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When trying to call the `.from_dict()` method for elfcar, aeccar0, and aeccar2 files, the following error appears:
It seems like only the chgcar constructor accepts the `data_... | {
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} | I didn't really understand how `starting_magnetization` in PWInp is supposed to be specified other than in site_properties, but I eventually did not find a way to let the input generator fill the input with the data I specify in site properties.
This is the original code
https://github.com/materialsproject/pymatg... | {
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} | I have been having issues with the `pylint` linting failing `(no-else-return)` and was trying to find out if I have configured the pre-commit hook incorrectly or something. I stumbled across the `.github/Contributing.md` file and noted it was very out of date (the obvious thing being that the code has now dropped suppo... | {
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} | Hi,
Is there a way to remove the magnetic symmetry operation inside a magnetic mcif file to correspond to symmetry operations in a cif?
For example: check the code using both structure obtain from MAGNDATA (no: 1.16 [http://webbdcrista1.ehu.es/magndata/index.php?this_label=1.16](url) ) and COD (no: 4123009 [http://ww... | {
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"Thanks @jmmshn. Renamed `DbPhaseDiagram` to be more clear and to match `BaseElement`, also expanded the docstring."
] | 2020-12-02T03:25:38 | 2020-12-12T02:28:58 | 2020-12-12T02:28:16Z | CONTRIBUTOR | {
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} | ## Added automatic magmom validation during set creation.
Currently, if there is missing or incompatible magmom data you just get an error when the INCAR is written.
This is not ideal since this often happens on the remote cluster.
So adding an additional validation function should make the behavior smoother.
## ... | {
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"\n[](https://coveralls.io/builds/37832596)\n\nCoverage decreased (-0.7%) to 82.997% when pulling **65805e23e055377544126e3d936e81e4e2ae0552 on rkingsbury:default_mp2020** into **89e37f004bb1bfc9335552ee4fd3d08c57e67f22 on materialsproject:master**.\n",
... | 2020-12-02T04:58:39 | 2021-04-01T21:10:44 | 2021-03-25T20:16:12Z | CONTRIBUTOR | {
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} | ## Summary
Make `MaterialsProject2020Compatibility` the default energy correction scheme in pymatgen.
* `MPRester().get_entries()` and `MPRester().get_pourbaix_entries()` now use MP2020 to correct energies
* `MaterialsProjectAqueousCompatibility` now uses MP2020 instead of legacy MP as the `solid_compat`
* Update... | {
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"Thanks @rkingsbury "
] | 2020-12-02T05:20:50 | 2020-12-02T19:52:49 | 2020-12-02T19:20:25Z | CONTRIBUTOR | {
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"Note, this will be merged without `pylint` modified files test passing since, by definition, this PR touches many files. Examination of logs does reveal some areas for improvement, notably `chemenv` (missing docstrings), `boltztrap` (lingering Python 2 code)."
] | 2020-12-02T23:05:26 | 2020-12-03T01:10:47 | 2020-12-03T01:10:40Z | MEMBER | {
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} | ## Summary
To improve legibility of pull requests, this runs linting tools including formatting with `black` and import sorting with `isort` throughout pymatgen. Will merge after tests pass. | {
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"I tried your input files with vasp 5.4.4 and pymatgen 2020.7.3. I did the scf first followed by the band structure calculation. I read in the wavecar with the following code:\r\n```python\r\nfrom pymatgen.io.vasp.outputs import Wavecar\r\nw = Wavecar('WAVECAR')\r\n```\r\nThis worked with no problem. I then updated... | 2020-12-03T16:28:13 | 2020-12-08T05:32:30 | 2020-12-08T04:26:25Z | NONE | {
"total": 0,
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} | **Describe the bug**
Same as the title.
**To Reproduce**
Trying to do a band unfolding process with the attached inputs. Of course, a scf calculation is done first.
[inputs.zip](https://github.com/materialsproject/pymatgen/files/5637393/inputs.zip)
**Expected behavior**
Successful reading of WAVECAR
**Scre... | {
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"I think this was a problem with past versions. Try the newest version of pymatgen instead. (Or if that fails, you should use a py37 environment. Py36 is pretty old and a lot of packages already dropped support for it)",
"Yes, to expand a little here, `numpy` has now officially dropped support for Python 3.6 in t... | 2020-12-07T12:04:55 | 2021-01-30T20:26:07 | 2020-12-07T16:37:28Z | NONE | {
"total": 0,
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} | **Describe the bug**
Cannot install pymatgen==2019.7.2 on ubuntu 16.04 in a clean virtualenv with python3.6.11.
**To Reproduce**
```
(test-venv) jenkins@ip:~/workspace/PR-212$ python --version
Python 3.6.11
(test-venv) jenkins@ip:~/workspace/PR-212$ pip --version
pip 20.3.1 from /usr/src/test-venv/lib/python3.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2011 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2011/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2011/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2011/events | https://github.com/materialsproject/pymatgen/pull/2011 | 760,549,908 | MDExOlB1bGxSZXF1ZXN0NTM1MzYyOTA2 | 2,011 | Add IsayevNN near neighbor class | {
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"Thanks @utf!"
] | 2020-12-09T18:04:16 | 2020-12-09T21:05:29 | 2020-12-09T21:05:29Z | MEMBER | {
"total": 0,
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} | ## Summary
Added `IsayevNN`, a class for finding near neighbors based on: [10.1038/ncomms15679](http://www.nature.com/articles/ncomms15679).
Two sites are considered coordinated if: (i) they share a Voronoi face and (ii) the near neighbor distance is less than the sum of the covalent radii + 0.25 Å.
Also added... | {
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"NOte that db \"friendliness\" is a distant consideration to actual user-friendliness.\r\nIn this case, I do agree using dataclasses is better. The only reason why it wasn't done in the past is to maintain backwards compatibility. Since most other packages have abandoned py36, there is nothing stopping us from doin... | 2020-12-09T23:17:22 | 2020-12-12T20:30:14 | 2020-12-12T20:30:14Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
The current implementation of the insertion and conversion electrodes are not very db friendly.
The information that users will interface with is essentially the data defined in the abstract properties of each class in addition to the `_vpair` paramet... | {
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"Thanks @jmmshn, this is great"
] | 2020-12-10T03:50:11 | 2020-12-11T18:18:44 | 2020-12-11T18:18:41Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
PR to address #2012
- Changed the `AbstractVoltagePair` and `AbstractElectrode` into `dataclass`s
- Changed the `InsertionVoltagePair` and `InsertionElectrode` into `dataclass`s
- For `InsertionVoltagePair` and `InsertionElectrode`, moved original entries based init into `from_entires` function
- ... | {
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"Thank you @CompRhys ! Looks like you're missing a newline character in pymatgen.entries.__init__.py. Otherwise looks good to me. I tested with the MP2020 corrections enabled as well and saw no issues.",
"> What is this new TransformedPDEntry logic for? What is `sp_mapping`? Can you add docstrings and maybe renam... | 2020-12-11T21:47:46 | 2021-01-27T13:18:50 | 2021-01-27T01:56:36Z | CONTRIBUTOR | {
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} | Split out the Entry changes as cleanly as possible from #1974 @rkingsbury | {
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"total": 0,
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} | **Describe the bug**
Reading a LAMMPS data file via `LammpsData.from_file()` does not read in the bond types, angle types, dihedral types, and improper types.
**To Reproduce**
```
from pymatgen.io.lammps.data import LammpsData
ld = LammpsData.from_file(filepath)
print(ld)
```
gives the output:
```
Generate... | {
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"Yes, please add a deprecation decorator to `as_dict_summary()`, and we can remove at a later date. Thanks!",
"@mkhorton I made some additional (independent) changes to the plotter.",
"Can you make `capacity` synonymous with `capacity_grav`? e.g. just add an `or` in line 73, for backwards compatibility (the doc... | 2020-12-14T04:08:43 | 2020-12-17T22:21:57 | 2020-12-17T22:21:54Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
- Change `ConversionElectrode` to type `dataclass` similar to the change to `InsertionElectrode` in #2013
- Added `x_charge` and `x_discharge` properties to report the number of working ion ver formula unit
- Standardized how the summary dictionary is created, now the base Electrode class has a `get_summ... | {
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"This looks useful but I'm trying not to merge new matplotlib plotting into pymatgen in favor of plotly-based plots which allow for more interactive data exploration. If you are using matplotlib, the [seaborn](https://seaborn.pydata.org) wrapper has some nice options for this kind of plot, including marginal histog... | 2020-12-15T19:58:27 | 2021-07-15T14:31:43 | 2020-12-18T01:13:47Z | CONTRIBUTOR | {
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} | ## Summary
Adds a new plotting function `pretty_parity_plot` to facilitate creating customizable and nicely-formatted plots that compare two quantities. An example is shown below.
* Most common plot customizations are exposed through explicitly documented kwargs
* Automatically plot or hide linear regression lin... | {
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"Thanks @jmmshn!"
] | 2020-12-21T17:22:56 | 2021-01-04T19:53:45 | 2021-01-04T19:53:38Z | CONTRIBUTOR | {
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} | ## Summary
Moved the entry_charge/discharge into the data model.
