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https://api.github.com/repos/materialsproject/pymatgen/issues/1501 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1501/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1501/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1501/events | https://github.com/materialsproject/pymatgen/pull/1501 | 458,277,132 | MDExOlB1bGxSZXF1ZXN0Mjg5OTIwNDQ5 | 1,501 | Run type method | {
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"Thanks. Pls look at the travis CI test. There is one failing test due to the new runtype tests.",
"@darnoceloc did you mean to delete maggroups.py?",
"I meant to delete the commit not the actual file since that is not part of my PR.\r\nSome of my commits appear redundantly as well due to some git pull commands... | 2019-06-20T00:09:21 | 2019-06-21T02:07:38 | 2019-06-21T00:57:50Z | CONTRIBUTOR | {
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} | ## Summary
- Modified run_type_method in Vasprun class within outputs.py script to account for wider range of functionals/levels of theory.
- Added tests within test_outputs.py script in io/vasp/tests directory and new test files relevant to various functionals/levels of theory.
## TODO (if any)
If this is a ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1502 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1502/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1502/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1502/events | https://github.com/materialsproject/pymatgen/pull/1502 | 458,391,545 | MDExOlB1bGxSZXF1ZXN0MjkwMDA1MTA1 | 1,502 | Fix for magnetic space groups | {
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"Thanks very much for fixing this bug @simonward86 (the space group cut-off was my error, I was not including the trigonal int numbers within that range, so thanks for catching that also!)\r\n\r\nI'll compare some more results to https://stokes.byu.edu/iso/magnetic_table_bns.txt via the `_write_all_magnetic_space_g... | 2019-06-20T07:15:45 | 2019-06-20T18:04:39 | 2019-06-20T18:04:39Z | NONE | {
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} | ## Summary
This fixes magnetic symmetry operations in pymatgen/symmetry/maggroups.py .
* Fix 1 : Hexagonal magnetic spacegroups start at 143 instead of 168. This can be verified by VESTA.
* Fix 2 : When reshaping data from https://stokes.byu.edu/iso/magnetic_data.txt , the data should be read in columns instead... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1503 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1503/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1503/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1503/events | https://github.com/materialsproject/pymatgen/issues/1503 | 458,737,566 | MDU6SXNzdWU0NTg3Mzc1NjY= | 1,503 | Pymatgen function to get XAS | {
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"@yimingchen95 Pls handle."
] | 2019-06-20T15:50:48 | 2019-06-27T15:24:35 | 2019-06-27T15:24:35Z | NONE | {
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} | There needs to be a pymatgen function to get XAS spectra from MP:
The format to get data by MP ID seems to be:
`f"/materials/{mpid}/xas/{absorbing_element}"` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1504 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1504/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1504/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1504/events | https://github.com/materialsproject/pymatgen/pull/1504 | 458,972,171 | MDExOlB1bGxSZXF1ZXN0MjkwNDM2MzMw | 1,504 | Modified run_type in outputs.py. | {
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"Thanks."
] | 2019-06-21T02:05:53 | 2019-06-21T18:43:26 | 2019-06-21T18:43:20Z | CONTRIBUTOR | {
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} | ## Summary
Updated run_type_method but phonoopy test giving error which is independent of my changes.
* Modified run_type_method in Vasprun class within outputs.py script to account for wider range of functionals/levels of theory.
* Added tests within test_outputs.py script in io/vasp/tests directory and new ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1505 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1505/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1505/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1505/events | https://github.com/materialsproject/pymatgen/pull/1505 | 459,384,578 | MDExOlB1bGxSZXF1ZXN0MjkwNzU3ODI0 | 1,505 | add get_xas_data method | {
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"The test is too basic. You cannot just test length of data. Test some of the internal structure."
] | 2019-06-21T21:48:21 | 2019-06-23T03:45:00 | 2019-06-23T03:45:00Z | CONTRIBUTOR | {
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} | ## Summary
This solves issue #1503 by implementing get_xas_data method in MPRester.
* Add get_xas_data method in MPRester
* Add unittest
## Additional dependencies introduced (if any)
* none
## TODO (if any)
* none | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1506 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1506/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1506/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1506/events | https://github.com/materialsproject/pymatgen/issues/1506 | 459,412,522 | MDU6SXNzdWU0NTk0MTI1MjI= | 1,506 | local_env.NearNeighbors and its subclasses are not serializable/deserializable | {
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"Hi @chc273, thanks for suggesting this. I’m currently re-working this class since the current class has a few issues. I can make it MSONable, but I think I want to include structure in the init too, which will perhaps cause its own problems too. There’s an open pull request and issue you may want to take a look at... | 2019-06-22T00:26:26 | 2023-08-10T15:01:05 | 2023-08-10T15:01:05Z | CONTRIBUTOR | {
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} | I wonder why `NearNeighbors` and its subclasses do not inherit from `monty.json.MSONable` so that the instances can be serialized/deserialized as other pymatgen objects?
I personally find a need for this in our `megnet` project, where we used the NearNeighbors as a way to find graphs and need to save the graph util... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1507 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1507/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1507/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1507/events | https://github.com/materialsproject/pymatgen/issues/1507 | 459,552,072 | MDU6SXNzdWU0NTk1NTIwNzI= | 1,507 | Delay warning of missing requirements in `io.cif` as a late as possible | {
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"Thanks. I fixed this. But instead of a warning, I simply make it throw an exception. The idea is that if someone is calling get_bibtex_string, they must actually be interested in a result and a runtime error should ensue if pybtex is not installed.",
"Thanks for the very quick response and action @shyuep :+1: "
... | 2019-06-23T08:51:16 | 2019-06-23T09:19:02 | 2019-06-23T09:15:49Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
Delay the printing of warnings as late as possible in `io.cif`.
Currently, just importing the module `io.cif` will print the warning if `pybtex` is not installed:
```
try:
from pybtex.database import BibliographyData, Entry
except ImportError:... | {
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"Thanks @Tinaatucsd! Would it be possible to rename `get_gb_data` to `get_grain_boundary_data` before we merge? Just to be more descriptive/more discoverable by people. Otherwise looks good!",
"@mkhorton I think get_gb is fine. gb is a very well-established abbreviation. We need to balance between descriptive and... | 2019-06-23T18:25:49 | 2019-06-24T04:04:10 | 2019-06-24T04:04:10Z | CONTRIBUTOR | {
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* add grain boundary MPRester to query grain boundary structure and energy data
* add unittest
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https://api.github.com/repos/materialsproject/pymatgen/issues/1509 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1509/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1509/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1509/events | https://github.com/materialsproject/pymatgen/pull/1509 | 460,028,801 | MDExOlB1bGxSZXF1ZXN0MjkxMjQyODIw | 1,509 | atat to_string method | {
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"Many thanks @dongsenfo!"
] | 2019-06-24T18:17:08 | 2019-06-24T23:07:09 | 2019-06-24T23:07:09Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1510 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1510/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1510/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1510/events | https://github.com/materialsproject/pymatgen/pull/1510 | 460,201,248 | MDExOlB1bGxSZXF1ZXN0MjkxMzc4MzE0 | 1,510 | add remove atoms option to the GrainBoundaryTransformation | {
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"Thanks @Tinaatucsd! Do you recommend setting \"quick_gen\" to True for the interactive app?",
"Yes, please. The \"quick_gen\" will accelerate the generation process but the generated GB maybe not the smallest possible cell. I think it's ok to do visualization using the larger cell. (The smallest cell is useful i... | 2019-06-25T04:22:08 | 2019-06-25T20:44:55 | 2019-06-25T20:33:44Z | CONTRIBUTOR | {
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* Update the GrainBoundaryTransformation such that remove atoms option is available. This option is useful if atoms around the grain boundary region are too close to each other. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1511 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1511/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1511/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1511/events | https://github.com/materialsproject/pymatgen/issues/1511 | 460,350,146 | MDU6SXNzdWU0NjAzNTAxNDY= | 1,511 | Obey and fix deprecation warnings | {
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"As far as I know, this was fixed some time ago. If you believe this not to be true, pls go ahead and implement a fix. As for using six, we already abandoned Py2 support from 2019. ",
"Yes, in fact they should be present since `v2019.3.13`. Sorry for the noise."
