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https://api.github.com/repos/materialsproject/pymatgen/issues/1201 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1201/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1201/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1201/events | https://github.com/materialsproject/pymatgen/pull/1201 | 341,103,335 | MDExOlB1bGxSZXF1ZXN0MjAxMzU2Mzc2 | 1,201 | change gb location | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1202 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1202/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1202/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1202/events | https://github.com/materialsproject/pymatgen/pull/1202 | 341,196,515 | MDExOlB1bGxSZXF1ZXN0MjAxNDI4MzA3 | 1,202 | add get_fermi_interextrapolated method to FermiDos | {
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} | ## Summary
when the value of doping concentration, c, is too low or too high, the get_fermi method may not converge in which case it raises error which is expected. To support a wider range of c even for a coarse CompleteDos with an energy range that is not wide enough, get_fermi_interextrapolated is introduced that... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1203 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1203/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1203/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1203/events | https://github.com/materialsproject/pymatgen/issues/1203 | 341,285,842 | MDU6SXNzdWUzNDEyODU4NDI= | 1,203 | spacegroup error in rhombohedral lattice | {
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"Sorry for the late reply. To force rhom setting, set your spacegroup to 'R32:R'. This will result in no errors and the right structure.",
"It works! Thank you.",
"Hi, I also have the similar error when I constructed the structure based on the groupspace, \r\n![image](https://github.com/materialsproject/pymatge... | 2018-07-15T02:15:46 | 2023-10-25T15:31:52 | 2018-07-16T22:35:09Z | CONTRIBUTOR | {
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} | Hello,
I encountered spacegroup issue about rhombohedral lattice as follows.
I read the source code of `pymatgen.symmetry.groups` for a while, but I don't know about what should I do about this.
Do you have any good ideas?
## System
* Pymatgen version: 2018.6.27
* Python version: 3.6.2
* OS version: Ubuntu 16.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1204 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1204/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1204/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1204/events | https://github.com/materialsproject/pymatgen/pull/1204 | 341,624,769 | MDExOlB1bGxSZXF1ZXN0MjAxNzE4NzIy | 1,204 | Set Matplotlib backend in CircleCI | {
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"Already did it."
] | 2018-07-16T18:21:56 | 2018-07-24T00:39:45 | 2018-07-17T14:29:44Z | NONE | {
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Set the matplotlib backend in circleCi to fix DISPLAY variable issues | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1205 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1205/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1205/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1205/events | https://github.com/materialsproject/pymatgen/pull/1205 | 341,714,653 | MDExOlB1bGxSZXF1ZXN0MjAxNzg3NzE3 | 1,205 | Optimize the symmetry analyzer | {
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} | Use pymatgen Spacegroup to analyze the symmetry of the structure.
Uses can provide any cell they want (swap a, b, c or angles in tetragonal or hexagonal systems). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1206 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1206/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1206/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1206/events | https://github.com/materialsproject/pymatgen/pull/1206 | 342,026,657 | MDExOlB1bGxSZXF1ZXN0MjAyMDI0Mzgy | 1,206 | Add FunctionalGroupExtractor | {
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"This broke code. Can you fix and submit a new PR?",
"Can you tell me what it broke? I'd be happy to fix whatever went wrong.",
"Go to CircleCI and look at the latest build.",
"I'm sorry, I'm not super used to these build tools. I see that Travis-CI failed for a timeout, and AppVeyor succeeded. Where can I fi... | 2018-07-17T18:07:34 | 2018-07-19T16:39:02 | 2018-07-19T12:37:01Z | CONTRIBUTOR | {
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} | ## Summary
Added a new file (functional_groups.py) and class (FunctionalGroupExtractor) in pymatgen.analysis. This new class uses an algorithm developed by Ertl (2017) to identify atoms of interest (heteroatoms and certain special carbons) and then combine connected atoms of interest to form functional groups. It is... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1207 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1207/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1207/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1207/events | https://github.com/materialsproject/pymatgen/pull/1207 | 342,049,948 | MDExOlB1bGxSZXF1ZXN0MjAyMDQyNTA3 | 1,207 | Testbranch | {
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"What is this about?",
"I'm sorry, I thought I was working on my own fork. Closing this now."
] | 2018-07-17T19:18:36 | 2018-07-17T19:45:24 | 2018-07-17T19:45:24Z | CONTRIBUTOR | {
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} | ## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1208 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1208/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1208/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1208/events | https://github.com/materialsproject/pymatgen/pull/1208 | 342,484,736 | MDExOlB1bGxSZXF1ZXN0MjAyMzc0MzI5 | 1,208 | QChem Refactor and Update | {
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"There are still failing tests. Pls fix. Thanks.",
"Pretty sure this will fix the appveyor / travis-ci build, but it required that I put an unused attempted import openbabel just to know whether or not to include that test, which now makes codacy upset. If this isn't acceptable, please advise. Thanks!"
] | 2018-07-18T20:43:34 | 2018-07-19T12:36:26 | 2018-07-19T12:36:26Z | CONTRIBUTOR | {
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} | * QChem IO functionalities have been refactored to be named consistently with other IO packages
* Default sets have been improved, including changing the default SCF strategy from DIIS to GDM
* Multiple new functionalities have been added to the output parser, including the ability to classify different types of stru... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1209 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1209/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1209/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1209/events | https://github.com/materialsproject/pymatgen/pull/1209 | 342,520,334 | MDExOlB1bGxSZXF1ZXN0MjAyNDAyNDg4 | 1,209 | Add new feature to GB generator | {
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} | In this new version,
A new class method 'get_ratio' is added to help user obtain the axial ratio from the structure needed for GB generator. Users can also supply the ratio directly by making their own approximations.
In addition, a new tag 'max_search' is added. This is to avoid crash for large GB with large sigma... | {
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} | ## Summary
Previous pull request left one test for pymatgen.analysis.graphs.MoleculeGraph broken. This pull request fixes those broken tests. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1211 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1211/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1211/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1211/events | https://github.com/materialsproject/pymatgen/issues/1211 | 342,902,109 | MDU6SXNzdWUzNDI5MDIxMDk= | 1,211 | Obtaining what materials-project ids are available | {
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"The method you are looking for is `MPRester.get_materials_ids`. Mids is simply a running number based on time of calculation. There is no system of assignment.\r\n\r\nIn future, please post questions on the Google groups. Github Issues are meant for reporting issues/bugs/feature requests. Thanks.",
"Questions re... | 2018-07-19T21:51:32 | 2018-07-19T22:04:19 | 2018-07-19T21:58:37Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1212 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1212/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1212/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1212/events | https://github.com/materialsproject/pymatgen/issues/1212 | 343,110,387 | MDU6SXNzdWUzNDMxMTAzODc= | 1,212 | Cythonized linear assignment algorithm very slow ONLY with negative costs | {
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} | Unexpectedly, in `pymatgen.optimization`, the cythonized linear assignment algorithm LAPJV, inside `linear_assignment.pyx`, becomes extremely slow when the cost matrix has some negative values. Adding a constant to the cost matrix does not change the solution and when the constant is high enough, the equivalent matrix ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1213 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1213/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1213/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1213/events | https://github.com/materialsproject/pymatgen/pull/1213 | 343,181,346 | MDExOlB1bGxSZXF1ZXN0MjAyOTA1OTk0 | 1,213 | Create GB object | {
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} | Similar to Slab object, we create a Gb object, which stores additional information compared with structure object, e.g. rotation axis, angle, gb_plane, etc., all are gb properties.
Gb object generator also adds ab_shift, which is the in-plane shift of two grains, particularly useful for twist GB. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1214 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1214/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1214/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1214/events | https://github.com/materialsproject/pymatgen/issues/1214 | 343,719,196 | MDU6SXNzdWUzNDM3MTkxOTY= | 1,214 | Band structure checks if HF in order to determine if self-consistent | {
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"Thanks for the report @ajjackson !"