This allows the from_dict to recover the entries after serialization.
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"This is great, thanks for adding @munrojm !"
] | 2020-12-21T23:53:56 | 2021-01-04T19:54:29 | 2021-01-04T19:54:28Z | MEMBER | {
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} | ## Summary
This PR improves the `get_continuous_path` method of `HighSymmKpath` by returning a new complete `BandStructureSymmLine` object instead of just the new path labels and distance segment mappings.
Additionally, the docstring for `KPathLatimerMunro` has been updated to list the appropriate publication.
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"\n[](https://coveralls.io/builds/40638027)\n\nCoverage decreased (-0.6%) to 83.093% when pulling **ba54f14de5d865f3ae941a0344ee3c4ff716f537 on arepstein:ae_Crest** into **14150a9d631996686cdc386c36272f96cf8d7e99 on materialsproject:master**.\n",
"I'm ... | 2020-12-24T18:18:41 | 2021-06-17T00:26:51 | 2021-06-17T00:26:51Z | NONE | {
"total": 0,
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} | ## Summary
- Added CRESTOutput to parse CREST output directories in pymatgen.io.xtb.outputs
- Added CRESTInput to write CREST input files in pymatgen.io.xtb.inputs
- Added tests and test files for CRESTOutput and CRESTInput
## Additional dependencies introduced (if any)
- None
## TODO (if any)
- XTB i/... | {
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"Hi @mdforti, thanks for reporting this. Would you willing to prepare a PR to fix?",
"yes, of course. hope I do it correctly.",
"Note to @janosh: The correct description here should be that Pymatgen does not support reading EIGENVAL files from pre-VASP 5.4, as noted in #2403."
] | 2020-12-26T17:02:25 | 2023-08-13T16:34:12 | 2023-08-13T16:34:12Z | NONE | {
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the line referenced skips if the eigenvalue table for a kpoint has only two columns. an option should be added for non spin polarized calculations where only two columns are present, one for b... | {
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"Thanks for the fix @drew-parsons!\r\n\r\nSince this is your first contribution, please do fill out [the form here](https://forms.gle/JnisFb38QDR8QTFTA) so that we can [acknowledge you appropriately](https://pymatgen.org/team.html). I know this is only a quick fix, but we want to make sure we acknowledge all contri... | 2020-12-28T07:30:13 | 2021-01-04T19:56:23 | 2021-01-04T19:56:23Z | CONTRIBUTOR | {
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} | test file is MoS2_single.pdf not MOS2_single.pdf
"MOS2_single.pdf" triggers an error: "No such file or directory: 'MOS2_single.pdf'" from `os.remove(test_file)`
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} | WulffShapeTest (via test_get_plotly) from test_wulff.py is failing on Debian systems (python3.9, numpy 1.19.4)
The error message is
```
ERROR: test_get_plotly (pymatgen.analysis.tests.test_wulff.WulffShapeTest)
----------------------------------------------------------------------
Traceback (most recent call las... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2024 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2024/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2024/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2024/events | https://github.com/materialsproject/pymatgen/issues/2024 | 775,468,761 | MDU6SXNzdWU3NzU0Njg3NjE= | 2,024 | feff_input_generation executable is broken: No module named 'pymatgen.cli.feff_input_generation' | {
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"Yes, this has been deprecated and removed. Pls use the modules directly to generate the input files.",
"But the executable scripts are still being generated. They are listed in the entry_points list in setup.py. Hence this bug is still open.",
"Yes, I just removed them in a new commit. This will be fixed in ... | 2020-12-28T15:59:26 | 2020-12-29T01:15:03 | 2020-12-28T17:01:45Z | CONTRIBUTOR | {
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} | pymatgen generates a handful of executable files invoking various pymatgen functionality, including pmg,
gaussian_analyzer, feff_input_generation
feff_input_generation appears to be broken and fails on attempting to load self-referential python submodule:
```
$ feff_input_generation
Traceback (most recent cal... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2025 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2025/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2025/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2025/events | https://github.com/materialsproject/pymatgen/issues/2025 | 775,669,834 | MDU6SXNzdWU3NzU2Njk4MzQ= | 2,025 | enable installation CI testing | {
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"Generally the tests are meant to be operated on a cloned repository of pymatgen, rather than being run on a pip install version. None of the test files are provided in the standard wheels or tar.gz distributions because they are hundreds of Mb. So these are mainly provided just in the repository for cloning by dev... | 2020-12-29T02:54:15 | 2021-08-23T21:55:37 | 2020-12-31T01:16:20Z | CONTRIBUTOR | {
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} | For Linux (and other) distributions, it would be good to be able to regularly test the pymatgen installation is working correctly (configuration integration CI testing).
pymatgen already provides an extensive amount of tests. They can't really be used with CI testing however. The location of input files is hardcod... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2026 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2026/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2026/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2026/events | https://github.com/materialsproject/pymatgen/issues/2026 | 780,674,968 | MDU6SXNzdWU3ODA2NzQ5Njg= | 2,026 | Calling specie from a site gives two different object classes | {
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"I would need a bit more context the inconsistent behavior you are referring to. Python uses duck typing. Objects that basically implement a common subset of methods/properties can substitute for each other.\r\n\r\nThere are instances where people want to just use Element to represent the site, e.g., when they are ... | 2021-01-06T16:19:29 | 2021-01-07T18:42:52 | 2021-01-07T18:42:51Z | NONE | {
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} | Depending on the source of the structure the return value for "Site.specie" is either an specie object or an element object. When I'm working with a database of pymatgen structures this seems to vary depending on the data source. This causes inconsistent behaviour with attempting to access the atomic number with .Z as ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2027 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2027/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2027/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2027/events | https://github.com/materialsproject/pymatgen/pull/2027 | 780,854,369 | MDExOlB1bGxSZXF1ZXN0NTUwNjc4NzI4 | 2,027 | QuasiRRHO Thermochemistry Analysis | {
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} | ## Summary
Added quasirrho.py to the analysis subpackage to calculate the Quasi-RRHO free energy from a Gaussian or QChem frequency calculation.
* Calculates Grimme's Quasi-RRHO free energy
* Option for also correcting for solvent concentration
## Additional dependencies introduced (if any)
*None
## TO... | {
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"@arepstein is this PR ready for review to be merged?",
"I believe so. The only pending update in my mind is automated detection of the rotational symmetry number, but I think it's okay as an input parameter for now.",
"Hey @arepstein , I get to know this PR in today's subgroup meeting. I am just wondering how ... | 2021-01-07T00:19:44 | 2023-08-22T14:58:05 | 2023-08-21T22:02:27Z | NONE | {
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} | ## Summary
Added quasirrho.py to the analysis subpackage to calculate the Quasi-RRHO free energy from a Gaussian or QChem frequency calculation.
* Calculates Grimme's Quasi-RRHO free energy
* Option for also correcting for solvent concentration
## Additional dependencies introduced (if any)
*None
## TO... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2029 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2029/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2029/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2029/events | https://github.com/materialsproject/pymatgen/pull/2029 | 782,165,995 | MDExOlB1bGxSZXF1ZXN0NTUxNzcxMTk5 | 2,029 | fix: typo in get_cbm docstring | {
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"Hi @kjappelbaum, thanks for this! Even for small fixes or edits, please do fill out our [developer attribution form](https://forms.gle/JnisFb38QDR8QTFTA) so we can [acknowledge you appropriately on our website](https://pymatgen.org/team.html), improvements to pymatgen are always appreciated."
] | 2021-01-08T14:42:16 | 2021-01-11T20:04:24 | 2021-01-08T15:44:48Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2030 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2030/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2030/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2030/events | https://github.com/materialsproject/pymatgen/issues/2030 | 782,380,061 | MDU6SXNzdWU3ODIzODAwNjE= | 2,030 | Test coverage for cmd line stuff | {
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"I can deal with `mcsqs` and `critic2` since I am familiar with both and compilations are straight-forward. I don't know who's responsible for the `aconvasp` and `zeo` interfaces?",
"Sure, we can start with those 2. The other two are not that important for now.",
"Rather than committing compiled versions in the... | 2021-01-08T20:33:49 | 2023-08-13T16:34:58 | 2023-08-13T16:34:58Z | MEMBER | {
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} | Right now, the unit tests are not being run for a number of those requiring certain cmd line utilities. (see recent tests).
1. mcsqs
2. critic2
3. aconvasp
4. zeo
I would like to address at least a number of those, esp 1-3. We do not need executables for all platforms, but at the minimum, the Ubuntu tests sh... | {
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"This should speed up import by 2x to 548,074 µs.\r\n\r\nRemoving all top-level imports from pymatgen would be the more forward-looking approach, and would maybe add an extra 10x speed-up. This would break backwards compatibility for anyone doing a root import (e.g. `from pymatgen import Structure` would have to be... | 2021-01-13T03:47:10 | 2021-02-13T17:29:22 | 2021-01-28T22:15:21Z | MEMBER | {
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} | ## Summary
This PR will be to explore strategies for optimizing pymatgen's start-up and import times.
Current root-level import is ~ 1 second (specifically, 1,100,534 µs as profiled by `python -X importtime`). Reducing this will also have consequences for speed of test suite.