] | 2019-06-25T10:47:56 | 2019-06-25T12:22:58 | 2019-06-25T11:30:28Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
Please consider to fix all relevant deprecation warnings. One example:
```
pymatgen/core/sites.py:31: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop workin... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1512 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1512/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1512/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1512/events | https://github.com/materialsproject/pymatgen/issues/1512 | 460,393,253 | MDU6SXNzdWU0NjAzOTMyNTM= | 1,512 | BabelMolAdaptor should be able to return all molecules found in a file | {
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"Tagging @samblau here since he's been working a lot with the OpenBabel adapter.",
"@samblau and I were chatting and it looks like the easiest solution would be to add a new keyword argument, `return_all_molecules=False`, that when set to `True` would just return the entire list (we should set it to False by defa... | 2019-06-25T12:25:54 | 2019-07-23T14:32:27 | 2019-07-23T14:32:27Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
The way it's currently implemented, ``pymatgen.io.babel.BabelMolAdaptor`` will only ever return the first molecule it finds in a file and discard the rest:
https://github.com/materialsproject/pymatgen/blob/5006e2c92d669a05775fcf67dd9b1f0b972c9636/pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1513 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1513/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1513/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1513/events | https://github.com/materialsproject/pymatgen/issues/1513 | 460,791,792 | MDU6SXNzdWU0NjA3OTE3OTI= | 1,513 | Vasprun does not discriminate both Kpoint sets when LVEL flag is set | {
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"Thanks for reporting this. I have no idea what the LVEL tag does. If this is an issue, I would suggest you perhaps fork the repo and implement a quick fix?",
"The actual purpose of the LVEL flag is also unclear to me, as it is undocumented.\r\n\r\nIn my particular case, I want to use it as it will write the full... | 2019-06-26T06:48:02 | 2019-06-27T19:14:43 | 2019-06-27T19:14:43Z | CONTRIBUTOR | {
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} | **Describe the bug**
When running VASP with the LVEL flag set, two kpoint sets are generated (probably IBZ and FBZ).
The Vasprun class will read both to the same variable overwriting the first that has been read.
Unfortunately, the set that is overwritten is the one associated to the eigenvalue array.
In the vaspru... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1514 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1514/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1514/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1514/events | https://github.com/materialsproject/pymatgen/pull/1514 | 461,371,076 | MDExOlB1bGxSZXF1ZXN0MjkyMzA5NjQ1 | 1,514 | Fix reading the SC K-Point set when LVEL flag is set. | {
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"Thanks @JRSuckert. I'm not familiar with the LVEL flag, I was about to ask what this is for and then saw the discussion in the issue :)"
] | 2019-06-27T07:46:45 | 2019-06-27T19:07:42 | 2019-06-27T19:07:42Z | CONTRIBUTOR | {
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} | ## Summary
This PR tries to fix the issue of #1513.
When running vasp with the LVEL flag enabled, two kpoint sets are written to the vasprun.xml file.
One quite far up in the file, containing the kpoints in the irreducible Brillouin zone, and one after the self-consistent calculation inside the electronvelocities ta... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1515 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1515/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1515/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1515/events | https://github.com/materialsproject/pymatgen/pull/1515 | 461,697,652 | MDExOlB1bGxSZXF1ZXN0MjkyNTYyNjI4 | 1,515 | Add option to translate molecule to origin in add_adsorbate | {
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"Thanks @oxana-a ! We'll wait for the CI tests to pass otherwise looks good to merge"
] | 2019-06-27T18:58:31 | 2019-06-27T20:20:37 | 2019-06-27T20:20:37Z | CONTRIBUTOR | {
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} | ## Summary
Updated _add_adsorbate_ to work with a copy of the adsorbate molecule and added the _translate_ keyword - if _True_, the molecule is translated to the origin before being added to the surface.
* Updated _add_adsorbate_ to work with a copy of the molecule passed as an argument. Previously, if _reorient_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1516 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1516/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1516/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1516/events | https://github.com/materialsproject/pymatgen/pull/1516 | 461,729,336 | MDExOlB1bGxSZXF1ZXN0MjkyNTg4MDQ5 | 1,516 | add options to query certain surface plane, and work of separation | {
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"Thanks @Tinaatucsd !"
] | 2019-06-27T20:19:12 | 2019-06-28T01:55:16 | 2019-06-28T01:55:16Z | CONTRIBUTOR | {
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} | ## Summary
* When query surface data, a new option to query certain surface plane is added by providing the Miller index.
* When query grain boundary data, users can also choose to include the work of separation value (unit: J/m^2) of the corresponding grain boundary. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1517 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1517/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1517/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1517/events | https://github.com/materialsproject/pymatgen/pull/1517 | 462,582,659 | MDExOlB1bGxSZXF1ZXN0MjkzMjM0MzAy | 1,517 | Waveder reading changed from FortranFile to directly reading binary. | {
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"Thanks @JRSuckert !"
] | 2019-07-01T08:30:46 | 2019-07-02T20:34:29 | 2019-07-02T20:34:29Z | CONTRIBUTOR | {
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} | ## Summary
This change was made due to the fact that FortranFile can not read records with the number of
entries exceeding int32 limits (filesize >~ 2GB). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1518 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1518/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1518/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1518/events | https://github.com/materialsproject/pymatgen/pull/1518 | 462,949,606 | MDExOlB1bGxSZXF1ZXN0MjkzNTI4MTM1 | 1,518 | Add ShengBTE IO Functions | {
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"Quick note. Any factory functions should be class methods. This ensures that if you just inherit from them the factory function generates the inherited class.",
"Thanks for the info @shyamd \r\n\r\n@rees-c Can you make the `from_file` function a class method again. Also make this method call the `cls.from_dict` ... | 2019-07-01T23:11:16 | 2019-07-11T20:25:46 | 2019-07-11T20:25:46Z | CONTRIBUTOR | {
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} | ## Summary
@utf
Initial commit for interfacing Pymatgen with ShengBTE. More features will be added later.
ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. It is capable of using 2nd and 3rd order interatomic force constants to calculate lattice thermal conductivities of... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1519 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1519/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1519/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1519/events | https://github.com/materialsproject/pymatgen/pull/1519 | 462,950,318 | MDExOlB1bGxSZXF1ZXN0MjkzNTI4NzA0 | 1,519 | Added CSLD functionality | {
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"Hi Rees, the tests are still failing. Can you have a look and try and fix please.",
"@mkhorton \r\n\r\nThis PR is no longer WIP.",
"Thanks @utf and @rees-c, this looks really useful! I had a request for something along the lines of CubicSupercellTransformation very recently in the context of creating input cel... | 2019-07-01T23:14:14 | 2019-07-09T23:13:51 | 2019-07-09T23:13:36Z | CONTRIBUTOR | {
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} | This branch adds functionality to ultimately be used in a high-throughput workflow implementing compressed sensing lattice dynamics for rapidly computing interatomic force tensors.
10.1103/PhysRevLett.113.185501
https://arxiv.org/abs/1805.08904
https://arxiv.org/abs/1805.08903
## Summary
@utf
Added 'CubicS... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1520 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1520/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1520/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1520/events | https://github.com/materialsproject/pymatgen/issues/1520 | 463,761,473 | MDU6SXNzdWU0NjM3NjE0NzM= | 1,520 | pymatgen<=2018.12.12 build broken on fresh python 2.7 | {
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"Thanks for reporting this, but I am not inclined to issue a fix for this. Newer versions of pymatgen are Py3 only, and other packages like numpy have dropped Py27 support already. From the deprecation message, it seem that pip is going to drop it on Jan 1 2020 as well. So whatever fixes issues is going to be relev... | 2019-07-03T13:43:47 | 2019-07-03T16:17:52 | 2019-07-03T13:55:55Z | CONTRIBUTOR | {
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} | **Describe the bug**
The installation of pymatgen <= 2018.12.12 from source is currently broken in fresh python2.7 environments.