] | 2018-07-23T17:10:28 | 2018-07-31T18:36:27 | 2018-07-31T18:36:27Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 2018.5.14
* Python version: 3.6.3
* OS version: Linux Mint 17.3
## Summary
* I am a developer of the `sumo` package which uses pymatgen's Vasp parsers for band stucture plotting
* When attempting to plot self-consistent band structures, the undesired k-points are included in th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1215 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1215/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1215/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1215/events | https://github.com/materialsproject/pymatgen/pull/1215 | 343,751,820 | MDExOlB1bGxSZXF1ZXN0MjAzMzA5ODQ1 | 1,215 | Elastic Revision | {
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"Need to fix a few tests. Will work through and update when done.",
"I think this is ready on my end. The travis tests seem to be failing because of an enumlib issue which I believe is unrelated to this PR."
] | 2018-07-23T18:50:18 | 2019-04-04T02:45:10 | 2018-07-25T18:52:13Z | CONTRIBUTOR | {
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} | * Tensors are MSONable, with optional flag for using voigt notation dict representation (this stores them more efficiently, but would only be used if the user explicitly chose to do so, as information may be lost)
* Revises determination of coefficient of linear expansion to use compliance tensor rather than inverse o... | {
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} | ## Summary
Adds the ability to determine which neighbors in VoronoiNN are adjacent.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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"Doesn't work. I tried the conda install openbabel before. There are too many issues with that package and compatibility with different systems.",
"OK... I'm going to try a couple more things because I'm curious, and because I did manage to get it working with custodian, but unless I have a major breakthrough, I'... | 2018-07-24T23:52:12 | 2018-07-25T18:15:28 | 2018-07-25T18:15:28Z | CONTRIBUTOR | {
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} | All tests that require OpenBabel are currently skipped. Having figured out how to avoid this and successfully run Babel-based tests in Custodian, I'm now trying to do the same in Pymatgen. | {
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} | A legacy portion of the pourbaix code filtered ion-including MultiEntries from pourbaix diagrams when their reaction coefficients were lower than their attached concentration attribute, which I can't think of a good reason to do. This resulted in pourbaix diagrams with high ion concentrations (e. g. > 0.5) filtering o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1219 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1219/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1219/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1219/events | https://github.com/materialsproject/pymatgen/pull/1219 | 344,979,804 | MDExOlB1bGxSZXF1ZXN0MjA0MjQ2NzEw | 1,219 | Add GrainBoundaryTransformation and test in advanced_transformations | {
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GrainBoundaryTransformation is used to generate grain boundary structure, which will be used in atomate grain boundary workflow. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1220 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1220/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1220/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1220/events | https://github.com/materialsproject/pymatgen/pull/1220 | 345,489,927 | MDExOlB1bGxSZXF1ZXN0MjA0NjE3NTYz | 1,220 | added spin polarization support | {
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"Thanks!",
"Would you like me to fix that one assertion that caused the Codacy/PR Quality Review check to fail?",
"that's fine. It is nto a big deal."
] | 2018-07-29T00:37:06 | 2018-07-29T17:55:00 | 2018-07-29T02:22:11Z | CONTRIBUTOR | {
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} | ## Summary
Added support for spin polarized WAVECARs.
## Additional dependencies introduced (if any)
N/A
## TODO (if any)
N/A | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1221 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1221/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1221/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1221/events | https://github.com/materialsproject/pymatgen/pull/1221 | 345,490,850 | MDExOlB1bGxSZXF1ZXN0MjA0NjE4MTM0 | 1,221 | check for 0 weight kpoints for hybrid-type band structures | {
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} | ## Summary
Added a check for 0 weight kpoints in pymatgen.io.vasp.outputs.Vasprun.get_band_structure. This is useful for meta-GGA calculations. Addresses Issue #1214 .
## Additional dependencies introduced (if any)
N/A
## TODO (if any)
N/A | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1222 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1222/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1222/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1222/events | https://github.com/materialsproject/pymatgen/pull/1222 | 345,563,249 | MDExOlB1bGxSZXF1ZXN0MjA0NjYxNzA1 | 1,222 | Changes to JMolNN class | {
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"tests are failing.",
"@jdagdelen there was a query from Hillary/Anubhav recently about whether the Jmol emulation in pymatgen faithfully matched the behavior in Jmol itself; were you able to find a good reference for Jmol's algorithm? If so, would be good to add a reference to the docstring.\r\n\r\nThe best I wa... | 2018-07-29T21:13:57 | 2018-08-08T23:07:29 | 2018-08-08T23:07:29Z | MEMBER | {
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Jmol's spelling was incorrect (the developer explicitly says not to capitalize "mol") and there was a redundant constant used to determine bond lengths.
* JMol -> Jmol
* One tolerance instead of two. | {
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"Why not use pip install?",
"I would like to use the new part of analysis particularly local_env and it doesn't seem to be available on the pip install version.",
"local_env is available on the pip installed version, try `pip install pymatgen --upgrade` ? We recommend using Python 3+ also since Python 2.x suppo... | 2018-07-30T19:49:08 | 2022-06-13T23:58:33 | 2018-09-29T20:09:53Z | NONE | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: <master>
* Python version: <Only 2.7.* and 3.* supported.>
* OS version: <Ubuntu 16.04>
## Summary
* 1-2 short bullet points stating... | {
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} | ## Summary
Occasionally, it makes sense to have a repeated atomic specie in the POTCAR (e.g., defect calculations). This will cause the charge to be calculated incorrectly with the past implementation. This PR handles this edge case and adds a test to check for it.
## Additional dependencies introduced (if any)
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https://api.github.com/repos/materialsproject/pymatgen/issues/1225 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1225/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1225/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1225/events | https://github.com/materialsproject/pymatgen/issues/1225 | 345,981,053 | MDU6SXNzdWUzNDU5ODEwNTM= | 1,225 | A small number of band structures have doubled k-point labels. | {
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"Sorry for the extremely late reply. I can no longer reproduce this (even using the old `MPRester`). Either the issue was fixed in the meantime or I'm not looking in the right place.\r\n\r\n```py\r\nfor mp_id in (\"mp-8601\", \"mp-4100\", \"mp-853153\", \"mp-765720\"):\r\n bandstructure = MPRester().get_bandstru... | 2018-07-30T23:49:26 | 2023-08-08T21:26:52 | 2023-08-08T21:26:52Z | NONE | {
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} | Hi again Materials Project folks,
Not a major concern, but while we've been running through the electronic structures in the database, we've found that a small number of them have doubled labels for high-symmetry k-points. For example, the k-path will be \Gamma -> X -> X -> \Sigma instead of \Gamma -> X -> \Sigma.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1226 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1226/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1226/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1226/events | https://github.com/materialsproject/pymatgen/pull/1226 | 346,483,879 | MDExOlB1bGxSZXF1ZXN0MjA1MzM1Mjc1 | 1,226 | io.lammps updates | {
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"Good. But are there supposed to be some sample templates/scripts? I don't seem to see them in there.",
"Sure, there will be examples on the usage of input script template updated in matgenb separately. ",
"This is better, but still not what I meant. THink about it from a new user perspective - I am clueless ab... | 2018-08-01T07:41:32 | 2018-08-03T22:31:00 | 2018-08-03T22:31:00Z | CONTRIBUTOR | {
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} | ## Summary
Major updates to `io.lammps`. The entire module is now flexible enough to handle most lammps related tasks.
* Simplified code for handling input script, which should just behave just like a string template.
* Revised log parser, and added many tests.