Initial investigations suggest thi... | {
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"Thanks @samblau !"
] | 2021-01-14T22:43:44 | 2021-01-16T00:33:18 | 2021-01-16T00:33:14Z | CONTRIBUTOR | {
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Adding Q-Chem cube file plotting and small tweaks to the output parser | {
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"Thanks."
] | 2021-01-15T01:27:05 | 2021-01-15T04:16:29 | 2021-01-15T04:16:23Z | MEMBER | {
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} | ## Summary
The electrostatic core potentials in the OUTCAR file are written based on a fix width format. The potentials are numbered from 1 to natoms, and sometimes the fixed width means there is no space between the index and the potential. For example:
```
average (electrostatic) potential at core
the test... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2034 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2034/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2034/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2034/events | https://github.com/materialsproject/pymatgen/pull/2034 | 786,756,678 | MDExOlB1bGxSZXF1ZXN0NTU1NTgzMzgw | 2,034 | Wavefunctions from Lobster | {
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"From my side, this code would now be ready to merge. Let me know, if there is anything else to do.",
"Thanks @JaGeo, this looks great!\r\n\r\nI did have a question on the `set_volumetric_data`, wasn't sure what the `runner` variable and the following block was doing.",
"I need to filter out some values from th... | 2021-01-15T09:47:21 | 2021-01-19T21:16:06 | 2021-01-16T00:29:31Z | MEMBER | {
"total": 0,
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} | ## Summary
This is a implementation of the new class Wavefunction for the Lobster module that can read in Lobster wavefunctions and transfer them to a VolumetricData object (This allows plotting with VESTA and compability with other VASP files). It can also calculate densities based on the Lobster output.
Thanks ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2035 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2035/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2035/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2035/events | https://github.com/materialsproject/pymatgen/pull/2035 | 788,239,263 | MDExOlB1bGxSZXF1ZXN0NTU2Nzg0MzI0 | 2,035 | Fixed coordination_geometry_finder. | {
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"Hello,\r\nis there anything left to do for this pull request? It would help me with another implementation if it could be merged? Thanks.\r\n\r\nBest, \r\nJG\r\n\r\n",
"Pls fix all missing documentation. I already put #TODO in all the relevant places in the chemenv package. We would like to make sure that all py... | 2021-01-18T12:43:23 | 2021-02-05T15:39:13 | 2021-02-05T15:39:12Z | CONTRIBUTOR | {
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* Fixed small bug in coordination_geometry_finder
* Fixed mutable argument in method for separation plane algorithm
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2036 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2036/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2036/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2036/events | https://github.com/materialsproject/pymatgen/issues/2036 | 788,984,013 | MDU6SXNzdWU3ODg5ODQwMTM= | 2,036 | Issue in `Structure.get_neighbor_list()` returning sites as their own neighbours | {
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"tolerence is already in pymatgen"
] | 2021-01-19T12:31:12 | 2021-01-19T14:45:25 | 2021-01-19T13:50:49Z | CONTRIBUTOR | {
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} | **Describe the bug**
According to the OCP codebase `Structure.get_neighbor_list()` can sometimes return self neighbours in some edge cases.
https://github.com/Open-Catalyst-Project/ocp/blob/899de1c1f46f44bf99e3ccd190b9a37795b60b67/ocpmodels/preprocessing/atoms_to_graphs.py#L99-L114
They resolve this by setting ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2037 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2037/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2037/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2037/events | https://github.com/materialsproject/pymatgen/pull/2037 | 789,492,578 | MDExOlB1bGxSZXF1ZXN0NTU3ODMwMzk2 | 2,037 | HighSymmKpath Hinuma setting bug fix | {
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"Thanks @munrojm "
] | 2021-01-20T00:08:38 | 2021-01-21T20:00:25 | 2021-01-21T20:00:23Z | MEMBER | {
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} | ## Summary
This PR contains a small bug fix for the `HighSymmKpath` class. Currently, the k-path from this class produced by the Hinuma et al. convention is not properly transformed into the basis of the reciprocal lattice of the input structure in all cases. This has been fixed, and a warning has been added to tell... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2038 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2038/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2038/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2038/events | https://github.com/materialsproject/pymatgen/issues/2038 | 790,363,805 | MDU6SXNzdWU3OTAzNjM4MDU= | 2,038 | Composition shows weird things when reading in unknown element | {
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"This is a feature, not a bug. It is common practice to use symbols to represent abstract species, e.g., vacancies or just some group of elements. ",
"For more context on this, read the documentation on `DummySpecies`. It is possible to initialize a DummySpecies without oxidation state, e.g. `DummySpecies('M', ox... | 2021-01-20T21:58:51 | 2021-01-22T07:35:21 | 2021-01-20T22:01:02Z | NONE | {
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} | **Describe the bug**
When I make a new Composition from a string that contains a chemical formula with non valid (but still often e.g. as placeholder used symbols) like "M", this pseudo element gets represented with the string "M0+" which is not the expected behaviour.
**To Reproduce**
Steps to reproduce the behav... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2039 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2039/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2039/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2039/events | https://github.com/materialsproject/pymatgen/pull/2039 | 790,855,410 | MDExOlB1bGxSZXF1ZXN0NTU5MDAyMjQw | 2,039 | [WIP] add kwarg to pass in a plt ax to plot_brillouin | {
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"I noticed that `get_ax3d_fig_plt` still prevents Brillouin zones from being plotted into a subplot because matplotlib appears unable to find the current figure and instead creates a new one:\r\n\r\n```py\r\ndef get_ax3d_fig_plt(ax=None, **kwargs):\r\n \"\"\"\r\n Helper function used in plot functions support... | 2021-01-21T09:18:37 | 2021-03-09T16:22:52 | 2021-03-09T16:22:52Z | MEMBER | {
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} | ## Summary
Adds the ability to plot Brillouin zones into a `plt.subplot`
## TODO (if any)
- Does this need a test?
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](ht... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2040 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2040/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2040/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2040/events | https://github.com/materialsproject/pymatgen/pull/2040 | 792,849,527 | MDExOlB1bGxSZXF1ZXN0NTYwNjQyMTQ3 | 2,040 | fix: #1985 and add test to stop computed entry being used for get_quasi_e_to_hull | {
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"Thanks @CompRhys ! I appreciate you doing this and I know that #2014 has become more involved than originally expected. This fixes #1985 at least insofar as it affects my use cases and looks like a very reasonable stopgap solution. @mkhorton , do you have any concerns about merging this as a temporary fix?",
"@r... | 2021-01-24T17:29:07 | 2021-01-27T09:32:02 | 2021-01-27T09:00:31Z | CONTRIBUTOR | {
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As the proper fix in #2014 seems like it might still take a while to get merged this is the temp fix I should have done for #1985 when I first saw it. It avoids the bug that I introduced by not (at that point) being aware that `ComputedEntry` was supposed to be interoperable with `PDEntry` and adds a ca... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2041 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2041/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2041/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2041/events | https://github.com/materialsproject/pymatgen/pull/2041 | 793,457,302 | MDExOlB1bGxSZXF1ZXN0NTYxMTQyMTE0 | 2,041 | add documentation for QChemDictSet | {
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"@samblau @espottesmith would love to get your feedback on this. As I started using the QChem workflows I found myself having to do a lot of code diving and searching the QChem manual to understand how to set things properly. That's what motivated me to do this; hoping to provide some clarification for new users ab... | 2021-01-25T15:02:53 | 2021-02-24T15:40:06 | 2021-02-24T15:24:08Z | CONTRIBUTOR | {
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TODO:
- [x] Clarify type of `pcm_dielectric`. The original docstring specified a `str` but I believe a `float` is more appropriate and intuitive
- [x] Copy docstring to child sets
- [x] complete documentation of `opt_variables` and `scan_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2042 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2042/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2042/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2042/events | https://github.com/materialsproject/pymatgen/pull/2042 | 795,123,898 | MDExOlB1bGxSZXF1ZXN0NTYyNTI0NTQ3 | 2,042 | [WIP] Add PatchedPhaseDiagram to accelerate handling of large approximately disjoint data sets | {
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"> @CompRhys I was just working on filtering large chemical spaces and tested out the PatchedPhaseDiagram class.\r\n> \r\n> I ran it on all entries in the \"Y-Mn-O-Li-Cl-C-Na-Fe-W-Bi-Ti-Be-S\" chemical system (as acquired from MP), which has 13 elements and about 3,595 entries. The PatchedPhaseDiagram code performe... | 2021-01-27T13:57:16 | 2021-04-30T15:21:47 | 2021-04-28T12:15:31Z | CONTRIBUTOR | {
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} | ## Summary
This PR takes over from #1974.