I believe the reason is the following:
Since pymatgen includes wheels only for the macos platform, extensions will be built from source on other platforms. pymatgen specifies the build... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1521 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1521/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1521/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1521/events | https://github.com/materialsproject/pymatgen/pull/1521 | 463,959,522 | MDExOlB1bGxSZXF1ZXN0Mjk0MzM1NDg4 | 1,521 | Pseudo_zval bugfix | {
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"@sthartman Thanks for catching the bug and making the fixes!",
"Thanks!"
] | 2019-07-03T21:23:49 | 2019-07-04T02:34:47 | 2019-07-04T02:33:33Z | CONTRIBUTOR | {
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} | Fixes a rare bug in the Outcar.read_pseudo_zval method of pymatgen.io.vasp.outputs. The new method doesn't make any assumptions about the POSCAR's title line, since this has no meaning in VASP. If adding a new OUTCAR test file is unwanted, I can modify the existing OUTCAR.BaTiO3.polar to check this issue instead. Th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1522 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1522/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1522/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1522/events | https://github.com/materialsproject/pymatgen/issues/1522 | 464,607,137 | MDU6SXNzdWU0NjQ2MDcxMzc= | 1,522 | Python 3.6 as hard requirement | {
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"Thanks @ajjackson, we’ll correct this.\r\n\r\nThe Py3.6 notice is quite new, mostly as a result of our own CI and to reduce our maintenance burden, but we’re open to explicitly supporting earlier versions of Py3 if there was a need for it in the community. Do you have any opinions on this? ",
"3.6 is the most re... | 2019-07-05T11:57:47 | 2019-07-15T12:07:36 | 2019-07-06T21:09:58Z | CONTRIBUTOR | {
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} | **Describe the bug**
I'm getting CI failures when testing a package that depends on Pymatgen with Python 3.5. It is announced in the README file that only Python 3.6 is supported, but the setup.py refers to older versions and nothing is being enforced for Pip. Please use `python_requires` to prevent Python3.5 users fr... | {
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} | ## Summary
Prompted by [user post](https://discuss.materialsproject.org/t/cli-error-occur-using-mpg-potcar-r/2429) to MP's forum.
There is no `spec` arg destination. Fixes this. Also, argparser help text indicates one directory only should be given, and `cli.pmg_potcar.proc_dir` appears to expect only one as well... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1524 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1524/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1524/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1524/events | https://github.com/materialsproject/pymatgen/pull/1524 | 467,624,776 | MDExOlB1bGxSZXF1ZXN0Mjk3MjQzODYw | 1,524 | Fix reading frequency dependent dielectric constant from VASP 6.0.8 output | {
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"Thanks @utf "
] | 2019-07-12T22:34:56 | 2019-07-15T03:48:30 | 2019-07-15T03:48:30Z | MEMBER | {
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} | In VASP 6.0.8, the frequency dependent dielectric constant is written to the vasprun.xml in a slightly different format from previous versions.
This PR makes a slight modification to support parsing the new dielectric format.
I've added a test and example vasprun.xml to catch the the broken behavior. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1525 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1525/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1525/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1525/events | https://github.com/materialsproject/pymatgen/pull/1525 | 468,362,442 | MDExOlB1bGxSZXF1ZXN0Mjk3ODA5NTE1 | 1,525 | [WIP] Heisenberg | {
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"Thanks @ncfrey !",
"I propose that you name the pymatgen wrappers around vampire \"lestat\". :-)",
"Looks pretty good, some tests need to be updated (e.g. see test_round_magmoms in CollinearMagneticStructureAnalyzerTest), a few minor PEP8 violations (mostly line length), HeisenbergScreener class definition has... | 2019-07-15T22:25:59 | 2019-07-17T23:47:46 | 2019-07-17T23:47:46Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
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} | ## Summary
@mkhorton
New functionality to take low energy magnetic orderings, map them to a Heisenberg model, compute exchange parameters, and perform Monte Carlo with the VAMPIRE package to calculate critical temperatures.
* Heisenberg model mapping of magnetic materials for calculating exchange parameters.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1526 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1526/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1526/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1526/events | https://github.com/materialsproject/pymatgen/pull/1526 | 468,861,528 | MDExOlB1bGxSZXF1ZXN0Mjk4MjA5MjUx | 1,526 | [WIP] TEM Diffraction | {
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} | ## Summary:
Working draft of TEM calculator. Have noticed some problems with the intensity calculations (that seem to stem from get_atoms not working as it should).
* Feature: Calculates and displays electron diffraction patterns for any regular crystalline object in any of the seven classes of crystals. Displays... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1527 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1527/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1527/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1527/events | https://github.com/materialsproject/pymatgen/pull/1527 | 468,878,987 | MDExOlB1bGxSZXF1ZXN0Mjk4MjIzNjE3 | 1,527 | Get symmetrically equivalent Miller indices | {
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"Thanks @richardtran415 ! I maintain some of this would be more appropriate in core.lattice, perhaps in future",
"Yeah I see what you mean, that would make it easier to get rid of some of overlap I mentioned.\r\n\r\nThanks\r\n",
"Let's move it to lattice then.",
"Yes, if you ever decide you'd like to move it,... | 2019-07-16T21:44:51 | 2019-07-19T22:47:55 | 2019-07-17T17:46:55Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Added a new function in surface.py called get_symmetrically_equivalent_miller_indices which takes in a structure and Miller index and returns a list for the family of hkl. Useful for searching for Miller index specific entries on MPRester (surface data, GB data, Wsep) as the user does not need to enter th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1528 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1528/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1528/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1528/events | https://github.com/materialsproject/pymatgen/pull/1528 | 469,250,354 | MDExOlB1bGxSZXF1ZXN0Mjk4NTE5NDAy | 1,528 | New class for lobster module and small other changes | {
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"Looks good, thanks @JaGeo !"
] | 2019-07-17T14:30:13 | 2019-07-17T17:45:52 | 2019-07-17T17:45:51Z | MEMBER | {
"total": 0,
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} | ## Summary
Hello!
I have created a new class to read in bandOverlaps.lobster files that are created during some Lobster runs. The class can check certain properties of these files and thereby judge the quality of the projection in the lobster run.
Furthermore, I have refactored a bit in the Lobsterin class to ma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1529 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1529/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1529/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1529/events | https://github.com/materialsproject/pymatgen/pull/1529 | 469,373,892 | MDExOlB1bGxSZXF1ZXN0Mjk4NjE1Mjc1 | 1,529 | Fix bug in bandoverlaps class | {
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"No problem!"
] | 2019-07-17T18:22:41 | 2019-07-17T18:32:26 | 2019-07-17T18:31:47Z | MEMBER | {
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I am sorry. I have already found a small bug in the bandoverlaps class. It should be fixed now and I have also adapted the tests to avoid this problem in the future.
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"**Describe the bug & To Reproduce**\r\nvasprun= Vasprun(path_vasprun, parse_dos=True)\r\ndos = vasprun.complete_dos\r\ndos.get_site_orbital_dos(dos.structure.sites[0],OrbitalType.d)\r\ndos.get_spd_dos()\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"/home/noki/anaconda... | 2019-07-18T14:45:24 | 2023-06-03T02:17:50 | 2023-06-03T02:17:50Z | NONE | {
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} | **Describe the bug & To Reproduce**
vasprun= Vasprun(path_vasprun, parse_dos=True)
dos = vasprun.complete_dos
dos.get_site_orbital_dos(dos.structure.sites[0],OrbitalType.d)
dos.get_spd_dos()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/noki/anaconda3/envs/procar/lib/pyth... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1531 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1531/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1531/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1531/events | https://github.com/materialsproject/pymatgen/issues/1531 | 470,271,959 | MDU6SXNzdWU0NzAyNzE5NTk= | 1,531 | sum_densities(*densities) | {
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"This can be done using Python's built-in reduce function. We shouldn't implement a special method for this. Try `reduce(add_densities, densities)`"
] | 2019-07-19T11:13:11 | 2019-07-19T16:26:24 | 2019-07-19T16:25:39Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
When I first encountered too simple function `add_densities(density1, density2)`,
I needed to sum multiple a list of density. But there is no feature something like `sum_densities(*densities)`
**Describe the solution you'd like**
I suggest below
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1532 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1532/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1532/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1532/events | https://github.com/materialsproject/pymatgen/pull/1532 | 470,648,133 | MDExOlB1bGxSZXF1ZXN0Mjk5NTQ2MDA1 | 1,532 | Moved some functions as a Lattice object method. | {
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} | ## Summary
Added unit testing for querying work of separation. Also moved get_recp_symmetry_operation function as a Lattice method.
