.com/materialsproject/pymatgen/issues/1829 | 601,164,797 | MDU6SXNzdWU2MDExNjQ3OTc= | 1,829 | ComputedEntry repr / as_dict display uncorrected energy | {
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"@ayushsgupta can you investigate?",
"@mkhorton @shyamd intended behavior would be to show the corrected energy under the 'Energy' key at least in the `repr`, right?",
"I suppose it makes sense to have uncorrected energy in `as_dict`, because that's what one would use to initialize a new entry with `from_dict`,... | 2020-04-16T15:27:24 | 2020-04-30T14:19:33 | 2020-04-30T14:19:33Z | CONTRIBUTOR | {
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} | **Describe the bug**
The `repr` and `as_dict` methods of `ComputedEntry` display the `uncorrected_energy` attribute under the `energy` key instead of the `energy` attribute (uncorrected energy plus corrections). Energies are still calculated correctly when reconstructing entries using `as_dict()` / `from_dict`, so thi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1830 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1830/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1830/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1830/events | https://github.com/materialsproject/pymatgen/issues/1830 | 602,161,216 | MDU6SXNzdWU2MDIxNjEyMTY= | 1,830 | Cif Parser improvement | {
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"I added an error message to detail unparseable structures. In this case, 18th structure in the file was problematic because there were essentially no atoms defined. You can check that for yourself by opening the CIF file and eyeballing it. \r\n\r\nPymatgen's CIF parser is reasonably robust against a lot of errors.... | 2020-04-17T18:37:01 | 2020-04-18T13:35:51 | 2020-04-17T22:47:17Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
I'm working with text files that contain multiple cif files (always 20) and would like to parse them with the Cif Parser, see example file. [1.txt](https://github.com/materialsproject/pymatgen/files/4494649/1.txt)
However, reading them into a dict or ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1831 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1831/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1831/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1831/events | https://github.com/materialsproject/pymatgen/pull/1831 | 602,250,546 | MDExOlB1bGxSZXF1ZXN0NDA1MzU0NjQ1 | 1,831 | SpacegroupOperations Description Fix | {
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"Thanks,"
] | 2020-04-17T21:45:00 | 2020-04-17T22:36:57 | 2020-04-17T22:36:56Z | CONTRIBUTOR | {
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} | ## Summary
* Fixed description for SpacegroupOperations.are_symmetrically_equivalent(). Input set of sites requires a list of PeriodicSite objects (not a Site objects).
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* n/a
## Checklist
Work-in-progress pull requests are enco... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1832 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1832/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1832/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1832/events | https://github.com/materialsproject/pymatgen/pull/1832 | 603,562,415 | MDExOlB1bGxSZXF1ZXN0NDA2MzI0NDcy | 1,832 | Get neighbors save memory | {
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"Thanks @chc273 !"
] | 2020-04-20T21:58:27 | 2020-04-20T22:50:28 | 2020-04-20T22:50:21Z | CONTRIBUTOR | {
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} | ## Summary
This is a minor change to the previous `optimization.neighbors.find_points_in_sphere` cython method to save memory.
The critical step for finding neighbors is the generation of candidate atoms that are potentially within the cutoff radius of some atoms. This is achieved by repeating the unit cell in 3... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1833 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1833/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1833/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1833/events | https://github.com/materialsproject/pymatgen/issues/1833 | 603,813,833 | MDU6SXNzdWU2MDM4MTM4MzM= | 1,833 | nullability-completeness related pymatgen build errors on Mac OS X | {
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"Please use conda to install pymatgen. ",
"Hi @paulfons, I can't reproduce -- I'm also on latest macOS (10.15.4) and Xcode (11.4), however I'll keep an eye on this.\r\n\r\n@shyuep is correct that the conda install is more reliable, since there are many more pre-built binary wheels available across platforms."
] | 2020-04-21T08:34:19 | 2020-04-21T16:56:06 | 2020-04-21T08:50:23Z | NONE | {
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} | **Describe the bug**
pymatgen update fails on OS X 10.15.4 and more importantly Xcode version 11.4.1 (11E503a)
**To Reproduce**
Steps to reproduce the behavior:
pip3 install --upgrade pymatgen
The full output is listed below:
[error.txt](https://github.com/materialsproject/pymatgen/files/4508677/error.txt)
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1834 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1834/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1834/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1834/events | https://github.com/materialsproject/pymatgen/pull/1834 | 604,215,810 | MDExOlB1bGxSZXF1ZXN0NDA2ODUxMjQ3 | 1,834 | KPathLM labels bug fix | {
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"Thanks @munrojm. Is there an existing KPath labels test this case could be added to?",
"> Thanks @munrojm. Is there an existing KPath labels test this case could be added to?\r\n\r\nGood point! I will make one and update the existing test. ",
"Should be fixed now if you merge latest changes from master. Seems ... | 2020-04-21T19:06:48 | 2020-04-28T00:52:07 | 2020-04-28T00:52:07Z | MEMBER | {
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} | ## Summary
This PR fixes a small bug in the `KPathLM` class where the code would hang when assigning labels to each of the points in a k-path for some complex cases. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1835 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1835/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1835/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1835/events | https://github.com/materialsproject/pymatgen/pull/1835 | 605,205,656 | MDExOlB1bGxSZXF1ZXN0NDA3NjUzNjY5 | 1,835 | Sqs caller, io, and transformation changes | {
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"Thanks @rwoodsrobinson, this looks great. Will merge once tests pass.",
"Thanks!"
] | 2020-04-23T03:11:10 | 2020-04-24T03:25:57 | 2020-04-24T03:25:50Z | NONE | {
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} | ## Summary
* Added parallel functionality and directory
* Added Monte Carlo kwargs
* Added new test files for mcsqs_caller, SQSTransformation and atat.io
* Added cluster generation based on structure
* Added file parsing to SQSTransformation
* Added sqs 'Perfect match' handling capabilities
* Updated docstring... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1836 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1836/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1836/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1836/events | https://github.com/materialsproject/pymatgen/pull/1836 | 606,809,801 | MDExOlB1bGxSZXF1ZXN0NDA4OTM3MDU3 | 1,836 | patch to allow scientific notation dielectric function, with possibil… | {
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"Can we have a unitest of this. No need for a full OUTCAR. Just testing the regex alone would be sufficient.",
"The regex is within the ```read_freq_dielectric()``` function in the OUTCAR class - which means I can't run the regex without first parsing an entire OUTCAR. As far as I can tell, my options are:\r\n\r\... | 2020-04-25T16:48:22 | 2020-04-28T18:20:08 | 2020-04-28T18:20:05Z | MEMBER | {
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} | ## Summary
Some versions of VASP (notably, run with MedeA) have a different format to dielectric function tensor output in the OUTCAR file. Notably, the format:
- uses scientific notation
- may not have any spaces or delimiter character in between adjacent values on a line
For example, the OUTCAR may contain ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1837 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1837/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1837/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1837/events | https://github.com/materialsproject/pymatgen/pull/1837 | 606,900,960 | MDExOlB1bGxSZXF1ZXN0NDA5MDAzNjUy | 1,837 | Add site_weighted_spectrum for XAS | {
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} | ## Summary
Enable generation of site-weighted XAS object based on site multiplicity for each absorbing index and its corresponding site-wise spectrum.