Introduce a new `PatchedPhaseDiagram` based class to handle large disjoint data sets. Calculation of the convex hull of a data set scales with the dimensions and amount of data. Breaking up disjoint datasets into smaller patches reduces the complexity in both these regar... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2043 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2043/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2043/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2043/events | https://github.com/materialsproject/pymatgen/pull/2043 | 795,156,952 | MDExOlB1bGxSZXF1ZXN0NTYyNTUyMzQ1 | 2,043 | Read Eigenval for Vasp non spin polarized Calculations | {
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"Thanks @mdforti! Do you have an example non-spin-polarized EIGENVAL file to hand too? We can include it as a test case",
"(Note: I've edited my comment now that I understand what is going on.)\r\n\r\nRegarding this PR and #2021 by @mdforti, I believe VASP might have changed how the EIGENVAL file is formatted sev... | 2021-01-27T14:37:14 | 2023-05-08T19:51:49 | 2023-05-08T19:51:49Z | NONE | {
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} | ## Summary
Include a summary of major changes in bullet points:
* add a ine to include the case where the eigenval corresponds to non spin polarized
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https://api.github.com/repos/materialsproject/pymatgen/issues/2044 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2044/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2044/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2044/events | https://github.com/materialsproject/pymatgen/pull/2044 | 795,641,394 | MDExOlB1bGxSZXF1ZXN0NTYyOTU0OTE3 | 2,044 | method to estimate NBANDS + tests | {
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"Thanks @rwoodsrobinson !",
"If possible, I'd also take into account whether spin-orbit coupling is included in the calculation (`LSORBIT = True`), as that will approximately double NBANDS.",
"Thanks for mentioning @utf, I'll add it. Know of any other cases where VASP changes the NBANDS value, or how they are e... | 2021-01-28T03:46:45 | 2021-01-28T20:45:34 | 2021-01-28T04:23:02Z | NONE | {
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} | ## Summary
* created method to estimate NBANDS for VASP input set
* simplified `nelect` property
* added tests
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://fla... | {
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"Pls report your OS when reporting issues. For this, I would recommend you try using conda installation as recommended in the official pymatgen documentation first. ",
"OS is Windows 10. ",
"The issue was resolved after i updated Microsoft Visual C++ greater than 14.0. Thank you."
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} | I tried to install 'pymatgem' using 'pip install pymatgem' command. It threw an error saying
"ERROR: Failed building wheel for spglib
Failed to build spglib
ERROR: Could not build wheels for spglib which use PEP 517 and cannot be installed directly"
The python version i am using is, python 3.8
Can you please ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2046 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2046/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2046/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2046/events | https://github.com/materialsproject/pymatgen/pull/2046 | 797,523,093 | MDExOlB1bGxSZXF1ZXN0NTY0NTA0OTQ5 | 2,046 | [WIP] build system: adopt PEP-518 | {
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"Ironic that the switch to the `pyproject.toml` surfaces the issue described in https://github.com/materialsproject/pymatgen/issues/2010#issuecomment-770274405 ;-)\r\nI'll try to have a look what's going on",
"@shyuep perhaps one of your recent commits broke the macos build; if I remember correctly they were work... | 2021-01-30T20:22:45 | 2021-01-31T16:52:44 | 2021-01-31T01:01:20Z | CONTRIBUTOR | {
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## Summary
The setup.py was using the deprecated `setup_requires` keyword, which
can result in dependencies being installed via `easy_install`.
`easy_install` is outdated and should no longer be used to install
packages.
This commit adopts PEP 518 and uses the `pyproject.toml` file to specify
the... | {
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"> But maybe since testing is lacking we should just add a deprecation warning for now?\r\n\r\nDeprecation warning is only for if we're going to remove the function. A general warning that it is untested would be useful; we should either add tests asap or remove though, untested code shouldn't be in pymatgen.",
... | 2021-01-30T21:47:06 | 2023-08-13T16:34:58 | 2023-08-13T16:34:58Z | CONTRIBUTOR | {
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} | The code might have an issue.
https://github.com/materialsproject/pymatgen/blob/4f906e3578cc20372ff4f12fcda9db3aaebec975/pymatgen/analysis/path_finder.py#L388
I used a Si CHGCAR and ran
```
from pymatgen.analysis.path_finder import StaticPotential
sp = StaticPotential(chgcar.structure, pot=chgcar.data['total']... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2048 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2048/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2048/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2048/events | https://github.com/materialsproject/pymatgen/pull/2048 | 798,966,795 | MDExOlB1bGxSZXF1ZXN0NTY1NjkxNzg2 | 2,048 | [WIP] Input/output for CASTEP | {
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} | ## Summary
Uses some code from the MIT-licensed [sumo](https://github.com/SMTG-UCL/sumo/blob/master/sumo/io/castep.py) implementation by @ajjackson, [used with permission](https://github.com/SMTG-UCL/sumo/pull/61#issuecomment-567632927) (thank you!).
I've re-worked the .cell implementation to make it more consist... | {
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"Thank you @mt-huebsch! This looks like an incredibly useful contribution, I would be happy to see this merged.\r\n\r\nI will take some time to review the PR carefully to provide comments and a response to your question on testing.\r\n\r\n> I noticed that this file does not get installed when installing pymatgen fr... | 2021-02-02T11:16:46 | 2024-08-03T19:01:57 | NONE | {
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} | ## Summary
Added MagneticSpacegroupAnalyzer that given a magnetic structure
* finds all magnetic spacegroup operations
* determines the magnetic spacegroup
* can return the magnetic pointgroup
* can compute all magnetic domains
Added ApplyMagSymmOpTransformation to standard transformations
* apply MagSymmOp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2050 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2050/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2050/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2050/events | https://github.com/materialsproject/pymatgen/issues/2050 | 799,451,307 | MDU6SXNzdWU3OTk0NTEzMDc= | 2,050 | Typing for pymatgen | {
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"1. I've been looking for solutions for this problem too. I found [nptyping](https://github.com/ramonhagenaars/nptyping) which defines a set of types for Numpy arrays of specific shapes. I'd rather not rely on a third-party here though. We can simply alias `Vector` and `Matrix` to `ArrayLike` for now, so at least i... | 2021-02-02T16:41:59 | 2023-05-30T16:58:02 | 2023-05-30T16:58:01Z | MEMBER | {
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} | I think we should try to get at least the core aspects of pymatgen typed. Here are some thoughts:
1. Numpy 1.20 has introduced the numpy.typing.ArrayLike type, which we can rely on for many instances. I created one in pymatgen.util.typing that uses ArrayLike where available and falls back to a default creation where... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2051 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2051/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2051/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2051/events | https://github.com/materialsproject/pymatgen/issues/2051 | 800,472,711 | MDU6SXNzdWU4MDA0NzI3MTE= | 2,051 | Issue with EnumlibAdaptor during doping transformation | {
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"This error typically occurs if the enumeration was unsuccessful. Either the cell is too large to be enumerated or the enum.x exited with error. "
] | 2021-02-03T16:07:38 | 2021-02-04T10:31:06 | 2021-02-04T10:31:06Z | NONE | {
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} | While trying to perform a doping transformation, I get the following attribute error:
'EnumlibAdaptor' object has no attribute 'structures'.
The error occurs on line 457 of "https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/transformations/advanced_transformations.py#L1095-L1258".
It seems ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2052 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2052/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2052/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2052/events | https://github.com/materialsproject/pymatgen/issues/2052 | 800,573,311 | MDU6SXNzdWU4MDA1NzMzMTE= | 2,052 | get_computed_entry() is failing in the Vasprun | {
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"Thanks for reporting this. @rkingsbury I believe this was added by you? Can you fix it pls? Thanks.",
"Thanks for reporting @kshumilov . @shyuep see #2054 for a fix."
] | 2021-02-03T18:09:59 | 2021-02-03T22:53:05 | 2021-02-03T22:53:05Z | NONE | {
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If `io.vasp.outputs.Vasprun()` is describing a run with IVDW tag set to `int` the function `get_computed_entry()` is failing.
The bug is hiding in the line [759](https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/io/vasp/outputs.py#L759) where the output of `get()` method on th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2053 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2053/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2053/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2053/events | https://github.com/materialsproject/pymatgen/issues/2053 | 800,700,595 | MDU6SXNzdWU4MDA3MDA1OTU= | 2,053 | Bug: GibbsComputedStructureEntry returning incorrect energies, running slowly | {
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"The phase diagram parts running more slowly will be due to the equality now checking the structure in getting stable_entries. It might be worth removing the structure check from the `__eq__` if the slow down in prohibitive? \n\nI can't think of any edge cases with the gibbs energy correction I went through all th... | 2021-02-03T21:06:22 | 2021-02-16T20:32:51 | 2021-02-05T23:32:11Z | MEMBER | {
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} | **Describe the bug**
`GibbsComputedStructureEntry` is now returning incorrect formation energies and running very slowly, I think due to refactoring in #2014 (tagging @CompRhys for reference, but I should be able to address).
