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https://api.github.com/repos/materialsproject/pymatgen/issues/2825 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2825/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2825/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2825/events | https://github.com/materialsproject/pymatgen/pull/2825 | 1,566,716,654 | PR_kwDOACgets5JCjOK | 2,825 | Fix pre-commit.ci isort error | {
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"\n[](https://coveralls.io/builds/56525588)\n\nCoverage: 78.875% (-0.5%) from 79.414% when pulling **332e26ee51fcd9ee70d44076754afb7fe9756b06 on fix-precommit-ci-isort** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n"
] | 2023-02-01T19:45:47 | 2023-02-01T23:01:15 | 2023-02-01T22:58:06Z | MEMBER | {
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} | Error is due to https://github.com/PyCQA/isort/pull/2078.
Updating `black` also introduced some formatting changes. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2826 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2826/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2826/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2826/events | https://github.com/materialsproject/pymatgen/issues/2826 | 1,567,242,599 | I_kwDOACgets5dajln | 2,826 | The hkl index outputted by XRDCalculator is incorrect. | {
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"I am not able to reproduce this error. Here is the XRD pattern that I get from the latest pymatgen. As far as I can tell, the labelling of the peaks corresponds to the VESTA ones.\r\n\r\n\r\n\r\nFor future ... | 2023-02-02T03:11:50 | 2023-02-04T14:36:20 | 2023-02-02T15:09:39Z | NONE | {
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} | # Describe the bug
An XRD expert, as pointed out on Twitter (https://bit.ly/3X4RFfa),
the hkl index is obviously incorrect as shown in the attached image.
We hope for improvement.
# Screenshots
---
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2827 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2827/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2827/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2827/events | https://github.com/materialsproject/pymatgen/issues/2827 | 1,567,339,102 | I_kwDOACgets5da7Je | 2,827 | Is the Debye-Waller correction in XRDCalculator correct? | {
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"Could you share a reference for the expression in the exponential? I'm not an expert in XRD but can help out if I have a resource to look at.",
"Thank you for your reply.\r\n\r\nI only have the text written in Japanese by Fujio Izumi.\r\n\r\nInstead, I asked ChatGPT4, and the answer is below.\r\nI'm no expert in... | 2023-02-02T05:19:42 | 2023-06-03T13:52:36 | NONE | {
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} | # Describe the bug
I am not an expert in XRD.
An XRD expert on Twitter(https://bit.ly/3jhhoDi) pointed out that
rough X-ray diffraction intensity calculations ignoring Debye-Waller factors are not valid.
Therefore, I tried simulating by changing the Debye-Waller factors as shown in the attached figure. Even ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2828 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2828/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2828/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2828/events | https://github.com/materialsproject/pymatgen/issues/2828 | 1,568,226,677 | I_kwDOACgets5deT11 | 2,828 | Search Bar not working on site | {
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"Thanks for reporting this. I just pushed a fix. For some reason, jQuery disappeared from current pymatgen docs. @janosh is this related to the update of the docs you did recently?",
"@shyuep Don't think so but maybe I missed something? Last time I updated the docs was for the [v2023.1.9 release](https://github.c... | 2023-02-02T15:07:08 | 2023-02-02T16:05:12 | 2023-02-02T15:16:48Z | NONE | {
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} | When I go to the pymatgen website(https://pymatgen.org/) and type a search term in the search bar, the search never finishes.
This occurs under firefox version: Mozilla Firefox version mint-001 - 1.0 109.0.1(64-bit)
as well as under Chromium version: 109.0.5414.119 (Official Build) for Linux Mint (64-bit)
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"As the error states, `inter_cutoff` is not a variable of the `CrystalNN` class. You can see the variable names here: [link](https://github.com/materialsproject/pymatgen/blob/v2023.3.10/pymatgen/analysis/local_env.py#L3772). You want to use `distance_cutoffs` instead which has to be a tuple with 2 values.\r\n\r\nI ... | 2023-02-03T04:10:00 | 2023-05-19T20:18:47 | 2023-05-19T20:18:37Z | NONE | {
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} | Hello everyone, I am a freshman in pymatgen. Recently, a colleague share with me the following script to generate all tetrahedral sites in a bcc unit cell
```py
from pymatgen.core import Structure
from pymatgen.core import Lattice
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pym... | {
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"\n[](https://coveralls.io/builds/56608789)\n\nCoverage: 74.3% (-5.2%) from 79.463% when pulling **7606c36e7b268a9de33ba0531ffb7693a03f094f on peikai:EntriesCopy** into **c6f9bba0cf6d3040d630cf083da2d1963a658e6c on materialsproject:master**.\n",
"The u... | 2023-02-04T00:59:07 | 2023-02-12T05:37:40 | 2023-02-04T04:14:23Z | CONTRIBUTOR | {
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} | Here to submit changes to avoid change input entries in place.