* Add `site_weighted_spectrum` for generation of site-weighted spectrum from site-wise spectra
* Add tests | {
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"Just upgrade to Py37 and it will be fine. ",
"Please have a look at the link as well (https://circleci.com/gh/hackingmaterials/atomate/2517?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link): the failing atomate tests are in a python 3.7 environment and it the error is clearly co... | 2020-04-28T13:16:31 | 2020-04-28T16:07:26 | 2020-04-28T14:41:19Z | MEMBER | {
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Hi,
we are currently working on including a workflow in atomate. Unfortunately, some of the tests fail with the current development version of pymatgen: https://circleci.com/gh/hackingmaterials/atomate/2517?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link
It looks like... | {
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"In the call to get_structures, set primitive=False. When primitive is True (the default), the code performs a search for primitive lattice vectors and that can change the setting.",
"Oh, I wasn't aware of that tag. Thank you for the quick solution @shyuep !",
"Have verified this seems to be a bug in CifParser,... | 2020-04-30T01:17:52 | 2020-06-30T17:11:05 | 2020-06-30T17:11:04Z | NONE | {
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} | Recently came across a strange bug when parsing a primitive cell (cif downloaded from MP). Parsing the cif with CifParser and then immediately exporting it again as a new cif (without any other operations in between) completely changed/distorted the unit cell and atomic positions.
```Python
from pymatgen.io.cif impor... | {
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"There is an XRDCalculator in pymatgen.analysis.diffraction.xrd.\r\nIn future, please use https://discuss.matsci.org/ for queries on usage. Github Issues is meant for reporting bugs and requesting new features."
] | 2020-04-30T07:30:11 | 2020-04-30T14:19:16 | 2020-04-30T14:19:16Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1841 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1841/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1841/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1841/events | https://github.com/materialsproject/pymatgen/issues/1841 | 611,257,238 | MDU6SXNzdWU2MTEyNTcyMzg= | 1,841 | Comment in KPOINTS generator | {
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"Hi Andrew; agreed, I think this could be better phrased. A pull request is welcome if you'd like to change it!\r\n\r\nAs a general comment, a lot of the default MP sets are kept as they are for historical, backwards compatibility reasons, including how we determine k-points. For our newer sets (e.g. SCAN) we're lo... | 2020-05-02T19:24:07 | 2020-05-09T15:22:08 | 2020-05-09T15:22:08Z | MEMBER | {
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} | **Describe the bug**
When using [`pymatgen.io.inputs.vasp.Kpoints.automatic_density()`](https://github.com/materialsproject/pymatgen/blob/v2020.4.29/pymatgen/io/vasp/inputs.py#L1237) (and likely related functions), the [comment line](https://github.com/materialsproject/pymatgen/blob/v2020.4.29/pymatgen/io/vasp/inputs.... | {
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"Thanks!"
] | 2020-05-02T22:25:41 | 2020-05-04T23:56:54 | 2020-05-04T23:56:54Z | MEMBER | {
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} | Change k-points / atom to k-points / number of atoms
## Summary
As mentioned in https://github.com/materialsproject/pymatgen/issues/1841, the comment line in the Pymatgen-generated VASP KPOINTS file is somewhat misleading. This PR changes it from being # kpoints/atom to # kpoints/number of atoms in the comment line... | {
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"Hi @JabinHao, there are many textbook references available on Ewald summation. The specific one linked from our documentation was:\r\n\r\n*Ewald summation techniques in perspective: a survey* by Abdulnour Y. Toukmaji and John A. Board Jr., doi: 10.1016/0010-4655(96)00016-1\r\n\r\nA pdf seems to be available here: ... | 2020-05-03T11:34:34 | 2020-05-03T19:24:40 | 2020-05-03T19:24:40Z | NONE | {
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```python
pymatgen.analysis.ewald module
class EwaldSummation(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)
Bases: object
Calculates t... | {
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I meet the following problem when installing the git master pymatgen: it freezes for ever during the installation progress. Then I use ` pip install -v ` to locate the problem and find that this is caused by spglib package. Simply to say, spglib needs numpy. If the numpy doesn't exist in the virtualenv where ... | {
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"Thanks for the report @roterojama. Can you paste in the two separate error messages you see?",
"@mkhorton I reinstalled the newest version of pymatgen to reproduce the error messages and just couldn't. In other words. Everything seems to be working fine. Im very sorry about this. I can't explain what changed. Th... | 2020-05-08T14:43:35 | 2020-05-11T16:57:31 | 2020-05-11T16:57:31Z | NONE | {
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} | **Describe the bug**
When using the newest version of pymatgen (v2020.4.29) the InterfacialReactivity() function produces an error. Two seperate errors can be generated depeding on whether the argument "include_no_mixing_energy=" is set to True or False. However this was not the case before the newest version of pymat... | {
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} | Hi,
Ubuntun 19.10 + git master version pymatgen and ipython. Fail to run some simple tests.
See [here](https://github.com/ipython/ipython/issues/12300) for more info.
Regards | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1847 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1847/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1847/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1847/events | https://github.com/materialsproject/pymatgen/pull/1847 | 616,474,192 | MDExOlB1bGxSZXF1ZXN0NDE2NTc3ODI2 | 1,847 | File update | {
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"I don't understand the difference between this and Element.Si.electronic_structure?",
"It looks like `Element.Si.electronic_structure` contains HTML tags, so is not as versatile?",
"Yes @mkhorton @shyuep, this was the only reason I created this function.\r\nAs for 'Fe'; _Element.Si.electronic_structure_ outpu... | 2020-05-12T08:43:37 | 2020-05-13T12:16:34 | 2020-05-13T12:14:49Z | NONE | {
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} | ### Summary
Depending on the element, the electronic configuration may be very long. Because of this, scientists have developed a shorthand notation that involves using a noble gas to represent electrons that are not valence electrons. This function does the same, it simplifies the electronic configuration for better... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1848 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1848/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1848/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1848/events | https://github.com/materialsproject/pymatgen/issues/1848 | 620,503,154 | MDU6SXNzdWU2MjA1MDMxNTQ= | 1,848 | Can't instantiate numpy array of Composition objects | {
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"I don't think a numpy array is a good container for a Composition object. The Composition object is in fact a dict-like object, which is iterable.\r\nYou can use lists if you wish, or pandas DataFrames, which are supposed to work with heterogenous objects works too. In general, numpy arrays are for numeric types.... | 2020-05-18T21:00:35 | 2020-05-18T21:07:15 | 2020-05-18T21:07:15Z | CONTRIBUTOR | {
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} | I'm on pymatgen version 2020.1.28 in JupyterLab, and I'm trying to instantiate a numpy array of Composition objects.
