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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 I executed to ensure my my branch was up to date with the upstream master.\r\nClosed this PR, deleted corresponding branch and opened another clean one which should be final."
] | 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 work-in-progress, write something about what else needs
to be done
- Add functionality to account for Many-Body perturbation theory (GW, GoWo, scGW, etc.), the Random Phase Approximation (ACDFT/RPA), Time-Dependent DFT (TD-DFT) and Time-Dependent Hartree-Fock equations (TDHF) via the Bethe Salpeter and Casida equations (BSE), and other higher levels of theory.
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| 458,391,545
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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_groups_to_file` method to double check."
] | 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 of rows.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
* Verify that the `_parse_transformation(b)` is giving expected results. Before/after the fix it was giving results which are the same as reference, but in a slightly different format. I'm unsure if this is intentional.
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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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MDExOlB1bGxSZXF1ZXN0MjkwNDM2MzMw
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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 test files relevant to various functionals/levels of theory.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Add functionality to account for Many-Body perturbation theory (GW, GoWo, scGW, etc.), the Random Phase Approximation (ACDFT/RPA), Time-Dependent DFT (TD-DFT) and Time-Dependent Hartree-Fock equations (TDHF) via the Bethe Salpeter and Casida equations (BSE), and other higher levels of theory.
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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
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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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MDU6SXNzdWU0NTk0MTI1MjI=
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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.",
"@mkhorton thanks for the pointer! I am not sure why structure should be in the init. If that is the case, then one `NearNeighbors` instance will only compute a specific structure. In my case, I would love to initialize the instance once and apply it to all structures I have. ",
"Because some of these classes require pre-processing on the structure\nitself that same processing then has to be repeated for every single site.\nIt means they scale badly for large structures.\n\nI agree this makes things difficult in other ways. I also use the class in\nthe same way you do.\n\nOn Fri, Jun 21, 2019 at 17:36, Chi Chen <notifications@github.com> wrote:\n\n> @mkhorton <https://github.com/mkhorton> thanks for the pointer! I am not\n> sure why structure should be in the init. If that is the case, then one\n> NearNeighbors instance will only compute a specific structure. In my\n> case, I would love to initialize the instance once and apply it to all\n> structures I have.\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1506?email_source=notifications&email_token=AAWWWRHRRRBUNUCCBU6P72LP3VX2FA5CNFSM4H2VRWM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYJ4DRQ#issuecomment-504611270>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRC27GN5XGDQXMQJNE3P3VX2FANCNFSM4H2VRWMQ>\n> .\n>\n",
"The alternative might be to offer some kind of standard structure\npreprocessing interface that could be cached, which is a bit more complex.\n\nOn Fri, Jun 21, 2019 at 17:50, Matthew Horton <mkhorton@lbl.gov> wrote:\n\n> Because some of these classes require pre-processing on the structure\n> itself that same processing then has to be repeated for every single site.\n> It means they scale badly for large structures.\n>\n> I agree this makes things difficult in other ways. I also use the class in\n> the same way you do.\n>\n> On Fri, Jun 21, 2019 at 17:36, Chi Chen <notifications@github.com> wrote:\n>\n>> @mkhorton <https://github.com/mkhorton> thanks for the pointer! I am not\n>> sure why structure should be in the init. If that is the case, then one\n>> NearNeighbors instance will only compute a specific structure. In my\n>> case, I would love to initialize the instance once and apply it to all\n>> structures I have.\n>>\n>> —\n>> You are receiving this because you were mentioned.\n>>\n>>\n>> Reply to this email directly, view it on GitHub\n>> <https://github.com/materialsproject/pymatgen/issues/1506?email_source=notifications&email_token=AAWWWRHRRRBUNUCCBU6P72LP3VX2FA5CNFSM4H2VRWM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYJ4DRQ#issuecomment-504611270>,\n>> or mute the thread\n>> <https://github.com/notifications/unsubscribe-auth/AAWWWRC27GN5XGDQXMQJNE3P3VX2FANCNFSM4H2VRWMQ>\n>> .\n>>\n>\n",
"@mkhorton thanks Matt! I will follow the updates on this. Now i guess I will need to find a way to work around. ",
"Keep this issue open.\n\nOn Sat, Jun 22, 2019 at 10:39 Chi Chen <notifications@github.com> wrote:\n\n> Closed #1506 <https://github.com/materialsproject/pymatgen/issues/1506>.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1506?email_source=notifications&email_token=AAEM4U6KSFJMDOXKLLH2243P3WGEZA5CNFSM4H2VRWM2YY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOSDYXZUY#event-2431745235>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAEM4U4AAMKM6QRAKG3VVGLP3WGEZANCNFSM4H2VRWMQ>\n> .\n>\n-- \nShyue Ping\n"
] | 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 utility during model saving. Help is very much appreciated!
Thanks
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MDU6SXNzdWU0NTk1NTIwNzI=
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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
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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:
warnings.warn("Please install optional dependency pybtex if you"
"want to extract references from CIF files.")
BibliographyData, Entry = None, None
```
However, the only function requiring it is `get_bibtex_string`.
**Describe the solution you'd like**
Since these warnings are not easy to suppress and show up even when not applicable it would be better to just move this warning to within the `get_bibtex_string` itself. One can simply extend the message of the `requires` decorator
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add grain boundary MPRester
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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 length of names...",
"@shyuep Given the choice I'd prefer to err on the side of verbosity (\"code is read more than it's written\", tab-completion exists, etc), but don't mind being over-ruled on this one."
] | 2019-06-23T18:25:49
| 2019-06-24T04:04:10
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2019-06-24T04:04:10Z
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CONTRIBUTOR
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## Summary
* add grain boundary MPRester to query grain boundary structure and energy data
* add unittest
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| 460,028,801
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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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Switched the lattice vector matrix with the scaling matrix, now in format compliant with atat
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MDExOlB1bGxSZXF1ZXN0MjkxMzc4MzE0
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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 if the structure will be used to perform DFT calculation)"
] | 2019-06-25T04:22:08
| 2019-06-25T20:44:55
|
2019-06-25T20:33:44Z
|
CONTRIBUTOR
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## Summary
* 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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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 working
class Site(collections.Hashable, MSONable):
```
Particularly annoying when running `pytest` and we do not want to ignore warnings.
**Describe the solution you'd like**
Fix these, for instance with six, e.g.
```
if six.PY2:
from collections import Hashable
else:
from collections.abc import Hashable
```
etc.
**Describe alternatives you've considered**
None
**Additional context**
None
|
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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 default to maintain backwards compatibility).\r\n\r\n@smheidrich would you be willing to implement this with a test and submit a pull request?",
"So it should return one instance of ``BabelMolAdaptor`` per molecule? I agree that this would be easiest to implement (as a matter of fact, that's what I've been doing as a workaround :P), although it's not very consistent with other ``io`` modules, which generally have only one filetype-specific object associated with each file (e.g. [``xyz.XYZ``](https://pymatgen.org/pymatgen.io.xyz.html#pymatgen.io.xyz.XYZ), [``cif.CifParser``](https://pymatgen.org/pymatgen.io.cif.html#pymatgen.io.cif.CifParser), [``vasp.outputs.Vasprun``](https://pymatgen.org/pymatgen.io.vasp.outputs.html#pymatgen.io.vasp.outputs.Vasprun)), which can then be used to obtain a list of molecules or structures ([``XYZ.all_molecules``](https://pymatgen.org/pymatgen.io.xyz.html#pymatgen.io.xyz.XYZ.all_molecules), [``CifParser.get_structures``](https://pymatgen.org/pymatgen.io.cif.html#pymatgen.io.cif.CifParser.get_structures), [``Vasprun.structures``](https://pymatgen.org/pymatgen.io.vasp.outputs.html#pymatgen.io.vasp.outputs.Vasprun.structures)). But implementing it in this way would be a bit more work, of course (could be done e.g. introducing ``_obmols`` instead of ``_obmol`` and making all the existing methods work on just ``_obmols[0]`` to maintain backwards-compatibility, then introducing plural versions for working with the full list).\r\n\r\nAnyway, if you're set on the one-instance-per-molecule solution, I'm happy to write it up and submit a PR.",
"Just a note that CIfParser supports multiple structures. For now, I would just suggest the from_file method returns a list of BabelMolAdaptors for each molecule. We should probably rethink the BabelMolAdaptor API.",
">Just a note that CIfParser supports multiple structures.\r\n\r\nAll the examples I listed do, but what I'm saying is that the API is different from what is proposed here.\r\n\r\n>For now, I would just suggest the from_file method returns a list of BabelMolAdaptors for each molecule.\r\n\r\nFair enough, I'll send a PR soon."
] | 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/pymatgen/io/babel.py#L314-L315
It still *loads* all of them though and holds them all in memory simultaneously, so in a way it's the worst of both worlds.
**Describe the solution you'd like**
It would be cool if all molecules found within a file could be accessed.
**Describe alternatives you've considered**
- not implementing this
**Additional context**
There is precedent for this e.g. in [``pymatgen.io.xyz``](https://pymatgen.org/pymatgen.io.xyz.html), which loads and stores everything by default and lets you access either only the last frame via the ``molecule`` property or all frames via ``all_molecules``.
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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 set of matrix elements <u|d/dk|u> for (ikpt, nbands, nbands) into the WAVEDER file, which by default is only done for a subset.\r\n\r\nI will attempt to fix it.",
"I'm not particularly experienced in parsing xml files, so maybe someone else can give me a hint.\r\nThe vasprun is parsed using the iterparse method of the ElementTree so it's not possible to determine the according parent.\r\n\r\nA quick fix would be to check if self.kpoints has already been set and then skip later tag matches.\r\n```python\r\nif not hasattr(self, 'kpoints'):\r\n self.kpoints, self.actual_kpoints, self.actual_kpoints_weights = self._parse_kpoints(elem)\r\n```\r\n\r\nRight now it should not break anything, since the kpoint set used for self-consistency is quite far up in the element tree, but I'm not sure how future proof it is, maybe someone else got an idea?"
] | 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 vasprun, the structure is somewhat like:
```
<modelling>
<kpoints>
....
</kpoints>
<electronvelocities>
<kpoints>
....
</kpoints>
</electronvelocities>
</modelling>
```
**To Reproduce**
Steps to reproduce the behavior:
1. Run vasp with LVEL and LOPTICS flag
2. Initialize Vasprun with resulting vasprun.xml
3. Compare size of eigenvalues in Vasprun().eigenvalues with size of Vasprun.actual_kpoints
**Expected behavior**
Separate kpoint variables, or a list of kpoint sets.
Edit: corrected xml tree
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| 461,371,076
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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 tag which contains points in the full Brillouin zone.
Here, I only prevent that the kpoint variables read for the first set in Vasprun are overwritten by the second set.
Also added a test that ensures that the kpoint dimension of the eigenvalues array is equal to the number of kpoints.
Short few sentences, and summary of the major changes in bullet
points
* Recover default behaviour, when LVEL flag in vasp calculation is set
## For a later PR
A later feature PR should introduce new variables for the second kpoint set in vasprun.xml, as well as for any quantities calculated due to the LVEL flag (if any).
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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_ was _True_ (it is by default), the molecule would be rotated in place. In the case of consecutive structure generation (such as in the adsorption workflow from atomate), the adsorbate would keep rotating after each structure generation.
* Added the option to translate the molecule to the origin before adding it to the surface. Previously, the position of the adsorbate was fully dependent on the position of the input molecule - which could lead to structures with adsorbates that are positioned too close to surface, or too far from the actual adsorption site. If _translate_ is _True_, the molecule is first translated so that the center of mass of the substructure made up of the atoms that have the most negative z coordinates is placed at the origin (and hence on the adsorption site). This allows for both head-on and side-on adsorbate placement while ensuring that no atoms are placed closer to the surface than the actual adsorption site.
* Added tests for both changes.
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MDExOlB1bGxSZXF1ZXN0MjkyNTg4MDQ5
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|
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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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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MDExOlB1bGxSZXF1ZXN0MjkzNTI4MTM1
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|
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` method.",
"@mkhorton This PR is no longer WIP.",
"Thanks @rees-c and @utf "
] | 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 bulk crystalline solids and nanowires. Full details can be found at the following link: https://doi.org/10.1016/j.cpc.2014.02.015
Added an IO for reading/writing/updating ShengBTE CONTROL files with Python dictionaries.
## Additional dependencies introduced (if any)
'f90nml' for reading FORTRAN namelists used as input for running ShengBTE.
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MDExOlB1bGxSZXF1ZXN0MjkzNTI4NzA0
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|
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 cells for STEM image simulations, so this is great.\r\n\r\nBefore merging, I have a request: @rees-c in the docstrings where you mention CSLD can you expand the acronym and provide the references you mention above? Also where any reference is made to the CSLD code, a link to their code/repo would also be useful.",
"@mkhorton re linking to the CLSD repo: the CLSD code is not available online just yet. We have an advance version of the code in our group, so are adding features to pymatgen and atomate with the expectation that it will be released publicly in the next month or so.",
"Ah ok, that's fine then -- explains why I couldn't find it myself :) If you could submit a quick PR to update the docstring when it's publicly released that'd be great.\r\n\r\nOnce the acronym/refs are added I'll go ahead and merge",
"@mkhorton updated the docstring :)",
"Thanks @rees-c!"
] | 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 'CubicSupercellTransformation' and 'PerturbedSupercellsTransformation' classes to 'advanced_transformations.py'.
'CubicSupercellTransformation' generates a transformation matrix (np.ndarray) and a supercell (Pymatgen Structure) that is as cubic as possible given a structure (Pymatgen Structure) and several parameter constraints. Constraints include a minimum number of atomic nearest neighbor distances that each dimension of the supercell must exceed, and bounds for the total number of atoms in the supercell.
'PerturbedSupercellsTransformation' generates a list of Pymatgen Structures with randomly displaced atomic coordinates given a Pymatgen Structure. Parameters are input describing the range and magnitude of the displacements as well as the number of displaced structures to generate.
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MDU6SXNzdWU0NjM3NjE0NzM=
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|
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 relevant only for the next 5 months.\r\n\r\nI recommend that everyone transits to py3 today, rather than continuing to work in Py27. With conda, it is relatively easy to create a py3 env even with Py27 system python.",
"Thanks for the write-up @ltalirz, I concur with @shyuep but I will make a note of this in the docs in case any users really need to get this working, and it's a good reminder to be more careful with the setup.py requirements in future."
] | 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 requirement using `setup_requires`, which actually pipes through to `easy_install`
https://github.com/materialsproject/pymatgen/blob/master/setup.py#L91
This line causes `easy_install` to install the latest numpy version available at the time of the build.
`easy_install` is not very picky and will actually install the very latest version of numpy -- even release candidates. The latest numpy release candidate 1.17.0rc1 requires python3.5, which then causes the build of pymatgen to fail.
**To Reproduce**
```
(py27) pip install pymatgen==2018.12.12 --no-binary pymatgen
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting pymatgen==2018.12.12
Using cached https://files.pythonhosted.org/packages/d6/b9/f386300f232c8523f562e39bf07bae0d9c4e6379f423f71df7cd622ddae7/pymatgen-2018.12.12.tar.gz
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/8y/7c7qkxcx5vxb749rt3sw5sh40000gp/T/pip-install-aUOCUB/pymatgen/setup.py", line 177, in <module>
'get_environment = pymatgen.cli.get_environment:main',
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/__init__.py", line 144, in setup
_install_setup_requires(attrs)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/dist.py", line 717, in fetch_build_eggs
replace_conflicting=True,
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
return self.obtain(req, installer)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
return installer(requirement)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/dist.py", line 784, in fetch_build_egg
return cmd.easy_install(req)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
run_setup(setup_script, args)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/Users/leopold/Applications/miniconda3/envs/py27/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/var/folders/8y/7c7qkxcx5vxb749rt3sw5sh40000gp/T/easy_install-gUdb4m/numpy-1.17.0rc1/setup.py", line 31, in <module>
self.include_dirs.append(numpy.get_include())
RuntimeError: Python version >= 3.5 required.
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/8y/7c7qkxcx5vxb749rt3sw5sh40000gp/T/pip-install-aUOCUB/pymatgen/
```
**Workaround**
It seems the problem can be solved by manually installing a compatible version of numpy (e.g. `pip install "numpy<1.17"`) *before* installing pymatgen.
**Note:**
* This needs to be done in a separate call to pip - `pip install numpy==1.16.4 pymatgen==2018.12.12` [does not work in general](https://travis-ci.org/ltalirz/aiida_core/jobs/553536605#L998).
* It is important that the version of numpy used to build the pymatgen extensions is the same version of numpy that is present when using pymatgen - otherwise you can run into issues like [these](https://travis-ci.org/aiidateam/aiida_core/jobs/484118664#L1472). When you have packages that require specific numpy versions, it is therefore important to install pymatgen *last*.
|
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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. Thanks to @blondegeek for the help!
* Outcars now get their zval_dict keys from more reliable part of the OUTCAR
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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 recent version available on most of the systems I have access to. The UCL Sumo users would definitely be ok. I'd be more worried about people doing Fireworks stuff on smaller institutional machines... Python 3.6 has only been out for 3 years, which seems to me the absolute minimum time that's ok to make it a hard requirement without a lot of pushback.\r\n\r\nI would love to start using f-strings in production code though...",
"Yes, I'd be lying if I said f-strings weren't a factor :) There's also dataclasses (a back port exists for 3.6 but not 3.5), ordered dicts by default etc. We're also trying to make heavier use of type hints in the core classes, though that's a 3.5 feature so we're fine there.\r\n\r\nIf you (or anyone else reading this) has significant issues with the 3.6 requirement however please let us know, we're definitely open to formally supporting 3.5 if necessary. To my knowledge there's nothing in pymatgen that shouldn't in principle work in 3.5 currently.\r\n\r\nAnd to clarify, this is for pymatgen specifically, there are no plans to change version requirements for fireworks, monty, etc.",
"Closed via https://github.com/materialsproject/pymatgen/commit/ed9396b385e9f5b262eb0289f69630893b7f72c1",
"Ok, thanks for clarity.\r\n\r\nJust a comment on ordered dicts: as of 3.6 they are an implementation detail of CPython and not guaranteed. Alternative implementations may not be ordered so you should still use OrderedDict wherever it matters (but in CPython it will pass through to the same implementation as _dict_). As of 3.7 it is part of the language spec, so you can assume all dicts are ordered once going to 3.7 as the minimum supported version.\r\n\r\n(Probably you knew all this already but it doesn't hurt to disseminate to passers-by ;-) )",
"Just a note that while I am on board for Dataclasses, I am less enamored of the idea of f-strings over say the standard str.format. I can certainly see convenience benefits, but in my opinion, it makes it hard to figure from context what the string actually is if the variable values are defined far away from the actual string. ",
"f-strings can be directly equivalent to format, I see it as more a syntax choice, e.g.:\r\n\r\n```\r\n\"Lattice params are {}, {} and {}\".format(a, b, c)\r\n```\r\n\r\nor\r\n\r\n```\r\n\"Lattice params are {a}, {b} and {c}\".format(a=a, b=b, c=c)\r\n```\r\n\r\nvs\r\n\r\n```\r\nf\"Lattice params are {a}, {b} and {c}\"\r\n```\r\n\r\nWhere a, b and c are defined is an implementation choice, at least in that sense I'm not sure I see why f-strings are any better/worse than .format",
"The .format forces you to specify at the location of the string what the values of a, b and c are. Of course a, b and c can be defined far away, but the more common application is \"{a}\".format(a=\"hello\").",
"I think it's on the programmer to use both f-strings and format() responsibly. If you're going to define a template and populate it elsewhere then format() is the better tool for the job. But I write a lot of code that looks like @mkhorton 's example and in that case the f-string is easiest to read and has the least potential for surprises.\r\n\r\nWith format() one has to read more carefully in case of something like\r\n```python\r\n\"lattice params are {a}, {b} and {c}\".format(a=b, b=c, c=a)\r\n```"
] | 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 from "upgrading" to a (from their perspective) broken version of Pymatgen.