**To Reproduce**
```python
from pymatgen.analysis.phase_diagram import PhaseDiagram
fro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2054 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2054/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2054/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2054/events | https://github.com/materialsproject/pymatgen/pull/2054 | 800,742,918 | MDExOlB1bGxSZXF1ZXN0NTY3MTc5NDc5 | 2,054 | fix IVDW bug in Vasprun.run_type | {
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"Thanks @rkingsbury "
] | 2021-02-03T22:12:23 | 2021-02-04T00:43:57 | 2021-02-03T22:53:05Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2055 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2055/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2055/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2055/events | https://github.com/materialsproject/pymatgen/pull/2055 | 801,705,466 | MDExOlB1bGxSZXF1ZXN0NTY3OTc0NTY4 | 2,055 | Additions to Q-Chem IO | {
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"Pls just run black through your code first. Also, can you try to add some type annotations? That would be helpful.",
"I'll work on the linting problems.\r\n\r\nAre there any specific areas that you think need type hints? Mostly I've just modified existing functions or made close copies (such as the new Sets clas... | 2021-02-04T23:12:35 | 2022-01-31T21:04:43 | 2021-02-08T17:27:56Z | CONTRIBUTOR | {
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} | Add ability to handle more diverse job types (including potential energy surface scans and transition-state optimizations) to the Q-Chem IO module.
One other small change was moving the metal_edge_extender function from pymatgen.analysis.fragmenter to pymatgen.analysis.local_env. As this function determines bonding ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2056 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2056/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2056/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2056/events | https://github.com/materialsproject/pymatgen/issues/2056 | 801,745,014 | MDU6SXNzdWU4MDE3NDUwMTQ= | 2,056 | latexify_ion is broken | {
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"Proposed fix:\r\n\r\nChanging the regex match pattern from\r\n`\r\nre.sub(r\"()\\[([^)]*)\\]\", r\"\\1$^{\\2}$\", formula)\r\n`\r\nto \r\n`\r\nre.sub(r\"([-+][\\d\\.]*)\", r\"$^{\\1}$\", )\r\n`\r\n\r\nSeems to work as expected. See [regex tester](https://regex101.com/r/HKAgL1/1).\r\n\r\nIt seems to me it might be ... | 2021-02-05T00:42:28 | 2021-02-06T21:18:08 | 2021-02-06T21:18:08Z | CONTRIBUTOR | {
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} | **Describe the bug**
The `latexify_ion` method in `analysis.pourbaix_diagram` does not work; it just returns the input formula.
**To Reproduce**
```
from pymatgen.analysis.pourbaix_diagram import latexify_ion
latexify_ion('Na+')
'Na+'
latexify_ion('SO4-2')
'SO4-2'
```
**Expected behavior**
The formula wo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2057 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2057/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2057/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2057/events | https://github.com/materialsproject/pymatgen/pull/2057 | 802,157,660 | MDExOlB1bGxSZXF1ZXN0NTY4MzQ4MTEy | 2,057 | Determine local environments based on bonding analysis | {
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"I would like to have a better organization of all the local environment analysis packages, including local_env and chemenv. Can we create a parent package called pymatgen.analysis.local_environment to house all of them. I would also prefer some common API that unifies all the different kinds of analysis and the va... | 2021-02-05T13:18:18 | 2021-02-26T08:20:37 | 2021-02-25T16:26:36Z | MEMBER | {
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} | ## Summary
This is work in progress to add an analysis of the local environments based on bonding analysis. The classes will allow to both use localenv and chemenv in combination with Lobster output. It will also provide additional methods to analyse the ICOHPs/COHPs for sites with neighbor atoms.
@mkhorton , let... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2058 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2058/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2058/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2058/events | https://github.com/materialsproject/pymatgen/pull/2058 | 802,393,101 | MDExOlB1bGxSZXF1ZXN0NTY4NTQzODY5 | 2,058 | Fix bug in GibbsComputedStructureEntry, add test | {
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"Thanks @mattmcdermott "
] | 2021-02-05T18:46:42 | 2021-02-05T19:27:15 | 2021-02-05T19:17:49Z | MEMBER | {
"total": 0,
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} | ## Summary
Addresses bug in #2053, where experimentally-derived Gibbs free energies (for gases like CO2) were being added incorrectly to DFT energies. Adds a test to check that energy of CO2 is correct, even after normalization of entry.
Note: a future PR should address the slow equality checking, as well as the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2059 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2059/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2059/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2059/events | https://github.com/materialsproject/pymatgen/pull/2059 | 802,578,266 | MDExOlB1bGxSZXF1ZXN0NTY4Njk2NjU3 | 2,059 | Remove custom entry normalize methods, solve via optional composition | {
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} | For **entry-equality branch**, to be reviewed by @mkhorton:
Solves the normalization issue by adding an optional composition parameter so that composition is not taken directly from the structure object. Also cleaned up a ton of other things!
This doesn't yet do the major entry refactor.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2060 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2060/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2060/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2060/events | https://github.com/materialsproject/pymatgen/pull/2060 | 803,747,604 | MDExOlB1bGxSZXF1ZXN0NTY5NjIzOTc3 | 2,060 | Some improvements to `Entry` | {
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} | ## Summary
* Makes `Entry` immutable, this vastly simplifies debugging
* `Entry.normalize()` always returns a new Entry
* Issues in `GibbsComputedStructureEntry` resolved
Thanks to @mattmcdermott for work on this and @CompRhys for discussion.
## TODO (if any)
* Introduce a new `.normalized_energy()` `.nor... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2061 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2061/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2061/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2061/events | https://github.com/materialsproject/pymatgen/pull/2061 | 804,034,195 | MDExOlB1bGxSZXF1ZXN0NTY5ODcxMzQ0 | 2,061 | Add tqdm as requirement | {
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"Thanks for bringing this to our attention @jan-janssen, I'll close this PR since I fixed it via https://github.com/materialsproject/pymatgen/commit/5126b5bc73173b911acb7d4c20a65655d2a9fe1c instead.\r\n\r\n`tqdm` should be an optional dependency, we have a wrapper called `PBar` which will fall back gracefully if tq... | 2021-02-08T22:50:56 | 2021-02-08T23:46:13 | 2021-02-08T23:46:12Z | CONTRIBUTOR | {
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} | Because it is used in pymatgen.analysis.pourbaix_diagram
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https://api.github.com/repos/materialsproject/pymatgen/issues/2062 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2062/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2062/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2062/events | https://github.com/materialsproject/pymatgen/pull/2062 | 805,631,712 | MDExOlB1bGxSZXF1ZXN0NTcxMjAxMDI0 | 2,062 | Fix KeyError when initializing XRDCalculator with integer wavelength | {
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"Thanks. Can you merge main master into your branch pls? I believe that's why your linting failed.",
"> Thanks. Can you merge main master into your branch pls? I believe that's why your linting failed.\r\n\r\nI just checked and it seems my master is based on the latest commit on the main master, so that wasn't th... | 2021-02-10T15:45:31 | 2021-02-11T16:24:39 | 2021-02-11T16:24:35Z | NONE | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Fix 1: attempting to create a XRDCalculator instance with an integer wavelength (e.g. 1, when wavelength is 1 Angstrom) throws a KeyError. Made changes to the __init__ method to accept integers for wavelength. Also raise TypeError if wavelength i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2063 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2063/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2063/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2063/events | https://github.com/materialsproject/pymatgen/issues/2063 | 807,646,919 | MDU6SXNzdWU4MDc2NDY5MTk= | 2,063 | pymatgen installation | {
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"Pls use the installation using conda as recommended in the pymatgen documentation."
] | 2021-02-13T01:32:33 | 2021-02-13T15:23:15 | 2021-02-13T15:23:15Z | NONE | {
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} | When I install pymatgen in windows 10 using "python setup.py install", I have the following error,
error: command 'C:\\Program Files (x86)\\Microsoft Visual studio\\2019\\Community\\VC\\Tools\\MSVC\\14.28.29333\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
Please, could you help me out?
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https://api.github.com/repos/materialsproject/pymatgen/issues/2064 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2064/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2064/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2064/events | https://github.com/materialsproject/pymatgen/issues/2064 | 808,968,002 | MDU6SXNzdWU4MDg5NjgwMDI= | 2,064 | cannot import pymatgen as mg | {
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"Pls try to install the latest pymatgen released yesterday. I believe it should solve this problem. It has to do with an incompatibility introduced in numpy 1.20.0 but solved in 1.20.1",
"Thank you. Pymatgen can be used now. "
] | 2021-02-16T04:13:36 | 2021-02-16T21:16:11 | 2021-02-16T21:16:11Z | NONE | {
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I use the command "conda install --channel conda-forge pymatgen" to install pymatgen in Conda Prompt as described in https://pymatgen.org/installation.html. After installation, I run a python script using "python pymatgen_sample.py". In the pymatgen_sample.py, I import pymatgen using "im... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2065 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2065/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2065/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2065/events | https://github.com/materialsproject/pymatgen/pull/2065 | 809,578,238 | MDExOlB1bGxSZXF1ZXN0NTc0NDE3MTM0 | 2,065 | Parse projected magnetisation from non-collinear calculations | {
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"I've run black on the files, so I don't know why linting is failing saying \"Black would make changes\". It doesn't...",
"\n[](https://coveralls.io/builds/37179362)\n\nCoverage decreased (-0.7%) to 79.63% when pulling **a71607a151a3b790142ec28f85c9d34... | 2021-02-16T19:15:07 | 2021-02-17T01:47:57 | 2021-02-16T21:20:11Z | MEMBER | {
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} | ## Summary
Added the ability to parse the projected magnetisation from VASP calculations that include spin-orbit coupling or non-collinear magnetism.