`import numpy as np
np.array([pymatgen.core.Composition('Ru')])` and several variants thereof result in an error
`TypeError: Invalid key 0, <class 'int'> for Composition
ValueError exception:
N... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1849 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1849/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1849/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1849/events | https://github.com/materialsproject/pymatgen/issues/1849 | 622,141,356 | MDU6SXNzdWU2MjIxNDEzNTY= | 1,849 | Negative electrostatic energy for charged cells | {
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"I don't think that is correct. A charged cell has a background charge of the opposite charge. That results in a negative electrostatic energy.",
"Ah, I see now. It is the energy of the structure + the compensating background. Thanks for the clarification @shyuep. \r\n\r\nI think the docstrings could be made more... | 2020-05-20T23:15:10 | 2020-05-28T15:59:43 | 2020-05-28T15:59:43Z | CONTRIBUTOR | {
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} | **Describe the bug**
I'm getting nonphysical negative values for the electrostatic energy of charged cells using `EwaldSummation`.
Seems the `_charged_cell_energy` needs to be adjusted by a minus sign?
https://github.com/materialsproject/pymatgen/blob/72d336d2d17ac140058fdcb74eb3336125bb12b7/pymatgen/analysis/ew... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1850 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1850/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1850/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1850/events | https://github.com/materialsproject/pymatgen/pull/1850 | 623,705,113 | MDExOlB1bGxSZXF1ZXN0NDIyMzAzMTg1 | 1,850 | Minor fix to as_dict and from_dict in StructureMatcher | {
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"Thanks."
] | 2020-05-23T17:28:15 | 2020-05-25T15:07:43 | 2020-05-25T15:07:43Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Saves missing attributes in `StructureMatcher.as_dict` so that `StuctureMatcher.from_dict` can faithfully recreate the original object.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request titl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1851 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1851/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1851/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1851/events | https://github.com/materialsproject/pymatgen/issues/1851 | 624,439,154 | MDU6SXNzdWU2MjQ0MzkxNTQ= | 1,851 | any function to get site-specific xas from MP? | {
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"Hi @davidcn21, we're currently developing a new API, and intend to add a site-specific API route for this. I'll update this thread when we have a public beta available. If you send us your email address, we may be able to share private access earlier if this is important to your research. My email is mkhorton@lbl.... | 2020-05-25T18:42:30 | 2023-08-13T16:33:41 | 2023-08-13T16:33:41Z | NONE | {
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} | I've been using "get_xas_data" to read the site-average XAS for a given adsorption element. Just curious if there is a function to read the site-specific XAS data? thanks! | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1852 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1852/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1852/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1852/events | https://github.com/materialsproject/pymatgen/issues/1852 | 624,523,719 | MDU6SXNzdWU2MjQ1MjM3MTk= | 1,852 | Option of plotter class to remove the grid lines on the background. | {
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"No there is no option. You can just adjust the grid yourself using the code given by @gVallverdu . In general, there are an infinite variety of customizations for plots. There is no way we can support all of them. ",
"Hi\r\nIn case somebody look for an answer, hereafter is the way to remove the grid. You need fi... | 2020-05-25T23:49:26 | 2020-05-26T08:39:35 | 2020-05-26T02:40:07Z | CONTRIBUTOR | {
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The pymatgen plotter class uses grid lines on the background in default. I try to remove the grid lines, say, for the example below:
from matplotlib import pyplot as plt
from pymatgen.electronic_structure.plotter import BSDOSPlotter
from pymatgen.ext.matproj import MPRester
```
a = MPRester()
bs = a.ge... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1853 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1853/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1853/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1853/events | https://github.com/materialsproject/pymatgen/issues/1853 | 625,013,493 | MDU6SXNzdWU2MjUwMTM0OTM= | 1,853 | module 'pymatgen' has no attribute 'DeformedStructureSet' | {
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"Hi Gus, welcome :-)\r\n\r\n`DeformedStructureSet` lives in `pymatgen.analysis.elasticity.strain' [here](https://pymatgen.org/pymatgen.analysis.elasticity.strain.html#pymatgen.analysis.elasticity.strain.DeformedStructureSet).\r\n\r\nRather than needing to include a long method call, it's usually easier to import ex... | 2020-05-26T16:23:51 | 2020-05-26T16:45:53 | 2020-05-26T16:45:04Z | NONE | {
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When I call the `DeformedStructureSet` function, I get the message shown in the title
```
hcp = mg.Lattice.hexagonal(3.23,5.14)
str = mg.Structure(hcp,["Zr","Zr"],[[0,0,0],[1/3,1/3,1/2]])
dfm = mg.DeformedStructureSet(... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1854 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1854/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1854/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1854/events | https://github.com/materialsproject/pymatgen/pull/1854 | 625,079,715 | MDExOlB1bGxSZXF1ZXN0NDIzMzY2NTcx | 1,854 | [WIP] Adding interpolation functionality to VolumetricData class | {
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"Hi @ayushsgupta , thanks for this, this looks useful.\r\n\r\nDo you think you could add a method to take a slice of a plane, returning a 2D numpy array? This could make use of the functionality in `Lattice` to provide a plane as a `(h, k, l)` tuple. If this feature would not be useful for your work however, please... | 2020-05-26T18:03:37 | 2020-06-22T22:01:46 | 2020-06-21T23:39:59Z | CONTRIBUTOR | {
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} | ## Summary
* Adds the ability to interpolate between discrete data points
* Adds the `val_at` method, which accepts three coordinates and returns the data value at the associated point (possibly interpolated)
* Adds the `linear_slice` method, which gives a linear slice of the volumetric data between two specified po... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1855 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1855/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1855/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1855/events | https://github.com/materialsproject/pymatgen/issues/1855 | 625,855,446 | MDU6SXNzdWU2MjU4NTU0NDY= | 1,855 | symmetry_reduce: AttributeError: 'Structure' object has no attribute 'transform' | {
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"The symmetry_reduce method is meant to operate on symmetry operations rather than a list of structures.\r\n\r\nFor the purposes of this method, you can simply initialize the DeformedStructureSet with the kwarg symmtry=True. E.g.,\r\n\r\n```\r\ndfm = DeformedStructureSet(structure, symmetry=True)\r\n```\r\n\r\nThis... | 2020-05-27T16:43:56 | 2020-05-27T18:00:22 | 2020-05-27T16:50:48Z | NONE | {
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} | This is probably my misuse of pymatgen or my weak python skills but...