**To Reproduce**
On a Python 3.5 system:
```
pip install pymatgen
python3 -c "import pymatgen.io.vasp.outputs"
```
**Expected behavior**
I'm not entirely sure what it looks like in practice but a `python_requires` in _setup.py_ should stop Pip from installing incompatible versions. There is a slight gotcha in that this feature has only been around since Pip 9.00.
|
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MDExOlB1bGxSZXF1ZXN0Mjk3MTcxMDYz
| 1,523
|
Fix bug in `pmg potcar` command
|
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[] | 2019-07-12T18:07:03
| 2019-07-12T18:12:02
|
2019-07-12T18:12:02Z
|
MEMBER
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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, so removes `nargs="+"` in the arg parsing.
## TODO (if any)
Test? I ran with a mock `POTCAR.spec` file with just the symbol `Ag` in it and got the error
> ValueError: No POTCAR for Ag with functional PBE found
so I think it's getting to the right point in the application logic. I have no interest in writing a proper test for this.
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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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MDExOlB1bGxSZXF1ZXN0Mjk3ODA5NTE1
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[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 extraneous parentheses etc. I haven't had a look at test coverage yet. Overall seems v high quality though + almost ready to merge. Thanks for the good code comments, made reviewing it easy!",
"Thanks for the review Matt! Working on those fixes now.",
"Find it really weird that ReactionDiagramTest failed here ... there's nothing in this PR that should affect that."
] | 2019-07-15T22:25:59
| 2019-07-17T23:47:46
|
2019-07-17T23:47:46Z
|
CONTRIBUTOR
|
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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.
* Wrapper for VAMPIRE atomistic simulations of magnetic materials package.
## Additional dependencies introduced (if any)
* Vampire5 command line tool for atomistic simulations of magnetic materials.
## TODO (if any)
* Added sophistication to screening/sanitization of input low energy ordering data.
* Cleanup VAMPIRE files after execution.
|
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MDExOlB1bGxSZXF1ZXN0Mjk4MjA5MjUx
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[WIP] TEM Diffraction
|
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[] | 2019-07-16T20:59:50
| 2019-10-31T00:34:05
|
2019-10-31T00:34:05Z
|
CONTRIBUTOR
|
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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 in nice "futuristic" format.
## Additional dependencies introduced:
*PrettyTable: needed to display TEM diffraction details in clean format
## TODO:
Re-examine cell_scattering_factors to make sure it's not double counting (though I believe this
should only affect calculations by a factor of two which cancels out anyway in the normalization of
cell intensity). (high priority)
Optimize runtime for patterns. Runtime is solid for simple structures like CsCl, but long (~10s) for complicated structures like rotaxanes and "molecules that chemists deal with". (best bet is to memoize certain calculations that reoccur many times) (mid-low priority)
Rearrange code so that the user decides only the structure to be tested, the Laue zone to be tested, and the point range to be tested for a given initialized calculator using the get_2d_pattern function.
Finish writing tests for the other functions. (low priority)
Make MSONable. (high priority)
Add type hints for every method. (low priority)
Start running this code on 120k-ish structures and doing cluster analyses on them. (high priority)
Write a function that gets all unique crystal planes based on crystal symmetries (?) (high priority)
|
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MDExOlB1bGxSZXF1ZXN0Mjk4MjIzNjE3
| 1,527
|
Get symmetrically equivalent Miller indices
|
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[] | null |
[
"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, I would support that. Although of course very important to surfaces, Miller indices and planes are fundamentally a property of a Lattice and relevant to non-surface applications too so I think it would make sense.",
"Will do"
] | 2019-07-16T21:44:51
| 2019-07-19T22:47:55
|
2019-07-17T17:46:55Z
|
CONTRIBUTOR
|
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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 the exact same Miller index as the one associated with an entry. Modified get_surface_data using this function to make it easier to obtain work of separation from GB data.
* Feature 1 get_equivalent_miller_indices(structure, miller_index)
* Fix 1: Can now get specific surfaces without needing the exact same Miller index
## TODO (if any):
Some overlap between get_symmetrically_equivalent_miller_indices and get_symmetrically_distinct_miller_indices.
|
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MDExOlB1bGxSZXF1ZXN0Mjk4NTE5NDAy
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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
|
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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 make the creation of an additional LobsterSet easier in the future.
Tests are also included.
JG
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| 469,373,892
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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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Hello again,
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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MDU6SXNzdWU0Njk4MTIyOTE=
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|
get_spd_dos() doesn't work?
|
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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/anaconda3/envs/procar/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py\", line 745, in get_spd_dos\r\n add_densities(spd_dos[orbital_type], pdos)\r\n File \"/home/noki/anaconda3/envs/procar/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py\", line 998, in add_densities\r\n for spin in density1.keys()}\r\n File \"/home/noki/anaconda3/envs/procar/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py\", line 998, in <dictcomp>\r\n for spin in density1.keys()}\r\nKeyError: <Spin.up: [1>]\r\n\r\n(My calculation result contains only Spin.up info.)\r\n\r\nThere are similar errors when typing\r\n\r\n`dos.get_element_dos()`\r\n`dos.get_element_spd_dos(dos.structure.symbol_set[0])`\r\n`dos.get_site_dos(dos.structure.sites[0])`\r\n\r\nafter executing \r\n\r\n `dos.get_site_orbital_dos(dos.structure.sites[0],OrbitalType.d)`\r\n\r\nBut if I re-bulid \r\n`vasprun= Vasprun(path_vasprun, parse_dos=True)`\r\n`dos = vasprun.complete_dos`\r\n(not from `dos = vasprun.complete_dos`)\r\nIt works again.\r\n\r\n**Desktop (please complete the following information):**\r\nCentOS 7\r\n\r\n**Additional context**\r\nName / Version / Build / Channel\r\npymatgen / 2019.7.2 / pypi_0 / pypi\r\n\r\ncopy.deepcopy works neither. Only after recalling the file, then it works.\r\n\r\nBy the way, I wonder that the below commands mutually influence or not for the output results e.g. densities.\r\n\r\ndos.energies\r\ndos.densities\r\ndos.get_densities()\r\ndos.pdos\r\ndos.get_element_dos() *\r\ndos.get_element_spd_dos(dos.structure.symbol_set[0]) *\r\ndos.get_site_dos(dos.structure.sites[0]) *\r\ndos.get_site_orbital_dos(dos.structure.sites[0], OrbitalType.d)\r\ndos.get_site_t2g_eg_resolved_dos(dos.structure.sites[0])\r\ndos.get_smeared_densities(0.1)\r\ndos.get_spd_dos()\r\n\r\n'*' means they are in troubles with mutual effect according to orders.",
"@janosh: I think this can be closed. `.get_spd_dos()` is widely used by MP and I've tested it more than probably any function in MP. We can re-open if someone has an issue."
] | 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/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 745, in get_spd_dos
add_densities(spd_dos[orbital_type], pdos)
File "/home/noki/anaconda3/envs/procar/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 998, in add_densities
for spin in density1.keys()}
File "/home/noki/anaconda3/envs/procar/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 998, in <dictcomp>
for spin in density1.keys()}
KeyError: <Spin.up: [1>]
(My calculation result contains only Spin.up info.)
There are similar errors when typing
`dos.get_element_dos()`
`dos.get_element_spd_dos(dos.structure.symbol_set[0])`
`dos.get_site_dos(dos.structure.sites[0])`
after executing
`dos.get_site_orbital_dos(dos.structure.sites[0],OrbitalType.d)`
But if I re-bulid
`vasprun= Vasprun(path_vasprun, parse_dos=True)`
`dos = vasprun.complete_dos`
(not from `dos = vasprun.complete_dos`)
It works again.
**Desktop (please complete the following information):**
CentOS 7
**Additional context**
Name / Version / Build / Channel
pymatgen / 2019.7.2 / pypi_0 / pypi
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MDU6SXNzdWU0NzAyNzE5NTk=
| 1,531
|
sum_densities(*densities)
|
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[] | null |
[
"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
```
def sum_densities(*densities):
if len(densities) == 1:
return densities[0]
else:
density_0 = denstiies[0]
density_1 = denstieis[1]
return sum_densities(add_densities(density_0, density_1),
*densities[2:])
```
|
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MDExOlB1bGxSZXF1ZXN0Mjk5NTQ2MDA1
| 1,532
|
Moved some functions as a Lattice object method.
|
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[] | null |
[] | 2019-07-20T07:56:59
| 2019-07-20T16:52:41
|
2019-07-20T16:52:40Z
|
CONTRIBUTOR
|
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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 requires a local import of Structure and SpacegroupAnalyzer to work which may be unwieldy?
* I want to make get_symmetrically_equivalent_miller_indices and get_symmetrically_distinct_miller_indices as a Lattice method as well, however there is the issue of getting Miller indices for trigonal systems which at the moment requires searching through the rhombohedral basis instead of the hexagonal basis to identify all the Miller indices. This is an issue because a lattice object won't know to look at a rhombohedral setting when given a hexagonal setting when looking for Miller indices. Will need to think of a more elegant way to refactor all these Miller index operations.
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| 471,442,974
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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/python2.7/site-packages/pymatgen/__init__.py:89: UserWarning:
Pymatgen will drop Py2k support from v2019.1.1. Pls consult the documentation
at https://www.pymatgen.org for more details.
at https://www.pymatgen.org for more details.""")
Traceback (most recent call last):
File "/usr/local/bin/pmg", line 7, in <module>
from pymatgen.cli.pmg import main
File "/usr/local/lib/python2.7/site-packages/pymatgen/cli/pmg.py", line 19, in <module>
from pymatgen.cli.pmg_plot import plot
File "/usr/local/lib/python2.7/site-packages/pymatgen/cli/pmg_plot.py", line 13, in <module>
from pymatgen.analysis.diffraction.xrd import XRDCalculator
File "/usr/local/lib/python2.7/site-packages/pymatgen/analysis/diffraction/xrd.py", line 15, in <module>
from .core import DiffractionPattern, DiffractionPatternCalculator, \
File "/usr/local/lib/python2.7/site-packages/pymatgen/analysis/diffraction/core.py", line 50, in <module>
class DiffractionPatternCalculator(abc.ABC):
AttributeError: 'module' object has no attribute 'ABC'
**Desktop (please complete the following information):**
- OS: MacOS
**Additional context**
Add any other context about the problem here.
|
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| 471,548,517
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MDExOlB1bGxSZXF1ZXN0MzAwMTc2OTY5
| 1,534
|
Fix ixc == 0 in from_abinit_ixc
|
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[] | 2019-07-23T08:13:47
| 2019-07-23T14:59:12
|
2019-07-23T14:33:01Z
|
CONTRIBUTOR
|
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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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| 471,676,012
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MDExOlB1bGxSZXF1ZXN0MzAwMjc5NDE5
| 1,535
|
Add return_all_molecules option to BabelMolAdaptor
|
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[] | null |
[
"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 always return just the first molecule found and discard the rest, which this PR leaves as the default behavior for backwards-compatibility.
Fixes #1512.
|
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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 AbstractTransformation apply_transformation docstring or other one-to-many transformations for an example).\r\n\r\nIn the long term, I think we could probably clean up the AbstractTransformation base class to make the method signature more consistent between one-to-one and one-to-many transformations, but for now PerturbSites should be fixed to make it consistent with other transformations, else it will not be able to be used e.g. for TransmuterFW in workflows etc.",
"@rees-c Can you respond to Matts comments/fix the transformation.",
"Hey @mkhorton ! Sorry for the late reply - I'm a bit new to Git and my gmail seems to silence my Github notifications. I'll send another pull request with the JSON serialization fixes and the corrected one-to-many format for PerturbSitesTransformation.\r\n\r\nI see now that PerturbSitesTransformation can replicate the output of PerturbStructureTransformation. On the flip side, I feel that if a user only needs a single perturbed structure, then reading through a one-to-many transformation with its corresponding variable names could be nonintuitive (i.e. if a user wanted to replicate the output of PerturbStructureTransformation using PerturbSitesTransformation, they would have to set `return_ranked_list=False` in `apply_transformation`, `min_random_distance=None` in the init, and `min_disp` to the desired distance). Do you have any thoughts about what would be the best way to merge the two while maintaining backwards compatibility if we choose to do so?",
"No worries, and thanks for the fix.\r\n\r\nRegarding merging them, they *should* be merged, but I'm agnostic to the specific method.\r\n\r\nThe `PerturbStructureTransformation` is basically a wrapper around the `Structure.perturb` method, so one option would be to improve that method to make it more powerful.\r\n\r\nI find the current docstring for `PerturbSitesTransformation` a little confusing actually, it's possibly trying to do too much (e.g. if you want multiple structures for multiple displacement distances, why not create multiple transformations to do that? so `max_disp`, `min_disp`, `num_disps` may not be necessary, or at least maybe accept a list of displacements instead and let the user figure out how to do them? It took me a few reads to understand the distinction between `min_disp` and `min_random_distance` which I think is partly why I found it confusing.) Open to ideas on this!",
"My view: PerturbSitesTransformation should be a one-to-one transformation. If someone wants multiple site perturbations, they can call it multiple times with different displacements. Class design should be for the most common use case, not a strangely powerful use case that is used 0.0001% of the time.",
"I agree -- I don't mind it being one-to-many if the \"many\" are just different random perturbations for the same displacement magnitude. But if the \"many\" are different random perturbations but also for *different* displacement magnitudes, I think that's just confusing, because you're varying two different variables.",
"Thanks for the helpful feedback! I agree with all your points - I'll submit a pull request."
] | 2019-07-23T19:24:37
| 2023-08-10T15:08:00
|
2023-08-10T15:08:00Z
|
MEMBER
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@utf @rees-c
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()`, `.from_dict()` etc
|
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MDU6SXNzdWU0NzIwODY3NzI=
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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 of scope."
] | 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 pymatgen.analysis.diffraction.xrd import XRDCalculator
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
fn_cif = "Ice6.cif"
fn_jcpds = 'Ice6.jcpds'
comments_jcpds = "Ice6"
material = mg.Structure.from_file(fn_cif)
**Error message**
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-14-99a894ef35cb> in <module>
----> 1 material = mg.Structure.from_file(fn_cif)
~\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_file(cls, filename, primitive, sort, merge_tol)
2092 return cls.from_str(contents, fmt="cif",
2093 primitive=primitive, sort=sort,
-> 2094 merge_tol=merge_tol)
2095 elif fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
2096 s = cls.from_str(contents, fmt="poscar",
~\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_str(cls, input_string, fmt, primitive, sort, merge_tol)
2026 if fmt == "cif":
2027 parser = CifParser.from_string(input_string)
-> 2028 s = parser.get_structures(primitive=primitive)[0]
2029 elif fmt == "poscar":
2030 s = Poscar.from_string(input_string, False,
~\Anaconda3\lib\site-packages\pymatgen\io\cif.py in get_structures(self, primitive)
1109 warnings.warn(error)
1110 if len(structures) == 0:
-> 1111 raise ValueError("Invalid cif file with no structures!")
1112 return structures
1113
ValueError: Invalid cif file with no structures!
**Files**
[Ice6.zip](https://github.com/materialsproject/pymatgen/files/3425151/Ice6.zip)
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MDExOlB1bGxSZXF1ZXN0MzAwNjAzODg1
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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 to use pymatgen on a server without an external internet connection, then any tools that depend on this pymatgen functionality will cease to work. We are exploring other avenues for determination of magnetic space group symmetry.",
"Actually, to clarify, if you wanted to write this and contribute to pymatgen we *would* gratefully accept it (provided this is done with Bilbao's permission, or otherwise queries their website in a polite way), however we wouldn't write this ourselves.\r\n\r\nIf you do want to contribute an interface an appropriate place to put the code would be `pymatgen.ext.bilbao` to emphasize this is calling an external service.",
"Finally, magnetic CIF writing should currently be supported by pymatgen -- if you're encountering bugs though please do open a bug report issue.",
"Hi @mkhorton! \r\n\r\nWhat do you mean by exploring other avenues to determine the magnetic space group (mspg)? Are you working on an implementation to get the mspg from the list of xyzt operations? \r\n\r\nContacting Bilbao and implementing `pymatgen.ext.bilbao` would be a simple solution. But I agree with your argument about offline availability and robustness. Personally, I would also prefer more transparency. Maybe it's me, but I could not find the algorithm behind their tool. Finally, to open a new module suggests t write complete interfaces, which I was not planing to do.\r\n\r\nConcerning the mcif functionality. The P 1 case works well, but when I want to use the magnetic symmetry detected, sf.get_refined_structure() does not work. As far as I understand, spglib is applying all operations to get all positions perfectly symmetric and return the conventional structure. For a non-collinear structure we need to do that for xyzt operations, which is not implemented in spglib. To be honest, I didn't grasp how spglibs refined_structure method works, when I looked at the code, so I am not sure how it can be extended to the xyzt case.\r\nThen instead of '_symmetry_equiv_pos_as_xyz' -> '_space_group_symop_magn_operation.xyz' and '_space_group_symop_magn_centering.xyz' should be written, I think. '_space_group_symop_magn_operation.xyz' are simply the xyzt strings, but I am not sure how to go about the latter. '_space_group_symop_magn_centering.xyz' is the non-primitiv translation that leaves the structure invariant, right? How can I find them in an efficient way...\r\n\r\nAnother question I am trying to answer is how to get '_atom_site_moment.symmform' (based on the xyzt operations?). It seems to be an xyzt like string, but in terms of mx, my, mz.\r\n\r\nI hope you are interested in some of my thoughts. Instead of working on my own little project, I would like to share what I am doing during my PhD. In the (very) long run, I am hoping to contribute a new ansatz, that we are currently perusing. But for now, I would be happy to contribute small functionalities that come in handy for my project and may benefit others.",
"Can we just run this for everything and build some sort of dictionary to reference to decouple from Bilbao?",
"Quick update, I am going to be working with Guy Moore (@guymoore13, grad student in our group) to try and write a native pymatgen MagneticSymmetryAnalyzer, we already have 90% of what we need I think.\r\n\r\n@mt-huebsch In terms of your other questions above, I'll get back to these! Apologies to the delay.",
"Closing for now, happy to re-open later if more progress is made on this."
] | 2019-07-24T07:56:49
| 2020-02-12T04:12:20
|
2020-02-12T04:12:20Z
|
NONE
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Hello!
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 structure.
This is used in the other new object, MagneticSpaceGroupAnalyzer, which can determine the magnetic space group in two steps:
* Find the magnetic space group operations, which leave the structure invariant.
* Use the tool IDENTIFY MAGNETIC GROUP made available by the Bilbao Crystallographic Server on the website www.cryst.ehu.es
## Additional dependencies introduced
mechanize: Introduced in order to navigate on the web interface of the tool IDENTIFY MAGNETIC GROUP.
I want to emphasize, that I am not affiliated with the Bilbao Crystallographic Server and that we may better get in touch with them before interfacing their tool. Though I wanted to make sure you are interested in my proposal, before asking them. Hope that's all right?
## TODO
(Or rather ideas what to work on:)
In MagneticSpaceGroupAnalyzer
* Get rid of circular dependencies btw pymatgen.transformations and pymatgen.symmetry
* Add a function get_refined_structure(self) analogous to SpacegroupAnalyzer
* Add function to return Magnetic Laue group
* Use Magnetic Laue Group + Seemann et al (2015) to determine symmetry-imposed shape of linear response tensor.