## TODO (if any)
* I would prefer to have get_recp_symmetry_operation as a Lattice method since its more related to lattices and not just surfaces, however at the moment it requi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1533 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1533/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1533/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1533/events | https://github.com/materialsproject/pymatgen/issues/1533 | 471,442,974 | MDU6SXNzdWU0NzE0NDI5NzQ= | 1,533 | calling pmg command line interface throws exception when using Python 2.7 | {
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"Pymatgen no longer supports Python 2.X."
] | 2019-07-23T01:25:54 | 2019-07-23T01:27:03 | 2019-07-23T01:26:32Z | MEMBER | {
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} | **Describe the bug**
calling pmg command line interface throws exception
**To Reproduce**
Steps to reproduce the behavior:
1. Install pymatgen for system python (python 2.7)
2. On command line, enter "pmg -h"
**Expected behavior**
pmg cli displays help information.
**Error Message**
usr/local/lib/python2.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1534 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1534/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1534/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1534/events | https://github.com/materialsproject/pymatgen/pull/1534 | 471,548,517 | MDExOlB1bGxSZXF1ZXN0MzAwMTc2OTY5 | 1,534 | Fix ixc == 0 in from_abinit_ixc | {
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} | ## Summary
The current implementation of `from_abinit_ixc` breaks for `ixc == 0`, which is the value ABINIT uses for "no XC functional". The proposed implementation just returns `None` instead of asking the dict explicitly. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1535 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1535/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1535/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1535/events | https://github.com/materialsproject/pymatgen/pull/1535 | 471,676,012 | MDExOlB1bGxSZXF1ZXN0MzAwMjc5NDE5 | 1,535 | Add return_all_molecules option to BabelMolAdaptor | {
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"The errors in CI look like they aren't my fault, so I'm marking this as ready for review.",
"Looks good. Thanks.",
"Thanks for merging! :+1: "
] | 2019-07-23T12:45:23 | 2019-07-23T14:38:45 | 2019-07-23T14:32:27Z | CONTRIBUTOR | {
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} | ## Summary
As suggested in https://github.com/materialsproject/pymatgen/issues/1512#issuecomment-506859409, this PR adds a ``return_all_molecules`` option to ``BabelMolAdaptor``, which, when set to ``True``, will return one instance of the adaptor for each molecule found in a file. The previous behavior was to alway... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1536 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1536/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1536/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1536/events | https://github.com/materialsproject/pymatgen/issues/1536 | 471,886,756 | MDU6SXNzdWU0NzE4ODY3NTY= | 1,536 | CubicSupercellTransformation and PerturbSitesTransformation not MSONable | {
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"I also realize there's something overlap between `PerturbStructureTransformation` and `PerturbSitesTransformation`; thoughts on merging these?",
"Additionally, I just realized that PeturbSitesTransformation is a one-to-many but it doesn't follow the correct format of a one-to-many transformation (see the Abstrac... | 2019-07-23T19:24:37 | 2023-08-10T15:08:00 | 2023-08-10T15:08:00Z | MEMBER | {
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This should be trivially fixable, just make sure the class attribute names match the keyword arg names and that the default values are JSON serializable (e.g. `None` for a default and set `np.Inf` in the body of the init), and then it should "just work." @rees-c you can check this by calling `.as_dict(... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1537 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1537/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1537/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1537/events | https://github.com/materialsproject/pymatgen/issues/1537 | 472,086,772 | MDU6SXNzdWU0NzIwODY3NzI= | 1,537 | Failed to read cifs files | {
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"I imagine it's failing because it doesn't contain positions of individual atoms, only of water molecules (\"Wat\"), pymatgen doesn't really know what to do here. We could reasonably put a water molecule on these positions but the orientations would be arbitrary.",
"@janosh: Can probably close this as being out o... | 2019-07-24T05:32:49 | 2023-06-03T02:19:41 | 2023-06-03T02:19:41Z | NONE | {
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} | **System**
Python version: 3.5.2
OS version: Windows 10
**Summary**
I download the cif file in AMCSD. And pymatgen failed to read the cif file
I was trying to convert cif to jcpds.
I don't know what is the problem
**Example code**
import pymatgen as mg
from pymatgen import Lattice, Structure
from pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1538 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1538/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1538/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1538/events | https://github.com/materialsproject/pymatgen/pull/1538 | 472,134,348 | MDExOlB1bGxSZXF1ZXN0MzAwNjAzODg1 | 1,538 | Magnetic Space Group Symmetry | {
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"Hi @mt-huebsch -- it would be good if we were able to determine magnetic space groups, and we're all fans of Bilbao's tools here and I use them myself regularly. The problem is that we can't rely on an external service to offer this functionality. If the Bilbao server is slow or goes offline, or if a user attempts... | 2019-07-24T07:56:49 | 2020-02-12T04:12:20 | 2020-02-12T04:12:20Z | NONE | {
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The following suggestions should be useful when dealing with non collinear magnetism. It's my first time proposing something to another project. Please, let me know what you think!
## Summary
Implemented an ApplyMagSymmOpTransformation object, that can apply a magnetic space group operation to a struct... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1539 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1539/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1539/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1539/events | https://github.com/materialsproject/pymatgen/issues/1539 | 472,379,801 | MDU6SXNzdWU0NzIzNzk4MDE= | 1,539 | Is there projected band structure on a site? | {
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"The \"projections\" attribute of the BandStructure object should have the projections:\r\n\r\n```\r\n projections: dict of orbital projections as {spin: ndarray}. The\r\n indices of the ndarrayare [band_index, kpoint_index, orbital_index,\r\n ion_index].If the band structure is not spi... | 2019-07-24T16:26:25 | 2019-07-24T20:13:15 | 2019-07-24T20:13:15Z | NONE | {
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} | Only two functions are pooling on elements or elements with orbital? I'm looking for a function working with the projected band structure on a particular site or a group of sites plus OrbitalType.
Also, I couldn't see the function on Orbital: s, px, py, ... (not OrbitalType: s, p, d, f)
In DOS objects, some functio... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1540 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1540/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1540/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1540/events | https://github.com/materialsproject/pymatgen/issues/1540 | 472,879,207 | MDU6SXNzdWU0NzI4NzkyMDc= | 1,540 | Improper pdos for the result from SOC calculation (VASP) | {
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"I'd add this issue is also present with band structure projections. You first have orbital projections and then mx, my, mz spin projections. The spin projection information is not stored for SOC calculations."