I created an hcp structure:
```
>>> hcpZr
Structure Summary
Lattice
abc : 3.23 3.2300000000000004 5.14
angles : 90.0 90.0 119.99999999999999
volume : 46.440704076633324
A : 3.23 0.0 1.9778045806229754e-16
B : -1.6149999... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1856 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1856/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1856/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1856/events | https://github.com/materialsproject/pymatgen/issues/1856 | 626,749,243 | MDU6SXNzdWU2MjY3NDkyNDM= | 1,856 | Illegal Instruction on neighbors.cpython-38-x86_64-linux-gnu.so for pymatgen==2020.4.29 | {
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"Hi @hibagus, thanks for the report -- we'll need more information to be able to fix this though, specifically a small/reproducible example of a specific call to the neighbor finding code. The CGCNN repo is not maintained by us, so we can't track down how exactly it's using pymatgen.\r\n\r\n@chc273 wrote many of th... | 2020-05-28T19:17:51 | 2020-05-28T19:47:39 | 2020-05-28T19:47:39Z | NONE | {
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} | We encounter illegal instruction when we are running the regression sample of [https://github.com/txie-93/cgcnn](url) that uses pymatgen.
We use the latest pymatgen version (2020.4.29).
Our gdb output is as follows.
```
(gdb) run main.py --train-ratio 0.6 --val-ratio 0.2 --test-ratio 0.2 data/sample-regre... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1857 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1857/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1857/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1857/events | https://github.com/materialsproject/pymatgen/pull/1857 | 627,273,293 | MDExOlB1bGxSZXF1ZXN0NDI1MTA3MTI4 | 1,857 | Fix labels in plot_thermodynamic_properties | {
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"Thanks for noticing and submitting the fix @ab5424!"
] | 2020-05-29T13:35:06 | 2020-05-29T18:08:34 | 2020-05-29T18:08:19Z | CONTRIBUTOR | {
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} | The labels seem to be incorrect (see https://github.com/materialsproject/pymatgen/blob/72d336d2d17ac140058fdcb74eb3336125bb12b7/pymatgen/phonon/dos.py#L229-L236 and https://github.com/materialsproject/pymatgen/blob/72d336d2d17ac140058fdcb74eb3336125bb12b7/pymatgen/phonon/dos.py#L263-L270 respecitvely) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1858 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1858/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1858/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1858/events | https://github.com/materialsproject/pymatgen/issues/1858 | 627,527,743 | MDU6SXNzdWU2Mjc1Mjc3NDM= | 1,858 | Elfcar.as_dict() from pymatgen.io.vasp.outputs not working | {
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} | **Describe the bug**
I could be doing something wrong, but the `as_dict()` method of the `Elfcar` class doesn't appear to work. `Elfcar` ultimately inherits `as_dict()` from `monty.MSONable`, which requires that every argument passed to the constructor be an attribute of that class. However, one argument for the `Elfc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1859 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1859/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1859/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1859/events | https://github.com/materialsproject/pymatgen/pull/1859 | 627,579,642 | MDExOlB1bGxSZXF1ZXN0NDI1MzYxMjU1 | 1,859 | Add poscar attribute to Elfcar modeled after Chgcar | {
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"Thanks for identifying the bug and for the fix, @ayushsgupta ! Can you add a test to verify that `elfcar = elfcar.from_dict(elfcar.as_dict())` ?\r\n",
"@rkingsbury ok I added tests & updated the docstring. Did you want the new tests in a different method or are they fine as is?",
"> \r\n> \r\n> @rkingsbury ok ... | 2020-05-29T22:32:28 | 2020-06-22T22:01:57 | 2020-06-01T18:49:34Z | CONTRIBUTOR | {
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} | ## Summary
* Add a `poscar` attribute to the `Elfcar` class patterned after the `Chgcar` constructor
* Fixes bug described in #1858
@rkingsbury @mkhorton | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1860 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1860/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1860/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1860/events | https://github.com/materialsproject/pymatgen/issues/1860 | 628,937,996 | MDU6SXNzdWU2Mjg5Mzc5OTY= | 1,860 | Getting different INCAR files for 'mp-22590' using MPRester.query() within pymatgen and from materials-project website | {
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I am getting different INCAR files for ID 'mp-22590' using **MPRester.query()** within pymatgen and from the **materials-project website**.
**using MPRester.query():**
mpr = MPRester('My_API_key')
data=mpr.query('mp-22590',['input.incar'])[0]
INCAR that i get is:
ALGO = Normal
A... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1861 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1861/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1861/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1861/events | https://github.com/materialsproject/pymatgen/pull/1861 | 629,731,306 | MDExOlB1bGxSZXF1ZXN0NDI2OTkyMjk0 | 1,861 | SOC WAVECARs and general cleanup | {
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"The tests are failing because of sympy (not related to my work so far). Looks like check_assumptions is no longer in sympy.core.assumptions.",
"Thanks @mturiansky. As far as I can see it _is_ still in sympy.core.assumptions, been meaning to take a look at this. Nevertheless not related to this PR, is this ready ... | 2020-06-03T06:33:36 | 2020-06-23T19:33:28 | 2020-06-08T19:53:49Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
* add ability to read SOC WAVECARs
* seemingly robust ability to determine if WAVECAR is from std, gam, or ncl binary
* add conversion from WAVECAR to UNK files for wannier90 (will add needed support for UNKs from ncl calculations)
## Additional dependencies introduced (if any)
None.
## TODO (i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1862 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1862/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1862/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1862/events | https://github.com/materialsproject/pymatgen/issues/1862 | 630,096,127 | MDU6SXNzdWU2MzAwOTYxMjc= | 1,862 | Restore structures from their pymatgen __str__ representation | {
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"While we can certainly implement a parser for the `Structure.__str__`, the general preference is to use one of the other formats for storing structures, e.g., CIF, POSCAR or json. These are well-established representations that people have been using widely. The structure string is more for the purposes of readabi... | 2020-06-03T15:32:17 | 2020-06-03T16:56:50 | 2020-06-03T16:56:50Z | CONTRIBUTOR | {
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} | `Structure` has a str representation defined below that can be written to a file however I can't find an easy way to restore a `Structure` from that string, is there one? it doesn't appear to be an option when using `Stucture.from_str()`
The need for such functionality arises when restoring a dataframe of structure... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1863 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1863/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1863/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1863/events | https://github.com/materialsproject/pymatgen/issues/1863 | 631,158,327 | MDU6SXNzdWU2MzExNTgzMjc= | 1,863 | Bug: Finding nn distances in the pymatgen_diffusion package | {
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"Pls make sure ou have the latest pymatgen and pymatgen-diffusion packages. Also, for pymatgen-diffusion, pls post on the Github issues of that package. "
] | 2020-06-04T21:25:28 | 2020-06-05T15:28:23 | 2020-06-05T15:28:23Z | NONE | {
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} | **Describe the bug**
Hello Pymatgen Dev,
There appears to be an error in the pymatgen_diffusion package. Exactly it is finding nn distances with the pymatgen_diffusion package. That has not been updated in a long time and it appears to be broken.