In io.cif
* Implement an magnetic CIF file writer. (First attempt failed because it needs get_refined_structure(self) )
(About me: My name is Marie-Therese. I am a PhD student in Ryotaro Aritas group at the University of Tokyo. Hard to guess, but my work focuses on non collinear magnetism. )
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MDU6SXNzdWU0NzIzNzk4MDE=
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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 spin polarized, we only\r\n store one data set under Spin.u\r\n```\r\n\r\nThere doesn't seem to be a convenience method to collect together the data on a single ion_index and orbital_index so you'd have to write your own that is similar to elements / elements with orbital."
] | 2019-07-24T16:26:25
| 2019-07-24T20:13:15
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2019-07-24T20:13:15Z
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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 functions are extracting on a site plus Orbital and OrbitalType.
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| 472,879,207
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MDU6SXNzdWU0NzI4NzkyMDc=
| 1,540
|
Improper pdos for the result from SOC calculation (VASP)
|
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[] | null |
[
"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 from spin polarization.
**Desktop (please complete the following information):**
CentOS 7
pymatgen / 2019.7.2 / pypi_0 / pypi
**Additional context**
Add any other context about the problem here.
|
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| 475,260,350
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MDExOlB1bGxSZXF1ZXN0MzAzMDQ4Mjg1
| 1,541
|
WIP: Fixed MSONability CubicSupercellTransformation and PerturbSitesTransformation
|
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[] | null |
[
"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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@utf
## 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 PerturbStructureTransformation (one-to-one transform). Not sure about the best way to do this
|
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| 475,299,961
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MDU6SXNzdWU0NzUyOTk5NjE=
| 1,542
|
SlabGenerator.get_slabs() fails on pure metal FCC crystals
|
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[] | null |
[
"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_index=(2, 1, 1),\r\n min_vacuum_size=12,\r\n min_slab_size=3,\r\n)\r\n```\r\n\r\nYou should be constructing the slab with your initial cell and then scaling as appropriate later. This is the purpose of the slab generator (in fact, if you use a supercell in the slab generator your choice of plane may well be incorrect relative to the conventional cell depending on your choice of supercell).\r\n\r\nIf you change this to:\r\n\r\n```\r\nmg_sg = SlabGenerator(\r\n initial_structure=fcc_basic,\r\n miller_index=(2, 1, 1),\r\n min_vacuum_size=12,\r\n min_slab_size=3,\r\n)\r\n```\r\n\r\nAnd then later create the supercell (`mg_sg * (2,2,1)` for example), it will work.",
"The reason is that you generated a supercell first before running the SlabGenerator with primitive=True. The search for primitive cells take a long time when there are many atoms. Use fcc_basic as an input to the slab generator. If you insist on using the supercell, you should then set primitive=False. But using supercells is not a good idea since the Miller indices may be completely different (depending on how you construct the supercell).",
"Okay, I see. If the supercell has the same aspect ratio as the unit cell (e.g., a 2 x 2 x 2 supercell of a cubic FCC unit cell), wouldn't the same Miller indices yield the same facets? I ask because I'm doing a doping study where I need a large supercell to simulate < 25% of the FCC atoms being doped, and I need the (211) surface for that particular composition.",
"Yes, if you maintain the same cubic cell, the Miller indices are the same (subject to a scaling factor). In any case, if you want to do doped fcc surfaces, I suggest you just set primitive = False, or alternatively, you generate the slab using the primitive cell first before you generate a supercell of the slab and then do the doping.",
"Sounds good. Thanks so much!"
] | 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 different species enables the slab generator to succeed.
**To Reproduce**
Minimal working example:
```python
import pymatgen as mg
from pymatgen.core.surface import SlabGenerator, generate_all_slabs, Structure, Lattice
# Create a FCC unit cell, conventional standard, cubic, not orthorhombic.
fcc_basic = mg.Structure(
lattice=mg.Lattice.cubic(a=4.2),
species=["Pt"] * 4,
coords=[[0, 0, 0], [0.5, 0, 0.5], [0.5, 0.5, 0], [0, 0.5, 0.5]],
)
# fcc_basic:
#
# Structure Summary
# Lattice
# abc : 4.2 4.2 4.2
# angles : 90.0 90.0 90.0
# volume : 74.08800000000001
# A : 4.2 0.0 0.0
# B : 0.0 4.2 0.0
# C : 0.0 0.0 4.2
# PeriodicSite: Pt (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
# PeriodicSite: Pt (2.1000, 0.0000, 2.1000) [0.5000, 0.0000, 0.5000]
# PeriodicSite: Pt (2.1000, 2.1000, 0.0000) [0.5000, 0.5000, 0.0000]
# PeriodicSite: Pt (0.0000, 2.1000, 2.1000) [0.0000, 0.5000, 0.5000]
mg_supercell = fcc_basic * (2,2,2)
# mg_supercell:
#
# Structure Summary
# Lattice
# abc : 8.4 8.4 8.4
# angles : 90.0 90.0 90.0
# volume : 592.7040000000001
# A : 8.4 0.0 0.0
# B : 0.0 8.4 0.0
# C : 0.0 0.0 8.4
# PeriodicSite: Pt (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
# PeriodicSite: Pt (0.0000, 0.0000, 4.2000) [0.0000, 0.0000, 0.5000]
# PeriodicSite: Pt (0.0000, 4.2000, 0.0000) [0.0000, 0.5000, 0.0000]
# PeriodicSite: Pt (0.0000, 4.2000, 4.2000) [0.0000, 0.5000, 0.5000]
# PeriodicSite: Pt (4.2000, 0.0000, 0.0000) [0.5000, 0.0000, 0.0000]
# PeriodicSite: Pt (4.2000, 0.0000, 4.2000) [0.5000, 0.0000, 0.5000]
# PeriodicSite: Pt (4.2000, 4.2000, 0.0000) [0.5000, 0.5000, 0.0000]
# PeriodicSite: Pt (4.2000, 4.2000, 4.2000) [0.5000, 0.5000, 0.5000]
# PeriodicSite: Pt (2.1000, 0.0000, 2.1000) [0.2500, 0.0000, 0.2500]
# PeriodicSite: Pt (2.1000, 0.0000, 6.3000) [0.2500, 0.0000, 0.7500]
# PeriodicSite: Pt (2.1000, 4.2000, 2.1000) [0.2500, 0.5000, 0.2500]
# PeriodicSite: Pt (2.1000, 4.2000, 6.3000) [0.2500, 0.5000, 0.7500]
# PeriodicSite: Pt (6.3000, 0.0000, 2.1000) [0.7500, 0.0000, 0.2500]
# PeriodicSite: Pt (6.3000, 0.0000, 6.3000) [0.7500, 0.0000, 0.7500]
# PeriodicSite: Pt (6.3000, 4.2000, 2.1000) [0.7500, 0.5000, 0.2500]
# PeriodicSite: Pt (6.3000, 4.2000, 6.3000) [0.7500, 0.5000, 0.7500]
# PeriodicSite: Pt (2.1000, 2.1000, 0.0000) [0.2500, 0.2500, 0.0000]
# PeriodicSite: Pt (2.1000, 2.1000, 4.2000) [0.2500, 0.2500, 0.5000]
# PeriodicSite: Pt (2.1000, 6.3000, 0.0000) [0.2500, 0.7500, 0.0000]
# PeriodicSite: Pt (2.1000, 6.3000, 4.2000) [0.2500, 0.7500, 0.5000]
# PeriodicSite: Pt (6.3000, 2.1000, 0.0000) [0.7500, 0.2500, 0.0000]
# PeriodicSite: Pt (6.3000, 2.1000, 4.2000) [0.7500, 0.2500, 0.5000]
# PeriodicSite: Pt (6.3000, 6.3000, 0.0000) [0.7500, 0.7500, 0.0000]
# PeriodicSite: Pt (6.3000, 6.3000, 4.2000) [0.7500, 0.7500, 0.5000]
# PeriodicSite: Pt (0.0000, 2.1000, 2.1000) [0.0000, 0.2500, 0.2500]
# PeriodicSite: Pt (0.0000, 2.1000, 6.3000) [0.0000, 0.2500, 0.7500]
# PeriodicSite: Pt (0.0000, 6.3000, 2.1000) [0.0000, 0.7500, 0.2500]
# PeriodicSite: Pt (0.0000, 6.3000, 6.3000) [0.0000, 0.7500, 0.7500]
# PeriodicSite: Pt (4.2000, 2.1000, 2.1000) [0.5000, 0.2500, 0.2500]
# PeriodicSite: Pt (4.2000, 2.1000, 6.3000) [0.5000, 0.2500, 0.7500]
# PeriodicSite: Pt (4.2000, 6.3000, 2.1000) [0.5000, 0.7500, 0.2500]
# PeriodicSite: Pt (4.2000, 6.3000, 6.3000) [0.5000, 0.7500, 0.7500]
# This seems to run forever and doesn't finish...
mg_sg = SlabGenerator(
initial_structure=mg_supercell,
miller_index=(2, 1, 1),
min_vacuum_size=12,
min_slab_size=3,
)
slabs = mg_sg.get_slabs()
# Times out.
```
But if you change just one atom to Ru, it works fine:
```python
mg_supercell[5] = "Ru"
mg_sg = SlabGenerator(
initial_structure=mg_supercell,
miller_index=(2, 1, 1),
min_vacuum_size=12,
min_slab_size=3,
)
slabs = mg_sg.get_slabs()
# CPU times: user 3.93 s, sys: 1.19 s, total: 5.11 s
# Wall time: 1.33 s
```
Similar behavior occurs when you use `generate_all_slabs` to do the task.
```python
# Create a FCC unit cell, conventional standard, cubic, not orthorhombic.
fcc_basic = mg.Structure(
lattice=mg.Lattice.cubic(a=4.2),
species=["Pt"] * 4,
coords=[[0, 0, 0], [0.5, 0, 0.5], [0.5, 0.5, 0], [0, 0.5, 0.5]],
)
mg_supercell = fcc_basic * (2,2,2)
# This times out.
test_slabs = generate_all_slabs(
mg_supercell,
max_index=2,
min_slab_size=3,
min_vacuum_size=12
)
```
But again, if you switch even one atom to Ru, things work:
```python
mg_supercell[5] = "Ru"
test_slabs = generate_all_slabs(
mg_supercell,
max_index=2,
min_slab_size=3,
min_vacuum_size=12
)
# CPU times: user 5.09 s, sys: 1.33 s, total: 6.42 s
# Wall time: 2.47 s
```
**Expected behavior**
When acting on the pure Pt FCC crystal, the slab generator should be able to generate the one unique (211) termination that exists.
**Desktop (please complete the following information):**
- OS: CentOS 7.6.1810
- Browser: Google Chrome 75.0.3770.142 (Official Build) (32-bit)
- Version: Pymatgen 2019.4.11 running in Python 3.7.3 and JupyterLab 1.0.2
- Have also observed the same behavior on a machine running Windows 10 1709, Python 3.7.3, Google Chrome 75.0.3770.142 (Official Build) (32-bit), Pymatgen 2019.4.11, and JupyterLab 0.35.4.
**Additional context**
Traceback when I interrupted the kernel during one failed slab generation:
```
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
<timed exec> in <module>
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/surface.py in get_slabs(self, bonds, ftol, tol, max_broken_bonds, symmetrize, repair)
1075 if r[0] <= shift <= r[1]:
1076 bonds_broken += 1
-> 1077 slab = self.get_slab(shift, tol=tol, energy=bonds_broken)
1078 if bonds_broken <= max_broken_bonds:
1079 slabs.append(slab)
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/surface.py in get_slab(self, shift, tol, energy)
950 "alpha": slab_l.alpha,
951 "beta": slab_l.beta,
--> 952 "gamma": slab_l.gamma})
953
954 return Slab(slab.lattice, slab.species_and_occu,
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/structure.py in get_primitive_structure(self, tolerance, use_site_props, constrain_latt)
1585 p = s.get_primitive_structure(
1586 tolerance=tolerance, use_site_props=use_site_props,
-> 1587 constrain_latt=constrain_latt
1588 ).get_reduced_structure()
1589 if not constrain_latt:
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/structure.py in get_primitive_structure(self, tolerance, use_site_props, constrain_latt)
1585 p = s.get_primitive_structure(
1586 tolerance=tolerance, use_site_props=use_site_props,
-> 1587 constrain_latt=constrain_latt
1588 ).get_reduced_structure()
1589 if not constrain_latt:
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/structure.py in get_primitive_structure(self, tolerance, use_site_props, constrain_latt)
1585 p = s.get_primitive_structure(
1586 tolerance=tolerance, use_site_props=use_site_props,
-> 1587 constrain_latt=constrain_latt
1588 ).get_reduced_structure()
1589 if not constrain_latt:
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/structure.py in get_reduced_structure(self, reduction_algo)
1211 """
1212 if reduction_algo == "niggli":
-> 1213 reduced_latt = self._lattice.get_niggli_reduced_lattice()
1214 elif reduction_algo == "LLL":
1215 reduced_latt = self._lattice.get_lll_reduced_lattice()
~/.conda/envs/samueldy_base/lib/python3.7/site-packages/pymatgen/core/lattice.py in get_niggli_reduced_lattice(self, tol)
838 k = -1 if n == -1 else 1
839 M = [[i, 0, 0], [0, j, 0], [0, 0, k]]
--> 840 G = dot(transpose(M), dot(G, M))
841 elif l * m * n == 0 or l * m * n == -1:
842 # A4
KeyboardInterrupt:
```
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| 475,359,433
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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 reproduce the behavior:
1. Download this file into some directory
[POSCAR-aconvasp_Mg3Sb2.txt](https://github.com/materialsproject/pymatgen/files/3453869/POSCAR-aconvasp_Mg3Sb2.txt)
2. Run the following python code in the same directory:
```python
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
structure = Structure.from_file('POSCAR-aconvasp_Mg3Sb2.txt')
print('ORIGINAL STRUCTURE')
print(structure)
sga = SpacegroupAnalyzer(structure, symprec=0.01)
structure = sga.get_primitive_standard_structure()
print('NEW STRUCTURE')
print(structure)
```
4. Notice from the printed output that the Sb atoms are placed on top of the Mg atoms in the new structure:
```python
ORIGINAL STRUCTURE
Full Formula (Mg3 Sb2)
Reduced Formula: Mg3Sb2
abc : 7.280122 4.589982 4.598335
angles: 60.060961 90.000000 90.000000
Sites (5)
# SP a b c
--- ---- -------- -------- --------
0 Mg 0.631749 0.333719 0.332562
1 Mg 0.368251 0.666281 0.667438
2 Mg 0 0 0
3 Sb 0.22557 0.332859 0.332859
4 Sb 0.77443 0.667141 0.667141
NEW STRUCTURE
Full Formula (Mg3 Sb2)
Reduced Formula: Mg3Sb2
abc : 4.594160 4.594160 7.280122
angles: 90.000000 90.000000 119.938984
Sites (5)
# SP a b c
--- ---- -------- -------- ---
0 Mg 0.333141 0.666859 0
1 Mg 0.666859 0.333141 0
2 Mg 0 0 0
3 Sb 0.332859 0.667141 0
4 Sb 0.667141 0.332859 0
```
**Expected behavior**
The original structure is already primitive (it was output from `AFLOW`) so we expected the structure to not change.
**Desktop (please complete the following information):**
- OS: iOS
**Additional context**
The code was run in PyCharm
|
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MDExOlB1bGxSZXF1ZXN0MzAzNDg5NDIx
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Update CubicSupercellTransformation and merge PerturbSitesTransformation into PerturbStructureTransformation
|
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[] | null |
[
"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 the transformation will be implemented in your own code by calling the standard transformation multiple times.",
"Thanks for working on this, it's looking much better! Quick note that since we're modifying the `.perturb()` method there will also need to be a test in `pymatgen.core` for the method also, otherwise after @utf's comments are resolved I think this looks good.",
"Perhaps one way to improve legibility would be to change the arg name on `perturb` to `min_amplitude` and say \"if None, all displacements will be equal amplitude\" (just a small note because we're changing from using the word \"amplitude\" to the word \"random_distance\" to describe essentially the same thing).",
"@mkhorton currently the main perturb argument is called “distance”, should we also change this to amplitude? \r\n\r\nPersonally, I think distance is a more obvious naming choice. However, if we were to use this throughout it would be a breaking change as amplitude is a named argument in the transformation class. ",
"Ah, apologies -- I was looking at the StandardTransformation args, not the perturb args. I'd want to rename that ideally to be consistent with the perturb argument not sure if it will break backwards compatibility somewhere though. (I have no opinion on \"amplitude\" vs \"distance\", as long as it's consistent)",
"Hey @mkhorton ! I implemented alex's comments, added to the Structure.perturb unit test, changed the doc string wording for `perturb` and `PerturbStructureTransformation` to \"if None, all displacements will be equal amplitude\", and refactored `amplitude` and `min_amplitude` in `PerturbStructureTransformation` to `distance` and `min_distance` (to match the arg names in `Structure.perturb`). Does this look ok? I can undo the refactoring of `amplitude` and `min_amplitude` if we think that might break something",
"As long as tests pass I’m ok with this change, it’s not a big difference if\nwe need to update something in atomate etc. Thanks again!\n\nOn Thu, Aug 1, 2019 at 12:24, rees-c <notifications@github.com> wrote:\n\n> Hey @mkhorton <https://github.com/mkhorton> ! I implemented alex's\n> comments, added to the Structure.perturb unit test, changed the doc string\n> wording for perturb and PerturbStructureTransformation to \"if None, all\n> displacements will be equal amplitude\", and refactored amplitude and\n> min_amplitude in PerturbStructureTransformation to distance and\n> min_distance (to match the arg names in Structure.perturb). Does this\n> look ok? I can undo the refactoring of amplitude and min_amplitude if we\n> think that might break something\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1544?email_source=notifications&email_token=AAWWWRHNLV42QG2YFNABH4DQCM2AHA5CNFSM4IITALOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3LUHCA#issuecomment-517424008>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRHM3YUPG5TCDLM2YCTQCM2AHANCNFSM4IITALOA>\n> .\n>\n",
"Thanks for your help @mkhorton! The checks passed and I think the code is ready",
"Hi @mkhorton ! The checks have passed so I think we're ready to merge :)"
] | 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 #1536)
- Removed PerturbSitesTransformation and its unit test from advanced_transformations
- Added an option to PerturbStructureTransformation and Structure.perturb that allows for the displacements to be randomly distributed between two values.
- Added to unit tests for PerturbStructureTransformation and Structure.perturb() to reflect the new option
- The rest of the advanced features of the old PerturbSitesTransformation will be implemented into my CSLD atomate workflow by calling the standard transformation multiple times
- Changed the args of PerturbStructureTransformation to match those of Structure.perturb (i.e. changed `amplitude` to `distance`). *****NOTE THIS IS POTENTIALLY A BREAKING CHANGE FOR ANY ATOMATE WORKFLOW USES `PerturbStructureTransformation`.**
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MDExOlB1bGxSZXF1ZXN0MzA0MDMwMTE1
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[WIP] Mcsqs_caller
|
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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 criterion here / how do we know when we have a decent SQS?\r\n\r\n* I saw this takes clusters as an input, is there a separate function coming to generate the clusters themselves?",
"@mkhorton I'll write that up! \r\n\r\nThe stopping criterion is currently just set by finding a perfect SQS or stopping after the max time, but I should probably edit that so it still spits out the best SQS it finds after the max time.\r\n\r\nThe clusters are generated with an initial call to mcsqs so you just need to specify the cluster cutoffs your're looking for ",
"Test failure is just a few PEP8 code style issues: https://travis-ci.org/materialsproject/pymatgen/builds/580508562#L1051\r\n\r\nRunning this through [Black](https://github.com/psf/black) or similar should fix most of them, but there are a few that might need manually changing like `E711 comparison to None should be 'if cond is None:'`",
"Thanks again @dongsenfo !",
"@mkhorton Lol thanks for fixing my formatting! "
] | 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 converting into a pymatgen structure.