] | 2019-07-25T13:52:48 | 2023-08-13T16:32:54 | 2023-08-13T16:32:54Z | NONE | {
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} | **Describe the bug**
There are four spin numbers in vasprun.xml when we calculate DOS with SOC. They represent 'total, mx, my, and mz' for each OrbitalType. But DOS Object only considers Up and Down as Total and mx (no more than two spin numbers). And, I think Up and Down are not proper namings because they don't come... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1541 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1541/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1541/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1541/events | https://github.com/materialsproject/pymatgen/pull/1541 | 475,260,350 | MDExOlB1bGxSZXF1ZXN0MzAzMDQ4Mjg1 | 1,541 | WIP: Fixed MSONability CubicSupercellTransformation and PerturbSitesTransformation | {
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"Thanks for this fix @rees-c "
] | 2019-07-31T17:10:13 | 2019-07-31T21:23:30 | 2019-07-31T21:23:29Z | CONTRIBUTOR | {
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## Summary
Fix for issue #1536
- Fixed class attribute names to match keyword args in inits
- Revised PerturbSitesTransformation to have the correct format for a 'one-to-many' transformation
## TODO (if any)
Potentially merge PerturbSitesTransformation (one-to-many transform) with PerturbStructureTransfo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1542 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1542/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1542/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1542/events | https://github.com/materialsproject/pymatgen/issues/1542 | 475,299,961 | MDU6SXNzdWU0NzUyOTk5NjE= | 1,542 | SlabGenerator.get_slabs() fails on pure metal FCC crystals | {
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"It's possible this is not a bug but rather poor scaling of the algorithm, we would have to investigate further. However, there are better ways to use this class. In particular, you should not be using the supercell here:\r\n\r\n```\r\nmg_sg = SlabGenerator(\r\n initial_structure=mg_supercell,\r\n miller_inde... | 2019-07-31T18:44:22 | 2019-07-31T19:16:51 | 2019-07-31T18:52:35Z | NONE | {
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} | **Describe the bug**
Neither `pymatgen.core.surface.SlabGenerator` nor `pymatgen.core.surface.generate_all_slabs` appear to not be able to generate slabs from FCC structures in which all atoms are of one element. When attempting to do so, the program crashes. Changing just one atom in the structure to be of a differen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1543 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1543/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1543/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1543/events | https://github.com/materialsproject/pymatgen/issues/1543 | 475,359,433 | MDU6SXNzdWU0NzUzNTk0MzM= | 1,543 | SpacegroupAnalyzer.get_primitive_standard_structure()'s default symprec value returns a faulty structure for Mg3Sb2 | {
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"Can you report this at https://github.com/atztogo/spglib ? This is basically an issue for spglib to solve."
] | 2019-07-31T21:11:33 | 2023-08-13T16:32:54 | 2023-08-13T16:32:54Z | CONTRIBUTOR | {
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} | **Describe the bug**
When using `SpacegroupAnalyzer.get_primitive_standard_structure()` with the default `symprec=0.01` option on a Mg3Sb2 structure, the structure returned places the Sb atoms on top of the Mg atoms. This issue does not occur when `symprec=0.001` or `symprec=0.1`.
**To Reproduce**
Steps to reprodu... | {
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"You should mention that your way of merging the two classes was to:\r\n- Remove the advanced transformation.\r\n- Add an option to `PerturbStructureTransformation` and `Structure.perturb` that allows for the displacements to be randomly distributed between two values.\r\n\r\nThe rest of the advanced features of th... | 2019-08-01T17:48:56 | 2019-08-06T23:56:28 | 2019-08-06T23:56:27Z | CONTRIBUTOR | {
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} | ## Summary
- Added a boolean argument to CubicSupercellTransformation that can constrain the transformation matrix to be diagonal
- Made a bug fix in CubicSupercellTransformation regarding how the smallest dimension is found
- Merged PerturbSitesTransformation into PerturbStructureTransformation (as discussed in #1... | {
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"Thanks for working on this @dongsenfo! \r\n\r\nWould it be possible to add a Transformation interface to it for convenience also? (along the same lines that enumlib_caller has EnumerateStructureTransformation, mcsqs_caller could have SQSTransformation)\r\n\r\nFew other questions:\r\n\r\n* what’s the stopping crite... | 2019-08-03T22:53:17 | 2019-09-04T22:08:51 | 2019-09-04T22:08:18Z | CONTRIBUTOR | {
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} | Returns a special quasirandom structure in the pymatgen structure format given an initial structure with partial occupancies. Not quite sure how to handle the files that come out of the mcsqs caller in the tests. In addition, there is a sleep time built into the code to allows the mcsqs code to build the files before c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1546 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1546/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1546/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1546/events | https://github.com/materialsproject/pymatgen/pull/1546 | 476,844,863 | MDExOlB1bGxSZXF1ZXN0MzA0MjkwMjAz | 1,546 | Xdatcar optimize | {
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} | ## Summary
* Fixed view_environments in chemenv (python2=>python3)
* Fixed return mode in chemenv strategies
* Added a break when reaching ionicstep_end when reading an XDATCAR file | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1547 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1547/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1547/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1547/events | https://github.com/materialsproject/pymatgen/pull/1547 | 478,076,652 | MDExOlB1bGxSZXF1ZXN0MzA1MjY4NzYw | 1,547 | Small change to conversion electrodes | {
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"What does Master mean?",
"ooops I didn't see that get populated by github somehow..."
] | 2019-08-07T18:29:08 | 2019-08-07T19:23:50 | 2019-08-07T19:23:50Z | CONTRIBUTOR | {
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} | ## Small change to conversion electrodes
- added kwarg that allows unstable entry to be used in the constructor. This allows us to get a conversion voltage estimate any new cathode materials, not just ones on the convex hull.
- changed the output of all_pairs and adj_pairs to lists not iterators
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https://api.github.com/repos/materialsproject/pymatgen/issues/1548 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1548/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1548/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1548/events | https://github.com/materialsproject/pymatgen/pull/1548 | 478,087,890 | MDExOlB1bGxSZXF1ZXN0MzA1Mjc3OTA1 | 1,548 | Bond valence sum unordered function fix | {
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"Thanks."
] | 2019-08-07T18:56:09 | 2019-08-07T19:23:15 | 2019-08-07T19:23:10Z | CONTRIBUTOR | {
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} | ## Summary
New Structure `get_neighbors` returns namedtuples which breaks usage of `calculate_bv_sum_unordered`. It appears `calculate_bv_sum` was fixed previously though.
* Fix `test_calculate_bv_sum_unordered`
* Add tests for both bv_sum functions (previously missing, hence why this bug existed)
* Cleaned up ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1549 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1549/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1549/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1549/events | https://github.com/materialsproject/pymatgen/pull/1549 | 478,633,814 | MDExOlB1bGxSZXF1ZXN0MzA1NzA0NDI5 | 1,549 | Fix the name of attribute in Outcar class's documentation | {
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"Thanks!"
] | 2019-08-08T18:52:34 | 2019-08-10T07:07:48 | 2019-08-10T07:07:45Z | CONTRIBUTOR | {
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} | ## Summary
* One of the duplicated attributes for `unsym_cs_tensor` was replaced to `cs_g0_contribution` in the documentation for `Ourcar` class.
* Add blank lines to correctly parse documentation. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1550 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1550/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1550/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1550/events | https://github.com/materialsproject/pymatgen/pull/1550 | 478,723,702 | MDExOlB1bGxSZXF1ZXN0MzA1Nzc5MDkw | 1,550 | Fix multi-line :param: and :return: directives in docstrings | {
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"I commited MPCompatibility.yaml by mistake; it should not be in here. Trying to fix now.",
"Thanks @rkingsbury!\r\n\r\nTechnically both modules mentioned in this PR are using RST docstrings where (by our own convention) we should be using Google-style docstrings. This easily happens since many IDEs default to RS... | 2019-08-08T23:01:45 | 2019-08-14T19:03:36 | 2019-08-10T07:07:27Z | CONTRIBUTOR | {
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} | ## Summary
* Fix docstrings with multi-line :param: and :return: directives not being rendered correctly. This was due to an (undocumented) quirk in sphinx discussed [here](https://stackoverflow.com/questions/32566466/multi-line-description-of-a-parameter-description-in-python-docstring).
* I also fixed a few is... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1551 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1551/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1551/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1551/events | https://github.com/materialsproject/pymatgen/pull/1551 | 479,093,609 | MDExOlB1bGxSZXF1ZXN0MzA2MDc3MDk4 | 1,551 | Fix number of returned entries in apply_transformation | {
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_apply_transformation()_ now returns _num_to_return_ entries as described in the doctoring. | {
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} | ## Summary
Hello!