For calculations that include orbital projections (`LORBIT = 11`), the projections are written to the vasprun.xml file in the same format as in the PROCAR file (htt... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2066 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2066/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2066/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2066/events | https://github.com/materialsproject/pymatgen/pull/2066 | 809,771,195 | MDExOlB1bGxSZXF1ZXN0NTc0NTc2NzMy | 2,066 | Add convenience interface for OPTIMADE-compliant APIs | {
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"\n[](https://coveralls.io/builds/37188701)\n\nCoverage decreased (-0.1%) to 79.514% when pulling **8447c788d514233aa5c060f80392c2c0b863d80b on optimade** into **5c5628265429bf33d1181d58add13a77e405a919 on master**.\n"
] | 2021-02-17T01:14:49 | 2021-03-09T01:04:01 | 2021-02-17T02:34:15Z | MEMBER | {
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} | ## Summary
An `OptimadeRester` in `pymatgen.ext.optimade`.
This is by no means the final version of this class, but it is functional and a starting point for future improvements. | {
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"I tried on another system with older GCC 4.8.5 but got the same errors. The errors are:\r\n\r\nzeo/netstorage.cpp: In function ‘PyObject* __Pyx_PyCFunction_FastCall(PyObject*, PyObject**, Py_ssize_t)’:\r\nzeo/netstorage.cpp:8776:69: error: too many arguments to function\r\n return (*((__Pyx_PyCFunctionFast)met... | 2021-02-17T17:45:57 | 2021-02-17T18:24:38 | 2021-02-17T18:24:38Z | NONE | {
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} | I am following your instructions here for the pymatgen.io.zeopp module:
https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps
I get gcc errors when attempting step 5(c). The first error is:
zeo/netstorage.cpp: In function ‘PyObject* __Pyx_PyCFunction_FastCall(PyObject*,
zeo/netstorage.cpp:8776:69... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2068 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2068/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2068/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2068/events | https://github.com/materialsproject/pymatgen/issues/2068 | 811,048,761 | MDU6SXNzdWU4MTEwNDg3NjE= | 2,068 | Outcar parsing for vasp 6.2.0 is broken | {
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"> I can create a pull request that does exactly that if needed.\r\n\r\nThat would be great, thank you!\r\n\r\nI would modify it slightly:\r\n\r\n```\r\ntry:\r\n run_stats[tok[0].strip()] = float(tok[1].strip())\r\nexcept ValueError:\r\n run_stats[tok[0].strip()] = None\r\n```\r\n",
"Pull request was made a... | 2021-02-18T12:19:43 | 2023-06-03T02:22:04 | 2023-06-03T02:22:04Z | CONTRIBUTOR | {
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} | **Describe the bug**
I recently used VASP version 6.2.0 (newest official release afaik) and found that the Outcar parser of pymatgen (class `Outcar`, `__init__` method, in pymatgen.io.vasp.outputs.py) is not compatible with it.
The problem is a tiny change in the OUTCAR format concerning memory, especially the line... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2069 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2069/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2069/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2069/events | https://github.com/materialsproject/pymatgen/pull/2069 | 811,892,866 | MDExOlB1bGxSZXF1ZXN0NTc2MzQ4NzI3 | 2,069 | Fix Outcar parsing for VASP 6.2.0 | {
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"\n[](https://coveralls.io/builds/37280078)\n\nCoverage decreased (-0.7%) to 79.241% when pulling **f7c9e2553668ea2f07224c7220185a89ebcdca21 on MichaelWolloch:Fix_issue_#2068** into **c9a7e9810b539d13398219ff06e333682881184e on materialsproject:master**.... | 2021-02-19T10:16:55 | 2023-06-03T02:22:26 | 2021-02-19T18:29:54Z | CONTRIBUTOR | {
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} | Close https://github.com/materialsproject/pymatgen/issues/2068 as [discussed](https://github.com/materialsproject/pymatgen/issues/2068#issuecomment-781645771) with @mkhorton. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2070 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2070/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2070/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2070/events | https://github.com/materialsproject/pymatgen/issues/2070 | 812,045,333 | MDU6SXNzdWU4MTIwNDUzMzM= | 2,070 | Make CrystalNN work with fractional occupation | {
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"No. That is the wrong approach. The basic premise is that people should code for disordered structures, rather than assume that all structures will always be ordered. In this case, `specie` was the wrong attribute to use in the first place. Feel free to just change the code to work with disordered structures and s... | 2021-02-19T13:58:24 | 2022-08-30T21:21:30 | 2022-08-30T21:21:30Z | CONTRIBUTOR | {
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} | When the CrystalNN neighbor-finding method is applied to a structure with fractional occupation (in the test case from a CIF file), it exits with an attribute error:
File "pymatgen/pymatgen/analysis/local_env.py", line 4010, in get_cn
return super().get_cn(structure, n, use_weights)
File "pymatgen/pymatgen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2071 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2071/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2071/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2071/events | https://github.com/materialsproject/pymatgen/issues/2071 | 812,185,988 | MDU6SXNzdWU4MTIxODU5ODg= | 2,071 | Installation problem in Google colab | {
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"The issue is that Google won't let you install numpy 1.20.1 (try `!pip install numpy==1.20.1` to verify), I think because it's not supported by Python 3.6 (the default interpreter). For now, I would advice you install an older version of pymatgen e.g. using `pip install pymatgen==` until Google supports this.",
... | 2021-02-19T17:03:27 | 2021-02-19T20:17:15 | 2021-02-19T20:17:15Z | NONE | {
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} | Hi. I was using pymatgen in google colab.
In google colab, pymatgen is not installed , so I was using pymatgen by installing every time when I need to use it.
"!pip3 install pymatgen" or "!pip install pymatgen" command was normally working a few days ago, but now it's not working so I can't use pymatgen in colab.
I... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2072 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2072/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2072/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2072/events | https://github.com/materialsproject/pymatgen/pull/2072 | 812,859,023 | MDExOlB1bGxSZXF1ZXN0NTc3MTE0MDM1 | 2,072 | Gaussian: allow None for functional, bset, charge and multiplicity | {
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"\n[](https://coveralls.io/builds/37304418)\n\nCoverage decreased (-0.7%) to 79.244% when pulling **9f9ab99653cb6b5e9c86530460ca557d5077b640 on eimrek:master** into **19d7f56ba07850ce7cef743cc60272057a289c43 on materialsproject:master**.\n",
"Thanks!"
... | 2021-02-21T13:44:00 | 2021-02-21T23:41:33 | 2021-02-21T23:41:31Z | CONTRIBUTOR | {
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} | Hi pymatgen community!
I would like to use the Gaussian input generator for post-processing runs, such as this one
~~~
%chk=g.chk
%oldchk=../g.chk
#P chkbasis geom=allcheck guess=(only,read) pop=naturalorbital
test
~~~
This would read the geometry, functional, basis set, charge and multiplicity from `.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2073 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2073/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2073/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2073/events | https://github.com/materialsproject/pymatgen/issues/2073 | 813,886,152 | MDU6SXNzdWU4MTM4ODYxNTI= | 2,073 | pymatgen.analysis.defects.point_defects doesn't exist | {
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"It's because you copied it with an extra space at the start :-) This is generally true wherever you copy and paste Python code, be careful of leading tabs or spaces. I would recommend reading some general Python tutorials before getting started with pymatgen specifically.\r\n\r\nThat example is out of date for a s... | 2021-02-22T21:38:31 | 2021-02-22T21:46:45 | 2021-02-22T21:46:45Z | NONE | {
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```
$ python3.7
Python 3.7.9 (default, Dec 12 2020, 01:25:17)
[Clang 8.0.1 (tags/RELEASE_801/final 366581)] on freebsd12
Type "help", "copyright", "credits" or "license" for more information.