* Minor changes to dump parser. Now dump data f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1227 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1227/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1227/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1227/events | https://github.com/materialsproject/pymatgen/pull/1227 | 346,776,010 | MDExOlB1bGxSZXF1ZXN0MjA1NTU4NjQ0 | 1,227 | Minor refactoring in DFPT part. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1228 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1228/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1228/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1228/events | https://github.com/materialsproject/pymatgen/issues/1228 | 347,344,988 | MDU6SXNzdWUzNDczNDQ5ODg= | 1,228 | Saving to .mcif fails if oxidation_state is not set | {
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"@RoberTnf Thanks for fixing!\r\n\r\nThis bug actually comes partly from the fact that in pymatgen we can specify magnetic moments in two different ways: a `magmom` site property, or adding `spin` to `Specie`. So, for your first example, the line `s.add_spin_by_site([1, -1])` could have been replaced by `s.add_site... | 2018-08-03T10:30:51 | 2018-08-04T17:34:33 | 2018-08-04T16:20:28Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 2018.7.23
* Python version: 3.6.6
* OS version: Manjaro
## Summary
* Trying to save to .mcif will fail if oxidation_state is not set
## Example code
```python
import pymatgen as mg
s = mg.Structure(mg.Lattice.cubic(4.2), ["Cs", "Cl"],[[0, 0, 0], [0.5, 0.5, 0.5]])
s.ad... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1229 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1229/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1229/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1229/events | https://github.com/materialsproject/pymatgen/pull/1229 | 347,346,459 | MDExOlB1bGxSZXF1ZXN0MjA1OTkxMzkx | 1,229 | Use TypeError as oxi_state is set to None, not unset | {
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"The tests were failing as loading from a .mcif file would not set oxi_state to None. I'm checking for both `AtributeError` and `TypeError`.\r\n\r\nAlso I added new tests to check for this issue.",
"Travis was failing a test that in my machine passed, it was a timeout related one, so it might be a hardware differ... | 2018-08-03T10:36:05 | 2018-08-04T17:31:30 | 2018-08-04T12:54:33Z | CONTRIBUTOR | {
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} | ## Summary
Fixing #1228
* Change to TypeError, as this is the one we want to catch, `oxi_state` is set to `None`, not unset
* Remove unnecessary code | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1230 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1230/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1230/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1230/events | https://github.com/materialsproject/pymatgen/issues/1230 | 347,994,372 | MDU6SXNzdWUzNDc5OTQzNzI= | 1,230 | Unintuitive behavior when saving to .cif related to space groups | {
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"My personal opinion on this is that Structure.to is a convenience method and if you want more customization you should use CifWriter directly.\r\n\r\nYour proposed solution of adding a symprec kwarg to Structure.to is fairly harmless, but it’s also very specific to just CIF output. This could also be confusing if ... | 2018-08-06T16:29:40 | 2018-08-07T02:48:16 | 2018-08-07T02:48:16Z | CONTRIBUTOR | {
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} | ## Summary
* Space group information lost when saving to cif
## Example code
```
import pymatgen as mg
from pymatgen import Lattice, Structure, Molecule
# Set up a cubic structure and write to a CIF.
lattice = mg.Lattice.cubic(4.2)
s1 = mg.Structure(lattice, ["Cs", "Cl"],[[0, 0, 0], [0.5, 0.5, 0.5]])
s1.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1231 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1231/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1231/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1231/events | https://github.com/materialsproject/pymatgen/pull/1231 | 347,998,644 | MDExOlB1bGxSZXF1ZXN0MjA2NDU1OTgx | 1,231 | add 'symprec' to method 'to' of 'Structure' | {
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"Pls do not introduce a new keyword symprec to Structure.to. You can simply pass the **kwargs to where you are putting symprec in CifWriter, and that would allow the symprec keyword to work.",
"I fixed it in https://github.com/materialsproject/pymatgen/commit/5f0f80984d54b8d2549bf829342608c8587721e1"
] | 2018-08-06T16:42:58 | 2018-08-07T00:47:52 | 2018-08-07T00:47:51Z | CONTRIBUTOR | {
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} | ## Summary
A memory friendly version of dump parser, reading a file line by line instead of reading the entire file into memory. Computers used to hang when dealing with GB size file, now parsing can be done in a few minutes w/ `pandas.read_csv`, tested to be faster than `numpy.loadtxt`.
## Additional dependencie... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1233 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1233/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1233/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1233/events | https://github.com/materialsproject/pymatgen/pull/1233 | 349,281,623 | MDExOlB1bGxSZXF1ZXN0MjA3NDM2NzQ4 | 1,233 | from_file: recognize ".vasp" extension as POSCAR-type | {
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"Unittest pls. I know this change seems trivial, but I will still need tests for it."
] | 2018-08-09T20:39:25 | 2018-08-10T12:47:01 | 2018-08-10T12:47:01Z | CONTRIBUTOR | {
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} | POSCAR-type files with `.vasp` extension can be read by VESTA but not by pymatgen. One has to rename the file because the `from_file` method doesn't provide a `fmt=` flag.
This change makes life easier. | {
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"I'm guessing the timeout failure in the enumlib test is unrelated?"
] | 2018-08-09T23:31:27 | 2018-08-10T02:00:39 | 2018-08-10T02:00:39Z | CONTRIBUTOR | {
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} | ## Summary
Determining whether a structure is equal to itself can be very expensive for large structures. A structure with 100 atoms can take seconds to verify, and the cost scales with the square of the number of atoms. This change adds a check in the equality operation if the "other" class refers to the same objec... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1235 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1235/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1235/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1235/events | https://github.com/materialsproject/pymatgen/pull/1235 | 349,347,620 | MDExOlB1bGxSZXF1ZXN0MjA3NDg2NzI5 | 1,235 | add init to gb | {
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} | `__init__.py` is generally unnecessary for including packages in editable installs of pymatgen in python 3, but seems to be necessary for non-editable installs (e. g. with pip or `python setup.py install`). I think this should fix the issue. Currently the pip-installed release doesn't include the analysis.gb module, ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1236 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1236/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1236/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1236/events | https://github.com/materialsproject/pymatgen/issues/1236 | 349,485,618 | MDU6SXNzdWUzNDk0ODU2MTg= | 1,236 | Band structure fails to load if vasprun is gzipped and KPOINTS isn't | {
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"Not sure why this is assigned to me (pretty sure I had no part in the original code)?\r\n\r\nBut anyway, I am not sure what os.path.pardir refers to in the above example.\r\n\r\nI would suggest to just use monty zpath (https://pythonhosted.org/monty/_modules/monty/os/path.html) \r\n\r\n\r\nMaybe something like thi... | 2018-08-10T11:48:33 | 2018-12-17T16:22:18 | 2018-12-17T16:22:17Z | CONTRIBUTOR | {
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} | ## System
* Pymatgen version: 2018.7.23
* Python version: 3.6
* OS version: Linux Mint 17.3 64-bit
## Summary
* Using the `BSVasprun` class to import a band structure calculation
* If vasprun.xml and KPOINTS files are present, it loads ok
* If both vasprun.xml and KPOINTS files have been gzipped (i.e. vasp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1237 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1237/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1237/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1237/events | https://github.com/materialsproject/pymatgen/issues/1237 | 349,544,464 | MDU6SXNzdWUzNDk1NDQ0NjQ= | 1,237 | Documentation: Slab surface normal explanation seems fishy to me | {
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"The documentation is correct as is. When you generate a slab, the c vector is out of the a-b plane, which is defined to be parallel to the plane of interest. It does not mean that c is perpendicular to the a-b plane. It will be perpendicular for certain planes, e.g., the (100) plane of the cubic structure or (001)... | 2018-08-10T14:47:33 | 2018-08-11T15:18:55 | 2018-08-10T19:23:52Z | CONTRIBUTOR | {
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* Pymatgen version: v2018.8.10-4-g10cf55a00 (10cf55a00)
* Python version: 3.5.3
* OS version: Debian GNU/Linux 9 (stretch)
## Summary
In the documentation for the [pymatgen.core.surface.Slab](http://pymatgen.org/pymatgen.core.surface.html#pymatgen.core.surface.Slab) class, it says:
> Note that all... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1238 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1238/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1238/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1238/events | https://github.com/materialsproject/pymatgen/pull/1238 | 349,669,214 | MDExOlB1bGxSZXF1ZXN0MjA3NzMxNzM5 | 1,238 | Fix #1237 (docs: slab surface normal explanation) | {
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"What else do I need to do so that one can merge this? The Travis CI check seems to fail because of a time limit.\r\nThanks in advance."