I have changed the DOSCAR class of the lobster io module and the corresponding tests. This will allow to adapt the class for other DFT programs in the future. I will also update the tutorial soon.
I hope it is okay that I am still making these kinds changes but I think this will make the class... | {
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"I'm actually long overdue on a general pymatgen PR, and one of the things I've done is substantially overhaul the fragmenter as well as made some key additions to graphs, both of which result in substantial speedups. That test now takes 43 seconds on my laptop. I can work on getting the PR together on Monday.",
... | 2019-08-15T23:16:06 | 2023-08-10T15:05:06 | 2023-08-10T15:05:06Z | MEMBER | {
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} | There are some tests which are ridiculously slow on pymatgen. Based on pytest, these are the slowest tests. Most are for the defect package, which I have highlighted quite a few times already. But the fragmenter test also takes a full 4 mins to run (@samblau can you speed this up?).
```
244.87s call pymatgen/a... | {
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"I think there are still many people that use BZT 1.0 and not BZT 2.0\r\n\r\n- BZT 2.0 has been harder to install for many people, especially on Mac, despite it being Python (although with C bindings, the problematic part) and BZT 1.0 being Fortran.\r\n- BZT 1.0 allows for command-line style usage which is what a l... | 2019-08-16T19:40:55 | 2019-08-16T23:05:51 | 2019-08-16T23:05:51Z | MEMBER | {
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} | Is there a reason to keep both bzt2 and bzt1? Or can we junk bzt1 code?
@computron
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https://api.github.com/repos/materialsproject/pymatgen/issues/1555 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1555/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1555/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1555/events | https://github.com/materialsproject/pymatgen/pull/1555 | 483,114,370 | MDExOlB1bGxSZXF1ZXN0MzA5MjU2NjAz | 1,555 | Enhancements to ComputedEntry and MPRester | {
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"Wait, I just noticed that there are no tests for the two methods. Pls submit a second PR with the relevant tests for the two methods.",
"I have temporarily reverted this PR until the tests are added. Thanks.",
"@shyuep test cases are ready (see #1561 ), but are failing because the PR is on top of the reverted ... | 2019-08-20T22:35:11 | 2019-08-22T18:20:20 | 2019-08-21T20:45:17Z | CONTRIBUTOR | {
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} | ## Summary
* By analogy to the `energy_per_atom` property, it would be useful for ComputedEntry objects to have an energy per formula unit property to unambiguously return the energy associated with a single formuala unit or reduced formula. The first commit adds this property
* `get_entries_in_chemsys` currently... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1556 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1556/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1556/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1556/events | https://github.com/materialsproject/pymatgen/pull/1556 | 483,577,520 | MDExOlB1bGxSZXF1ZXN0MzA5NjI1NzYz | 1,556 | Updates to Fragmentation, Graphs, and Q-Chem IO | {
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"All updates and cleanup finished. Once all the tests run (and assuming they pass), this is ready for review and / or merging.",
"Travis test has failed because of OpenBabel dependency. You need to put a skipIf for openbabel. That is not a core dependency for pmg.",
"Thanks. Merged.",
"BTW, if igraph is suppo... | 2019-08-21T18:20:57 | 2019-08-21T22:59:09 | 2019-08-21T20:36:05Z | CONTRIBUTOR | {
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} | ## Summary
* Molecule fragmentation substantially sped up by using more efficient data structures and leveraging the faster igraph library. Additional functionality added to allow a list of previously identified fragments to be accounted for.
* Some graph functionality modified or improved in order to facilitate fr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1557 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1557/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1557/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1557/events | https://github.com/materialsproject/pymatgen/pull/1557 | 483,644,159 | MDExOlB1bGxSZXF1ZXN0MzA5NjgxMDI2 | 1,557 | Revert "Enhancements to ComputedEntry and MPRester" | {
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"I think I need a longer summary to know what this is for?",
"Hi, sorry I'll elaborate.\r\n\r\nThe corrections in MPCompatibility.yaml were refit and now have standard error values associated with them (from imperfect fits as well as uncertainty in experimental data). I'll add the code that calculates the correct... | 2019-08-21T22:02:09 | 2020-08-14T22:22:51 | 2020-08-14T22:22:34Z | CONTRIBUTOR | {
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} | ## Summary
Added uncertainty quantification for energy corrections in compatibility module.
* additional yaml file that contains uncertainties for each correction
* get_correction() methods now return (correction, uncertainty)
* process_entry() adds correction uncertainty to entry.data dictionary under key: 'co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1559 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1559/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1559/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1559/events | https://github.com/materialsproject/pymatgen/pull/1559 | 483,688,422 | MDExOlB1bGxSZXF1ZXN0MzA5NzE3ODEy | 1,559 | Turning back on fragmenter tests | {
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When fixing the metal_edge_extender test to not use babel, I turned off the other fragmenter tests and forgot to turn them back on. This fixes that. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1560 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1560/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1560/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1560/events | https://github.com/materialsproject/pymatgen/pull/1560 | 483,731,773 | MDExOlB1bGxSZXF1ZXN0MzA5NzUyMTgx | 1,560 | Minor improvements to plot_fermi_surface | {
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"Yikes, a lot of that code looks quite old. Thanks for fixing.\r\n\r\nDoes this work with BoltzTraP 2 or is this 1 only? I seem to remember seeing a function to plot Fermi surfaces in there too. Also, is it possible to plot using any uniform band structure, or does it require a special BoltzTraP-friendly input?",
... | 2019-08-22T02:09:45 | 2019-08-28T00:07:31 | 2019-08-28T00:07:31Z | CONTRIBUTOR | {
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} | ## Summary
1. `plot_fermi_surface` did not easily work with multiple transparency factors and colors at the same time. This PR makes plotting multiple energy levels with plot_fermi_surface easier by accepting a list of colors and transparencies, one for each desired surface. The core plotting code is identical to pr... | {
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"Tests failed because of a bug in the get_reduced_formula. Pls fix. (And also, this is why unittests are needed).",
"I decided to go with an alternative implementation. Instead of having energy_per_formula_unit, which is not very well-defined (since forumula unit can mean different things to different people). I ... | 2019-08-22T17:17:39 | 2019-08-22T22:40:14 | 2019-08-22T20:35:27Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1562 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1562/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1562/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1562/events | https://github.com/materialsproject/pymatgen/pull/1562 | 484,214,415 | MDExOlB1bGxSZXF1ZXN0MzEwMTQxOTc4 | 1,562 | Add options and docs to periodic_table_heatmap | {
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"Thanks @rkingsbury !"
] | 2019-08-22T21:01:05 | 2019-08-23T17:19:04 | 2019-08-23T17:19:04Z | CONTRIBUTOR | {
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Add options to adjust the range of the colorbar and the size of the label in `periodic_table_heatmap`. The ability to adjust the scale is useful if you want to generate multiple plots for comparison to one another, and make sure they all use the same scale.
Also corrected some inaccuracies in the docst... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1563 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1563/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1563/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1563/events | https://github.com/materialsproject/pymatgen/pull/1563 | 484,634,291 | MDExOlB1bGxSZXF1ZXN0MzEwNDcxNTMz | 1,563 | Remove charge from composition | {
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"Thanks @kmu, this looks useful!",
"Thanks @kmu!"
] | 2019-08-23T17:25:40 | 2019-08-25T18:12:41 | 2019-08-25T18:12:41Z | CONTRIBUTOR | {
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- The method that removes charges from the composition.
- It is useful to compare the composition of the oxidized structure and the composition derived from other sources such as ICSD metadata. | {
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"Tests have failed because of codestyle. We are enforcing codestyle going forward. Pls fix them before we merge. Thanks.",
"Not sure why there's a failing test in test_phase_diagram all of a sudden when all I've changed is parsing a new error in my Q-Chem IO. This should be ready to merge. "
] | 2019-08-23T22:28:22 | 2019-08-25T21:42:30 | 2019-08-25T21:42:30Z | CONTRIBUTOR | {
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} | ## Summary
* igraph functionality is now handled more elegantly, removing the need for the use_igraph input argument in the fragmenter.