>>> from pymatgen.analysis.defects.point_de... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2074 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2074/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2074/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2074/events | https://github.com/materialsproject/pymatgen/pull/2074 | 815,418,754 | MDExOlB1bGxSZXF1ZXN0NTc5MjUxNzQ3 | 2,074 | More Informative Message with PhaseDiagramError | {
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"\n[](https://coveralls.io/builds/37416969)\n\nCoverage decreased (-0.7%) to 79.244% when pulling **9b83131e07eb95e6d049e82949e805dcd212199e on CompRhys:pderror** into **47c2bef6d01c6d2fd53e950931b923b94bf6f175 on materialsproject:master**.\n",
"Please... | 2021-02-24T12:10:03 | 2021-02-24T17:34:29 | 2021-02-24T16:31:17Z | CONTRIBUTOR | {
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update `PhaseDiagramError` message to tell users which elements are missing.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2075 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2075/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2075/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2075/events | https://github.com/materialsproject/pymatgen/pull/2075 | 815,860,095 | MDExOlB1bGxSZXF1ZXN0NTc5NjE5NzQ0 | 2,075 | [WIP] reconfigure `get_quasi_e_to_hull` when polymorphs are present | {
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"\n[](https://coveralls.io/builds/37587648)\n\nCoverage decreased (-0.6%) to 79.523% when pulling **d038832f61d0e70dda4a8953f49777e3124e9f7c on CompRhys:decomp** into **877715f11f72457bafca6346b0378c5cfc7d1131 on materialsproject:master**.\n",
"@mkhort... | 2021-02-24T21:24:10 | 2021-03-02T20:01:26 | 2021-03-02T19:06:16Z | CONTRIBUTOR | {
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} | ## Summary
Currently for the stable entry in the toy hull shown below in the presence of a polymorph (blue filled circle) the current code returns the red energy from `get_quasi_e_to_hull` whilst the intended behaviour should be that it gives the orange energy. I have checked this with @CJBartel who agrees that the ... | {
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"A good hash function has two qualities:\r\n1) It's fast\r\n2) It hashes very similar but different things to completely different hashes. The more granual that definition of similar is, the better the hash function.\r\n\r\nYour 3rd example is a good test to implement IMHO. Something like:\r\n``` python\r\nassert h... | 2021-02-25T14:55:50 | 2021-02-25T23:14:12 | 2021-02-25T23:14:12Z | CONTRIBUTOR | {
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} | For a project I am doing I have produced a large screening library of compositions, to reduce the computation I need to do at the next stage I want only the unique compositions. Unique compositions will be determined by hashing and then within each hashbin checking the n(n-1) equality options. The current hash ends up ... | {
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"\n[](https://coveralls.io/builds/37458509)\n\nCoverage decreased (-0.7%) to 79.517% when pulling **9e09cf9526eca1d064ac98ff0ecd98d22fbb03de on CompRhys:comphash** into **6cb45f5fbb1bde78aef668c48582a92f7a910604 on materialsproject:master**.\n",
"Thank... | 2021-02-25T18:37:07 | 2021-02-25T21:03:31 | 2021-02-25T20:19:21Z | CONTRIBUTOR | {
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} | ## Summary
New more discriminative hash see #2076 for discussion
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2078 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2078/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2078/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2078/events | https://github.com/materialsproject/pymatgen/pull/2078 | 817,752,237 | MDExOlB1bGxSZXF1ZXN0NTgxMTk1MzI1 | 2,078 | QChem Input OPT Section | {
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"\n[](https://coveralls.io/builds/37495101)\n\nCoverage decreased (-0.6%) to 79.521% when pulling **b3e37b460207ec7bb639717bc6f8f27ed00b8d29 on arepstein:ae_qchem** into **ccd04311c957b03cfbe3735348d57842c51cabc6 on materialsproject:master**.\n",
"Than... | 2021-02-26T23:41:41 | 2021-03-04T16:05:27 | 2021-03-04T16:05:21Z | NONE | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Allows QChem OPT input file section to be written from OptSet
## Additional dependencies introduced (if any)
*None
## TODO (if any)
*None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pul... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2079 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2079/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2079/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2079/events | https://github.com/materialsproject/pymatgen/issues/2079 | 818,251,122 | MDU6SXNzdWU4MTgyNTExMjI= | 2,079 | pymatgen 2021.2.16 documentation: get_spacegroup_symbol() seems to be typo for get_space_group_symbol() | {
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} | **Describe the bug**
In Section "Usage" of [pymatgen project top page](https://pymatgen.org/),
part of
`# Integrated symmetry analysis tools from spglib.`
`from pymatgen.symmetry.analyzer import SpacegroupAnalyzer`
`finder = SpacegroupAnalyzer(structure)`
`finder.get_spacegroup_symbol()`
returns
> AttributeErro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2080 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2080/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2080/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2080/events | https://github.com/materialsproject/pymatgen/pull/2080 | 821,427,103 | MDExOlB1bGxSZXF1ZXN0NTg0MjE5MTYw | 2,080 | Modify Critic2Caller for more modular use | {
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"\n[](https://coveralls.io/builds/37628931)\n\nCoverage decreased (-0.6%) to 79.5% when pulling **0780b2a4a2f33d9761ad8e50c21980b876ee63fe on samblau:qchem** into **b8d63d20728deed91d02d507e739d05f3d49a61e on materialsproject:master**.\n",
"@mkhorton I... | 2021-03-03T19:44:31 | 2021-03-03T20:18:05 | 2021-03-03T20:10:22Z | CONTRIBUTOR | {
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} | Modifications per discussions with @mkhorton in Atomate PR #598. Made `Critic2Caller.__init__` only responsible for actually calling `Critic2`, and put the rest of the chgcar-specific details into a `from_chgcar` class method. | {
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"Based on preliminary testing, the new API would be about twice as fast as the current one, probably due to not [creating new `Site`s to overwrite existing ones in `translate_sites`](https://github.com/materialsproject/pymatgen/blob/33ad121f3ad99ab5e61d4142d4200e7519e12d28/pymatgen/core/structure.py#L3995) but simp... | 2021-03-04T11:58:05 | 2021-03-04T17:33:14 | 2021-03-04T17:33:14Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
[`Structure.perturb()`](https://pymatgen.org/pymatgen.core.structure.html#pymatgen.core.structure.Structure.perturb) and [`Structure.translate_sites()`](https://pymatgen.org/pymatgen.core.structure.html#pymatgen.core.structure.Structure.translate_sit... | {
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"@mbkumar can you update pls?",
"@shyuep,\r\n\r\nThere are two parts. a) The installation for Zeo++, which could be still valid. b) The validation example which uses the Interstitial class is outdated. The defects subpackage was rewritten by Shyam and Danny. They were using a new algorithm introduced by Nils Zimm... | 2021-03-04T15:37:11 | 2023-08-13T16:34:58 | 2023-08-13T16:34:58Z | NONE | {
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} | **Describe the bug**
The example given in the documentation making use of `pymatgen.analysis.defects.core.Interstitial` seems to be outdated or incorrect. Following the example shown on the installation page yields to the following error message:
```
Traceback (most recent call last):
File "<stdin>", line 1, in... | {
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"> These problems would be solved by switching back to [semantic versioning](https://semver.org/)\r\n\r\nShould note that this solves problems _provided_ that minor and patch versions do not break backwards compatibility. Might be obvious given the definition of semantic versioning but is in practice not always eas... | 2021-03-05T12:58:56 | 2021-03-09T19:34:34 | 2021-03-05T15:21:26Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
As the github landing page nicely illustrates, `pymatgen` is used as a dependency in many other projects, some of which are again used a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2084 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2084/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2084/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2084/events | https://github.com/materialsproject/pymatgen/issues/2084 | 823,542,014 | MDU6SXNzdWU4MjM1NDIwMTQ= | 2,084 | Outdated docstrings related to PeriodicNeighbor | {
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"Thanks for reporting this. I have updated the doc.",
"Thank you very much for your quick reply and fix. Also, I appreciate the functions for getting neighbor atoms in pymatgen, which have helped my research a lot."
] | 2021-03-06T02:41:45 | 2021-03-07T05:56:59 | 2021-03-07T05:46:33Z | CONTRIBUTOR | {
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} | **Describe the bug**
The docstrings for member functions of `IStructure` to get neighbor atoms are seemed to be outdated.
Related to `get_sites_in_sphere`, `get_neighbors`, `get_neighbors_old`, `get_all_neighbors`, `get_all_neighbors_py`, and `get_neighbors_in_shell`.
The difference between docstrings and codes ar... | {
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"Thanks @pjf295, this is due to a recent change in #2080. The call on line 301 just needs to be changed to `cls.from_chgcar(...)`.",
"Actually, my mistake, this precedes that PR. Let me look into it"
] | 2021-03-08T06:14:08 | 2023-08-13T16:34:59 | 2023-08-13T16:34:59Z | NONE | {
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} | Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
Properly return with a Critic2Caller object.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following in... | {
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"I don't think the writeup is necessarily true. I don't want to give up calendar version just because we are temporarily doing semantic versioning due to the switch over to a namespace package. In future, it will still be calendar versioned.\r\n\r\nI think a more important statement is that if you happen to just us... | 2021-03-08T18:15:37 | 2021-03-09T16:45:49 | 2021-03-09T16:20:08Z | CONTRIBUTOR | {
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} | ## Summary
Drafting an update of the Compatibility guide as requested by @mkhorton in
https://github.com/materialsproject/pymatgen/issues/2083#issuecomment-791597868
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be mer... | {
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} | Hello,
The defects package in Pymatgen doesn't seem to be aware of the PBE + U correction terms used in the Materials Project for certain transition metal compounds. Supposing that I'm calculating the formation energy of a Fe vacancy in Fe3O4, pymatgen will calculate the uncorrected energy of a Defect_entry just as t... | {
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"Thanks.",
"\n[](https://coveralls.io/builds/37787014)\n\nCoverage decreased (-0.7%) to 82.993% when pulling **ded832a04ab268c1169c3b3a05d70bca6291d7ce on janosh:docs** into **f02c081348e17f0ecbd1d87b109710ade520ba4f on materialsproject:master**.\n"
] | 2021-03-09T16:01:41 | 2021-03-09T17:53:37 | 2021-03-09T16:12:36Z | MEMBER | {
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} | `Structure.get_neighbor_list` claims to be orders of magnitude faster than `get_all_neighbors` which probably refers to `get_all_neighbors_old`. It's actually only about 2-3x faster than `get_all_neighbors`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2089 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2089/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2089/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2089/events | https://github.com/materialsproject/pymatgen/issues/2089 | 826,534,680 | MDU6SXNzdWU4MjY1MzQ2ODA= | 2,089 | ImportError: cannot import name 'Molecule' from 'pymatgen' (unknown location) | {
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"Hi @jr31na,\r\n\r\nThis is part of a recent breaking change with pymatgen version 2022 onwards.\r\n\r\nThe older import `from pymatgen import Molecule` is what's known as a \"convenience import\", and was short-hand for the canonical import which is `from pymatgen.core.molecule import Molecule`. For technical reas... | 2021-03-09T19:45:21 | 2021-03-09T20:49:04 | 2021-03-09T20:49:04Z | NONE | {
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} | **Describe the bug**
I am practicing with the Intro to Pymatgen workshop. I create a virtual environment on my computer and download [pip install pymatgen] in it, create a pymatgen.py file and write the first lines of code in Visual Studio Code.