In both of GGA/GGA+U and GGA/GGA+U/R2SCAN mixing processes, the methods below not only return adjusted entries, but also change input entries in place. Is it necessary? I think this may cause bugs in programming.
MaterialsProjectDFTMixingScheme.proces... | {
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"I've run into the same problem. I definitely agree that API could be improved. But it would be a substantial change, so not something to do on a whim. I think any modifications would need the green light from @shyuep, @mkhorton and @rkingsbury.",
"I agree, the process_entries() still works if people use with awa... | 2023-02-04T05:06:26 | 2023-02-13T06:39:13 | 2023-02-13T06:39:12Z | CONTRIBUTOR | {
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In the case that running **processed_entryList = compatibility.process_entries(entryList, clean=True),** entryList will be changed as well. The method not only returns adjusted entries, but also change input entries in place. Is it necessary? I think this may ca... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2833 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2833/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2833/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2833/events | https://github.com/materialsproject/pymatgen/issues/2833 | 1,571,667,129 | I_kwDOACgets5drby5 | 2,833 | CifWriter writes standard-incompliant chemical formulae and cell formula | {
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"Thanks for reporting this. But I would like to understand what is the actual implication of this beyond \"non-standards\" compliance. Does it affect the use of the CIF in any software out there?\r\n\r\nI am happy for someone to write a PR to fix this. But unless there is a pressing compatibility problem, I don't f... | 2023-02-05T23:47:24 | 2023-02-14T06:29:05 | CONTRIBUTOR | {
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} | **Describe the bug**
A clear and concise description of what the bug is.
Chemical formulae-related items written by `CifWriter` do not comply with the specification.
**To Reproduce**
Steps to reproduce the behavior:
Run the following script (POSCAR of CH₃NH₃PbI₃ from <https://materialsproject.org/materials/m... | {
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updates:
- [github.com/MarcoGorelli/cython-lint: v0.11.1 → v0.12.4](https://github.com/MarcoGorelli/cython-lint/compare/v0.11.1...v0.12.4)
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"Could you move the test into the existing [`pymatgen/io/tests/test_cif.py`](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/tests/test_cif.py)? And add the new kwarg to the doc string? Would be great to have a sentence in there explaining when this might be useful.",
"Hello @janosh, My most ... | 2023-02-07T19:32:20 | 2023-08-22T01:34:16 | 2023-08-22T01:34:16Z | CONTRIBUTOR | {
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} | If `check_occu=False`, site occupancy will not be checked, allowing unphysical occupancy != 1. Useful for experimental results in which occupancy was allowed to refine to unphysical values. Warning: unphysical site occupancies are incompatible with many pymatgen features.
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"A Structure's charge can be different from the sum of the oxidation states (e.g., if you are doing electron or hole doping of the structure).\r\nIn this case, the reason is that the API sets the charge. I am not sure why this is the case. @munrojm can you check? As far as I know, MP does not do non-neutral structu... | 2023-02-08T16:26:47 | 2023-02-11T01:55:13 | 2023-02-08T16:53:57Z | NONE | {
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} | **Describe the bug**
The structure.charge function sometimes does not print the right charge
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.ext.matproj import MPRester
with MPRester("kVbufThFdGlpePa0IbqjnimfyIHc5Ng2") as m:
# Structure for material id
str_test = m.get_structure_by... | {
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"I think a simple solution would be to multiply the lattice matrix and vectors by -1?"