Dependency on mcsqs from ATAT.
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MDExOlB1bGxSZXF1ZXN0MzA0MjkwMjAz
| 1,546
|
Xdatcar optimize
|
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[] | 2019-08-05T12:57:40
| 2019-08-05T17:09:29
|
2019-08-05T17:09:28Z
|
CONTRIBUTOR
|
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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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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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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 the docstrings for these two functions to match the implementation
## TODO:
There is probably a way to combine these into one function for a little less boilerplate, but that's maybe something for a future PR. This is just a minimum changes necessary fix.
|
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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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MDExOlB1bGxSZXF1ZXN0MzA1Nzc5MDkw
| 1,550
|
Fix multi-line :param: and :return: directives in docstrings
|
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[] | null |
[
"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 RST, and I have some older code in pymatgen where I’ve done just that myself and have been meaning to update (e.g. see magnetism module also).\r\n\r\nA better fix might be to use a tool like [pyment](https://github.com/dadadel/pyment/) to auto-convert to the Google style.",
"Thanks!\r\n"
] | 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 issues with the display of some numbered lists.
See screenshots of the incorrect rendering attached.
@shyuep - I've tested this with ```invoke make-docs```. Do you want me to commit the built docs as well, or just the code?
|
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MDExOlB1bGxSZXF1ZXN0MzA2MDc3MDk4
| 1,551
|
Fix number of returned entries in apply_transformation
|
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[] | 2019-08-09T17:33:31
| 2019-08-10T07:06:07
|
2019-08-10T07:06:07Z
|
CONTRIBUTOR
|
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## Summary
_apply_transformation()_ now returns _num_to_return_ entries as described in the doctoring.
|
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MDExOlB1bGxSZXF1ZXN0MzA3MjY0MDIy
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|
Changes to DOSCAR class of the lobster io module
|
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[] | 2019-08-14T10:23:47
| 2019-08-14T11:08:07
|
2019-08-14T11:08:07Z
|
MEMBER
|
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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 more flexible.
Best
JG
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MDU6SXNzdWU0ODEzNzY1ODY=
| 1,553
|
Slow tests on pymatgen
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[] | null |
[
"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.",
"The defects stuff is never going to be fast. If it's causing a significant failure of tests, then we need to put it on a conditional skip to run every once in a while. ",
"Never is a word used too often. There was once a time when people said distance computations were never going to be fast. \r\n\r\nThe idea is to design the tests to ensure correct functionality using small model systems. ",
"OK, **I** will not be spending time to make them faster since they already work fast enough for defect calculations. The defect thermodynamics are already constructed using QHull, so they're unlikely to get much faster. The defect corrections will take a decent bit of understanding and effort to convert from python to Cython. The interstitial generator algorithms are just hard to develop. Danny and I spent a lot of time getting this all to something reasonable. ",
"@shyamd It is the responsibility of all coders to write reasonable tests. No one is asking you to rewrite the code in cython. I am asking for the *tests* to be sped up, not the code. \r\n\r\nJust for reference, I merely changed one thing from setup to setupClass in one of the defect tests, and that essentially took a full 4mins or so off the tests because the same defect generator is used for all tests - the tests were not changing the defect class at all. \r\n\r\nThese are the kind of common sense things that should be done. Rather than just fighting me on this trivial stuff. \r\n\r\nIf you want me to disable the defect tests or to junk the entire defect code, that is fine by me. ",
"I'm pretty sure the interstitial generator algorithms specifically could be significantly sped up (by an order of magnitude or more). They are excessively slow and missing some obvious optimizations. But I echo @shyamd; there's nobody currently working on this who can take the lead.",
"@mkhorton @shyamd If no one is working on the defects, I will begin to deprecate the entire functionality. I will remove the package in Oct 2019.",
"I don't think that's necessary, the defects package is broadly excellent and a result of a substantial body of work, it just doesn't have a primary maintainer to add new features or performance optimizations right now. We can commit to address any bugs as necessary however.",
"@mkhorton As I said, I don't expect major performance optimizations - I am expecting working and reasonable tests that does not affect the overall ability to iterate on the rest of pmg code. Right now, that is not the case. I would rather sacrifice the defects package than sacrifice our ability to iterate quickly.\r\n\r\nSo someone - anyone - has to take the lead to make it happen.",
"We already have `EXCLUDE_TESTS` so that we can skip long-running tests in Travis that would otherwise slow down development. This is not ideal, but it seems like a sensible, pragmatic solution until the tests can be improved rather than removing an entire submodule which is deeply integrated into our workflows and has been peer-reviewed, referenced in papers, etc.",
"There is a contradiction here. If it is \"deeply integrated\" into MP, then I would assume there is at least one person who is actively using and working on it, and that person can fix this. If there is \"no one who has time to fix this\", then it is essentially static code that no one is really caring about. Seriously, the time we spent debating on this, someone could have already done a 80% fix to satisfy what I asked for.\r\n\r\n",
"I am using the defects package regularly and am responsible for both this and interfaces. I'm currently focused on MP infrastructure since this is `on-fire`. Please just skip these tests for now, and I'll come back and fix them. "
] | 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/analysis/tests/test_fragmenter.py::TestFragmentMolecule::test_babel_PC_with_RO_depth_0_vs_depth_10
93.16s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_suggest_charges
88.57s call pymatgen/analysis/defects/tests/test_corrections.py::DefectsCorrectionsTest::test_kumagai
68.99s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_suggest_larger_supercells
67.63s setup pymatgen/analysis/tests/test_interface.py::InterfaceBuilderTest::test_film_and_substrate_sites
64.83s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_solve_for_non_equilibrium_fermi_energy
61.05s call pymatgen/analysis/defects/tests/test_defect_compatibility.py::DefectCompatibilityTest::test_check_kumagai_delocalized
60.37s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_solve_for_fermi_energy
55.63s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_plot
54.23s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_good_test_data
53.58s call pymatgen/analysis/defects/tests/test_generators.py::InterstitialGeneratorTest::test_int_gen
53.43s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_get_dopability_limits
53.43s call pymatgen/analysis/defects/tests/test_thermo.py::DefectsThermodynamicsTest::test_entries
45.04s call pymatgen/analysis/tests/test_structure_analyzer.py::MiscFunctionTest::test_average_coordination_number
36.73s call pymatgen/analysis/elasticity/tests/test_elastic.py::DiffFitTest::test_fit
30.93s call pymatgen/command_line/tests/test_bader_caller.py::BaderAnalysisTest::test_automatic_runner
```
|
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MDU6SXNzdWU0ODE3NTcyNzg=
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|
Remove BZT 1.0 support?
|
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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 lot of scientists use and prefer. BZT 2.0 is really about working with the Python objects which is more useful but not as popular.\r\n\r\nIf look on Google Scholar for citations of Boltztrap 1.0 vs Boltztrap 2.0 since 2019 only (well into the release of Boltztrap 2.0), there are 34 *pages* of results for Bolztrap 1.0 versus 3 *pages* of of results for BZ2. i.e., 11 times more citations in 2019 to BZT 1.0.\r\n\r\nSo I think people are going to want BZT 1.0 support for awhile ...\r\n",
"Ok...... the bzt1.0 is poorly covered by tests though....."
] | 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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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 PR #1555 (meaning the associated methods are no longer in pymatgen). Can you reopen this PR so I can add the necessary commits here?",
"@rkingsbury I can't seem to reopen the PR. I think the easiest way is for you to use `git checkout 35f222512ee90446b2516e68b99f163eca548548 <relevant file paths>` to get back the changes you made to entries and MPRester and commit them with the test PR.\r\n"
] | 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 requires a list input e.g. ['Li','O'], but the `chemical_system` attribute of Composition returns a str separated by dashes e.g. 'Li-O'. To improve interoperability, it should be possible to pass the dash-separated string into `get_entries_in_chemsys` in addition to lists. The second commit makes this possible
|
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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 supposed to be used, shouldn't it be in setup.py and requirements-optional.txt? I see it as a separate install in circleci/config.yml. ",
"Why is igraph being used(?)",
"It’s a lot faster than networkx since it’s core routines are written in C++\n(I think) instead of python. This improved performance can be critical when\ndoing large numbers of isomorphism checks such as when finding all unique\nfragments from many molecules. However, igraph does not provide any\nadditional functionality beyond networkx, just performance, thus I did not\nthink it merited being an actual requirement.\n\nOn Wed, Aug 21, 2019 at 1:50 PM Matthew Horton <notifications@github.com>\nwrote:\n\n> Why is igraph being used(?)\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1556?email_source=notifications&email_token=ABYWINYBKMTGRFL6CEAX7XDQFWTAFA5CNFSM4IOLZCS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD43CU3Y#issuecomment-523643503>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ABYWIN3WZVFNITLDPAFKAL3QFWTAFANCNFSM4IOLZCSQ>\n> .\n>\n",
"Thanks @samblau, sounds great! I like how igraph will gracefully fall back to networkx if it's not installed"
] | 2019-08-21T18:20:57
| 2019-08-21T22:59:09
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2019-08-21T20:36:05Z
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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 fragmentation upgrades.
* Q-Chem IO improvements given changes in the latest version of the software. Parsing more errors, warnings, and properties. Default sets also updated given latest convergence tests.
## Additional dependencies introduced (if any)
* Now using the igraph python graph library, although like OpenBabel, it is not technically a dependency. If it cannot be imported, networkx will be used instead.
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Revert "Enhancements to ComputedEntry and MPRester"
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[] | 2019-08-21T20:47:35
| 2021-02-13T17:29:08
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2019-08-21T20:47:45Z
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MEMBER
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Reverts materialsproject/pymatgen#1555
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uncertainty quantification in energy corrections
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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 corrections and their errors soon. The Correction classes which previously given an entry returned a correction now also return the error on that correction. The Compatibility classes which previously processed an entry by calculating a total correction to the energy value now also include the error on that correction.",
"Just to make some introductions, @awvio is working with us (@shyamd, Persson group) to help improve the MP corrections.\r\n\r\n@awvio I wasn't familiar with your GitHub handle, so I was also confused for a moment :)",
"@mkhorton @kristinpersson @shyamd I think this needs to be discussed. I do understand of course that corrections can be changed/improved. I have no problems with putting uncertainties in. But this is a rather extensive set of changes and it is possible that there are codes out there relying on the existing correction values. Some of the corrections are not small at all.\r\n\r\nWe should have a proper review of all the correction values, as well as a possible strategy to have versioned corrections based on MP database versions. This cannot be done just by someone editing the code.",
"Yes, agreed this cannot be done solely in code. Perhaps worth discussing in next MP dissemination meeting; it'll need to be staged with the next database release, and have accompanying docs. Agreed also we need to store the MPCompatibility version (which could be pymatgen version even) in the database, and potentially in the resulting ComputedEntries also.",
"There are plans for a docs page and a paper discussing these corrections and their effects. For the most part these don't change the old values by much. The big difference is that these corrections can be reproduced in comparison to the old numbers, which I've never been able to recreate. ",
"The changes are large, by ~0.5 eV/atom in some cases.\r\n\r\nMP has gone from 2012 to 2019 with many generations of db changes along the way. I do not doubt that it would be difficult to reproduce the old values (some of which were done using proper AFM structures). The original values were actually documented in the pymatgen publication.\r\n\r\nThe point remains this is an exercise that requires careful discussion and vetting. A doc page and publication would be good. But this will not be merged until all the pieces are in place. ",
"Just to give an example, Fe3O4 in MP seems to be ferromagnetic. The actual ground state is ferrimagnetic. The energy diffs are not small. This is a point I have made since 2013.\r\n\r\nThe original corrections are fitted to binary oxides that were properly charge-ordered and magnetized.",
"I would say you could carry 1 extra digit for the uncertainty (so, round uncertainty to 0.1 meV)\n\n\n\nRyan Kingsbury, Ph.D., P.E.\n\nPostdoctoral Researcher\nThe Material Project\nC: 713-851-7231\nE: RKingsbury@lbl.gov\nOn Aug 30, 2019, 2:27 PM -0700, awvio <notifications@github.com>, wrote:\n> @awvio commented on this pull request.\n> In pymatgen/entries/MPCompatibility.yaml:\n> > @@ -2,55 +2,46 @@ Name: MP\n> Advanced:\n> UCorrections:\n> O:\n> - Mn: -1.68085015096 #Fit to MnO, Mn3O4 and MnO2 (BURP:-1.687)\n> - Fe: -2.733 #Fit to FeO and Fe2O3 (Fe3O4 probably wrong)\n> - Co: -1.874 #Fit to CoO, Co3O4 (BURP:-1.751)\n> - Cr: -2.013 #Fit to Cr2O3 (CrO3 missing) (BURP: -2.067)\n> - Mo: -3.531 #Fit to MoO3 and MoO2 (BURP: -2.668)\n> - W: -4.351 #Fit to WO2 and WO3 (BURP: -2.762)\n> - V: -1.682 #Fit to V2O3 and V2O5 (VO2 fit is way off) (BURP: -1.764)\n> - Ni: -2.164 #Based on burp version as of Feb 28 2011\n> + V: -1.634860584846134\n> Does this also apply to the correction errors? Rounding to 3 decimal places often results in only 1 sigfig (error = 0.00x), at most 2.\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub, or mute the thread.\n",
"I can't figure out why my last commit about polysulfide caused the Travis Build to fail. The test that's failing (ReactionDiagramTest.test_formed_formula) doesn't touch any of the code I changed as far as I can tell.",
"A good start may be to modify the ReactionDiagramTest.test_formed_formula -- it doesn't look like a very good test to me because it's not clear what's changed when it fails (I appreciate you haven't modified this file/it's not your test).\r\n\r\nCurrently it's:\r\n\r\n`self.assertTrue(formula in formed_formula)`\r\n\r\nMaybe:\r\n\r\n`self.assertIn(formula, formed_formula)`\r\n\r\nI don't know who wrote that test originally.",
"@mkhorton OK, I can try that. The test runs successfully on my local machine and on AppVeyor though (without modifying the assertion statement). Could it be something about the Travis environment?",
"Yeah, it looks like the kind of test that might have machine-specific precision issues but I'm not sure, I suspect the test could be improved.",
"Yes, that test has been failing randomly. Just ignore it for now. @mkhorton Can you talk to whoever is responsible and get him to fix it.",
"That said the test has been around for two years so I'm not sure why it would start failing now. @paulgholin it looks like you wrote this test, do you have any ideas why this may be failing?",
"Were the linting tests recently added to the build checks? It looks like we're failing on mypy / pycodestyle / flake8 now, but that wasn't an issue a few weeks ago.",
"Yes, linting is now enforced on all PRs.",
"Note that the linting is fairly relaxed. Codestyle in general is quite basic. mypy enforces type checks on the few classes where we actually have type annotations (they are mostly core classes that have well-defined APIs). This needs to be strict since it catches very egregious errors in code.\r\n\r\nFlake8 adds a few minor checks. Pydocstyle again just ensures that you have proper docstrings for all public modules, classes and methods - no a huge ask. We do not enforce pylint at all, though that is the most comprehensive. Pylint is to encourage you to fix the code, but if you pass the other four linters, we will not insist on passing pylint.",
"One of the errors from mypy is that it can't find the plotly module:\r\npymatgen/entries/corrections_calc.py:3: error: Cannot find module named 'plotly'\r\nAfter referring to the mypy docs ([https://mypy.readthedocs.io/en/latest/running_mypy.html#missing-imports](url)), this seems to be caused by the fact that plotly doesn't have type hints. Is it ok to silence this import error?\r\n",
"Whether plotly has type hints or not isn't relevant. The error is present because plotly is not a pymatgen dependency -- you need to add it to the requirements.txt as a dependency otherwise it will not be installed during testing. Note that while in general we're reluctant to add new dependencies, I think plotly makes a lot of sense for us so this is fine.",
"After adding plot.ly, you might need to add them to the mypy exclusions in the setup.cfg file. There are plenty of examples there. See https://github.com/materialsproject/pymatgen/blob/master/setup.cfg",
"At least that'd be my guess -- I was looking to see if the regular tests pass but nothing in `corrections_calc.py` seems to have tests yet, so we can take another look after they've been added.",
"@awvio can you add plotly under \"additional dependencies introduced\" in the first comment on this PR? ",
"Plotly is getting added anyway from #1685",
"I created a 2020 version of MITCompatibility.yaml even though the MIT corrections have not been changed - the only difference between MITCompatibility2020.yaml and MITCompatibility.yaml is CompoundEnergies (N2, F2, Cl2, H2, SO3, SO2) have been changed to GasCorrections. However I'm not sure if it's appropriate to create a 2020 version if the value of the corrections themselves have not changed, just the formatting/the way they are applied.",
"If they give 1:1 equivalent outputs I would omit the 2020 label.\n\nOn Wed, Dec 4, 2019 at 16:48, awvio <notifications@github.com> wrote:\n\n> I created a 2020 version of MITCompatibility.yaml even though the MIT\n> corrections have not been changed - the only difference between\n> MITCompatibility2020.yaml and MITCompatibility.yaml is CompoundEnergies\n> (N2, F2, Cl2, H2, SO3, SO2) have been changed to GasCorrections. However\n> I'm not sure if it's appropriate to create a 2020 version if the value of\n> the corrections themselves have not changed, just the formatting/the way\n> they are applied.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1558?email_source=notifications&email_token=AAWWWRDGFTXBG3B4DM2OGVTQXBFVNA5CNFSM4IOOYLS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF7CHTA#issuecomment-561914828>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRGH4Y6R7MC5KKKGR63QXBFVNANCNFSM4IOOYLSQ>\n> .\n>\n",
"@shyuep we are ready to begin code review on this PR. I'll explain in bullet points what it does; feel free to request more info offline if that would be helpful. @awvio and @shyamd feel free to chime in as well.\r\n\r\n- This PR updates the existing GGA/GGA+U mixing scheme to incorporate uncertainty quantification.\r\n- We extend the list of anions to which corrections are fit, adding Br, I, Se, Si, Sb, and Te to the existing list of corrected elements.\r\n- The updated scheme is implemented as `MaterialsProjectCompatibility2020` to avoid conflicts with the existing `MaterialsProjectCompatibility`, which we intend to deprecate in the future\r\n- For clarity, in the new scheme we consolidate the `AnionCorrection` and `GasCorrection` into the `CompositionCorrection` class, because all are linear functions of the elemental composition of a compound. \r\n- Corrections are fit to experimental formation energy data as before. However, in the -2020 scheme all corrections are solved simultaneously via a linear system of equations. This approach makes it possible to include more compounds (e.g., ternaries with multiple corrected atoms like KFeO2.)\r\n- In addition to fitting energy corrections, the linear system allows us to quantify the uncertainty in the fits arising from 1) uncertainty in the experimental data and 2) the number of observations used to fit each correction. It also generates information about cross-correlation effects between energy corrections\r\n- `ComputedEntry` objects that are corrected now have a `correction_uncertainty` item added to their `.data` dict \r\n- We include a new `CorrectionCalculator` class that illustrates how to generate the .yaml file containing the corrections. We hope this new class will make our correction procedure more transparent and easier for users to understand.\r\n\r\nWe look forward to your feedback. Hope you have a nice holiday break!",
"@mkhorton is `IonTest.test_as_dict()` failing in master? I don't think any changes here should have affected it.",
"Yup, looks like it broke alongside another bug fix (https://github.com/materialsproject/pymatgen/commit/dec6ecb6a9a80dbd4bfdfb924040cdfc7fe4ebb3)",
"We removed the 'polysulfide' type because it was not being used by the old corrections and it had caused a bug that in some cases caused corrections not to be applied correctly.\n\n\nOn Jul 9, 2020, 12:39 PM -0700, Matthew Horton <notifications@github.com>, wrote:\n> @mkhorton commented on this pull request.\n> In pymatgen/analysis/tests/test_structure_analyzer.py:\n> > latt = Lattice.tetragonal(9.59650, 11.78850)\n> species = [\"Na\"] * 2 + [\"S\"] * 2\n> coords = [[0.00000, 0.00000, 0.17000],\n> [0.27600, 0.25000, 0.12500],\n> [0.03400, 0.25000, 0.29600],\n> [0.14700, 0.11600, 0.40000]]\n> struct = Structure.from_spacegroup(122, latt, species, coords)\n> - self.assertEqual(sulfide_type(struct), \"polysulfide\")\n> + self.assertEqual(sulfide_type(struct), \"sulfide\")\n> Was this incorrect previously?\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub, or unsubscribe.\n"
] | 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: 'correction_uncertainty'
## Additional dependencies introduced (if any)
Plotly
## TODO (if any)
WIP (needs review)
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MDExOlB1bGxSZXF1ZXN0MzA5NzE3ODEy
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Turning back on fragmenter tests
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[] | 2019-08-21T22:53:41
| 2019-08-21T23:45:06
|
2019-08-21T23:45:06Z
|
CONTRIBUTOR
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## Summary
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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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?",
"@mkhorton yeah the code is all terribly ancient.\r\n\r\nMy understanding is that there are two separate versions. plot_fermi_surface in boltztrap.py (for BoltzTrap 1) and BztPlotter class in boltztrap2.py which does not look fully implemented.\r\n\r\nLuckily. if I am not mistaken @utf is working on (fixing? improving?) the Boltztrap2 version which will likely supercede everything current boltztrap fermi surface does.\r\n\r\nFor this Boltztrap 1 version at least, it is not possible to plot with any uniform BS. You need to do a separate Boltztrap 'FERMI' mode run beforehand. I assume this is because the fermi surf of your typical uniform BS will be too low resolution, hence why boltztrap is needed to interpolate? Specifically, the plotter needs a 3D array \"cube\" flle in order to work\r\n\r\nIt would be great if there was instead a simple `plot_fermi_surface` method of `BSPlotter`...perhaps some more physics-minded people could weigh in on whether that would or would not be a good idea. \r\n",
"tests failing bc mayavi can't install on travis, I guess I'll remove the requirement...",
"tests now failing for unrelated reasons, as far as I can tell...`ReactionDiagramTest.test_formed_formula` is failing",
"Seems to be a merge conflict on this now?",
"@mkhorton ok it is fixed now to my knowledge\r\n\r\nNow to see if tests will pass? Which is weird because atm plot_fermi_surface has no test...",
"🤦🏻♂️\n\nOn Mon, Aug 26, 2019 at 09:54, Alex Dunn <notifications@github.com> wrote:\n\n> @mkhorton <https://github.com/mkhorton> ok it is fixed now to my knowledge\n>\n> Now to see if tests will pass? Which is weird because atm\n> plot_fermi_surface has no test...\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1560?email_source=notifications&email_token=AAWWWRA7URFHFYOYVJ5A7R3QGQDGFA5CNFSM4IOQABX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5E62IQ#issuecomment-524938530>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRGMZ4CWSAJOSV3HQADQGQDGFANCNFSM4IOQABXQ>\n> .\n>\n",
"Lol I feel the same\r\n\r\nWas considering writing one but the current plotter requires data from a BolztrapAnalyzer with either a BT1 pre-generated fort.30 file, which is typically ~500+MB or creating this file via actually running Boltztrap. + the fact that mayavi does not seem installable on travisCI? So not sure what would be the best way of including a test. \r\n\r\n",
"Correct answer is that you can help us add Fermi surface plotting to crystal toolkit instead and skip mayavi completely :P Doesn't really help with the onerous Boltztrap requirements though.\r\n\r\nWill merge once CI has completed",
"There are codestyle issues that are independent of the test failures (use pycodestyle to check it, and also it is recommended you use the pre-commit hook provided). Also, you can do the tests until circleCI if you sign in there. ",
"@shyuep @mkhorton Fixed.\r\n"
] | 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 previous versions. No features were added.