] | 2018-08-13T10:31:51 | 2018-08-17T09:57:51 | 2018-08-17T09:57:51Z | MEMBER | {
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} | ## Summary
I have included a class to read "DOSCAR.lobster" created with Lobster and VASP and another class to evaluate the results so that one could plot "DOSCAR.lobster" with the help of the class DosPlotter.
I have also written tests for both classes.
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1240 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1240/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1240/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1240/events | https://github.com/materialsproject/pymatgen/pull/1240 | 350,198,642 | MDExOlB1bGxSZXF1ZXN0MjA4MTA3NTUy | 1,240 | Changing JMolNN -> JmolNN and fixing algorithm to be consistent with Jmol. | {
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"@shyuep All tests pass now. Ready to be merged. "
] | 2018-08-13T21:20:56 | 2018-08-26T04:32:14 | 2018-08-26T04:32:14Z | MEMBER | {
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} | ## Summary
This PR fixes a naming issue with the Jmol-like NN tool in local_env and makes the algorithm work more consistently with Jmol's algorithm. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1241 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1241/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1241/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1241/events | https://github.com/materialsproject/pymatgen/pull/1241 | 350,995,768 | MDExOlB1bGxSZXF1ZXN0MjA4NzAzMjky | 1,241 | get_cohesive_energy() added to MPRester() and other updates | {
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} | - Added missing metallic radii to periodic table. See:
http://www.wiredchemist.com/chemistry/data/metallic-radii
- WulffShape objects now returns total number of corners and edges on the shape. Useful for studies into nanoparticle catalysis.
- Minor changes to surface_analysis.py to make it less dependent on sym... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1242 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1242/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1242/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1242/events | https://github.com/materialsproject/pymatgen/issues/1242 | 351,128,034 | MDU6SXNzdWUzNTExMjgwMzQ= | 1,242 | Why the BandStructure and BandStructureSymmLine classes have different format of ["bands"] in as_dict() | {
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"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-08-16T09:35:00 | 2023-08-08T21:27:13 | 2023-08-08T21:27:13Z | NONE | {
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I have found the following difference handling the band structure data:
https://github.com/materialsproject/pymatgen/blob/2e03585538072b9e71adaaaa659029f4beaa0a68/pymatgen/electronic_structure/bandstructure.py#L855
https://github.com/materialsproject/pymatgen/blob/2e03585538072b9e71adaaaa659029f4beaa0a68... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1243 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1243/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1243/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1243/events | https://github.com/materialsproject/pymatgen/pull/1243 | 351,610,040 | MDExOlB1bGxSZXF1ZXN0MjA5MTYwMDU5 | 1,243 | Fixes bug in VoronoiNN where atoms in unit cell are not bonded | {
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## Summary
Fixes a bug with VoronoiNN. Under cases where an atom is not bonded to any other atoms in its own image of a unit cell, VoronoiNN will fail to analyze the NN environment of that atom. To fix this problem, we ensure that all sites are in the list of atoms to include in a tessellation
- Added a unit ... | {
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"@montoyjh ",
"The cited lattice isn't cubic, the second vector has a nonzero x-component, which is deformed the same way as the first vector.",
"Put differently, the deformation gradient is a vector mapping, it's applied to each of the three lattice vectors independently.",
"Sounds good, thanks for the expla... | 2018-08-17T19:56:46 | 2018-08-20T12:52:22 | 2018-08-20T12:52:22Z | CONTRIBUTOR | {
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} | Possibly related to this commit: https://github.com/materialsproject/pymatgen/commit/2c3a8dc72dddc72c72ed0dd0b417edc29a76a844
In the test_apply_to_structure unit test (https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/tests/test_strain.py#L43) lattice is defined as:
```
lattice ... | {
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} | ## Added pourbaix functionality for parallel processing of multientries and serialization
* Adds functionality for parallel processing of MultiEntry generation, activated via a `nproc` argument supplied to the PourbaixDiagram constructor. This enables ternary diagrams to be generated much more quickly and quaternar... | {
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"Thanks for the report @bonfus! If you spot any other docstring errors you're also welcome to submit a fix directly (GItHub has an integrated text editor which makes this easy to do)."
] | 2018-08-22T12:02:03 | 2018-08-22T16:40:38 | 2018-08-22T16:40:38Z | NONE | {
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} | Line 291 misleadingly states that the default value of tol is 0.01
https://github.com/materialsproject/pymatgen/blob/8cb71acda73b1544a08a087351edf30d68ed18da/pymatgen/core/structure.py#L283-L291
while it is actually defined as `DISTANCE_TOLERANCE=0.5` above.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1247 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1247/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1247/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1247/events | https://github.com/materialsproject/pymatgen/pull/1247 | 352,964,707 | MDExOlB1bGxSZXF1ZXN0MjEwMTQyMTc3 | 1,247 | Improve Functional Group Substitution/Replacement, aiming to resolve Issue #1072 | {
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"No errors have arisen, but it seems that Travis timed out. What is the best way to move forward and resolve this problem?"
] | 2018-08-22T13:55:11 | 2018-08-22T20:17:26 | 2018-08-22T20:17:25Z | CONTRIBUTOR | {
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} | ## Summary
Previously, functional group substitution was only possible for Molecules, not Structures. In addition, functional group replacements (substituting a functional group for another functional group, rather than an atom for a functional group) was impossible across both classes. This pull request adds functi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1248 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1248/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1248/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1248/events | https://github.com/materialsproject/pymatgen/pull/1248 | 353,187,640 | MDExOlB1bGxSZXF1ZXN0MjEwMzA4NDA4 | 1,248 | Fix Outcar's MSONable pattern | {
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"note the travis-ci test failed due to a timeout. Should we increase this to get all the tests to complete?",
"This is tricky, because this breaks the MSONable contract. ~~I'm assuming you want to keep the MSONable subclass so that dumpfn will correctly use its as_dict() method.~~ (Edit: I realize MontyEncoder wi... | 2018-08-23T01:43:55 | 2020-05-12T15:47:25 | 2018-08-27T02:37:38Z | NONE | {
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} | ## Summary
Outcar is subclassed from MSONable, but is not intended to fully implement this pattern as its not designed to instantiated from the dictionary it generates. This ensures that Monty doesn't try to auto convert the dictionary into an Outcar object, for instance when using loadfn from a jsonified Outcar or ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1249 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1249/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1249/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1249/events | https://github.com/materialsproject/pymatgen/pull/1249 | 353,192,942 | MDExOlB1bGxSZXF1ZXN0MjEwMzExMzUx | 1,249 | bug fix for exporting structure out of LammpsData | {
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} | ## Summary
Fixed a bug where exported structure has Ni or Co in the composition. Thanks to the report by @ucsdlxg
## Additional dependencies introduced (if any)
None
## TODO (if any)
None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1250 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1250/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1250/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1250/events | https://github.com/materialsproject/pymatgen/issues/1250 | 353,319,610 | MDU6SXNzdWUzNTMzMTk2MTA= | 1,250 | suggestion in periodic.py | {
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} | ## Suggested solution (if any)
In the Element class, there are plenty of grouping functions like
* is_transition_metal
* is_noble_gas
...