**To Reproduce**
Steps to reproduce the behavior:
Unzip file
1. C... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1864 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1864/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1864/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1864/events | https://github.com/materialsproject/pymatgen/pull/1864 | 632,204,566 | MDExOlB1bGxSZXF1ZXN0NDI4OTc4ODgw | 1,864 | pip sympy instead of conda sympy | {
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"Thanks!"
] | 2020-06-06T04:48:45 | 2020-06-08T20:05:46 | 2020-06-08T20:00:51Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Attempt to fix circleci.
## 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/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1865 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1865/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1865/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1865/events | https://github.com/materialsproject/pymatgen/issues/1865 | 634,712,173 | MDU6SXNzdWU2MzQ3MTIxNzM= | 1,865 | Illegal instruction error when running VoronoiNN.get_nn_info() | {
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"Please install using pip install the latest version of pymatgen.",
"Hi @mtdunstan , I can't reproduce this -- note that VoronoiNN relies on qhull integrated into scipy, try upgrading your scipy and/or your Python version also."
] | 2020-06-08T15:18:23 | 2020-06-08T16:46:50 | 2020-06-08T15:19:07Z | NONE | {
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} | I had older code using VoronoiNN.get_nn_info on structures that I tried to use today, and it is giving an illegal instruction error. Minimal code is below. Normally it should produce substructural information for each site in the structure.
Do you know what I can try to do to fix this?
```
from pymatgen.ext.matp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1866 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1866/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1866/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1866/events | https://github.com/materialsproject/pymatgen/pull/1866 | 634,991,814 | MDExOlB1bGxSZXF1ZXN0NDMxNDQzMTM2 | 1,866 | Fix appveyor | {
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"We're probably overdue removing AppVeyor now anyway, we used it because it offered Windows testing, but we can do that within Github Actions now and reduce our CI overload.",
"Yeah, probably worth it. I was just annoyed that the appveyor badge said the build was failing :-)",
"Haha, I admire your diligence"
] | 2020-06-08T23:09:25 | 2020-06-08T23:20:10 | 2020-06-08T23:15:54Z | CONTRIBUTOR | {
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} | I assume it has the same problem as CircleCI with conda sympy. | {
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"After further testing, using the previous version `pymatgen-2020.4.29`, the script as:\r\n```\r\nparser = CifParser(\"FIQCEN.cif\", occupancy_tolerance=100)\r\n```\r\nworks fine.\r\nPlease check if the is a bug in the latest version and document the need of `occupancy_tolerance=somehighnumber` in https://pymatgen.... | 2020-06-09T09:51:38 | 2020-06-11T16:07:09 | 2020-06-11T08:43:56Z | NONE | {
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```
from pymatgen.io.cif import CifParser
parser = CifParser("FIQCEN.cif")
structure = parser.get_structures()[0]
```
with FIQCEN being a structure from the CSD database (https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/), the script returns the error:
```
/home/daniele/anaconda3/envs... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1868 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1868/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1868/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1868/events | https://github.com/materialsproject/pymatgen/issues/1868 | 636,109,762 | MDU6SXNzdWU2MzYxMDk3NjI= | 1,868 | StructureMatcher.get_rms_dist illegal instruction on release pymatgen==2020.6.8. | {
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"If you installed pymatgen via conda, pls try to do pip install --upgrade pymatgen. This error is usually a symptom that something is wrong with the compilation of the C extensions and happens quite frequently on Linux based systems.",
"I have not installed pymatgen through conda. I have simply pip installed it. ... | 2020-06-10T09:54:34 | 2020-06-10T15:44:16 | 2020-06-10T15:44:16Z | NONE | {
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} | **Describe the bug**
On the most recent release of pymatgen (2020.6.8) I am now getting "Illegal instruction" when running the `pymatgen.structure_matcher.StructureMatcher.get_rms_dist`. This did not happen on the previous release (2020.4.29).
**To Reproduce**
The following script
```
from ase.build import bulk
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https://api.github.com/repos/materialsproject/pymatgen/issues/1869 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1869/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1869/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1869/events | https://github.com/materialsproject/pymatgen/issues/1869 | 636,432,533 | MDU6SXNzdWU2MzY0MzI1MzM= | 1,869 | Invalid entries in MPRester | {
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} | When querying for entries in MPRester, e.g., for phase diagram construction, I keep getting lots of "Entry mp-*** has invalid run type None or LDA+rVV10. Discarding.". I have no idea why there are so many runs with invalid run types. But shouldn't a better way be to exclude these from the query, e.g., by setting the cr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1870 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1870/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1870/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1870/events | https://github.com/materialsproject/pymatgen/issues/1870 | 637,151,485 | MDU6SXNzdWU2MzcxNTE0ODU= | 1,870 | pymatgen.Composition, Invalid formula when atom fraction is < 1e-4 | {
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} | **Describe the bug**
The `Compostion.to_data_dict` property will report `CompositionError: e-05 is an invalid formula!` error when any atom fraction is less than 1e-4.
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen import Composition
comp = Composition('Fe0.00009Ni0.99991')
print(comp.to... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1871 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1871/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1871/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1871/events | https://github.com/materialsproject/pymatgen/pull/1871 | 637,200,663 | MDExOlB1bGxSZXF1ZXN0NDMzMjMyNzgz | 1,871 | Add "unit" to plot_compare in PhononBSPlotter | {
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"Hello, \r\n\r\nis there anything else we would need to do before this can be merged? I think, only py3test is currently failing but this has nothing to do with this change.\r\n\r\nBest, \r\nJG",
"Thanks @ab5424! And apologies both @ab5424 and @JaGeo, been a little slow reviewing PRs this week. We currently have ... | 2020-06-11T17:28:06 | 2020-06-20T20:28:54 | 2020-06-20T17:24:07Z | CONTRIBUTOR | {
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} | The frequency unit can only be changed for a single bandstructure plot: https://github.com/materialsproject/pymatgen/blob/604d59c93f21c4a180663bdc6cd64bf1329c5239/pymatgen/phonon/plotter.py#L329 This is missing for plot_compare. I also provided a test (although it is not very useful to compare a bandstructure object wi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1872 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1872/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1872/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1872/events | https://github.com/materialsproject/pymatgen/pull/1872 | 638,209,804 | MDExOlB1bGxSZXF1ZXN0NDM0MDQwNzM3 | 1,872 | Adding the option to plot other side of slab | {
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"Thanks @mhsiron, some linting failures here otherwise looks useful",
"Hi @mhsiron, any updates on this?",
"Thanks @mhsiron !"