] | 2023-02-08T21:31:16 | 2023-02-12T15:38:07 | 2023-02-12T15:38:07Z | CONTRIBUTOR | {
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} | For certain structures, pymatgen's `SpacegroupAnalyzer.get_conventional_to_primitive_transformation_matrix()` is returning a matrix with a negative determinant, which is causing issues when trying to use this transformation matrix in codes like `phonopy`. I know that the symmetry elements for trigonal space groups are ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2839 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2839/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2839/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2839/events | https://github.com/materialsproject/pymatgen/issues/2839 | 1,576,850,763 | I_kwDOACgets5d_NVL | 2,839 | StressTest.test_properties uses equality for floating point comparison | {
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} | **Describe the bug**
StressTest.test_properties in analysis/elasticity/tests/test_stress.py uses equality '==' to test mean_stress values at https://github.com/materialsproject/pymatgen/blob/134722b20ca24e6ff3d01aaa194fb51e296966b6/pymatgen/analysis/elasticity/tests/test_stress.py#L21 . This inevitably fails since ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2840 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2840/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2840/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2840/events | https://github.com/materialsproject/pymatgen/issues/2840 | 1,577,251,120 | I_kwDOACgets5eAvEw | 2,840 | PatchedPhaseDiagram.get_decomp_and_e_above_hull() performance bottle neck | {
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} | This `if` statement in `PatchedPhaseDiagram.get_decomp_and_e_above_hull()` scales very poorly with the size of the `stable_entries` `set`.
https://github.com/materialsproject/pymatgen/blob/134722b20ca24e6ff3d01aaa194fb51e296966b6/pymatgen/analysis/phase_diagram.py#L741-L747
For a PPD constructed from all entries ... | {
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"@peikai Really nice work! Thanks for adding tests. 👍 ",
"Great :clap:"
] | 2023-02-12T05:29:05 | 2023-02-13T06:43:05 | 2023-02-12T16:58:04Z | CONTRIBUTOR | {
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} | With regard to the discussion in #2832, this PR is submitted to avoid always adjusting entries in place.
- A flag `inplace` is added into `process_entries` method for several compatibility schemes, including `Compatibility()`, `MaterialsProjectDFTMixingScheme`, and `MaterialsProjectAqueousCompatibility`. If `inplac... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2843 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2843/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2843/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2843/events | https://github.com/materialsproject/pymatgen/issues/2843 | 1,582,133,912 | I_kwDOACgets5eTXKY | 2,843 | It should be possible to use a setter for coords on a neighbor object | {
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"Well, Neighbors are essentially container objects that bypass some of the checks that PeriodicSite runs by default. It is meant to be a unchangeable storage. If you prefer sites that are modifiable, I suggest you convert the neighbor objects to site objects (the information are all the same, you just need to run P... | 2023-02-13T11:02:57 | 2023-02-13T16:30:33 | 2023-02-13T16:30:33Z | NONE | {
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} | **The problem**
If I get all the ligands around a central cation using the structure method `get_neighbors`:
```
ligands = structure.get_neighbors(core_site,3.0)
```
and I then want to change the position of one of these ligands, i.e.:
```
ligand = ligands[0]
new_coords = ligand.coords
new_coords[2] = new_... | {
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"Thanks @kaueltzen! 👍 ",
"Let me know when this is ready to merge.",
"Hey @janosh , this is ready to merge(:",
"`mypy` is failing. you can try and fix the errors or (if that's too much hassle) decorate the plot function with\r\n\r\n```py\r\nimport typing\r\n\r\n@typing.no_type_check\r\n```",
"Thanks, I dec... | 2023-02-13T13:23:38 | 2023-03-29T17:42:40 | 2023-03-29T17:26:21Z | CONTRIBUTOR | {
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} | - added arguments in Dosplotter class to plot DOS w. inverted axes (as common in chemistry) and to plot beta spin channel w. dashed line
- debugged CohpPlotter class: limit determination and display of energy axis
- added tests for automatic limit determination in DosPlotter class (especially to test if DOS and energ... | {
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"I have gone down a different route. I use `input_cell.remove_sites()` to remove the site, and then `input_cell.insert()` to add the same site with different coordinates. this seems to work"
] | 2023-02-13T21:07:44 | 2023-02-13T21:33:02 | 2023-02-13T21:33:02Z | NONE | {
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} | **Problem**
Changing the coordinates of a `PeriodicSite` within a structure does not change the coordinates of that `PeriodicSite` object shown elsewhere.