These are very good functions for one who wants to quickly obtain the select elements by properties. However, there was a special group of 'post_transition_metal' missing he... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1251 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1251/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1251/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1251/events | https://github.com/materialsproject/pymatgen/pull/1251 | 355,063,124 | MDExOlB1bGxSZXF1ZXN0MjExNjc3NTQz | 1,251 | Boltztrap2 interface | {
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"Pls fix failing tests.",
"The main error is due to the missing package boltztrap2 that is required to make the interface work.\r\nHow can we do?",
"@fraricci Add it to requirements-optional.txt and then the test should install it.",
"I added BoltzTraP2 to requirements-optional.txt but it seems not working ye... | 2018-08-29T08:59:00 | 2018-09-07T15:58:05 | 2018-09-07T14:02:37Z | CONTRIBUTOR | {
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} | Here a first version of the interface to BoltzTraP2.
The interface provides the user with three main classes:
- BztInterpolator: it takes care of the interpolation of the bands, giving access to coefficients of the interpolation, eigenvalues on the new denser grid, and others properties. In the same class get_band_st... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1252 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1252/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1252/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1252/events | https://github.com/materialsproject/pymatgen/issues/1252 | 355,388,581 | MDU6SXNzdWUzNTUzODg1ODE= | 1,252 | Bug in API related to tasks? | {
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"@dwinston Can you check on this bug and fix it (with a unittest)? Thanks.",
"@shyuep bug is fixed on MP backend, and #1254 guards against regression. Can close this."
] | 2018-08-30T01:21:42 | 2018-08-30T21:41:30 | 2018-08-30T21:41:30Z | CONTRIBUTOR | {
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} | ## Summary
* `GET https://www.materialsproject.org/rest/v2/tasks/` faild with a error
* the error states `NoneType object is not iterable`
## Example code
```python
url = "https://www.materialsproject.org/rest/v2/tasks/mp-1"
r=requests.get(url, {"API_KEY" : api_key})
```
or
```python
with MPRester(api... | {
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} | Adds a few methods to the base tensor class for projection, integration/averaging, and summaries that are useful for higher-order tensors.
* Tensor.project projects a given tensor into a provided direction
* Tensor.average_over_unit_sphere averages the projection over the unit sphere
* Tensor.get_grouped_indices g... | {
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} | * test getting supported properties
* test aliasing
Guards against #1252 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1255 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1255/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1255/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1255/events | https://github.com/materialsproject/pymatgen/pull/1255 | 355,959,468 | MDExOlB1bGxSZXF1ZXN0MjEyMzY2NzM1 | 1,255 | New Lobster version | {
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} | ## Adapted the classes to the new Lobster version (see www.cohp.de).
*New labels for the icohps and cohps from lobster were necessary since more than one bond per atom pair is possible now
*Added a class to read in "CHARGE.lobster"
*Fixed a bug in Cohpcar class that occured when there were f orbitals in Cohpcar.lob... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1256 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1256/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1256/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1256/events | https://github.com/materialsproject/pymatgen/pull/1256 | 356,014,533 | MDExOlB1bGxSZXF1ZXN0MjEyNDA5OTkw | 1,256 | Add converters to and from dictionary | {
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} | Implement PWInput.as_dict() and PWInput.from_dict(pwinput_dict) methods to the PWInput class.
## Summary
* as_dict method returns a dictionary with a dictionary-encoded Structure object, pseudopotential dictionary, input sections, and k points information
* from_dict method takes a dictionary from as_dict and re... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1257 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1257/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1257/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1257/events | https://github.com/materialsproject/pymatgen/pull/1257 | 356,149,240 | MDExOlB1bGxSZXF1ZXN0MjEyNTEzNTMz | 1,257 | Refactor tensors into core | {
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} | ## Refactor tensors into core
* refactor analysis.elasticity.tensors into core.tensors
* stub added to analysis.elasticity.tensors with a deprecation warning
* adds a rounding functionality that preserves class identity (numpy's default round attribute casts ndarray subclasses back into ndarrays).
* Cleans up a ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1258 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1258/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1258/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1258/events | https://github.com/materialsproject/pymatgen/issues/1258 | 356,360,690 | MDU6SXNzdWUzNTYzNjA2OTA= | 1,258 | bug in electronic_structure/bandstructure.py | {
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"@computron I think this is yours?",
"No I think this was all written by Geoffroy, with the last update to that line from you according to \"git blame\". I really didn't have much to do with writing the band structure classes apart from writing the specific BSDosPlotter and maybe a bugfix here or there",
"I tho... | 2018-09-03T05:17:27 | 2018-09-03T18:45:40 | 2018-09-03T17:39:43Z | NONE | {
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} | ## System
* Pymatgen version: 2018.9.1
* Python version: 2.7.14 and 3.6.3
* OS version: CentOS 7.4.1708
## Summary
* On line 251, v is a Python list but called as a Numpy array
## Example code
```python
#!/usr/bin/env python
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.io.vasp.outputs ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1259 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1259/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1259/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1259/events | https://github.com/materialsproject/pymatgen/pull/1259 | 356,444,077 | MDExOlB1bGxSZXF1ZXN0MjEyNzAzMDI5 | 1,259 | Minor bug fix in wulff.py | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1260 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1260/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1260/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1260/events | https://github.com/materialsproject/pymatgen/pull/1260 | 357,226,124 | MDExOlB1bGxSZXF1ZXN0MjEzMjkxMzMy | 1,260 | Change default value of fix_qcritical | {
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} | ## Summary
* Change default value of fix_qcritical in scheduler (False instead of True)
* Pass `**kwargs` to plt.figure in get_ax_fix_plot and get_ax3d_fig_plt
* Ignore sendmail return code in scheduler | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1261 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1261/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1261/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1261/events | https://github.com/materialsproject/pymatgen/issues/1261 | 357,417,188 | MDU6SXNzdWUzNTc0MTcxODg= | 1,261 | MPRester query for band_gap does not return full dict | {
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"This is an issue with the new builders on emmet, not directly an MPRester issue. Previously gaps from all tasks were included, now only the 'highest-ranked' gap is included:\r\n\r\nhttps://github.com/materialsproject/emmet/blob/master/emmet/vasp/settings/materials_settings.json#L12",
"Will raise an issue on emme... | 2018-09-05T21:49:21 | 2023-08-08T21:27:23 | 2023-08-08T21:27:23Z | NONE | {
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} | ## System
* Pymatgen version: master
* Python version: 3
## Summary
* MPRester query output for 'band_gap' is not consistent with mapidoc
* expect a full dictionary of band gap information, but returns only a single band gap value (presumably from search_gap)
## Example code
```python
mpr.query({'mate... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1262 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1262/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1262/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1262/events | https://github.com/materialsproject/pymatgen/pull/1262 | 357,566,811 | MDExOlB1bGxSZXF1ZXN0MjEzNTQ4ODkz | 1,262 | TensorMapping | {
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} | Replaces some of the ad-hoc tensor mapping procedures with a more explicit TensorMapping class. These are often useful for cases when one has tensor datasets (e. g. stress-strain pairs) and when organizing symmetry-equivalent tensors. Also revises Strain objects to not include deformation matrix attributes, because t... | {
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"I don't think there is a bug. Try `python -c \"import pymatgen.io.vasp;print(dir(pymatgen.io.vasp))\"`",
"That did work!\r\n\r\nI don't fully understand why. for most packages and submodules I should be able to import the entire package (parent directory), i.e `import pymatgen` and subsequently be able to naviga... | 2018-09-06T12:59:29 | 2018-09-06T15:11:03 | 2018-09-06T13:04:26Z | NONE | {
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## System
* Pymatgen version: 2018.9.1
* Python version: 3.5, 3.6
* OS version: ubuntu 14.04
* environment: using conda python
* installed via pip
## Summary
* Missing the **io** submodule, i.e pymatgen.io
* I want to interact with vasp. Therefore I must use `import pymatgen.io.vasp.inputs`
* navigat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1264 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1264/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1264/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1264/events | https://github.com/materialsproject/pymatgen/pull/1264 | 357,745,068 | MDExOlB1bGxSZXF1ZXN0MjEzNjg3MTY3 | 1,264 | Minor bug fix in bandstructure | {
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} | Fixes a bug in the initialization of projections in bandstructure.py. This was causing an error in the boltztrap module test. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1265 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1265/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1265/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1265/events | https://github.com/materialsproject/pymatgen/pull/1265 | 358,413,307 | MDExOlB1bGxSZXF1ZXN0MjE0MTY1NDY1 | 1,265 | Minor CIF Parser Fixes | {
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} | Fixes some minor issues with CIF Parser's get_bibtex_string when dealing with ICSD CIFs
- ensure bibtex gets single strings and not arrays when dealing with _loop fields
- properly formats author field when not supplied via _loop
- simple test for get_bibtex_string so we can monitor incase it breaks | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1266 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1266/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1266/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1266/events | https://github.com/materialsproject/pymatgen/pull/1266 | 358,776,647 | MDExOlB1bGxSZXF1ZXN0MjE0NDMwMzYz | 1,266 | Add function to remove atoms when atoms are too close | {
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"Structure already has a merge_sites method. Is this different? There are so many changes in this code that I don't see where the specific code is.",
"I read the merge_site code in structure.py. It seems like that it is still different from what I want if I understand it correctly. e.g. if we have three atoms a, ... | 2018-09-10T20:14:06 | 2018-09-22T00:45:04 | 2018-09-22T00:45:04Z | CONTRIBUTOR | {
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} | The user now can set a criteria to remove atoms if the atoms are too close with each other.