* Further simplification of the fragmenter made one of the longest tests unnecessary. This test has been removed.
* Isomorphism checking between molecule graphs returned to a mol_... | {
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} | ## Summary
Hello!
I have written a new class for the lobster module to read in GROSSPOP.lobster files. Also, a new unit test is included.
Best,
JG
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"Thanks @htz1992213, this looks great + very useful!\r\n\r\nThere are a few places where `for i in range(len(...)):` loops are used where `for i, ... enumerate(...)` would be more appropriate (and would remove the need for some of the \"temp\" variables). If you could make that change we can go ahead and merge.",
... | 2019-08-26T22:36:11 | 2019-08-29T20:20:36 | 2019-08-29T20:20:36Z | CONTRIBUTOR | {
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} | ## Summary
* The CombinedData class is added to easily merge LammpsData objects or LAMMPS data files.
* The original LammpsData class is modified to handle hybrid style bond/angle/dihedral/improper coefficients merging.
* Fix: No. of significant figures to output for charges is changed to a more conservative numbe... | {
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"Hi, thanks for the contribution! But the test is failing due to both actual test errors as well as codestyle issues. Can you fix those? For codestyle, you can refer to http://pymatgen.org/contributing coding guidelines for how to deal with codestyle easily.",
"Ok sure, I'll look into it.",
"Thank for contribut... | 2019-08-28T21:27:35 | 2020-06-22T20:09:52 | 2020-06-22T20:08:56Z | CONTRIBUTOR | {
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} | ## Summary
- Analysis of solar-cell efficiency using spectroscopy limited maximum efficiency (SLME)
- Analysis of topological spillage for non-trivial materials
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"Can we have a unittest for the functionality pls? Thanks.",
"Thanks."
] | 2019-08-28T23:59:24 | 2019-09-03T04:55:49 | 2019-09-03T04:55:45Z | CONTRIBUTOR | {
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} | Vasp on nersc now produces extra text in front of the born effect charge which prevents parsing. Got rid of the line which differentiates the two old and new vasp text in front of the born effective charges | {
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"Ok, I see where the syntax error might be coming from. While I can fix it, I would suggest you move to Py 3.7 and use a newer version of pymatgen. Thanks."
] | 2019-08-30T09:02:02 | 2019-08-30T12:54:47 | 2019-08-30T12:54:47Z | NONE | {
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} | Installed 2019.7.2 via pip3 and got syntax errors from the WAVEDER and WAVEDERF classes when testing the command line tool. Deleted both classes as I don't see that I need these and it works.
Have python 3.5.0 installed on a cluster runing linux 64 bit CentOS 6. | {
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"Thanks. This is great. I have merged it."
] | 2019-09-02T10:07:02 | 2019-09-03T04:55:27 | 2019-09-03T04:55:14Z | MEMBER | {
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} | ## Summary
Hello!
I have written a LobsterSet to create VASP inputs that can be used for lobster calculations later and I have also created tests.
Please let me know if I have followed all conventions for VASP sets. Also, let me know if I have overlooked something. The relationships between classes in this mod... | {
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*Sourced from [numpy's releases](https://github.com/numpy/numpy/releases).*
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*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.1.2
> pytest 5.1.2 (2019-08-30)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#2270](https:... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1577 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1577/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1577/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1577/events | https://github.com/materialsproject/pymatgen/pull/1577 | 488,894,171 | MDExOlB1bGxSZXF1ZXN0MzEzODIyNzg1 | 1,577 | Incar params | {
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"Thanks @richardtran415, this is fantastic"
] | 2019-09-04T01:29:28 | 2019-09-09T22:45:32 | 2019-09-04T02:38:35Z | CONTRIBUTOR | {
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} | ## Summary
* Added a JSON file containing a dictionary with INCAR flags as keys and the value indicating the object type. 380 flags scoured from the VaspWiki and vasprun.xml file. By no means is this all possible flags for the INCAR, but I will add on as I find more in future pull requests.
* Added Incar class me... | {
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"Could any help me to solve this problem?",
"I just pushed a fix. ",
"Thanks for the prompt reply. It works! "
] | 2019-09-04T13:36:29 | 2019-09-04T16:55:30 | 2019-09-04T16:55:30Z | NONE | {
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} | **System**
Python version: 3.7.3
OS version: macOS Mojave
monty 1.12.0
**Summary**
I installed the pymatgen through Conda-based install and in developmental mode as well.
When I was trying the execute "pmg analyze ." in a vasp calculaiton fold.
The following error message appears:
File "/Users/lvjian... | {
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} | Bumps [netcdf4](https://github.com/Unidata/netcdf4-python) from 1.5.1.2 to 1.5.2.
<details>
<summary>Changelog</summary>
*Sourced from [netcdf4's changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).*
> version 1.5.2 (tag v1.5.2rel)
> ==============================
> * fix for scaling bug whe... | {
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"Very happy to see this :) will merge when tests pass"
] | 2019-09-04T21:01:36 | 2019-09-05T05:46:35 | 2019-09-05T05:46:35Z | CONTRIBUTOR | {
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} | ## Refactor of pourbaix diagram module for significant speedup to many-element systems
The pourbaix diagram module is refactored for significant speedup for many element systems. The methodology is outlined [here](https://arxiv.org/abs/1909.00035).
* Many-element pourbaix diagrams pre-compute valid "MultiEntries... | {
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"Thanks, this is already known and has been fixed in master. A new file is missing from the packaged version, I’ll be pushing an updated release shortly.",
"Ok, then I close the PR. ",
"This should now be fixed in the supplemental v2019.9.8 release, thanks again for reporting."
] | 2019-09-08T05:14:30 | 2019-09-08T05:35:52 | 2019-09-08T05:26:45Z | CONTRIBUTOR | {
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} | Already the import of pymatgen fails, with the new release, as the file `pymatgen/io/vasp/incar_parameters.json` is missing.
https://github.com/conda-forge/pymatgen-feedstock/pull/8
```
import: 'pymatgen'
Traceback (most recent call last):
File "/home/conda/feedstock_root/build_artifacts/pymatgen_156791426025... | {
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} | Bumps [numpy](https://github.com/numpy/numpy) from 1.17.1 to 1.17.2.
<details>
<summary>Release notes</summary>
*Sourced from [numpy's releases](https://github.com/numpy/numpy/releases).*
> ## v1.17.2
> NumPy 1.17.2 Release Notes
> ==========================
>
> This release contains fixes for bugs reported again... | {
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<details>
<summary>Commits</summary>
- [`1156f5a`](https://github.com/h5py/h5py/commit/1156f5ac1ca38db85dcd906cf19a7aba90d0b39a) Updated CHANGELOG for 2.10.0
- [`8457701`](https://github.com/h5py/h5py/commit/84577017954e617c78b96a39938630445f8e96c4) bump... | {
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<details>
<summary>Changelog</summary>
*Sourced from [palettable's changelog](https://github.com/jiffyclub/palettable/blob/master/CHANGELOG.rst).*
</details>
<details>
<summary>Commits</summary>
- See full diff in [compare view](https:/... | {
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"I have no idea whether the gamma info is in the wavecar. But setting that argument seems to be a quick fix for the problem for now. Can you implement and then submit a PR with the requisite unittests pls? Thanks.",
"> On Sep 10, 2019, at 8:49 AM, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> I have no ... | 2019-09-10T00:54:22 | 2020-06-04T22:44:51 | 2020-06-04T22:44:51Z | CONTRIBUTOR | {
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} | When reading a WAVECAR that was generated by the gamma-point-only vasp executable, pymatgen.io.vasp.outputs.Wavecar fails with the error:
> File "/Users/bernstei/Library/Python/3.7/lib/python/site- packages/pymatgen/io/vasp/outputs.py", line 4170, in __init__
'number of G points {} {}'.format(len(self.Gpoints... | {
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} | ## Summary
Fixes a bug in AnionCorrections related to the 'polysulfide' sulfide_type.