] | 2020-06-13T18:34:07 | 2020-09-26T02:51:10 | 2020-09-26T02:51:04Z | CONTRIBUTOR | {
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} | Adding the option to plot other side of slab, that way the user has the option to plot either surface of the slab, especially if the two surfaces are different.
## Additional dependencies introduced (if any)
None
Before a pull request can be merged, the following items must be checked:
- [ x] Code is in the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1873 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1873/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1873/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1873/events | https://github.com/materialsproject/pymatgen/pull/1873 | 642,920,719 | MDExOlB1bGxSZXF1ZXN0NDM3ODE3NzE1 | 1,873 | Add new functionality to Lobsterin class and some fixes | {
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"Hi!\r\nI don't think the failing tests are from my changes.\r\n\r\nBest, \r\nJG",
"We've had an IonEntry bug in master for the past week, I think a PR from @knc6 just fixed it. Please try merging in from master and hopefully tests should pass, otherwise this looks great.\r\n\r\nWhat's the distinction between the... | 2020-06-22T09:45:34 | 2020-06-23T00:55:50 | 2020-06-23T00:55:40Z | MEMBER | {
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} | ## Summary
Include a summary of major changes in bullet points:
-I have introduced a new static method to the Lobsterin class that can return a list of possible basis sets for Lobster runs. And, I also added files that help creating theses basis sets.
-To restructure the code, I have also created a lobster fol... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1874 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1874/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1874/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1874/events | https://github.com/materialsproject/pymatgen/issues/1874 | 643,384,489 | MDU6SXNzdWU2NDMzODQ0ODk= | 1,874 | Link to Bader analysis code no longer working | {
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"Edit to docs_rst, thanks!"
] | 2020-06-22T21:54:36 | 2022-04-20T03:25:26 | 2022-04-20T03:25:26Z | CONTRIBUTOR | {
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} | **Describe the bug**
For the [Bader caller module](https://pymatgen.org/pymatgen.command_line.bader_caller.html) in the docs, the link to download the original fortran code for the Bader analysis is broken. The link should be http://theory.cm.utexas.edu/henkelman/code/bader/. Not sure how to fix (edit docs or docs_rst... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1875 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1875/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1875/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1875/events | https://github.com/materialsproject/pymatgen/issues/1875 | 643,394,586 | MDU6SXNzdWU2NDMzOTQ1ODY= | 1,875 | XYZ File Parser can incorrectly handle comment string, miscounting the number of sites | {
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"Update: I have discovered that removing the bottom lines does not solve the problem, nor did removing the comment lines, **but removing the scientific notation from the _first_ atomic coordinate does**. When the same coordinate is supplied to a different atom, the parsing appears to complete correctly; so the issu... | 2020-06-22T22:17:27 | 2020-06-22T22:51:59 | 2020-06-22T22:51:36Z | CONTRIBUTOR | {
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For some XYZ files, the parser will incorrectly use the end of the comment line as the number of sites present on the molecule, which can result in an `IndexError` if this exceeds the number of sites on the Molecule. (This could presumably also result in fewer atoms being loaded in then should be,... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1876 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1876/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1876/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1876/events | https://github.com/materialsproject/pymatgen/pull/1876 | 643,441,997 | MDExOlB1bGxSZXF1ZXN0NDM4MjQ0Nzcz | 1,876 | Add support for *^ scientific notation for XYZ parser (Useful for QM9 Database) | {
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"Thanks @stevetorr!"
] | 2020-06-23T00:30:58 | 2020-06-23T01:25:56 | 2020-06-23T01:25:55Z | CONTRIBUTOR | {
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The QM9 database uses a special format for scientific notation in their .xyz files, wherein e.g. `3.14e-6` would be represented `3.14*^-6`. This addresses issue #1875 (which was not a bug per se, but simply brushing up against unimplemented behavior).
- The XYZ file parser can now handle this formattin... | {
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"Thanks -- the only way to really test this would be a test that does a pip install + then runs the test suite, which is perhaps not a bad idea. The other thing is that we could change the setup.py to just include all .json/.yaml it finds, which might also be sensible (rather than the current method which just incl... | 2020-06-23T10:12:13 | 2020-06-23T18:15:16 | 2020-06-23T18:14:04Z | MEMBER | {
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Hi,
I forget to change the setup.py to reflect the correct folder structure of the new lobster module. Currently, the basis functions are not found when pymatgen is installed... (Is it maybe possible to check for this within an automatic test in the future?)
Best,
JG | {
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"Hi @Jaydu1996, what does your directory structure look like? Your `pseudopotentials` folder should have a `POT_GGA_PAW_PBE_52` folder inside it, and that has the POTCARs gzipped, e.g. `POTCAR.Ac.gz`",
"The directory structure is below:\r\n```\r\n[user@master POT_GGA_PAW_PBE_52]$ pwd\r\n/home/user/pseudopotential... | 2020-06-23T14:39:05 | 2020-06-25T19:14:25 | 2020-06-25T19:13:29Z | NONE | {
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} | **Describe the bug**
The pymatgen can't recognize the POTCAR(PBE_52), although I think I have set the correct pmgrc.yaml file.
The bug is
```
Traceback (most recent call last):
File "/home/user/app/anaconda3/envs/firework/lib/python3.7/site-packages/fireworks/core/rocket.py", line 262, in run
m_action = t.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1879 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1879/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1879/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1879/events | https://github.com/materialsproject/pymatgen/pull/1879 | 644,422,331 | MDExOlB1bGxSZXF1ZXN0NDM5MDQ2Mzgw | 1,879 | Boltztrap2 spin | {
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"Thanks!"
] | 2020-06-24T08:26:57 | 2020-06-25T13:41:02 | 2020-06-25T13:40:57Z | CONTRIBUTOR | {
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} | Here an upgrade of the boltztrap2 interface.
Major points are:
- transport properties, dos, and bands can be computed for spin polarized DFT computations
- PMGLoader should be used to load a vasprun/bandstructure pymatgen object, instead of the two previous loaders.