2. Some formatting and removal of the most obvious anti-patterns (imports in functions, mutable default kwargs). Docs are changed to be a bit clearer and more PEP8 compliant.
3. Added mayavi as an optional requirement (it was used but not optionally required before)
## Additional dependencies introduced (if any)
Technically `mayavi`, but this was already implicitly "required" by the module and would just throw a boltztrap error every time if mayavi wasn't installed.
|
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| 484,116,151
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MDExOlB1bGxSZXF1ZXN0MzEwMDYxOTMy
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[WIP] Add test cases for enhancements in PR #1555
|
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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 added a normalize method to ComputedEntry. This has been pushed."
] | 2019-08-22T17:17:39
| 2019-08-22T22:40:14
|
2019-08-22T20:35:27Z
|
CONTRIBUTOR
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Add test cases for enhancements in PR #1555
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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
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CONTRIBUTOR
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## Summary
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 docstring.
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MDExOlB1bGxSZXF1ZXN0MzEwNDcxNTMz
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|
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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## Summary
- 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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MDExOlB1bGxSZXF1ZXN0MzEwNTUyNjU5
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Better igraph integration, fragmenter and isomorphic cleanup
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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_graph.isomorphic_to() function call and the core isomorphic function in graphs was made internal _isomorphic.
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New Class to read GROSSPOP.lobster
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[] | 2019-08-26T15:30:07
| 2019-08-26T18:12:05
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2019-08-26T18:12:05Z
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MEMBER
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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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CombinedData class and hybrid style LAMMPS data file i/o
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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.",
"Hey @mkhorton! I have made commits changing the 1) `range(len())` for loop, 2) temp variable to meaningful names, 3) and from_files function. \r\nThank you for reviewing my code :)! Feeling good to get my feet wet in contributing to pymatgen!",
"No problem, and thanks for your contribution(!)"
] | 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 number (4).
## TODO
* To support i/o of the comments of coeff styles on the 'keyword' lines of LAMMPS data file
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[WIP] Added SLME and spillage analysis
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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 contributing these @knc6 !\r\n\r\nTo be more specific for some of the issues @shyuep mentioned, we have missing docstrings for some functions (e.g. in topological), some extraneous print statements (please use a logger if you want to print debug output), the `if __name__ == \"__main__\"` block is fairly harmless but shouldn't be there either, and some capitalization is not PEP8 compliant (classes should be capitalized, methods should have underscores not camelCase).\r\n\r\nOn a separate note, we already have a `Wavecar` class, is there anything in the `vaspwfc` class that would make sense to add to the `Wavecar` class instead?",
"Hi @mkhorton Thank you for the notes, I'll get back to this in a couple of days.",
"It seems like the current pymatgen's Wavecar module is not implemented for the spin-orbit case, which is important for spillage calculation. Could you please confirm? @mkhorton ",
"@mturiansky contributed the Wavecar functionality, I think he would know best whether it correctly handles the spin-orbit case.",
"You're correct; it does not handle spin-orbit WAVECARs nor does it handle gamma WAVECARs. It shouldn't be too difficult to modify the current code to also handle these cases; I was planning to do it once I can find some free time. #1585 references this and someone had started implementing it for the gamma case, but it was never finished.",
"Hi @knc6, this is very timely but @mturiansky just addressed loading of SOC WAVECARs with our existing `Wavecar` class via #1861, so it should now be possible to simplify this PR by removing `vaspwfc` and get this merged in if you were interested. Enjoyed your Optimade talk today!",
"Hi @mkhorton thanks for attending the talk. I'll look into the new Wavecar class. Or another option would be to make jarvis-tools an dependency/optional-dependency and just import the functionalities from there. Also, I would like to add a jarvis adaptor to pymatgen. What do you think?",
"We have several adaptors already inside pymatgen.io and a Jarvis adaptor would be very welcome. Regarding dependencies, we try not to add dependencies unless absolutely necessary, it's important to keep this minimal. An optional dependency for the adaptor would make sense (e.g. see the [ASE adaptor](https://github.com/materialsproject/pymatgen/blob/e42ae2911757c080a2b18d8b53bacff94630fd78/pymatgen/io/ase.py#L19)), I don't think a dependency should be necessary for the spillage code however.",
"I'm happy to help integrate with the Wavecar class. Let me know if you have any questions/need any help.\r\n\r\nOut of curiosity: why does jarvis-tools reimplement many of the things pymatgen has instead of just making pymatgen a dependency?\r\n\r\nI would point out that the Wavecar class here has a few extra features like constructing a PARCHG or converting to an UNK file. One thing that the jarvis-tools implementation has that is nice is that the bands are only read when called for, so the whole WAVECAR doesn't need to be stored in memory. If this is necessary, I can make some changes to make this implementation more memory efficient. There are a few places where I use lists instead of just defining an empty np.array. Second, I could add a \"bands\" tag to the reader so only certain bands are read in. This just adds a little extra work because then there needs to be a mapping from the input band coefficient to the array that is stored in memory; this can be accomplished with the property decorator, but as I said, just a little extra work.",
"@mkhorton , I have added the SOC-Spillage module with pymatgen Wavecar. The unittests are passing on my local computer. I think some other pymatgen modules are failing. Please take a look.\r\nNew modules added: pymatgen/analysis/solar/slme and pymatgen/analysis/topological/spillage.",
"Many thanks Kamal, I'll take a look. The first test that seems to be failing right now is the linter, which is usually some minor code style issues: https://github.com/materialsproject/pymatgen/runs/786553347#step:5:24 ",
"For context, the linters that run check for code style, documentation coverage, and also some type checking, so there are typically a few iterations of getting linter tests to pass before the full test suite is run. These can also be run offline if desired (via pycodestyle, flake8, pylint, pydocstyle etc.)",
"@mkhorton Thank you for the suggestions. In addition to the code style changes, fixed a small bug in core/ion.",
"Fantastic, thanks @knc6, and thanks for fixing the ion bug too. The only issue stopping this getting merged in I think is the missing descriptions for the args in `slme`.\r\n\r\nThere's another PEP8 issue but I can correct if necessary, this is `SOC_Spillage` should be `SOCSpillage` [(classnames don't have underscores)](https://www.python.org/dev/peps/pep-0008/#class-names) and similarly with `from pymatgen.io.vasp.outputs import Wavecar as pmg_wav`. {",
"Alright @mkhorton , I have made the suggested changes. Please let me know if any additional modifications are needed.",
"Thanks for addressing all the comments @knc6! This is a really useful PR, glad to be able to merge it :-)"
] | 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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Update born effective charge in outcar parsing
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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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pymatgen/io/vasp/outputs.py SyntaxError line 4534
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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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MDExOlB1bGxSZXF1ZXN0MzEzMjAwMTgy
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New vasp set
|
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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 module are quite complex due to the many class-subclass relationships.
Best,
JG
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Bump numpy from 1.16.4 to 1.17.1
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| 2019-09-02T20:26:52
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2019-09-02T20:26:44Z
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CONTRIBUTOR
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Bumps [numpy](https://github.com/numpy/numpy) from 1.16.4 to 1.17.1.
<details>
<summary>Release notes</summary>
*Sourced from [numpy's releases](https://github.com/numpy/numpy/releases).*
> ## v1.17.1
> NumPy 1.17.1 Release Notes
> ==========================
>
> This release contains a number of fixes for bugs reported against NumPy 1.17.0
> along with a few documentation and build improvements. The Python versions
> supported are 3.5-3.7, note that Python 2.7 has been dropped. Python 3.8b3
> should work with the released source packages, but there are no future
> guarantees.
>
> Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and
> OpenBLAS >= 3.7 to avoid problems on the Skylake architecture. The NumPy wheels
> on PyPI are built from the OpenBLAS development branch in order to avoid those
> problems.
>
>
> Contributors
> ============
>
> A total of 17 people contributed to this release. People with a "+" by their
> names contributed a patch for the first time.
>
> * Alexander Jung +
> * Allan Haldane
> * Charles Harris
> * Eric Wieser
> * Giuseppe Cuccu +
> * Hiroyuki V. Yamazaki
> * Jérémie du Boisberranger
> * Kmol Yuan +
> * Matti Picus
> * Max Bolingbroke +
> * Maxwell Aladago +
> * Oleksandr Pavlyk
> * Peter Andreas Entschev
> * Sergei Lebedev
> * Seth Troisi +
> * Vladimir Pershin +
> * Warren Weckesser
>
>
> Pull requests merged
> ====================
>
> A total of 24 pull requests were merged for this release.
>
> * [#14156](https://github-redirect.dependabot.com/numpy/numpy/issues/14156): TST: Allow fuss in testing strided/non-strided exp/log loops
> * [#14157](https://github-redirect.dependabot.com/numpy/numpy/issues/14157): BUG: avx2_scalef_ps must be static
> * [#14158](https://github-redirect.dependabot.com/numpy/numpy/issues/14158): BUG: Remove stray print that causes a SystemError on python 3.7.
> * [#14159](https://github-redirect.dependabot.com/numpy/numpy/issues/14159): BUG: Fix DeprecationWarning in python 3.8.
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`2975946`](https://github.com/numpy/numpy/commit/29759461091f9a4a40ff2f4ae2126e0a5af1fcdd) REL: NumPy 1.17.1 release.
- [`ad4a017`](https://github.com/numpy/numpy/commit/ad4a017cb378733c3314dc128fbd4cc8ea3376ca) Merge pull request [#14350](https://github-redirect.dependabot.com/numpy/numpy/issues/14350) from charris/prepare-1.17.1-release
- [`45d1cf1`](https://github.com/numpy/numpy/commit/45d1cf1b180f41749796160abbac35a0b2ef5fca) REL: Prepare for NumPy 1.17. release.
- [`73e4759`](https://github.com/numpy/numpy/commit/73e47591ad048c43f2b1851c8a83146c66a0bb4d) Merge pull request [#14345](https://github-redirect.dependabot.com/numpy/numpy/issues/14345) from charris/backport-14310
- [`4c87dd7`](https://github.com/numpy/numpy/commit/4c87dd716810fbda77233ee31b4700d8669fb84f) MAINT: fix behavior of structured_to_unstructured on non-trivial dtypes
- [`94a2142`](https://github.com/numpy/numpy/commit/94a2142b7c8accad9f9050b84faf119983c18f07) Merge pull request [#14339](https://github-redirect.dependabot.com/numpy/numpy/issues/14339) from eric-wieser/fix-if-fields-1.17
- [`66388aa`](https://github.com/numpy/numpy/commit/66388aab96f1acbef5fb028fce76785a09efa7b5) Merge pull request [#14338](https://github-redirect.dependabot.com/numpy/numpy/issues/14338) from charris/backport-14240
- [`8e310ec`](https://github.com/numpy/numpy/commit/8e310ecf3ed5163c11a5bb9cbdb2e3d0b5182441) Merge remote-tracking branch 'upstream/maintenance/1.17.x' into fix-if-fields
- [`4452556`](https://github.com/numpy/numpy/commit/4452556d70556f51f1967fe077be1d8596e90acc) BUG: don't fail when lexsorting some empty arrays ([#14228](https://github-redirect.dependabot.com/numpy/numpy/issues/14228))
- [`fa64aba`](https://github.com/numpy/numpy/commit/fa64ababda2f79ff3cfc00b7ce85ce17255e972c) Merge pull request [#14330](https://github-redirect.dependabot.com/numpy/numpy/issues/14330) from charris/backport-14241
- Additional commits viewable in [compare view](https://github.com/numpy/numpy/compare/v1.16.4...v1.17.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=numpy&package-manager=pip&previous-version=1.16.4&new-version=1.17.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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[//]: # (dependabot-automerge-end)
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[] | 2019-09-02T20:25:40
| 2019-09-02T20:27:04
|
2019-09-02T20:26:53Z
|
CONTRIBUTOR
|
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.34.0 to 4.35.0.
<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.35.0 stable
> - add `{bar}` format specifier ([#623](https://github-redirect.dependabot.com/tqdm/tqdm/issues/623) -> [#799](https://github-redirect.dependabot.com/tqdm/tqdm/issues/799))
> + `[width][type]`
> - add tests and documentation
> - update performance tests
</details>
<details>
<summary>Commits</summary>
- [`f856c57`](https://github.com/tqdm/tqdm/commit/f856c5747c87b6c44d6aa2c64fd5378f5300310d) bump version, merge branch 'bar-formatspec'
- [`6d1d38f`](https://github.com/tqdm/tqdm/commit/6d1d38fcad4c6a623b64f061cfba65374cdb250e) linting (flake8, codacy)
- [`ee68bac`](https://github.com/tqdm/tqdm/commit/ee68bac05e4f54fcd27ed8ff0e34269c2ca80aad) add bar formatspec documentation
- [`91c52e4`](https://github.com/tqdm/tqdm/commit/91c52e4d737716875b9ddc3c9aded04588912310) re-fix py2 unicode
- [`86db96c`](https://github.com/tqdm/tqdm/commit/86db96cf9b7dd06301980a07b2743d2a8c76019b) update perf test thresholds
- [`8888db4`](https://github.com/tqdm/tqdm/commit/8888db4cb8a5abd464b3a16b46692fe8f7670df7) tidy perf tests
- [`532d433`](https://github.com/tqdm/tqdm/commit/532d433f2032a6daf64a9946cced484d378dbf49) blank bar format spec type
- [`3c17710`](https://github.com/tqdm/tqdm/commit/3c177105d2f04dd16832303bb1b044f4e784a034) negative bar len for auto-trimming
- [`273e0c7`](https://github.com/tqdm/tqdm/commit/273e0c7ba2ad6227cf569a158a1058a47c314863) fix py26 tests
- [`1aa3745`](https://github.com/tqdm/tqdm/commit/1aa3745667677366749e36bee36c912617fe16bd) move and document empty format helper
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.34.0...v4.35.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.34.0&new-version=4.35.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
**Note:** This repo was added to Dependabot recently, so you'll receive a maximum of 5 PRs for your first few update runs. Once an update run creates fewer than 5 PRs we'll remove that limit.
You can always request more updates by clicking `Bump now` in your [Dependabot dashboard](https://app.dependabot.com).
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You can trigger Dependabot actions by commenting on this PR:
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MDExOlB1bGxSZXF1ZXN0MzEzMzYwNTk0
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Bump apscheduler from 2.1.0 to 3.6.1
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2019-09-02T20:26:00
| 2019-09-02T20:28:57
|
2019-09-02T20:28:47Z
|
CONTRIBUTOR
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Bumps [apscheduler](https://github.com/agronholm/apscheduler) from 2.1.0 to 3.6.1.