Matt M. in our group discovered that applying corrections to a polysulfide compound would yield different results depending on whether the ComputedEntry included a structure or not. If the structure was present, AnionCorrection ... | {
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"@jmmshn ?",
"Sorry, there should have been an example of how to us the FullPathMapper.\r\nI have created a PR to fix this.",
"@ws517037749 the following file should have an example.\r\nhttps://github.com/materialsvirtuallab/pymatgen-diffusion/blob/master/examples/neb_path_mapping.ipynb\r\nThe file not renderin... | 2019-09-11T00:45:31 | 2019-09-16T16:42:12 | 2019-09-16T16:42:12Z | NONE | {
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} | **Describe the bug**
when I try to use function of FullPathMapper.get_unique_hops_dict() the 'KeyError: 'hop'' appear, but other functions work well.
**Expected behavior**
Fix the bug
**Screenshots**
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https://api.github.com/repos/materialsproject/pymatgen/issues/1589 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1589/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1589/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1589/events | https://github.com/materialsproject/pymatgen/pull/1589 | 492,547,514 | MDExOlB1bGxSZXF1ZXN0MzE2Njk5NjI1 | 1,589 | Fixed some minor bugs in Trajectory and more features | {
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"Thanks. While you are fixing the errors (travis fails immediately with codestyle issues), can you add some basic type annotations for the main classes in Trajectory? Thanks.",
"Regarding \"frame_property,\" this is really a problem of associating metadata with a structure. We have specie properties, site propert... | 2019-09-12T02:12:18 | 2019-09-12T18:21:03 | 2019-09-12T05:17:51Z | CONTRIBUTOR | {
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} | ## Summary
- Fixed issue with slicing, wherein only fully specified slices work. example: traj[0 : -1 : 10] worked, but traj[ : : 10] and traj[ : -1 : 10] did not work.
- Added property to keep track of information of each time step such as Temperature, Pressure, and Energy. This variable is called 'frame_property'... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1591 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1591/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1591/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1591/events | https://github.com/materialsproject/pymatgen/issues/1591 | 493,572,704 | MDU6SXNzdWU0OTM1NzI3MDQ= | 1,591 | VoronoiNN failed for method `get_all_voronoi_polyhedra` but ok using `get_voronoi_polyhedra` on all site indices. | {
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"Hi Chi -- I didn't write this class, but this behavior is not completely unexpected with Voronoi.\r\n\r\nWhen asking to get the Voronoi polyhedra for a single site, only the sites immediately surrounding that site are given to the Voronoi tessellation algorithm, whereas when all sites are requested, all sites in t... | 2019-09-14T02:23:30 | 2019-09-16T16:40:23 | 2019-09-16T16:40:23Z | CONTRIBUTOR | {
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} | **pymatgen.analysis.local_env.VoronoiNN potential bug**
I tried to compute the Voronoi Tessellation of surface structures. Using `get_all_voronoi_polyhedra` it reports `pathological structure` error. However, there is no error if I run `get_voronoi_polyhedra` on each site index. I wonder if this is a bug?
**To R... | {
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"@shyuep ok "
] | 2019-09-16T15:31:55 | 2019-09-19T14:04:32 | 2019-09-19T14:04:32Z | MEMBER | {
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} | Recently, @chc273 implemented a much better distance computation algo that scales linearly with # of atoms Structure.get_neighbors. But some of the other methods seem to still use Lattice.get_points_in_sphere.
I would like to unify all these treatments. Basically port the general concept of get_neighbors to Lattice.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1593 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1593/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1593/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1593/events | https://github.com/materialsproject/pymatgen/pull/1593 | 494,761,708 | MDExOlB1bGxSZXF1ZXN0MzE4NDUxNzY3 | 1,593 | Bump tqdm from 4.35.0 to 4.36.0 | {
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<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.36.0 stable
> - expose more custom format params
> - potential thread safety fix ([#548](https://github-redirect.dependabo... | {
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"Thanks. Do you mind closing this PR and resubmititng another one? I am testing out Github Action workflows for PRs. I want to make sure that the Actions get run. You can just copy and paste the same PR text.",
"@shyuep ok"
] | 2019-09-17T17:57:27 | 2019-09-17T18:16:50 | 2019-09-17T18:16:50Z | CONTRIBUTOR | {
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} | ## Summary
This fixes #1592
1. Moved neighbor computations from `structure.py` to `lattice.py`
2. Added a function `lattice.get_points_in_spheres` that computes, for each `center_coords`, the neighboring points from `all_coords` within a cutoff `r`. All coordinates are cartesian. This function takes optionally... | {
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"Ok, there are some errors related to mypy that you need to fix. See the failed travis-ci build.\r\n\r\n@mkhorton For some reason, the Github actions are not running on PRs. Can you check?",
"Looks like this may be a limitation during the beta on PRs from forked repos.",
"Actually https://help.github.com/en/art... | 2019-09-17T18:17:47 | 2019-09-19T14:04:39 | 2019-09-19T14:04:32Z | CONTRIBUTOR | {
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} | This fixes #1592
Moved neighbor computations from structure.py to lattice.py
Added a function lattice.get_points_in_spheres that computes, for each center_coords, the neighboring points from all_coords within a cutoff r. All coordinates are cartesian. This function takes optionally boolean pbc to indicates periodic... | {
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"@mkhorton there seems to be some fragility with the magnetism tests. Can fix?",
"I'll take a look. This is a very old test so not clear why it should change now, it has not been fragile in the past. It is an enumlib test, has the conda enumlib been updated recently?",
"This started failing after the recent Lat... | 2019-09-19T17:23:19 | 2019-09-19T20:56:35 | 2019-09-19T20:12:58Z | CONTRIBUTOR | {
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<details>
<summary>Commits</summary>
- [`a0af066`](https://github.com/tqdm/tqdm/commit/a0af0666991b724abe1efdbb3958892771a21495) bump version, merge branch 'devel'
- [`ed82bf3`](https://github.com/tqdm/tqdm/commit/ed82bf38cb2f4abcc65f6d5f3192734f0cb97f1... | {
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"Even better, we have new Literal type hints now!\n\nWe have added MSONable support for Enums in the latest monty but I still\nfind it verbose/a little clumsy to have to init the Enum before you can\ninit the class. You can also create the Enum from a string kwarg inside the\nclass initializer and raise an error th... | 2019-09-19T23:44:24 | 2021-02-13T17:26:48 | 2020-03-15T19:25:55Z | MEMBER | {
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} | Bumps [ase](https://gitlab.com/ase/ase) from 3.18.0 to 3.18.1.
<details>
<summary>Changelog</summary>
*Sourced from [ase's changelog](https://gitlab.com/ase/ase/blob/master/CHANGELOG.rst).*
</details>
<details>
<summary>Commits</summary>
- [`07de356`](https://gitlab.com/ase/ase/commit/07de35654601ddbb2b23a4e7df70916... | {
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⚠️ **Dependabot is rebasing this PR** ⚠️
If you make any changes to it yourself then they will take precedence over the rebase.
---
[//]: # (dependabot-end)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.1.2 to 5.1.3.
<details>
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"This implies you do not have a spin down DOS. Is your run spin polarized?",
"Shyuep,\r\n\r\nI think I know what is wrong.\r\n\r\nThe calculation is spin polarized but with spin-orbit coupling \r\nso the spin up/down channels are not well defined anymore.\r\nParadoxically the Spin.down works for DOS but not for b... | 2019-09-23T20:38:45 | 2023-08-10T15:05:56 | 2023-08-10T15:05:56Z | NONE | {
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} | **Describe the bug**
When I try to get the projection on elements and orbitals for my bands
the spin down case does not work.
i.e.
Mn_bands = bands.get_projections_on_elements_and_orbitals({"Mn": ["s", "p","d"]})
print(Mn_bands[Spin.down][n_b][n_k]["Mn"]["s"])
I get the error:
KeyError: <Spin.down: -1>
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