This function is very useful for tilt GB generation. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1267 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1267/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1267/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1267/events | https://github.com/materialsproject/pymatgen/issues/1267 | 358,847,193 | MDU6SXNzdWUzNTg4NDcxOTM= | 1,267 | Is there a way that I can get a band structure projected on atom?s | {
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"@hautierg Can you answer pls.",
"any updates ?",
"Viet Anh, could you answer this?\r\n\r\nThanks,\r\n\r\nGeoffroy\r\n\r\nOn 20 Sep 2018, at 15:32, Shuyang Yang <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n\r\nany updates ?\r\n\r\n—\r\nYou are receiving this because you were mention... | 2018-09-11T00:57:21 | 2023-08-08T21:27:35 | 2023-08-08T21:27:35Z | NONE | {
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} | I can only get projected on element or orbitals when plotting the band structure. How can I project on atoms ? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1268 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1268/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1268/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1268/events | https://github.com/materialsproject/pymatgen/issues/1268 | 359,276,029 | MDU6SXNzdWUzNTkyNzYwMjk= | 1,268 | Is there a method to parse a formula containing "@" ? | {
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"Hi @tamuhey , this isn't supported right now but you'd be welcome to submit a pull request to add this feature.\r\n\r\nYou'd want to strip out any '@' symbols present in the formula here:\r\nhttps://github.com/materialsproject/pymatgen/blob/master/pymatgen/core/composition.py#L468\r\n\r\nAnd then it should work as... | 2018-09-12T00:56:07 | 2018-09-12T16:43:43 | 2018-09-12T16:43:43Z | CONTRIBUTOR | {
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} | I am searching a parser of chemical formula that can handle [Metallofullerene](https://en.wikipedia.org/wiki/Metallofullerene), whose formula contains "@" symbol.
For example, I tried to handle it with `pymatgen.core.composition.Composition` class, like below
```python
Composition("Dy3N@C80")
```
but this causes... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1269 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1269/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1269/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1269/events | https://github.com/materialsproject/pymatgen/pull/1269 | 359,327,400 | MDExOlB1bGxSZXF1ZXN0MjE0ODQ0MzM0 | 1,269 | Update composition parser able to handle "@" #1268 | {
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"Thanks."
] | 2018-09-12T06:02:26 | 2018-09-12T16:40:08 | 2018-09-12T16:39:48Z | CONTRIBUTOR | {
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} | ## Summary
See the issue #1268
* Update Composition._parse_formula able to handle "@", that is usually used in Metallofullerene formula (e.g. Y3N@C80)
* Add test_Metallofullerene to test the updated parser | {
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"Would it be possible to notify the BoltzTrap2 maintainers of this as well? A colleague was trying to install BoltzTrap2 recently via pip and was unable to do so / didn't realize additional CFLAGS had to be set.",
"Yes, it's a better solution actually. It can be useful in general.\r\nI'll do that so. Thanks\r\n",... | 2018-09-12T15:12:33 | 2018-09-17T20:49:05 | 2018-09-12T16:12:48Z | CONTRIBUTOR | {
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} | I found a bug in plotting the dos.
In case the densities array have zeros
in the first and last elements, the fill_between()
function fill the outer part of the dos and not the
inner one as it should.
In any case, since the dos plot has densities in the
x-axis, the proper function to use should be fill_betweenx... | {
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"Can you pls include a unittest with the code? Thanks.",
"A meaningful test will need to open files called \"KPOINTS\" and \"vasprun.xml.gz\". Where should these be located? Is there a convention in this project for making temporary files/folders during testing?",
"try using monty's ScratchDir\r\n```\r\nfrom mo... | 2018-09-12T17:45:27 | 2018-09-19T15:18:51 | 2018-09-19T15:18:51Z | CONTRIBUTOR | {
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} | ## Summary
Pull request corresponding to Issue #1236
Monty's `zpath` is used to find (un)compressed KPOINT files corresponding to (un)cimpressed vasprun path. This was the solution suggested by @computron and it seems to cover all the permutations; you can even use gzip for one file and bzip2 for the other.
#... | {
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"I completely second the idea of restructuring for molecules/disordered structures. Currently, any function in MoleculeGraph which interfaces with the local_env NearNeighbor strategies has to have reorder and extend_structure kwargs to play nicely with the NearNeighbor classes; most NearNeighbor classes will wrap a... | 2018-09-12T22:57:55 | 2023-08-08T21:28:01 | 2023-08-08T21:28:01Z | MEMBER | {
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} | A colleague had issues when trying to use analysis.local_env.NearNeighbor directly, which is not possible. This should be an abstract base class.
NearNeighbor could probably also be restructured a little to be friendlier to molecules and disordered structures, and avoid repeating any expensive structure operations (... | {
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"There are still errors. The vasprun test file provided is a bad one - the xml is invalid. See https://ci.appveyor.com/project/shyuep/pymatgen/build/1.0.2756"
] | 2018-09-13T12:13:55 | 2018-09-13T14:21:32 | 2018-09-13T13:28:19Z | CONTRIBUTOR | {
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"There are still failing tests. It says VasprunLoader is not defined.",
"weird... Is it loading boltztrap2 package?",
"I'm not sure how to set a variable in windows.\r\nCould you take care of that?\r\nWe could also skip installing boltztrap2 on windows, I added an IF that should skip the test in case\r\nit's no... | 2018-09-13T14:27:14 | 2018-09-14T09:52:17 | 2018-09-14T09:48:13Z | CONTRIBUTOR | {
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"Thre are failing tests related to the defect package. Pls fix first.",
"Apologies. Tests are fixed now."
] | 2018-09-13T18:39:13 | 2018-09-17T19:02:50 | 2018-09-17T19:02:50Z | CONTRIBUTOR | {
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} | **Non-defects related**
1) Add ability for Incar.from_string to import multiple settings in a single line separated by a semi-colon (Ex. "LHFCALC= True ; HFSCREEN = 0.2"), also add unit test to ensure this works
**Defects related**
2) Enforce lattice matching between defect site and structure inputs to Defect obje... | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: "master"
* Python version: 3.7
* OS version: Mac
## Summary
* Chemenv uses lots of np.matrix, resulting in the following deprecation ... | {
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"rofl @shyuep not following his own issue template :) \r\n@montoyjh \r\n\r\nEdit: I'm bad at reading. Expected the bottom bit of text at the top in place of the default block. ",
"Erm, I did...."