<details>
<summary>Changelog</summary>
*Sourced from [apscheduler's changelog](https://github.com/agronholm/apscheduler/blob/master/docs/versionhistory.rst).*
> 3.6.1
> =====
>
> - Fixed OverflowError on Qt scheduler when the wait time is very long
> - Fixed methods inherited from base class could not be executed by processpool executor (PR by Yang Jian)
>
> 3.6.0
> =====
>
> - Adapted `RedisJobStore` to v3.0 of the `redis` library
> - Adapted `RethinkDBJobStore` to v2.4 of the `rethink` library
> - Fixed `DeprecationWarnings` about `collections.abc` on Python 3.7 (PR by Roman Levin)
>
> 3.5.3
> =====
>
> - Fixed regression introduced in 3.5.2: Class methods were mistaken for instance methods and thus were broken during serialization
> - Fixed callable name detection for methods in old style classes
>
> 3.5.2
> =====
>
> - Fixed scheduling of bound methods on persistent job stores (the workaround of scheduling `YourClass.methodname` along with an explicit `self` argument is no longer necessary as this is now done automatically for you)
> - Added the FAQ section to the docs
> - Made `BaseScheduler.start()` raise a `RuntimeError` if running under uWSGI with threads disabled
>
> 3.5.1
> =====
>
> - Fixed `OverflowError` on Windows when the wait time is too long
> - Fixed `CronTrigger` sometimes producing fire times beyond `end_date` when jitter is enabled (thanks to gilbsgilbs for the tests)
> - Fixed ISO 8601 UTC offset information being silently discarded from string formatted datetimes by adding support for parsing them
>
> 3.5.0
> =====
>
> - Added the `engine_options` option to `SQLAlchemyJobStore`
> - Added the `jitter` options to `IntervalTrigger` and `CronTrigger` (thanks to gilbsgilbs)
> - Added combining triggers (`AndTrigger` and `OrTrigger`)
> - Added better validation for the steps and ranges of different expressions in `CronTrigger`
> - Added support for named months (`jan` – `dec`) in `CronTrigger` month expressions
> - Added support for creating a `CronTrigger` from a crontab expression
> - Allowed spaces around commas in `CronTrigger` fields
> - Fixed memory leak due to a cyclic reference when jobs raise exceptions (thanks to gilbsgilbs for help on solving this)
> - Fixed passing `wait=True` to `AsyncIOScheduler.shutdown()` (although it doesn't do much)
> - Cancel all pending futures when `AsyncIOExecutor` is shut down
>
> 3.4.0
> =====
>
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`1428971`](https://github.com/agronholm/apscheduler/commit/1428971e178f861a5d104e9cbf8ce936384089bc) Updated the changelog
- [`50a7e39`](https://github.com/agronholm/apscheduler/commit/50a7e3935b19e01ce58582c5aae2fe9ccbfda988) Fixed OverflowError on QT scheduler if the wait time is very long
- [`8d0e9aa`](https://github.com/agronholm/apscheduler/commit/8d0e9aa606fdda8a9b7fff788b4e6d44b2e3c7d4) Fixed wrong method name in documentation ([#374](https://github-redirect.dependabot.com/agronholm/apscheduler/issues/374))
- [`f2e039e`](https://github.com/agronholm/apscheduler/commit/f2e039e5584253282e2187c2efcdb86274ea6e06) Fixed methods inherited from base class could not be executed by processpool ...
- [`92dc6cf`](https://github.com/agronholm/apscheduler/commit/92dc6cfcb09529cbde60e9e7d30b76d51fee38e7) Refactored the Travis configuration
- [`33aa920`](https://github.com/agronholm/apscheduler/commit/33aa9206e094a240d478821c03dc911e6bbb4151) Added the release version
- [`8235c03`](https://github.com/agronholm/apscheduler/commit/8235c03d790b42104e2921d9cff376c9f53dd53d) Replaced [@​yield](https://github.com/yield)_fixture with [@​fixture](https://github.com/fixture)
- [`8b951a6`](https://github.com/agronholm/apscheduler/commit/8b951a658de3710f6fe3f4b1257ecad9e5f3f637) Adapted RethinkDBJobStore to rethinkdb library v2.4+
- [`3d8cd86`](https://github.com/agronholm/apscheduler/commit/3d8cd86f7898ea14acec5c889372220d170314d1) Removed skipping of Gevent tests on Python 3.7
- [`ab991eb`](https://github.com/agronholm/apscheduler/commit/ab991eb29eedb0943356c4d7ddca8320e7845965) Added a FAQ entry about serialization related ValueErrors
- Additional commits viewable in [compare view](https://github.com/agronholm/apscheduler/compare/v2.1.0...v3.6.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=apscheduler&package-manager=pip&previous-version=2.1.0&new-version=3.6.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
**Note:** This repo was added to Dependabot recently, so you'll receive a maximum of 5 PRs for your first few update runs. Once an update run creates fewer than 5 PRs we'll remove that limit.
You can always request more updates by clicking `Bump now` in your [Dependabot dashboard](https://app.dependabot.com).
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<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
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- `@dependabot merge` will merge this PR after your CI passes on it
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MDExOlB1bGxSZXF1ZXN0MzEzMzYwNjM0
| 1,574
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Bump netcdf4 from 1.4.2 to 1.5.1.2
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[] | 2019-09-02T20:26:20
| 2019-09-02T20:27:19
|
2019-09-02T20:27:05Z
|
CONTRIBUTOR
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Bumps [netcdf4](https://github.com/Unidata/netcdf4-python) from 1.4.2 to 1.5.1.2.
<details>
<summary>Changelog</summary>
*Sourced from [netcdf4's changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).*
> version 1.5.1.2 (tag v1.5.1.2rel)
> ==================================
> * fix another slicing bug introduced by the fix to issue [#906](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/906) (issue [#922](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/922)).
>
> version 1.5.1.1 (tag v1.5.1.1rel)
> ==================================
> * fixed __version__ attribute (was set incorrectly in 1.5.1 release).
> * fix for issue [#919](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/919) (assigning 2d array to 3d variable with singleton
> first dimension with v[:] = a).
> * minimum numpy changed from 1.9.0 to 1.10.0.
>
> version 1.5.1 (tag v1.5.1rel)
> ==============================
> * fix issue [#908](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/908) by adding workaround for incorrect value returned
> by nc_inq_var_fill for netcdf-c < 4.5.1.
> * fix bug writing slice to unlimited dimension that is not the first
> (leftmost). Issue [#906](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/906).
> * make sure data gets converted to type of scale_factor when add_offset=0
> and scale_factor=1 (issue [#913](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/913)).
> * fix for reading empty (NIL) string attributes (issue [#915](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/915)).
>
> version 1.5.0.1 (tag v1.5.0.1rel)
> ==================================
> * binary wheels for linux and macosx rebuilt against netcdf-c 4.6.3 (instead
> of 4.4.1.1).
> * add read-shared mode (mode='rs'). Significantly speeds up reads of NETCDF3
> files (pull request [#902](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/902)).
>
> version 1.5.0 (tag v1.5.0rel)
> ===============================
> * added support for parallel IO in the classic netcdf-3 formats through the
> pnetcdf library (pull request [#897](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/897)).
>
> version 1.4.3.2 (tag v1.4.3.2)
> ===============================
> * include missing membuf.pyx file in release source tarball.
>
> version 1.4.3.1 (tag v1.4.3.1)
> ===============================
> * fix bug in implementation of NETCDF4_CLASSIC support for parallel IO
> in v1.4.3 release.
>
> version 1.4.3 (tag v1.4.3rel)
> =============================
> * make set_always_mask work in MFDataset.
> * fix saving diskless files to disk with netcdf-c >= 4.6.2.
> * write to an in-memory Dataset, memoryview buffer returned by Dataset.close()
> (issue [#865](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/865), requires netcdf-c >= 4.6.2)
> * fix performance regression when using large sequences of consecutive
> integers for indexing with netcdf-c >= 4.6.2 (issue [#870](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/870)).
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- See full diff in [compare view](https://github.com/Unidata/netcdf4-python/commits)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=netcdf4&package-manager=pip&previous-version=1.4.2&new-version=1.5.1.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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[//]: # (dependabot-automerge-end)
---
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MDExOlB1bGxSZXF1ZXN0MzEzMzYwNjg5
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Bump phonopy from 1.11.12.121 to 2.3.2
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] | 2019-09-02T20:26:43
| 2019-09-03T15:35:52
|
2019-09-03T15:35:39Z
|
CONTRIBUTOR
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Bumps [phonopy](http://atztogo.github.io/phonopy/) from 1.11.12.121 to 2.3.2.
[](https://dependabot.com/compatibility-score.html?dependency-name=phonopy&package-manager=pip&previous-version=1.11.12.121&new-version=2.3.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzEzNjYxNTQy
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Bump pytest from 5.0.1 to 5.1.2
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2019-09-03T15:59:57Z
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.0.1 to 5.1.2.
<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://github-redirect.dependabot.com/pytest-dev/pytest/issues/2270): Fixed
> `self` reference in function-scoped fixtures defined plugin classes:
> previously `self` would be a reference to a *test* class, not the
> *plugin* class.
> - [\#570](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/570): Fixed long
> standing issue where fixture scope was not respected when indirect
> fixtures were used during parametrization.
> - [\#5782](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5782): Fix
> decoding error when printing an error response from `--pastebin`.
> - [\#5786](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5786): Chained
> exceptions in test and collection reports are now correctly
> serialized, allowing plugins like `pytest-xdist` to display
> them properly.
> - [\#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792): Windows:
> Fix error that occurs in certain circumstances when loading
> `conftest.py` from a working directory that has casing other than
> the one stored in the filesystem (e.g., `c:\test` instead of
> `C:\test`).
>
> ## 5.1.1
> pytest 5.1.1 (2019-08-20)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5751](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5751): Fixed
> `TypeError` when importing pytest on Python 3.5.0 and 3.5.1.
>
> ## 5.1.0
> pytest 5.1.0 (2019-08-15)
> =========================
>
> Removals
> --------
>
> - [\#5180](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5180): As per
> our policy, the following features have been deprecated in the 4.X
> series and are now removed:
>
> - `Request.getfuncargvalue`: use `Request.getfixturevalue`
> instead.
> - `pytest.raises` and `pytest.warns` no longer support strings as
></tr></table> ... (truncated)
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.1.2 (2019-08-30)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#2270](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/2270): Fixed `self` reference in function-scoped fixtures defined plugin classes: previously `self` would be a reference to a *test* class, not the *plugin* class.
> - [\#570](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/570): Fixed long standing issue where fixture scope was not respected when indirect fixtures were used during parametrization.
> - [\#5782](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5782): Fix decoding error when printing an error response from `--pastebin`.
> - [\#5786](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5786): Chained exceptions in test and collection reports are now correctly serialized, allowing plugins like `pytest-xdist` to display them properly.
> - [\#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792): Windows: Fix error that occurs in certain circumstances when loading `conftest.py` from a working directory that has casing other than the one stored in the filesystem (e.g., `c:\test` instead of `C:\test`).
>
> pytest 5.1.1 (2019-08-20)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5751](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5751): Fixed `TypeError` when importing pytest on Python 3.5.0 and 3.5.1.
>
> pytest 5.1.0 (2019-08-15)
> =========================
>
> Removals
> --------
>
> - [\#5180](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5180): As per our policy, the following features have been deprecated in the 4.X series and are now removed:
>
> - `Request.getfuncargvalue`: use `Request.getfixturevalue` instead.
> - `pytest.raises` and `pytest.warns` no longer support strings as the second argument.
> - `message` parameter of `pytest.raises`.
> - `pytest.raises`, `pytest.warns` and `ParameterSet.param` now use native keyword-only syntax. This might change the exception message from previous versions, but they still raise `TypeError` on unknown keyword arguments as before.
> - `pytest.config` global variable.
> - `tmpdir_factory.ensuretemp` method.
> - `pytest_logwarning` hook.
> - `RemovedInPytest4Warning` warning type.
> - `request` is now a reserved name for fixtures.
>
> For more information consult [Deprecations and Removals](https://docs.pytest.org/en/latest/deprecations.html) in the docs.
>
> - [\#5565](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5565): Removed unused support code for [unittest2](https://pypi.org/project/unittest2/).
>
> The `unittest2` backport module is no longer necessary since Python 3.3+, and the small amount of code in pytest to support it also doesn't seem to be used: after removed, all tests still pass unchanged.
>
> Although our policy is to introduce a deprecation period before removing any features or support for third party libraries, because this code is apparently not used at all (even if `unittest2` is used by a test suite executed by pytest), it was decided to remove it in this release.
>
> If you experience a regression because of this, please [file an issue](https://github.com/pytest-dev/pytest/issues/new).
>
> - [\#5615](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5615): `pytest.fail`, `pytest.xfail` and `pytest.skip` no longer support bytes for the message argument.
>
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`e56544c`](https://github.com/pytest-dev/pytest/commit/e56544cb587e8f288bea12aff01355b31aec92f7) Preparing release version 5.1.2
- [`f9cc704`](https://github.com/pytest-dev/pytest/commit/f9cc704b1a8cf475a02051b747b78897b13a83f7) Replace session duration to a fix value in regendoc
- [`bd57307`](https://github.com/pytest-dev/pytest/commit/bd57307a39bc3877f38f802cf6ed9aef22663c1f) Merge pull request [#5768](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5768) from robholt/fixture-class-instance
- [`667c646`](https://github.com/pytest-dev/pytest/commit/667c6463ab30b00fb942d6b3cde9f8a4a1693cc6) Merge pull request [#5803](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5803) from nicoddemus/flaky-5795
- [`4e59455`](https://github.com/pytest-dev/pytest/commit/4e594552eb74dc8c0ea891ffe0f01b2c22e0f9f9) Merge pull request [#5798](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5798) from aklajnert/570-indirect-fixtures
- [`955dc6d`](https://github.com/pytest-dev/pytest/commit/955dc6d18aca99184db3b5db85b9fb9f497c04a1) Merge remote-tracking branch 'upstream/master' into robholt/fixture-class-ins...
- [`3ddbc7f`](https://github.com/pytest-dev/pytest/commit/3ddbc7fb2a63f6ca505f64368d5bd4dd939f0ea9) Improve CHANGELOG and add some comments
- [`bb60736`](https://github.com/pytest-dev/pytest/commit/bb60736a6f76276b1a0295dee5cf70c99e2997e7) Run py35 without xdist on Travis
- [`35b3b10`](https://github.com/pytest-dev/pytest/commit/35b3b1097ffc576b11cd8ad205103666a90e2344) Improve CHANGELOG and make test easier to understand for [#570](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/570)
- [`01082fe`](https://github.com/pytest-dev/pytest/commit/01082fea12649384aab44306f49503de1374c4a1) Serialize/deserialize chained exceptions ([#5787](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5787))
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.0.1...5.1.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.0.1&new-version=5.1.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
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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 method called check_params(self) which will show 5 different types of warnings:
- Warning if a user provided flag in the incar does not exist in our json file.
- Warning if a parameter for a flag is not a real number when a real number is needed
- Warning if an object type of the parameter for a flag does not match that in the json file
- Warning if only a specific list of strings/parameters is valid for a specific tag and the user provided parameter is not present in the list
- Warning if the parameter should be a list but is not (a future pull request will check if the elements in the list are the correct object type, hence why this is a separate warning)
* Unittest for check_params
## TODO
* Will add more flags along the way
* Add a function for recommending specific flags if a user provides a non-existent flag (e.g. if the user has NBAND in the INCAR file instead of NBANDS, the warning will recommend using NBANDS instead)
* Custodian Outcar validator for checking if all parameters in the INCAR weere properly red (see issue #100 in materialsproject/custodian)
|
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MDU6SXNzdWU0ODkxNjU0NTc=
| 1,578
|
Error when execute pmg analyze .
|
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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/miniconda3/lib/python3.7/site-packages/monty/json.py", line 271, in default
d = o.as_dict()
AttributeError: 'property' object has no attribute 'as_dict'
...
...
File "/Users/lvjian/miniconda3/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Users/lvjian/miniconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
TypeError: Object of type property is not JSON serializable
|
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MDExOlB1bGxSZXF1ZXN0MzE0MDk5NTg2
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|
Bump netcdf4 from 1.5.1.2 to 1.5.2
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[] | 2019-09-04T15:36:54
| 2019-09-04T16:29:31
|
2019-09-04T16:29:09Z
|
CONTRIBUTOR
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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 when _Unsigned attribute is set and byteorder of data
> does not match native byteorder (issue [#930](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/930)).
> * revise documentation for Python 3 (issue [#946](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/946)).
> * establish support for Python 2.7, 3.5, 3.6 and 3.7 (issue [#948](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/948)).
> * use dict built-in instead of OrderedDict for Python 3.7+
> (pull request [#955](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/955)).
> * remove underline ANSI in Dataset string representation (pull request [#956](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/956)).
> * remove newlines from string representation (pull request [#960](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/960)).
> * fix for issue [#957](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/957) (size of scalar var is a float since numpy.prod(())=1.0).
> * make sure Variable.setncattr fails to set _FillValue (issue [#959](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/959)).
> * fix detection of parallel HDF5 support with netcdf-c 4.6.1 (issue [#964](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/964)).
</details>
<details>
<summary>Commits</summary>
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</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzE0MjI3MTM2
| 1,580
|
Fast pourbaix
|
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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" using a convex hull from a grand-canonical phase diagram which includes electrons and protons as free species.
* The `MPRester.get_entries_in_chemsys` method is refactored to use a MongoDB `$in` operation on the chemsys, rather than iteratively querying the rest endpoint. This is significantly faster for many-element systems, and similarly performant for small-element systems.
* The `PourbaixDiagram.get_decomposition_energy` (i. e. the "pourbaix hull" method) now returns eV/atom, rather than eV/formula unit.
* `PourbaixDiagram.get_decomposition_energy` is now constrained to use the same composition as the pourbaix diagram, rather than attempting to make an inference about which phase the user intends to compute in pourbaix space. I'd like to reintroduce this functionality at some point with a more concrete use case and example that has a more rigorous physical interpretation, but as it stood was costly and likely misleading. This may introduce some hiccups to existing data pipelines.
|
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| 1,581
|
2019.9.7 - fails during conda-forge build test
|
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[] | null |
[
"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_1567914260255/test_tmp/run_test.py", line 2, in <module>
import pymatgen
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/__init__.py", line 42, in <module>
from .ext.matproj import MPRester
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/ext/matproj.py", line 23, in <module>
from pymatgen.core.surface import get_symmetrically_equivalent_miller_indices
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/core/surface.py", line 28, in <module>
from pymatgen.analysis.structure_matcher import StructureMatcher
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/analysis/structure_matcher.py", line 23, in <module>
from pymatgen.analysis.defects.core import Interstitial, \
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/analysis/defects/core.py", line 15, in <module>
from pymatgen.analysis.defects.utils import kb
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/analysis/defects/utils.py", line 25, in <module>
from pymatgen.io.vasp.outputs import Chgcar
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/io/vasp/__init__.py", line 13, in <module>
from .inputs import *
File "/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/io/vasp/inputs.py", line 610, in <module>
with open(os.path.join(cwd, "incar_parameters.json")) as incar_params:
FileNotFoundError: [Errno 2] No such file or directory: '/home/conda/feedstock_root/build_artifacts/pymatgen_1567914260255/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/pymatgen/io/vasp/incar_parameters.json'
Tests failed for pymatgen-2019.9.7-py36h516909a_0.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
WARNING:conda_build.build:Tests failed for pymatgen-2019.9.7-py36h516909a_0.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
WARNING conda_build.build:tests_failed(2230): Tests failed for pymatgen-2019.9.7-py36h516909a_0.tar.bz2 - moving package to /home/conda/feedstock_root/build_artifacts/broken
TESTS FAILED: pymatgen-2019.9.7-py36h516909a_0.tar.bz2
```
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MDExOlB1bGxSZXF1ZXN0MzE1NjcxNjA1
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|
Bump numpy from 1.17.1 to 1.17.2
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[] | 2019-09-09T19:03:30
| 2019-09-09T19:05:39
|
2019-09-09T19:05:24Z
|
CONTRIBUTOR
|
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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 against NumPy 1.17.1 along with a
> some documentation improvements. The most important fix is for lexsort when the
> keys are of type (u)int8 or (u)int16. If you are currently using 1.17 you
> should upgrade.
>
> The Python versions supported in this release are 3.5-3.7, Python 2.7 has been
> dropped. Python 3.8b4 should work with the released source packages, but there
> are no future guarantees.
>
> Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and
> OpenBLAS >= 3.7 to avoid errors on the Skylake architecture. The NumPy wheels
> on PyPI are built from the OpenBLAS development branch in order to avoid those
> errors.
>
>
> Contributors
> ============
>
> A total of 7 people contributed to this release. People with a "+" by their
> names contributed a patch for the first time.
>
> * CakeWithSteak +
> * Charles Harris
> * Dan Allan
> * Hameer Abbasi
> * Lars Grueter
> * Matti Picus
> * Sebastian Berg
>
>
> Pull requests merged
> ====================
>
> A total of 8 pull requests were merged for this release.