- load and save methods of BztInterpolator and Bz... | {
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"Thanks for the bug fix @kavanase, my apologies for letting this sit for a while. I've merged this in now as-is since it's a fairly minimal change, but for future bug fixes including a minimal extra test that demonstrates the buggy behavior is always appreciated.\r\n\r\nPlease make sure to include your details in [... | 2020-06-24T15:32:46 | 2020-10-04T14:45:35 | 2020-10-03T03:07:49Z | CONTRIBUTOR | {
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} | ## Summary
There's a small bug in the `DefectPhaseDiagram.suggest_larger_supercells()` method (line 390 in `pymatgen/analysis/defects/thermodynamics.py`, where the current code is:
```python
for tl, chgset in self.transition_level_map.items():
```
which gives the wrong variables of Defect-Name, {Transition-Leve... | {
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} | ## Summary
Added folder to pymatgen/analysis called Fstar
contains script for generating f* diagrams, an example notebook, and scattering factor files
## TODO (if any)
add additional examples to show off more features.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
... | {
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} | ## Summary
* generator code
* example
* scattering factors
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* need more examples of features and workarounds
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pu... | {
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"Hi @jonathanjdenney, nice to see this PR. I noticed you were uploading these files manually. You may find [GitHub Desktop](https://desktop.github.com) useful to commit your changes locally.",
"Hi @mkhorton I will check that out. In the meantime I'm getting the error \"D100: Missing docstring in public module\" f... | 2020-06-25T17:46:38 | 2020-10-20T17:33:46 | 2020-10-20T17:33:46Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Script to generate f* diagrams
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* add more examples
## Checklist
Work-in-progress pull requests are encouraged, but please put [WI... | {
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"Hi Chi. I agree that it's unlikely it's a \"bad\" POTCAR -- in fact, I've recently changed this warning in master to be `UnknownPotcarWarning` instead, so as not to alarm people. I suspect the database of potcar hashes distributed with pymatgen is simply incomplete, we did use the latest potcars to generate them b... | 2020-06-26T23:28:58 | 2023-08-13T16:33:42 | 2023-08-13T16:33:42Z | CONTRIBUTOR | {
"total": 0,
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} | **Describe the bug**
I was trying to generate vasp input sets for a Na-containing system using io.vasp.sets.MPRelaxSet. However, it seems that the `Na_pv` potcar failed the potcar check.
I then go to my vasp potcar directory, `VASP_PSP/POT_GGA_PAW_PBE`, and run the following codes
```
from pymatgen.io.vasp.i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1885 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1885/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1885/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1885/events | https://github.com/materialsproject/pymatgen/pull/1885 | 646,714,976 | MDExOlB1bGxSZXF1ZXN0NDQwOTM1MDUy | 1,885 | parse scientific notation in OUTCAR (possibly without spaces in betwe… | {
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"Closing for now, since two features got intermingled in this PR"
] | 2020-06-27T16:47:53 | 2020-06-27T17:18:34 | 2020-06-27T17:18:34Z | MEMBER | {
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} | ## Summary
This PR is very similar to #1836 , except it now supports the dielectric tensor section of the OUTCAR as well (instead of just plasma frequencies)
The unit test from #1836 should also cover this one | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1886 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1886/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1886/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1886/events | https://github.com/materialsproject/pymatgen/pull/1886 | 646,720,208 | MDExOlB1bGxSZXF1ZXN0NDQwOTM4Nzg1 | 1,886 | two changes: parse scientific notation dielectric data, update cost information | {
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"Thanks @computron :) "
] | 2020-06-27T17:22:42 | 2020-06-27T22:04:02 | 2020-06-27T22:03:25Z | MEMBER | {
"total": 0,
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} | ## Summary
This PR includes two different changes (poor style, I know - but the Github UI makes it difficult to separate them into different PRs after the fact):
### Change 1:
This update for scientific notation is very similar to #1836 , except it now supports the dielectric tensor section of the OUTCAR as well... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1887 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1887/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1887/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1887/events | https://github.com/materialsproject/pymatgen/pull/1887 | 647,187,544 | MDExOlB1bGxSZXF1ZXN0NDQxMjU2ODQ2 | 1,887 | Fix regular expression of read_onsite_density_matrices | {
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"Thanks.",
"This had a linter failure, nothing major but the other linters didn't have chance to run.",
"I know. But the linter failure is in the test file."
] | 2020-06-29T07:35:27 | 2020-06-29T20:12:20 | 2020-06-29T20:05:22Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Fixed regular expression to parse density matrix
At Line 1476 -- 1490 in OUTCAR_merged_numbers2 file in test_files
-------------------------------------------------------
spin component 1
6.1320 -7.9985 9.9720 5.1366 -1.5481
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"Hi @bwjustus, nice to see this :-)\r\n\r\nIn terms of implementation, would a method to return all 24 Selling lattices be sensible?\r\n\r\nUltimately, the benefit of the Selling reduction is to calculate a distance between lattices `A` and `B`, which I believe takes the form of `min([dist(any_selling_lattice_A, a_... | 2020-06-29T18:40:25 | 2021-04-14T20:37:36 | 2021-04-14T20:37:27Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1889 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1889/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1889/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1889/events | https://github.com/materialsproject/pymatgen/issues/1889 | 647,609,062 | MDU6SXNzdWU2NDc2MDkwNjI= | 1,889 | Jupyter notebook bug. | {
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"Which vasprun.xml are you using?",
"The vasprun.xml file that is generated from running VASP. Im not sure how else to explain it, are there different vasprun.xml files.",
"The reason I ask is that usually this kind of error is the result of a mal-formed vasprun.xml file, e.g. one in which VASP didn't complete ... | 2020-06-29T19:25:00 | 2020-06-29T19:47:03 | 2020-06-29T19:47:02Z | NONE | {
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} | I am going through the Jupiter notebook tutorials and am trying to reproduce the 2013-01-01-Bandstructure of NiO tutorial. The issue I am running into is with the run = BSVasp("vasprun.xml", parse_projected_eigen=True) command. The error is ParseError: no element found: line 486, column 0.
That is the last line in the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1890 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1890/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1890/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1890/events | https://github.com/materialsproject/pymatgen/issues/1890 | 648,025,298 | MDU6SXNzdWU2NDgwMjUyOTg= | 1,890 | Error of Critic2Caller | {
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"Hi @yuuukuma, you need to compile a newer version of Critic2, the zpsp version isn't in older versions of the code.",
"Dear @mkhorton,\r\nthanks for your reply. \r\nI can only use the stable version of critic2 due to the compiler issue, so try to use the older version of Pymatgen.",
"Ok, you can also check wit... | 2020-06-30T09:36:04 | 2020-07-02T17:40:15 | 2020-07-02T17:40:15Z | CONTRIBUTOR | {
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[test.zip](https://github.com/materialsproject/pymatgen/files/4850861/test.zip)
**Describe the bug**
When using the critic2 with Critic2Caller, the result shows
```
%% load int.CHGCAR id chg_int zpsp Al 3 As 5 O 6
!error! id chg_int zpsp Al 3 As 5 O 6
ERROR(setfield): Unknown extra keyword
ERROR(setfield): ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1891 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1891/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1891/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1891/events | https://github.com/materialsproject/pymatgen/pull/1891 | 649,737,904 | MDExOlB1bGxSZXF1ZXN0NDQzMzU3NzA1 | 1,891 | Fix zpsp to have element names as its keys | {
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"Thanks!"