] | 2018-09-16T14:54:26 | 2023-08-08T21:28:41 | 2023-08-08T21:28:41Z | MEMBER | {
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} | When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: "Master"
## Summary
* See output from nose-timer below.
```
[success] 68.23% pymatgen.analysis.tests.test_pourbaix_diagram.PourbaixDi... | {
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"@samblau ",
"I sped up the QCOutput tests by about an order of magnitude a couple weeks ago. They now take ~16 seconds. A large QChem-centric pull request will be coming soon which will include those improvements along with many other updates. ",
"Thanks for fixing these in #1293 @samblau !"
] | 2018-09-16T15:40:21 | 2018-10-04T19:48:47 | 2018-10-04T19:48:47Z | MEMBER | {
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} | ## System
* Pymatgen version: "Master"
## Summary
* QCOutput tests take so much longer than the entire VASP test suite, including CHGCARs.
```
[success] 71.43% pymatgen.io.qchem.tests.test_outputs.TestQCOutput.test_all: 159.0792s
[success] 4.17% pymatgen.io.vasp.tests.test_outputs.OutcarTest.test_init: 9.28... | {
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"Tagging @blondegeek for this issue. This is news to me, but looks like numpy is deprecating np.matrix:\r\n\r\n> It is no longer recommended to use this class, even for linear algebra. Instead use regular arrays. The class may be removed in the future.",
"I really need this to be dealt with soon. The visual noise... | 2018-09-17T17:13:01 | 2018-11-19T02:54:47 | 2018-11-19T02:54:47Z | MEMBER | {
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} | ## System
* Pymatgen version: Master
## Summary
* Currently the polarization module uses np.matrix, which will be deprecated from py3.8 due to the introduction of the matrix multiplication operator (@).
* This leads of excessive deprecation messages.
## Suggested solution (if any)
* Replace all np.matri... | {
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"Looking at `VoronoiNN().get_voronoi_polyhedra()` in more detail. The code actually mentions the potential for a segfault to occur if the cutoff used is too small.\r\n\r\n```python\r\n while True:\r\n try:\r\n neighbors = structure.get_sites_in_sphere(\r\n center.... | 2018-09-17T20:39:30 | 2018-09-26T21:27:49 | 2018-09-26T21:27:49Z | MEMBER | {
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} | Calling `pymatgen.analysis.local_env.VoronoiNN.get_voronoi_polyhedra()` on a structure obtained via `MPRester` is causing Python to crash. Note that Python itself is crashing, not just returning an error message.
The structure in question is: https://materialsproject.org/materials/mp-978085/. It is a relatively smal... | {
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"Can you implement some unittests to confirm the new functionality pls? Thanks.",
"My apologies, tests are now added."
] | 2018-09-18T20:24:15 | 2018-09-19T18:02:25 | 2018-09-19T18:02:24Z | CONTRIBUTOR | {
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## Summary
* Semantically, `MolecularOrbitals` should only handle compositions with integer-valued subscripts.
* The doc strings for this class have been updated to reflect the intended use.
* A feature has been added that raises a `ValueError` when non-integer subscripts are used.
(the issue of non-integer s... | {
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} | ## Summary
* New WeightedNbSetChemenvStrategy (accepts an arbitrary number of "weights")
* New weights DistanceNbSetWeight and DeltaDistanceNbSetWeight
* Fix of func_utils (smoothstep/smootherstep problem)
* Additional tests for new functionalities
* Removed unnecessary and unused code | {
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"Thanks @jmmshn, will take a look at this when tests pass."
] | 2018-09-20T21:27:46 | 2018-09-21T01:40:22 | 2018-09-21T01:40:22Z | CONTRIBUTOR | {
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VolumetricData(object) -> VolumetricData(MSONable)
added tests for as_dict and from_dict | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1286 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1286/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1286/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1286/events | https://github.com/materialsproject/pymatgen/issues/1286 | 362,796,255 | MDU6SXNzdWUzNjI3OTYyNTU= | 1,286 | EnumerateStructureTransformation does not return structures with correct stoichiometries | {
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"For reference, the [topic on the pymatgen help group](https://groups.google.com/forum/#!topic/pymatgen/uK6kRiSqFEg)",
"I'm a bit confused by this too. It seems clear the first ordering sets one `Cu:0.4` site to 0, and the other `Cu:0.4` site to 1, which is not completely unreasonable but obviously the overall co... | 2018-09-21T22:46:48 | 2018-09-25T17:30:12 | 2018-09-25T00:13:52Z | CONTRIBUTOR | {
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} | **Describe the bug**
Using `EnumerateStructureTransformation` with the `max_disordered_sites` parameter specified does not return structures with correct stoichometry. For example, with the attached cif file for Cu2.8Te2 the output structures should be Cu7Te5; however, the output structures are Cu3Te2.
**To Reprodu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1287 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1287/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1287/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1287/events | https://github.com/materialsproject/pymatgen/pull/1287 | 362,969,568 | MDExOlB1bGxSZXF1ZXN0MjE3NTI2MDgx | 1,287 | Improvements to CifParser (finite precision, implicit hydrogens) + tests | {
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"Some of the CIF fixes inadvertently change FEFF tests, will close until FEFF tests updated.",
"Hi @czhengsci ,\r\n\r\nI have some improvements to CIF that break the FEFF tests, would it be possible to update the FEFF tests?\r\n\r\nBefore the CIF changes, CoO19128.cif parses as:\r\n\r\n```\r\nStructure Summary\r\... | 2018-09-23T19:21:30 | 2018-09-25T00:49:06 | 2018-09-25T00:49:06Z | MEMBER | {
"total": 0,
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} | ## Summary
* Fixes issue with finite precision in frac co-ords (0.6667 vs 0.6666666667) causing errors in resulting structure.
* Will warn/store warning if attached hydrogens detected.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* None | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1288 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1288/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1288/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1288/events | https://github.com/materialsproject/pymatgen/issues/1288 | 362,990,698 | MDU6SXNzdWUzNjI5OTA2OTg= | 1,288 | Are there any plans on adding plotly based plotting codes to pymatgen (or to the optional requirements) in the future? | {
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"I am all for adding plot.ly based GUIs. But as a longer term strategy, we probably cannot be implementing GUIs on a regular basis as frameworks and code changes.\r\n\r\nMy suggestion is to think of a \"universal\" plot data container, e.g., a Pandas Dataframe. Then we implement a few things that translate the univ... | 2018-09-24T00:18:18 | 2023-08-08T21:33:27 | 2023-08-08T21:30:58Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1289 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1289/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1289/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1289/events | https://github.com/materialsproject/pymatgen/pull/1289 | 364,202,867 | MDExOlB1bGxSZXF1ZXN0MjE4NDQ3OTQy | 1,289 | Change default VoronoiNN cutoff | {
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"Excellent, thanks @utf !"
] | 2018-09-26T20:40:45 | 2018-09-26T21:41:22 | 2018-09-26T21:27:49Z | MEMBER | {
"total": 0,
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} | ## Summary
Change default cutoff of `VoronoiNN` from 10.0 to 13.0. This fixes #1281 for all 85,000 materials currently in the materials project database.