>
> * [#14418](https://github-redirect.dependabot.com/numpy/numpy/issues/14418): BUG: Fix aradixsort indirect indexing.
> * [#14420](https://github-redirect.dependabot.com/numpy/numpy/issues/14420): DOC: Fix a minor typo in dispatch documentation.
> * [#14421](https://github-redirect.dependabot.com/numpy/numpy/issues/14421): BUG: test, fix regression in converting to ctypes
> * [#14430](https://github-redirect.dependabot.com/numpy/numpy/issues/14430): BUG: Do not show Override module in private error classes.
> * [#14432](https://github-redirect.dependabot.com/numpy/numpy/issues/14432): BUG: Fixed maximum relative error reporting in assert_allclose.
> * [#14433](https://github-redirect.dependabot.com/numpy/numpy/issues/14433): BUG: Fix uint-overflow if padding with linear_ramp and negative...
> * [#14436](https://github-redirect.dependabot.com/numpy/numpy/issues/14436): BUG: Update 1.17.x with 1.18.0-dev pocketfft.py.
> * [#14446](https://github-redirect.dependabot.com/numpy/numpy/issues/14446): REL: Prepare for NumPy 1.17.2 release.
>
> Checksums
> =========
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`fce34f5`](https://github.com/numpy/numpy/commit/fce34f559f17674e7a3301c46b0a9cc991c143d4) REL: NumPy 1.17.2 release.
- [`198b58c`](https://github.com/numpy/numpy/commit/198b58cf296ab7b28936466eb2e447c3b5c1cc05) Merge pull request [#14446](https://github-redirect.dependabot.com/numpy/numpy/issues/14446) from charris/prepare-1.17.2-release
- [`6e46f34`](https://github.com/numpy/numpy/commit/6e46f34ad3fffe1cfd7a90230e58430cc6afcb2c) REL: Prepare for NumPy 1.17.2 release.
- [`e1febea`](https://github.com/numpy/numpy/commit/e1febea7d30a3d5c6f0922c6b4d71029b8a6d129) Merge pull request [#14436](https://github-redirect.dependabot.com/numpy/numpy/issues/14436) from charris/backport-14279
- [`3752840`](https://github.com/numpy/numpy/commit/37528408521b4b64d5f173c27a27106f31a27475) MAINT: Update 1.17.x with 1.18.0-dev pocketfft.py.
- [`b6ed3f1`](https://github.com/numpy/numpy/commit/b6ed3f1e8d553009eb9e01e3231f832a8f9d7b2d) Merge pull request [#14433](https://github-redirect.dependabot.com/numpy/numpy/issues/14433) from charris/backport-14209
- [`ca55abc`](https://github.com/numpy/numpy/commit/ca55abca13947f2ecbe61be17e0672af33e304ae) Merge pull request [#14430](https://github-redirect.dependabot.com/numpy/numpy/issues/14430) from charris/backport-14429
- [`d6bd499`](https://github.com/numpy/numpy/commit/d6bd4997b6261575fc85b57f5e4c4406c212481c) Merge pull request [#14432](https://github-redirect.dependabot.com/numpy/numpy/issues/14432) from charris/backport-13802
- [`30bd4f8`](https://github.com/numpy/numpy/commit/30bd4f8b7bd86742b0a07deeed2256f11bee6a58) BUG: Fixed maximum relative error reporting in assert_allclose ([gh-13802](https://github-redirect.dependabot.com/numpy/numpy/issues/13802))
- [`5678c0b`](https://github.com/numpy/numpy/commit/5678c0b868e1dbd7e39930136def969a985047ed) BUG: Replace _linear_ramp with linspace
- Additional commits viewable in [compare view](https://github.com/numpy/numpy/compare/v1.17.1...v1.17.2)
</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzE1NjcxNzIx
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|
Bump h5py from 2.9.0 to 2.10.0
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[] | 2019-09-09T19:03:50
| 2019-09-10T15:53:01
|
2019-09-10T15:52:49Z
|
CONTRIBUTOR
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Bumps [h5py](https://github.com/h5py/h5py) from 2.9.0 to 2.10.0.
<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) bumped version to 2.10.0
- [`e64f611`](https://github.com/h5py/h5py/commit/e64f6112bdd7b664b354a60564d7c409b92464de) Updated authorship for 2.10.0
- [`1c3f1d0`](https://github.com/h5py/h5py/commit/1c3f1d0b01ebb9f7dea27d59dcd70bae2cbb2530) Merge pull request [#1250](https://github-redirect.dependabot.com/h5py/h5py/issues/1250) from takluyver/whatsnew-2.10-d
- [`ee8012a`](https://github.com/h5py/h5py/commit/ee8012a11c6733d975efa1d720f91341174ab78c) Merge branch 'master' into whatsnew-2.10-d
- [`6648f8a`](https://github.com/h5py/h5py/commit/6648f8a4371c6384f94ec800f0d46b6d82353432) Merge pull request [#1290](https://github-redirect.dependabot.com/h5py/h5py/issues/1290) from scopatz/rever
- [`d8b0f27`](https://github.com/h5py/h5py/commit/d8b0f27f87e86341b99b52fab0233bbab971f31b) prune news
- [`b8c53ec`](https://github.com/h5py/h5py/commit/b8c53ecb58271ffa63788659dbdfabfadd9d1736) fix manifest for rever
- [`dd2d278`](https://github.com/h5py/h5py/commit/dd2d278e7e2e3de08472af938886cde5e1e9013d) fix end of file newlines
- [`6a79bf1`](https://github.com/h5py/h5py/commit/6a79bf1da65eedb3058b4bf0be242a1dd2163983) move existing news
- Additional commits viewable in [compare view](https://github.com/h5py/h5py/compare/2.9.0...2.10.0)
</details>
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MDExOlB1bGxSZXF1ZXN0MzE1NjcxODU1
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|
Bump palettable from 3.2.0 to 3.3.0
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[] | 2019-09-09T19:04:12
| 2019-09-09T19:05:51
|
2019-09-09T19:05:41Z
|
CONTRIBUTOR
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Bumps [palettable](https://github.com/jiffyclub/palettable) from 3.2.0 to 3.3.0.
<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://github.com/jiffyclub/palettable/commits/v3.3.0)
</details>
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MDU6SXNzdWU0OTEzOTMzMzI=
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pymatgen.io.vasp.outputs.Wavecar fails to read WAVECAR from gamma-only VASP run
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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 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.\n> \n> \n\nI'll see what I can do.\n\n\t\t\t\t\t\tNoam\n\n____________\n||\n|U.S. NAVAL|\n|_RESEARCH_|\nLABORATORY\nNoam Bernstein, Ph.D.\nCenter for Materials Physics and Technology\nU.S. Naval Research Laboratory\nT +1 202 404 8628 F +1 202 404 7546\nhttps://www.nrl.navy.mil <https://www.nrl.navy.mil/>\n",
"I think there was another issue where this was discussed, I’ll try and find\nit...\n\nOn Tue, Sep 10, 2019 at 05:54, bernstei <notifications@github.com> wrote:\n\n> > On Sep 10, 2019, at 8:49 AM, Shyue Ping Ong <notifications@github.com>\n> wrote:\n> >\n> > I have no idea whether the gamma info is in the wavecar. But setting\n> that argument seems to be a quick fix for the problem for now. Can you\n> implement and then submit a PR with the requisite unittests pls? Thanks.\n> >\n> >\n>\n> I'll see what I can do.\n>\n> Noam\n>\n> ____________\n> ||\n> |U.S. NAVAL|\n> |_RESEARCH_|\n> LABORATORY\n> Noam Bernstein, Ph.D.\n> Center for Materials Physics and Technology\n> U.S. Naval Research Laboratory\n> T +1 202 404 8628 F +1 202 404 7546\n> https://www.nrl.navy.mil <https://www.nrl.navy.mil/>\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1585?email_source=notifications&email_token=AAWWWRDTWLAUZZDEVN7CBOLQI6KJDA5CNFSM4IVBTLU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6K7GTQ#issuecomment-529920846>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWREP24VP6O7MHFWQYYTQI6KJDANCNFSM4IVBTLUQ>\n> .\n>\n",
"I've worked out what needs to be done, although it's going to be a while before I would be able to release it. It required replicating the VASP logic for which plane waves to skip, and then reconstructing the missing complex conjugate coefficients.",
"Thanks @bernstei. Didn't realize it was so complicated!!! Do you know if there is a quick way to check whether a WAVECAR is gamma only? If so, we can first code a warning into the Wavecar class to at least warn people.",
"Ah, the previous issue I was thinking about was actually in relation to the Waveder class (pasted here for interest https://github.com/materialsproject/pymatgen/issues/1442), which might have similar issues.",
"From what I can tell, the only way to check is to look for mismatching numbers of plane waves (which is what the current code, and also WaveTrans, do), which isn't exactly feel like good practice, but it does seem to be the only way it can happen. My current code needs a \"gamma\" flag, but I suppose one could actually switch to assuming that it's gamma-only if the number of PW doesn't match.",
"I wrote the original implementation for pymatgen.io.vasp.outputs.Wavecar based on WaveTrans. There's no flag or any information in the WAVECAR that will tell you whether it's gamma only or a normal one. Putting the option as an input argument is the best option (in my opinion) because this is essentially what you do with VASP (you compile a separate binary for gamma only and the WAVECAR's from gamma only and normal are not cross compatible). Also, this leaves the check for the number of PW's in tact.\r\n\r\nLet me know if you have any questions or need any help with adding the gamma-only code.",
"Thanks. I think I have working code, but can someone point me at an example of a unit test, so I can develop one for this feature?\n\n\t\t\t\t\t\tthanks,\n\t\t\t\t\t\tNoam\n",
"[here](https://github.com/materialsproject/pymatgen/blob/bcd76b3e5e09983de52eb930799a192ef221db6a/pymatgen/io/vasp/tests/test_outputs.py#L1255-L1411) are the unittests that I wrote for the Wavecar class.",
"> On Sep 11, 2019, at 2:18 PM, Mark Turiansky <notifications@github.com> wrote:\n> \n> here <https://github.com/materialsproject/pymatgen/blob/bcd76b3e5e09983de52eb930799a192ef221db6a/pymatgen/io/vasp/tests/test_outputs.py#L1255-L141> are the unittests that I wrote for the Wavecar class.\n> \n> \n\nThanks. A couple of related questions. Does the unit test actually test the contents (PW coefficients and/or values of WF in real space) of the Wavecar object, or just its metadata? I only see the latter. Second, where does WAVECAR.N2 come from? Is that distributed in the pymatgen git repo, or does the test somehow cause it to be calculated on the fly?\n\n\t\t\t\t\t\t\t\t\tNoam\n\n",
"> On Sep 11, 2019, at 2:33 PM, Noam Bernstein <noam.bernstein@nrl.navy.mil> wrote:\n> \n> Thanks. A couple of related questions. Does the unit test actually test the contents (PW coefficients and/or values of WF in real space) of the Wavecar object, or just its metadata? I only see the latter.\n\nNever mind, I see the relevant tests.\n\n> Second, where does WAVECAR.N2 come from? Is that distributed in the pymatgen git repo, or does the test somehow cause it to be calculated on the fly?\n\nThis I still need to understand, to generate a gamma-only run WAVECAR.\n\n\t\t\t\t\t\t\tNoam\n\n",
"Yes, the WAVECAR.N2 lives in the test_files directory: https://github.com/materialsproject/pymatgen/blob/master/test_files/WAVECAR.N2\r\n\r\nSo the gamma-only WAVECAR would have to be added there also. Since git doesn't really like large files, the smallest sensible representative WAVECAR is definitely preferred.",
"> On Sep 11, 2019, at 3:00 PM, Matthew Horton <notifications@github.com> wrote:\n> \n> Yes, the WAVECAR.N2 lives in the test_files directory: https://github.com/materialsproject/pymatgen/blob/master/test_files/WAVECAR.N2 <https://github.com/materialsproject/pymatgen/blob/master/test_files/WAVECAR.N2>\n> So the gamma-only WAVECAR would have to be added there also. Since git doesn't really like large files, the smallest sensible representative WAVECAR is definitely preferred.\n> \n> \n\nI don’t suppose I could get whomever contributed the WAVECAR.N2 file to run a gamma-only calculation with exactly the same parameters and add it? Then my test could just compare it to the non-gamma-only run.\n\n\t\t\t\t\t\t\t\t\t\tNoam\n\n",
"@bernstei You can just run a very small calculation using gamma point only. The calculation does not have to be good. We are only making sure of parsing. E.g., just take the primitive cell of Li and run with gamma point to get WAVECAR. You don't even need to run it on a queue. It will be done in < 1 min.",
"> On Sep 11, 2019, at 3:23 PM, Shyue Ping Ong <notifications@github.com> wrote:\n> @bernstei <https://github.com/bernstei> You can just run a very small calculation using gamma point only. The calculation does not have to be good. We are only making sure of parsing. E.g., just take the primitive cell of Li and run with gamma point to get WAVECAR. You don't even need to run it on a queue. It will be done in < 1 min.\n> \n\nTrue, but the easiest way to check is to compare to a non-gamma calculation of the same thing, and if I can’t re-use the existing WAVECAR.N2, I’ll have to upload two WAVECARs. I can do that, but it’s more stuff in your repo.\n\n\t\t\t\t\t\t\t\t\tNoam",
"Also, are the any instructions for how to run the unit tests, ideally just the vasp io ones?\n\n\t\t\t\t\t\tNoam",
"Committing two small files is fine.\r\nTo run unittests, just type pytest test_outputs.py",
"\n\n> On Sep 11, 2019, at 3:33 PM, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> Committing two small files is fine.\n> To run unittests, just type pytest test_outputs.py\n> \n> \nIt’s failing with:\n> cd pymatgen/io/vasp/tests\n> pytest test_outputs.py \n\n===================================================================================================== ERRORS ======================================================================================================\n_____________________________________________________________________________ ERROR collecting pymatgen/io/vasp/tests/test_outputs.py _____________________________________________________________________________\nImportError while importing test module '/Volumes/bernstei/src/work/pymatgen/pymatgen/pymatgen/io/vasp/tests/test_outputs.py'.\nHint: make sure your test modules/packages have valid Python names.\nTraceback:\n../../../__init__.py:40: in <module>\n from pymatgen.core import *\n../../../core/__init__.py:8: in <module>\n from .structure import Structure, IStructure, Molecule, IMolecule\n../../../core/structure.py:25: in <module>\n from pymatgen.core.lattice import Lattice\n../../../core/lattice.py:22: in <module>\n from pymatgen.util.coord import pbc_shortest_vectors\n../../../util/coord.py:9: in <module>\n from . import coord_cython as cuc\nE ImportError: cannot import name 'coord_cython'\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n\nI did \"setup.py build” in the top level directory, but that didn’t help. \n\n\t\t\t\t\t\t\t\t\tNoam\n",
"THink you need to run python setup.py develop. Build is not gong to install the compiled cython code.",
"As they have said, I just generated the WAVECAR.N2 with horrendously low convergence parameters (ENCUT of 25 eV, 1 kpoint, 10 Angstrom cube cell with a N2 molecule in the center, just a single-shot calculation).\r\n\r\nIn my unittests, I really just check the metadata. It's not so practical to check the actual wavefunctions and coefficients. The best check in the end is to use the \"get_parchg\" function and look at the charge density using your favorite viewing software to make sure the charge density looks correct.",
"Months later, I finally have patches available to make reading gamma-point only wavefunctions possible. I'd be happy to do a pull request, but do I need some sort of permission first?",
"No permission required to open a pull request, thanks very much for taking the time to patch!",
"OK - I created a pull request, but something's still broken, so please ignore it for now. I'll try to link it to this issue once it's actually ready.",
"Great! You can put “[WIP]” (work in progress) in your PR title and remove it when you feel like it’s ready to merge",
"OK, I created pull request 1781 [https://github.com/materialsproject/pymatgen/pull/1781], but I haven't quite figured out whether it's ready. It seems to be failing the travis-ci step, but I see no sign that anything I modified is a problem."
] | 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[ink]), nplane))
ValueError: failed to generate the correct number of G points 891 446
(I added the numbers myself). The numbers are off by a factor of 2 (+1), suggesting that it's not aware of the "-DNGXhalf -DwNGXhalf" arguments passed for the gamma-only executable, and that's messing up the count. I don't know if that info is embedded in the WAVECAR, but if not, perhaps it might be necessary to add a "gamma=bool" argument to Wavecar.__init__? The values in the file may well be real rather than complex, as well.
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MDExOlB1bGxSZXF1ZXN0MzE1NzczNjY5
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Incar params fix
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[] | 2019-09-10T01:11:44
| 2019-09-10T15:48:39
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2019-09-10T15:48:39Z
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CONTRIBUTOR
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Simplified checks for 'list' type parameters in INCAR
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MDExOlB1bGxSZXF1ZXN0MzE2MTcyNDIy
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Remove polysulfide logic and correction
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[] | 2019-09-10T20:52:01
| 2019-09-10T20:52:46
|
2019-09-10T20:52:46Z
|
CONTRIBUTOR
|
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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 would determine the sulfide_type as 'polysulfide', for which there was no corresponding correction key in MPCompatibility.yaml. Without the structure, the sulfide_type would be 'sulfide' and a correction would be applied.
This commit removes 'polysulfide' as a return type from sulfide_type() and adds a unit test to ensure that a ComputedEntry and ComputedStructureEntry return the same corrections.
|
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| 491,960,832
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MDU6SXNzdWU0OTE5NjA4MzI=
| 1,588
|
Error report when using module of pymatgen_diffusion.neb.pathfinder
|
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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 rendering on github for me right now but if you download the file it should work. "
] | 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**
**Desktop (please complete the following information):**
- OS: [e.g. Red Hat Enterprise Linux Server release 6.10 (Santiago)]
- Browser [e.g. Chrome]
- Version [e.g. 6.10]
|
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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 properties, but no structure properties. This tends to lead to structure properties being created in an ad-hoc way, like charge, or here, with the energy/temperature/pressure.\r\n\r\nI think the solution proposed here with \"frame_property\" is fine, I'm just noting this as something we may want to think about since there are many cases where this might be useful.\r\n\r\nOn the other side of the issue, a problem with site_properties etc. at the moment is that it's a free-form dict and can't be type-hinted (or, rather, it's `Dict[str, List[Any]]`, which doesn't tell us much). This makes it powerful and versatile, but also makes it more difficult to reason about and prone to error, and would also be an issue here with frame_property.",
"@shyuep Fixed! :D\r\n\r\n@mkhorton I do see where the issue is with site_properties and \"frame_property\" being free-form. Perhaps there is a way to let the user know which keys are supported by default/ used by other bits of code in pymatgen, but still allow users to have the flexibility of using other properties? As for structure properties, I would be in support of creating structure properties.",
"Many thanks!",
"Yes, in regards to flexibility/strictness for properties, I think one route would be to have supported keys (such as what we currently have in Specie). These could be typed, and the types checked on initialization and/or when using e.g. the add_site_property() method. But if you want to add your own arbitrary keys that would be allowed.\r\n\r\nThere is actually a solution to this on the horizon with TypedDict https://www.python.org/dev/peps/pep-0589/ but unless this is back-ported I'm not sure to what extent we can use this."
] | 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', but if a better name is proposed, I have no problem changing it.
- Added more tests for slicing, site properties, and frame properties
|
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MDExOlB1bGxSZXF1ZXN0MzE2OTk0MDQx
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|
revert list of specific keys back to original list:
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[] | 2019-09-12T16:36:33
| 2019-09-12T19:59:00
|
2019-09-12T19:59:00Z
|
CONTRIBUTOR
|
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Change the list of specific parameters to handle in the Incar class method proc_val back to its original lists as this method can only read specific parameter types as certain objects.