] | 2020-07-02T08:24:09 | 2020-07-02T17:40:15 | 2020-07-02T17:40:15Z | CONTRIBUTOR | {
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This fix is needed as symbol shows the POTCAR label e.g. "Ca_pv" while element its name "Ca",
Fix #1890
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"Check out `jsanitize` in `monty.json` and see if that helps. There's a subtle distinction between `to_dict()` and `to_json()` methods, to insert into Mongo it needs to be JSON-compatible, you might try JSON with `MontyEncoder` too. Both these methods should just work without manual code tweaks required. If this do... | 2020-07-02T09:09:23 | 2020-07-03T15:12:10 | 2020-07-03T09:12:08Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
When I try to put a `Slab.as_dict()` into a MongoDB database within a FireWorks workflow it fails. The `as_dict()` method has to be MSON serializable according to the documentation, but apparently for pymongo this is not enough.
The problematic entrie... | {
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Correct bugfix if `nb` happens to come out as zero for a particular branch. | {
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"The code is correct. In your first example, there are TWO surfaces - one is the FePt terminated and the other is CuPt terminated. In your second figure, that is not even stoichiometric FeCuPt2 anymore. If you want to make sure the surfaces are symmetrized, you need the Tasker 2 reconstructed slabs.",
"Thanks Pr... | 2020-07-03T09:48:29 | 2020-07-03T15:33:09 | 2020-07-03T14:50:14Z | NONE | {
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} | Hi Pymatgen Developers,
I am using Pymatgen to generate the (1, 0, 0) surfaces of mp-3702 FeCuPt2 crystal, and I get confused why only one CuPt terminated surface is generated. Theoretically, there are two unique surfaces (terminated at (1, 0, 0) and (0.5, 0, 0) respectively)
```
from pymatgen.ext.matproj impor... | {
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"What you call \"decomposition\" enthalpy is simply some formation energy. This can be obtained from the Reaction Calculator quite easily. But if you want the functions that are reported by the paper, you can ask @computron ",
"Yep it's just a formation energy and for anything that isn't a vertex of the convex hu... | 2020-07-03T15:58:19 | 2020-10-03T03:28:48 | 2020-10-03T03:28:48Z | CONTRIBUTOR | {
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} | `e_above_hull` is zero for everything on the hull. Whereas the decomposition enthalpy provides a distribution of values for compounds on the hull, therefore, making it potentially more useful for some workflows.
**Describe the solution you'd like**
add a function similar to `get_decomp_and_e_above_hull` that calcul... | {
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"Just adding a note that I'll have some requests on the Bader portion of this code, seems like there's a lot of duplicated code from the current Bader caller. It seems like it'd be neater just to tidy up the code to factor out the common code (eg ACF.dat parsing) and allow it to initialize from either from Chgcar... | 2020-07-07T20:39:56 | 2020-10-19T19:52:34 | 2020-10-19T19:52:30Z | CONTRIBUTOR | {
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} | ## Summary
Re-opening a work in progress PR for my CP2K module. Main feature is pymatgen.io.cp2k, which includes modules for reading/writing cp2k input files, input sets, and output parsing.
1. **pymatgen.io.cp2k.inputs**: Handles the CP2K input file structure by mainly defining a "Section" and a "Keyword". Keywo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1897 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1897/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1897/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1897/events | https://github.com/materialsproject/pymatgen/pull/1897 | 652,761,041 | MDExOlB1bGxSZXF1ZXN0NDQ1Nzg0MzQz | 1,897 | Make EwaldSummation MSONable | {
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"If anything in the implementation looks fishy please comment...",
"Thanks but I am unclear about the value of this. The EwaldSummation is an analysis. Typically people execute it once for a particular structure. They may want to store the final results of it in some form (son or otherwise) but I fail to see when... | 2020-07-08T00:06:48 | 2020-07-14T16:53:48 | 2020-07-14T15:06:24Z | CONTRIBUTOR | {
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} | ## Summary
Computing the Ewald matrices for large structures can be very time consuming. By making the `EwaldSummation` class `MSONable` we can at least save time by reloading instances without recreating the matrices.
* `as_dict` method
* `from_dict` method
* To implement the above I changed the constructor to ... | {
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"What format are your structure files? Structure.is_ordered is the property method you are looking for.\r\nFor questions regarding usage, pls use https://matsci.org/c/pymatgen/9"
] | 2020-07-08T06:19:42 | 2020-07-08T14:44:51 | 2020-07-08T14:44:50Z | NONE | {
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} | Apologies if github is the wrong place to ask operational questions.
I have a large list of structures and I need to quickly identify the ones with partial occupancies and parse them / clean up. Is there a quick test for if a crystal contains partial occupancies? | {
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"```\r\nPDEntry : N4 Zn12 Zr12 with energy = -21.6244\r\n\r\nDecomposition reaction:\r\n(PDEntry : N1 Zr1 with energy = -3.5118, 1.8295715595655295)\r\n(PDEntry : N2 Zn2 Zr6 with energy = -9.2150, 1.0852142202171597)\r\n(PDEntry : Zn4 Zr2 with energy = -1.8542, 0.5739288989128745)\r\n(PDEntry : Zn6 Zr2 with energy ... | 2020-07-08T19:58:46 | 2020-10-03T03:30:02 | 2020-10-03T03:28:49Z | CONTRIBUTOR | {
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} | ## Summary
This PR addresses Issue #1895.
The finalised code should add the functionality to calculate the "decomposition" energy for materials on the convex hull. This is slightly different from the "equilibrium reaction" energy already implemented as it allows for compositions not previously on the hull to be i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1900 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1900/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1900/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1900/events | https://github.com/materialsproject/pymatgen/pull/1900 | 654,088,091 | MDExOlB1bGxSZXF1ZXN0NDQ2ODgyODcz | 1,900 | Changed tolerance for lattice match when creating defect objects | {
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"Can we have a unittest pls, since the claim is that the lattice match is causing functionality failure.",
"Unit test added demonstrating the failure with default lattice match and success with looser absolute tolerance.",
"Thanks."
] | 2020-07-09T14:05:19 | 2020-07-09T16:46:33 | 2020-07-09T16:46:29Z | CONTRIBUTOR | {
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} | ## Summary
Stringent atol of 1e-8 used in numpy.allclose function for lattice match is causing problems for users. The tolerance for lattice match check for defect instantiation is now made looser. This fixes many failures experienced by users of pycdt and atomate defect workflows
* Instead of using default lat... | {
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