I have also changed the way the max_cutoff is calculated. Previously, the max cutoff was incorrect for cells with angles not equal to 90 deg (e.g. for the examp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1290 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1290/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1290/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1290/events | https://github.com/materialsproject/pymatgen/pull/1290 | 364,723,241 | MDExOlB1bGxSZXF1ZXN0MjE4ODQwNjcw | 1,290 | [Waiting on tests] add BXSF support | {
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"Hi @specter119, thanks for your contribution! We will definitely need a test.\r\n\r\nAn appropriate place for this test would be `pymatgen.io.tests.test_xcrysden`, you can copy the existing `XSFTest` as a template to create a `BXSFTest`. To test your `from_vasprun()` method, you can reference one of the existing v... | 2018-09-28T02:58:33 | 2022-10-10T16:58:52 | 2022-10-10T16:56:48Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
vasp need to run with previous `CHGCAR`
start with nscf vis updated by
```python
user_incar_settings={
'SYM': -1,
'ICHARG': 11,
'ISMEAR': 0
}
```
and a [general grid](http://www.xcrysden.org/doc/XSF.html#genper) kpoints
for example:
```python
from itertools import product
import n... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1291 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1291/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1291/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1291/events | https://github.com/materialsproject/pymatgen/pull/1291 | 365,264,178 | MDExOlB1bGxSZXF1ZXN0MjE5MjI5Mzg3 | 1,291 | New StructureGraph analysis methods + speed up extract_molecules test | {
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} | ## Summary
* Adds three new methods to StructureGraph:
* `types_and_weights_of_connections` returns e.g. for MoS2 `{'Mo-S': [2.4169, 2.4169, 2.4169, 2.4169, 2.4169, 2.4169]`
* `weight_statistics` returns a dict summarizing statistics of weights in the graph (e.g. min, max, mean, variance)
* `types_of_coord... | {
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"I basically halved the time for tests by using multi-processing. Some of the io bound tests (e.g., getting data from MP / reading from files) are sped up enormously. But I sitll prefer to get total test time down below 10mins. Right now it is 20mins, down from 40mins.",
"This is great! I just re-ran nose-timer o... | 2018-09-30T21:41:54 | 2019-05-23T13:50:03 | 2019-05-23T13:50:03Z | MEMBER | {
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} | [success] 20.10% pymatgen.io.qchem.tests.test_outputs.TestQCOutput.test_all: 153.4455s
[success] 6.81% test_gb.Test_GBGenerator.test_gb_from_parameters: 52.0188s
[success] 3.77% pymatgen.ext.tests.test_matproj.MPResterTest.test_get_pourbaix_entries: 28.8016s
[success] 2.90% test_elastic.DiffFitTest.test_fit: 22.1355... | {
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"Thanks. I will merge this for this time. But in future, pls submit PRs in bite-size morsels. Otherwise, it makes review extremely difficult.",
"Will do - sorry about that!",
"The fragmenter tests are taking way too long. Can you fix them pls? Pls try to get tests down to less than 10s.\r\n\r\n[None] 16.61% pym... | 2018-10-01T19:27:05 | 2018-10-05T19:19:39 | 2018-10-02T23:46:06Z | CONTRIBUTOR | {
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} | ## Summary
* New molecule fragmenter in analysis/fragmentation.py. Can find all possible fragments of a molecule or only fragments obtained within a specific number of bond breakages, including ring openings. Relies heavily on molecule graphs, networkx, and open babel. Essential to a new fragmentation firetask in At... | {
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"Thank you for the comprehensive report. However, I don't think you are doing the slabs right in VESTA. First of all, you can logically reason (without any code) that it is an impossibility that (102) is not equivalent to (012) in hexagonal systems. By definition, hexagonal systems have a 3/6-fold rotational symmet... | 2018-10-02T11:33:29 | 2018-10-23T14:45:53 | 2018-10-23T14:21:50Z | NONE | {
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} | Dear community,
first of all I would like to thank you for the great work you put into the project. I started working with pymatgen a few months ago. I stumbled across the "bug" by accident and did quite some tests for verification.
The intention to use pymatgen was the availability of a slab generator for crys... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1295 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1295/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1295/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1295/events | https://github.com/materialsproject/pymatgen/issues/1295 | 366,189,360 | MDU6SXNzdWUzNjYxODkzNjA= | 1,295 | Possible issue with DLSVolumePredictor | {
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"Also tagging @tschaume here",
"Increasing cutoff by 10-20x (tried up to 80.0) also doesn't seem to change the result.",
"@computron Incidentally, why are we using DLS? In most instances, the RLS should work fine. As far as I know, we don't have any method of structure prediction from completely unknown crystal... | 2018-10-03T06:13:37 | 2019-02-12T21:01:24 | 2019-02-12T21:01:24Z | MEMBER | {
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} | **Describe the bug**
In a very small number of cases, `DLSVolumePredictor` seems to be giving non-sensical volumes.
**To Reproduce**
This structure almost made it to MP (though way off the hull!):
```
{'@module': 'pymatgen.core.structure',
'@class': 'Structure',
'charge': None,
'lattice': {'matrix': ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1296 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1296/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1296/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1296/events | https://github.com/materialsproject/pymatgen/issues/1296 | 366,872,939 | MDU6SXNzdWUzNjY4NzI5Mzk= | 1,296 | pip version 2018.9.30 is broken | {
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"Interesting, thanks for the report. I tested the release and it installs fine on my machine, both with the macOS wheel and direct from source. There is no Linux wheel at present which means your computer has to compile the Cython coord utils itself, so this is likely a compiler issue on your own machine.\r\n\r\nIf... | 2018-10-04T16:31:10 | 2021-07-01T15:50:08 | 2018-11-17T00:15:24Z | NONE | {
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**Describe the bug**
upgrading pymatgen to latest version breaks the build. The previous version works okay.
system details: python3.6 with intel
<ipython-input-2-ad23870f0a12> in <module>()
1 import numpy as np
----> 2 from pymatgen import Structure
~/.local/lib/python3.6/site-packages/pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1297 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1297/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1297/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1297/events | https://github.com/materialsproject/pymatgen/pull/1297 | 366,981,064 | MDExOlB1bGxSZXF1ZXN0MjIwNTI1NzE2 | 1,297 | Test ieee | {
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} | ## Summary
* Fixes bug in triclinic IEEE tensor conversion where c axis was being rotated into x instead of z axis.
* Adds test for triclinic conversion. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1298 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1298/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1298/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1298/events | https://github.com/materialsproject/pymatgen/pull/1298 | 367,954,088 | MDExOlB1bGxSZXF1ZXN0MjIxMjQ0MDcw | 1,298 | Insertion batt js | {
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"Test for a case that previously wasn't working?"
] | 2018-10-08T21:09:47 | 2018-10-13T05:49:08 | 2018-10-13T05:49:08Z | CONTRIBUTOR | {
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} | ## Small changes to the insertion battery module
* updated the artificial shift in energy to the non-working-ion elements so that we can always have a convex hull of with just the working-ion changing
* made the dicts for adj_pairs and all_paris return the actual list and not just the iterator.
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"Thanks for this!"
] | 2018-10-09T12:33:10 | 2018-10-09T23:21:03 | 2018-10-09T16:11:15Z | CONTRIBUTOR | {
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} | Recently, a build_MoleculeGraph function was added to pymatgen.analysis.graphs. This function allowed the user to create a MoleculeGraph either by specifying a pymatgen.analysis.local_env strategy, or by specifying the edges between nodes explicitly. This function was deemed unnecessary, as it effectively replicated th... | {
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"What's the difference between this method and Chgcar.get_integrated_diff?",
"This is meant to look at the data['total'] and just suggest the best site to insert an interstitial atom.\r\nThe Chgcar.get_integrated_diff is really meant for analysis of the data['diff'].\r\nThere is mention of get_integrated_diff bei... | 2018-10-13T00:46:20 | 2018-11-05T03:06:59 | 2018-11-05T03:06:59Z | CONTRIBUTOR | {
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"diff_url": "https://github.com/materialsproject/pymatgen/pull/1300.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1300.patch",
"merged_at... |
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