**Code**
import pymatgen
from pymatgen import Molecule
c_monox = ... | {
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"Hi @hitarth64 , make sure that the energy you use to create your extra `ComputedEntry` in this line\r\n\r\n`centry = ComputedEntry(Composition('Fe11 Co11 O64 Ru10'), -606.313)`\r\n\r\nis a _formation energy_ and not a raw DFT energy. All energies supplied to `PourbaixDiagram` need to be free energies of formation ... | 2021-03-13T07:18:29 | 2021-06-27T15:15:53 | 2021-06-27T15:15:53Z | NONE | {
"total": 0,
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} | **Describe the bug**
I am trying to model an alloy with three elements (Co11-Fe11-Ru10-O64) in it. I am working with a 96 atoms supercell. Calculating the Pourbaix diagram only yields that particular compound as the stable entity across the whole pH range which doesn't make sense.
**To Reproduce**
Steps to reprod... | {
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"We removed root level imports in the recent versions of pymatgen as part of a move to a more modular structure. Pls change from pymatgen import Structure to from pymatgen.core.structure import Structure."
] | 2021-03-14T20:41:46 | 2021-03-14T20:49:28 | 2021-03-14T20:49:28Z | NONE | {
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} | Unable to install Pymatgen properly on google collab,
```
!pip3 install pymatgen
from pymatgen import Structure
```
Could you please share a working code for a collab,
**To Reproduce**
Please run this [collab file](https://colab.research.google.com/drive/1XAb7q78cKf1n-MA3T9LjNscVgO0SRCsw?usp=sharing) for chec... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2092 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2092/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2092/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2092/events | https://github.com/materialsproject/pymatgen/issues/2092 | 832,687,270 | MDU6SXNzdWU4MzI2ODcyNzA= | 2,092 | Construct PointGroup class failed from the result of SpaceGroup for some space groups | {
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"Some of the point groups are just different settings of existing point groups. E.g., -4m2 is similar to -42m. Others are just more lengthy names. E.g., 321 is just 32. ",
"just as a comment, here is a way to convert them:\r\n```\r\npoint_group_conv = {'321' :'32', '312': '32', '3m1' :'3m', '31m': '3m',\r\n ... | 2021-03-16T11:17:09 | 2021-03-21T01:29:35 | 2021-03-17T21:43:43Z | NONE | {
"total": 0,
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} | **Describe the bug**
Construct PointGroup class failed from the result of SpaceGroup for some space groups.
Failed space groups: 115-120, 149-154, 156-159, 162-165, 189-190
**To Reproduce**
Steps to reproduce the behavior:
```python
from pymatgen.symmetry.groups import SpaceGroup, PointGroup
for spacegroup... | {
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"Looks like @shyuep has fixed, thanks for reporting!"
] | 2021-03-16T14:31:19 | 2021-03-16T19:18:09 | 2021-03-16T19:18:09Z | CONTRIBUTOR | {
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} | **Describe the bug**
The links in the documentation to the source code associated with that release currently give a 404 error, at least in the cases I have tried.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to https://pymatgen.org/pymatgen.analysis.local_env.html
2. Click on any "source" link
4. S... | {
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"We do make `pymatgen.core.__version__` to be the correct version number. However, it is not the best way to properly get version numbers for packages since it depends on the developer actually updating it. You should use importlib or pkgutil. See https://stackoverflow.com/questions/20180543/how-to-check-version-of... | 2021-03-18T15:35:54 | 2021-03-18T15:48:56 | 2021-03-18T15:46:27Z | NONE | {
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} | Hi, I have installed the latest version of pymatgen (v2022.0.4) in a fresh conda environment. Previously when checking the version I could open my command line, type `import pymatgen` and then `pymatgen.__version__` and I could obtain the version number. However, with the latest version (since the backwards incompatibl... | {
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"\n[](https://coveralls.io/builds/38064815)\n\nCoverage increased (+0.01%) to 83.652% when pulling **528ca078a121f8fced073529f43995ae5a5cdeef on graph-improvements** into **ac8f65e336008b6c219b8043f299cdeb50945c62 on master**.\n"
] | 2021-03-18T18:43:35 | 2021-03-18T20:48:38 | 2021-03-18T20:33:28Z | MEMBER | {
"total": 0,
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} | ## Summary
A fix to the graphs class that enforces a new convention to ensure duplicate edges are not added. This will only happen in rare instances normally (namely, small unit cells with NearNeighbor strategies where the cut-off is >> the length of a chemical bond).
Tagging @jmmshn @kim-jiyoon
While this con... | {
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"You need to use mode=\"delete\" for merging. It is impossible to know whether some files have duplicate sites because they were wrongly entered, or it was intentional. Further, it is quite often that H atoms are excluded from the atomic positions but included in the composition of a file. So asserting a compositi... | 2021-03-19T09:39:06 | 2021-03-21T20:10:28 | 2021-03-19T15:25:54Z | MEMBER | {
"total": 0,
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} | **Describe the bug**
`Structure.from_str` duplicates atoms.
**To Reproduce**
```py
import requests
resp = requests.get("http://www.crystallography.net/cod/1510206.cif")
with open("1510206.cif", 'w') as file:
file.write(resp.text)
```
The above writes a CIF file with contents
```cif
...
_chem... | {
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"Thanks. Feel free to submit a PR to modify the doc. I don't think the alternative is needed though. There are a lot of different settings for space groups. People who work with space groups understand the differences."
] | 2021-03-19T12:09:15 | 2021-03-22T18:53:44 | 2021-03-22T18:53:44Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
It is a bit confusing (i.e. I spent quite a bit of time under a false impression) that the get_conventional_standard_structure method in the SpacegroupAnalyzer class does not necessarily return a Structure instance that is in the standard settting desc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2098 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2098/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2098/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2098/events | https://github.com/materialsproject/pymatgen/issues/2098 | 836,552,872 | MDU6SXNzdWU4MzY1NTI4NzI= | 2,098 | Please don't deprecate latexify | {
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"Ok, this sounds fair to me, I can definitely see how these might be useful for people for formula strings that cannot be cast to Composition.\r\n\r\n> If you'd like to remove the duplication, I'd recommend that the Stringify mix-in class use these functions directly rather than duplicating the code in both places.... | 2021-03-20T01:14:17 | 2021-09-30T01:14:18 | 2021-09-30T01:14:18Z | MEMBER | {
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} | The `latexify`, `unicodeify`, etc have been deprecated in a recent update. We are now recommended to use the `Stringify` mix-in class.
Please can you not remove these functions. I use them fairly extensively in my code and in many cases switching to the `Stringify` mix-in class is not possible. For example, I have a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2099 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2099/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2099/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2099/events | https://github.com/materialsproject/pymatgen/issues/2099 | 837,058,773 | MDU6SXNzdWU4MzcwNTg3NzM= | 2,099 | [2022+] Structure predictor raises TypeError | {
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"Sorry invalid report "
] | 2021-03-21T12:03:00 | 2021-03-21T12:25:28 | 2021-03-21T12:25:28Z | NONE | {
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} | **Describe the bug**
If I decorate structures with oxidation stater and use them in Substitutor
(from pymatgen.analysis.structure_prediction.substitutor import Substitutor)
then call to
sub = Substitutor(threshold=1E-4)
species = [Species('Li', 1), Species('B', 3), Species('O', -2), Species('F', -1)] # just an... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2100 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2100/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2100/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2100/events | https://github.com/materialsproject/pymatgen/pull/2100 | 837,969,344 | MDExOlB1bGxSZXF1ZXN0NTk4MjI0NDE3 | 2,100 | Small clarification to get_conventional_standard_structure docstring in symmetry/analyzer.py | {
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"\n[](https://coveralls.io/builds/38148505)\n\nCoverage decreased (-0.6%) to 83.002% when pulling **8aae967617ad4b310f90d4b4140dca8457a8326d on tom-wood:master** into **2e5a4bb06950bf0d54bad07121435531eebc49a9 on materialsproject:master**.\n",
"Thanks ... | 2021-03-22T17:50:45 | 2021-03-22T18:55:09 | 2021-03-22T18:53:44Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
*Small addition to docstring of get_conventional_standard_structure to clarify that it does not produce the standard ITC setting (this is done by get_refined_structure).
Closes #2097.
## Additional dependencies introduced (if any)
* None
##... | {
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