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MDU6SXNzdWU0OTM1NzI3MDQ=
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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 the structure are given. Therefore it is entirely possible that asking for each site individually might work, but all sites together will not. Some combinations of co-ordinates can cause the Voronoi algorithm to fail, e.g. see this previous bug report https://github.com/scipy/scipy/issues/8929\r\n\r\nI imagine this might be fixed with a different choice of cut-off radius but I have not investigated. You may want to try changing the `cutoff` kwarg and the `allow_pathological` kwarg in the `VoronoiNN` constructor. Please report back if you manage to fix this!",
"Thanks @mkhorton. I understand that with all the points included in the voronoi tessellation, it is more prone to error. My expectation is only that the get all voronoi polyhedron should return a list the same way as I compute each site individually (its a reasonable expectation right?). The problem is more related to implementation than physics. I will test options and let you know. Thank you again.\r\n\r\nChi",
"Yes agreed, it’s a completely reasonable expectation. I don’t know if there\nare more robust Voronoi implementations out there, or if it’s a fundamental\nlimitation.\n\nOn Sat, Sep 14, 2019 at 15:29, Chi Chen <notifications@github.com> wrote:\n\n> Thanks @mkhorton <https://github.com/mkhorton>. I understand that with\n> all the points included in the voronoi tessellation, it is more prone to\n> error. My expectation is only that the get all voronoi polyhedron should\n> return a list the same way as I compute each site individually (its a\n> reasonable expectation right?). The problem is more related to\n> implementation than physics. I will test options and let you know. Thank\n> you again.\n>\n> Chi\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1591?email_source=notifications&email_token=AAWWWREIXHG7CWOC34KOARTQJVQUFA5CNFSM4IWVTKD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6XFJKY#issuecomment-531518635>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRD2ZEIZVSMM566BUADQJVQUFANCNFSM4IWVTKDQ>\n> .\n>\n",
"@mkhorton For the above example, it seems that increasing Voronoi cutoff to 20 Angstrom \"cured\" the pathological structure. Strange enough. I will close this issue. Thank you for the suggestion! "
] | 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 Reproduce**
```
from pymatgen.analysis.local_env import VoronoiNN
from pymatgen import Structure
s = Structure.from_str("""V12
1.0
2.459662 0.000000 0.000000
0.000000 4.471437 0.000000
0.000000 0.000000 29.515945
V
12
direct
0.000000 0.000000 0.916206 V
0.000000 0.000000 0.994721 V
0.500000 0.500000 0.959167 V
0.500000 0.500000 0.874547 V
0.000000 0.000000 0.749499 V
0.000000 0.000000 0.833633 V
0.500000 0.500000 0.792168 V
0.500000 0.500000 0.708033 V
0.000000 0.000000 0.582499 V
0.000000 0.000000 0.667120 V
0.500000 0.500000 0.625461 V
0.500000 0.500000 0.546946 V
""", fmt='POSCAR')
vnn = VoronoiNN()
try:
all_polys = vnn.get_all_voronoi_polyhedra(s)
except Exception as e:
print('get_all_voronoi_polyhedra error: ')
print(e)
try:
for i in range(len(s)):
poly = vnn.get_voronoi_polyhedra(s, i)
except Exception as e:
print('get_voronoi_polyhedra failed with index %d' %i)
print(e)
```
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MDU6SXNzdWU0OTQxMjQzMjY=
| 1,592
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Inconsistent Structure.get_distance and Lattice.get_distance methods.
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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.get_points_in_sphere and then have all relevant methods just call that. This is reduce code duplication and ensure we have one consistent algo.
@chc273 can do the honors?
|
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MDExOlB1bGxSZXF1ZXN0MzE4NDUxNzY3
| 1,593
|
Bump tqdm from 4.35.0 to 4.36.0
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[] | 2019-09-17T17:43:46
| 2019-09-17T17:44:35
|
2019-09-17T17:44:16Z
|
CONTRIBUTOR
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.35.0 to 4.36.0.
<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.dependabot.com/tqdm/tqdm/issues/548))
> - update submodule architecture ([#198](https://github-redirect.dependabot.com/tqdm/tqdm/issues/198) -> [#800](https://github-redirect.dependabot.com/tqdm/tqdm/issues/800))
> + backward-compatibility
> + expose `utils`
> + rename `main` -> `cli`
> + add/fix tests
> + fix minor cached var optimisation
> + `gui` partial upgrade ([#790](https://github-redirect.dependabot.com/tqdm/tqdm/issues/790))
> + `notebook` upgrade ([#790](https://github-redirect.dependabot.com/tqdm/tqdm/issues/790))
> * support `{bar}` in `bar_format` ([#594](https://github-redirect.dependabot.com/tqdm/tqdm/issues/594))
> * inherit methods including `set_*(refresh)` ([#740](https://github-redirect.dependabot.com/tqdm/tqdm/issues/740) -> [#741](https://github-redirect.dependabot.com/tqdm/tqdm/issues/741))
> + ready for `contrib` releases ([#252](https://github-redirect.dependabot.com/tqdm/tqdm/issues/252))
> - support custom `bar_format` with unknown `total`
> - fix `tqdm_notebook` red block on explicit `file=None`
> - update notebook to fully support custom `bar_format` ([#594](https://github-redirect.dependabot.com/tqdm/tqdm/issues/594), [#649](https://github-redirect.dependabot.com/tqdm/tqdm/issues/649))
> - misc tidy
> + warnings
> + linting
> + update submodule contribution guide ([#252](https://github-redirect.dependabot.com/tqdm/tqdm/issues/252))
> + parallel `(py)make test`
> + fix Zenodo metadata
> - update documentation
> + `pandas`, `notebook`, `gui` ([#245](https://github-redirect.dependabot.com/tqdm/tqdm/issues/245))
> + indentation
> + update multiprocessing and multithreading examples ([#796](https://github-redirect.dependabot.com/tqdm/tqdm/issues/796))
</details>
<details>
<summary>Commits</summary>
- [`89b73bd`](https://github.com/tqdm/tqdm/commit/89b73bdc30c099c5b53725806e7edf3a121c9b3a) bump version, merge branch 'devel'
- [`1bd486c`](https://github.com/tqdm/tqdm/commit/1bd486c6ca5bfe558a15a4ff6e70301bae2e3ad1) expose more custom format params
- [`05c02c5`](https://github.com/tqdm/tqdm/commit/05c02c517779b615f000bbd724bc11be88687f8d) linting
- [`6c5fb3b`](https://github.com/tqdm/tqdm/commit/6c5fb3bcdcb1c16914dd58c3f669bc179a816790) add warning msg
- [`a347706`](https://github.com/tqdm/tqdm/commit/a3477060f1974ef1413e5a2108fbdf60d4299be0) potential thread safety fix
- [`96cd73e`](https://github.com/tqdm/tqdm/commit/96cd73ec0322f09971c119a39013f0351d533c0c) minor doc indentaion update
- [`c4220fd`](https://github.com/tqdm/tqdm/commit/c4220fd162eba64ecacb0d657fa0697b03b2f4a5) update submodule contribution guide
- [`2d1a7f5`](https://github.com/tqdm/tqdm/commit/2d1a7f513b42f76a0f796af024cc27d318c04286) update pandas, notebook, gui docs
- [`831f44b`](https://github.com/tqdm/tqdm/commit/831f44b90dc1977aafe3960102dba5fead54e363) fix tests
- [`c54409b`](https://github.com/tqdm/tqdm/commit/c54409bdf588cb90a77e18ecaba79d7b639f90b8) update docs
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.35.0...v4.36.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.35.0&new-version=4.36.0)
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MDExOlB1bGxSZXF1ZXN0MzE4NDU2ODAz
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|
Unify lattice.get_points_in_sphere and structure.get_all_neighbors
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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 boolean `pbc` to indicates periodic boundary for each dimension. When any direction is periodic, a periodic `lattice` should be supplied. The function returns `List[List[Tuple[coord, distance, index, image]]]`
3. `Lattice.get_points_in_sphere` calls `get_points_in_spheres` by supplying only one `center_points`
4. Previous `Lattice.get_points_in_sphere` was moved to `Lattice.get_points_in_sphere_old` with deprecation decorator.
5. `Structure.get_all_neighbors` calls `get_points_in_spheres` and constructs the neighbor list with site properties.
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MDExOlB1bGxSZXF1ZXN0MzE4NDY0ODM0
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Unify lattice.get_points_in_sphere and structure.get_all_neighbors
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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/articles/events-that-trigger-workflows#pull-request-events-for-forked-repositories ",
"@mkhorton The article doesn't say how to get it to work. ",
"Yes, I'm finding conflicting information online -- it sounds like this was only recently added, e.g. see this thread https://github.com/sdras/awesome-actions/issues/98. I'm not seeing the answer in the documentation (aside to use push events, which we already do).",
"@chc273 There are still failing tests. These should be fixed.",
"@shyuep i am on it.",
"Thanks."
] | 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 boundary for each dimension. When any direction is periodic, a periodic lattice should be supplied. The function returns List[List[Tuple[coord, distance, index, image]]]
Lattice.get_points_in_sphere calls get_points_in_spheres by supplying only one center_points
Previous Lattice.get_points_in_sphere was moved to Lattice.get_points_in_sphere_old with deprecation decorator.
Structure.get_all_neighbors calls get_points_in_spheres and constructs the neighbor list with site properties.
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Bump tqdm from 4.36.0 to 4.36.1
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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 Lattice changes were merged, it seems more likely it's the Lattice changes that are responsible.",
"Nope.. The tests use a binary within the pymatgen repo. I have not changed the enum lib. It seems to me.",
"Possibly.\n\nOn Thu, Sep 19, 2019 at 11:21 Matthew Horton <notifications@github.com>\nwrote:\n\n> This started failing after the recent Lattice changes were merged, it\n> seems more likely it's the Lattice changes that are responsible.\n>\n> —\n> You are receiving this because your review was requested.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1596?email_source=notifications&email_token=AAEM4UZPLVYAR7HZXASVF7TQKO7LTA5CNFSM4IYN5H5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7EMFPA#issuecomment-533250748>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAEM4U4KSOOFJMQKDEVM7FLQKO7LTANCNFSM4IYN5H5A>\n> .\n>\n-- \nShyue Ping\n",
"If I had to guess, it could lead back to StructureMatcher ... like in a few transformations, it relies on using StructureMatcher.group_structures to discard duplicates. I imagine the Lattice changes have subtly changed how the ordering in group_structures works. I suspect this is probably not a bug, but it does highlight something subtle happening in the group_structures code.",
"I pushed a fix. The problem was that the test was comparing the lattice matrices directly (using assertEqual no less). When you compare the actual lattice parameters, the two lattices are identical. The lattice matrix is arbitrary and should not be used for comparison.",
"That’s fair. Still means the ordering of StructureMatcher grouping has\nchanged. That test is years old.\n\nOn Thu, Sep 19, 2019 at 13:32, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> I pushed a fix. The problem was that the test was comparing the lattice\n> matrices directly (using assertEqual no less). When you compare the actual\n> lattice parameters, the two lattices are identical. The lattice matrix is\n> arbitrary and should not be used for comparison.\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1596?email_source=notifications&email_token=AAWWWRGN57UZPU25TTUYXKLQKPOXVA5CNFSM4IYN5H5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7EXWJA#issuecomment-533297956>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRBNG3WRFJ6KSL2ZPBLQKPOXVANCNFSM4IYN5H5A>\n> .\n>\n"
] | 2019-09-19T17:23:19
| 2019-09-19T20:56:35
|
2019-09-19T20:12:58Z
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.36.0 to 4.36.1.
<details>
<summary>Commits</summary>
- [`a0af066`](https://github.com/tqdm/tqdm/commit/a0af0666991b724abe1efdbb3958892771a21495) bump version, merge branch 'devel'
- [`ed82bf3`](https://github.com/tqdm/tqdm/commit/ed82bf38cb2f4abcc65f6d5f3192734f0cb97f1d) fix console entry point
- [`46135ce`](https://github.com/tqdm/tqdm/commit/46135ce62799423f82d981e14702461cd2e80333) minor doc updates
- See full diff in [compare view](https://github.com/tqdm/tqdm/compare/v4.36.0...v4.36.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.36.0&new-version=4.36.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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[Needs test] Add vacuum mode to Bader caller
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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 that way if the option you choose in\nunsupported but again a lot of boilerplate.\n\nOn Wed, Oct 16, 2019 at 13:54, Shyam Dwaraknath <notifications@github.com>\nwrote:\n\n> *@shyamd* commented on this pull request.\n> ------------------------------\n>\n> In pymatgen/command_line/bader_caller.py\n> <https://github.com/materialsproject/pymatgen/pull/1597#discussion_r335703822>\n> :\n>\n> > @@ -106,7 +106,8 @@ class BaderAnalysis:\n> \" Please download the library at http://theory.cm.utexas\"\n> \".edu/vasp/bader/ and compile the executable.\")\n> def __init__(self, chgcar_filename, potcar_filename=None,\n> - chgref_filename=None, parse_atomic_densities=False):\n> + chgref_filename=None, parse_atomic_densities=False,\n> + vacuum_mode=\"auto\"):\n>\n> Can we make this an enum to provide some unambiguity? I think in general\n> we should do that for anything that is a selection of choices.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1597?email_source=notifications&email_token=AAWWWRGNT3BADERQZBTJC5TQO55RLA5CNFSM4IYRDMEKYY3PNVWWK3TUL52HS4DFWFIHK3DMKJSXC5LFON2FEZLWNFSXPKTDN5WW2ZLOORPWSZGOCIGXAAA#pullrequestreview-302870528>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRBZMZ22H4DL3VEHBYLQO55RLANCNFSM4IYRDMEA>\n> .\n>\n",
"Will re-open this pending changes to Bader from #1804 "
] | 2019-09-19T23:44:24
| 2021-02-13T17:26:48
|
2020-03-15T19:25:55Z
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Needs test before merging.
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Bump ase from 3.18.0 to 3.18.1
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[] | 2019-09-23T20:01:43
| 2019-09-23T21:07:04
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2019-09-23T21:06:51Z
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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/07de35654601ddbb2b23a4e7df7091696b0af108) ASE version 3.18.1
- [`4066b5f`](https://gitlab.com/ase/ase/commit/4066b5f2365f1fd2b855bfef3444a330bd0d36a6) add workaround for crash on macos due to library compatibility issue.
- [`912a5ff`](https://gitlab.com/ase/ase/commit/912a5fff0130776187786431f0f183577d663ddd) allow running newrelease from any branch
- [`1308594`](https://gitlab.com/ase/ase/commit/1308594f01455ff4e662e8f4657236ba202b56be) Alway pop _little_endian key so that users don't see it
- [`0df1f01`](https://gitlab.com/ase/ase/commit/0df1f018a4663ee87262c64d223585eed96a6b1b) raise error if band path cell vectors do not match atoms.pbc
- [`f2e943e`](https://gitlab.com/ase/ase/commit/f2e943e748959247eecc184c2fec136258cc17ee) make sure we don't complain about 2D bandpath for atoms with 2d-periodic rank...
- [`fa8a90e`](https://gitlab.com/ase/ase/commit/fa8a90ed943a7dc311c05b4452163c0a15caaef8) Use cell.any(1)
- [`9614aac`](https://gitlab.com/ase/ase/commit/9614aac45dc1e2d613f8d0c0d0fe7b665a4ab6d4) Don't use cell.pbc
- [`c3b86d4`](https://gitlab.com/ase/ase/commit/c3b86d4b42367e3f562c6a290997fdbcacc4804f) docstring
- [`705bcd0`](https://gitlab.com/ase/ase/commit/705bcd037a445ffa6bb82afa55f21109dd569042) cleanup
- Additional commits viewable in [compare view](https://gitlab.com/ase/ase/compare/3.18.0...3.18.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=ase&package-manager=pip&previous-version=3.18.0&new-version=3.18.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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Bump pytest from 5.1.2 to 5.1.3
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[] | 2019-09-23T20:02:03
| 2019-09-23T21:08:03
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2019-09-23T21:07:09Z
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CONTRIBUTOR
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[//]: # (dependabot-start)
⚠️ **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>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.1.3
> pytest 5.1.3 (2019-09-18)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5807](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5807): Fix
> pypy3.6 (nightly) on windows.
> - [\#5811](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5811): Handle
> `--fulltrace` correctly with `pytest.raises`.
> - [\#5819](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5819): Windows:
> Fix regression with conftest whose qualified name contains uppercase
> characters (introduced by [#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792)).
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.1.3 (2019-09-18)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5807](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5807): Fix pypy3.6 (nightly) on windows.
> - [\#5811](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5811): Handle `--fulltrace` correctly with `pytest.raises`.
> - [\#5819](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5819): Windows: Fix regression with conftest whose qualified name contains uppercase characters (introduced by [#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792)).
</details>
<details>
<summary>Commits</summary>
- [`1a9f4a5`](https://github.com/pytest-dev/pytest/commit/1a9f4a51cb2a3c3b1d8e3bd5189552a24a85f5f4) Preparing release version 5.1.3
- [`892bdd5`](https://github.com/pytest-dev/pytest/commit/892bdd59dc7cfbd5ebacf18ccfd7ecb6704bae08) Normalize all summary durations, including quiet ones
- [`702acdb`](https://github.com/pytest-dev/pytest/commit/702acdba4658ad0a7e732059d18b22b185c79e5c) Merge pull request [#5811](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5811) from blueyed/fulltrace-pytest-raises
- [`f832ac3`](https://github.com/pytest-dev/pytest/commit/f832ac3316e9f733990f619af8c0f0f4abdbdb69) Handle --fulltrace with pytest.raises
- [`9422e10`](https://github.com/pytest-dev/pytest/commit/9422e10322562b11cf626e2adde015f715fc429a) Fix regression due to different cases on Windows ([#5840](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5840))
- [`5c3b4a6`](https://github.com/pytest-dev/pytest/commit/5c3b4a6f528f206da449d3c379e33f549f3f66e8) Add CHANGELOG entry for [#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792)
- [`05850d7`](https://github.com/pytest-dev/pytest/commit/05850d73bd9dc77ad2c90cea9767523a2e9d18e0) Re-introduce Christian Neumüller to AUTHORS
- [`b48f51e`](https://github.com/pytest-dev/pytest/commit/b48f51eb031f1b35b7fd4cd5d9da774541e10ec1) Use Path() objects to store conftest files
- [`cf5b544`](https://github.com/pytest-dev/pytest/commit/cf5b544db35478afe540eb78d75ef97ed798e1f1) Revert "Merge pull request [#5792](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5792) from dynatrace-oss-contrib/bugfix/badcase"
- [`73c5b7f`](https://github.com/pytest-dev/pytest/commit/73c5b7f4b11a81e971f7d1bb18072e06a87060f4) Clarify docs by showing tox.ini considered before setup.cfg ([#5839](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5839))
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.1.2...5.1.3)
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MDU6SXNzdWU0OTczMTYwNTk=
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Spin down projection does not work
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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 bands\r\nit should not work for both right?",
"We would need the relevant file to be able to investigate this.\r\n\r\nWhat do you get if you print `print(Mn_bands.keys())`?",
"Hmmm... yes, that is paradoxical. \r\n\r\nThe most helpful thing would be to generalize the DOS and BS objects to support SOC calculations as well as non-SOC>"
] | 2019-09-23T20:38:45
| 2023-08-10T15:05:56
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2023-08-10T15:05:56Z
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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>
When I replace Spin.down with Spin.up I don't get errors
**To Reproduce**
Steps to reproduce the behavior:
Mn_bands = bands.get_projections_on_elements_and_orbitals({"Mn": ["s", "p","d"]})
print(Mn_bands[Spin.up][n_b][n_k]["Mn"]["s"])
**Desktop (please complete the following information):**
- OS: Mac
- Version [e.g. 10.14.6]
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