For instance, if I have a structure object `input_cell` containing several sites, where `input_cell[0].coords` is [0,0,0], and I then change it as follows:
``... | {
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"Awesome 😍",
"I replaced `flake8` and `pylint` with `ruff` in `.github/workflows/lint.yml`. Great news. That action used to take ~9 mins before and runs in 3.\r\n\r\nThe main time hog left now is `mypy` (which I update from 0.991 to v1 which supposedly is 40% faster). Before, the longest running step was `pylint... | 2023-02-15T19:16:05 | 2023-02-19T15:57:58 | 2023-02-19T15:57:57Z | MEMBER | {
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} | This PR adds Ruff as a new linter to be run in pre-commit.ci. Ruff is written in Rust and about 100x faster than our existing linters written in Python. Unlike `flake8`, it also auto-fixes many violations. It takes less than a second to check the entire pymatgen codebase:
```sh
time ruff check . --no-cache
ruff ch... | {
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} | ## Summary
Currently `OptimadeRester` defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means they will not be used if the user provides their own filtered list of aliases, without doing so... | {
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"3.11 is not officially supported at the moment as it is a bit new. We are working on it.",
"Related issue #2710 and PR #2714",
"Thanks for the information. I would like to add that the same problem was also present on my laptop which runs Fedora 36 (python 3.10). So, I am guessing that it will be first fixed ... | 2023-02-19T13:43:21 | 2023-05-19T20:19:51 | 2023-05-19T20:16:47Z | NONE | {
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} | I am trying to install pymatgen on a clear virtual environment on Fedora 37.
`python -m venv <virtual-environment-name>`
`source <virtual-environment-name>`
`pip install wheel`
`pip install pymatgen`
But I get the error shown on the attached image.
![Screenshot from 2023-02-19 15-42-18](https://user-images.gith... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2850 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2850/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2850/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2850/events | https://github.com/materialsproject/pymatgen/pull/2850 | 1,590,751,727 | PR_kwDOACgets5KSbza | 2,850 | Fix auto-fixable pydocstyle errors through ruff | {
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```sh
ruff check . --fix-only --select D
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2851 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2851/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2851/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2851/events | https://github.com/materialsproject/pymatgen/pull/2851 | 1,590,927,765 | PR_kwDOACgets5KS-K8 | 2,851 | Run pyupgrade and flake8-simplify through ruff | {
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[tool.ruff]
select = [
"B", # flake8-bugbear
"D", # pydocstyle
"E", # pycodestyle
"F", # pyflakes
"I", # isort
"PLE", # pylint error
"PLW", # pylint warning
"Q", # flake8-quotes
+ "SIM", # flake8-simplify
"TID", # tidy imports
+ "UP", # pyupgrade
"W", # pycodesty... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2852 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2852/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2852/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2852/events | https://github.com/materialsproject/pymatgen/issues/2852 | 1,590,930,477 | I_kwDOACgets5e06wt | 2,852 | OPTIMADE client generates malformed queries | {
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"(same thing also applies to string queries within the `filter` query parameter)",
"@ml-evs Sorry! That was my fault. We can definitely make a release before week's end. Thanks for #2853! 🙏 ",
"No problem, and thanks! Also found another bug where `chemical_formula_hill` was being passed incorrectly in queries ... | 2023-02-20T00:32:48 | 2023-02-20T03:04:55 | 2023-02-20T03:04:55Z | CONTRIBUTOR | {
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} | **Describe the bug**
At some point, the OPTIMADE client in this repo was linted (presumably) and `f'?response_fields="{response_fields}"...'` was replaced with `f'?response_fields={response_fields!r}'`, which generates query parameters with the wrong (according to the OPTIMADE spec, at least) kind of quotes:
https... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2853 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2853/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2853/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2853/events | https://github.com/materialsproject/pymatgen/pull/2853 | 1,590,938,386 | PR_kwDOACgets5KTAQ1 | 2,853 | Fix OPTIMADE client generated filters and URLs | {
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"Sorry, took a few attempts to get around the linter... this should be good to go."
] | 2023-02-20T00:50:16 | 2023-02-20T03:04:54 | 2023-02-20T03:04:54Z | CONTRIBUTOR | {
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Also fixes an issue where `chemical_formula_hill` was not queryable. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2854 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2854/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2854/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2854/events | https://github.com/materialsproject/pymatgen/pull/2854 | 1,592,733,759 | PR_kwDOACgets5KZAEM | 2,854 | Ruff c4+ruf rules | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2855 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2855/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2855/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2855/events | https://github.com/materialsproject/pymatgen/issues/2855 | 1,593,109,661 | I_kwDOACgets5e9Oyd | 2,855 | AttributeError in LinearAssignment.__init__(), pymatgen v. 2022.11.7, python 3.11.0 | {
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"Typically you will use the C version of linear assignment. This suggests that your pymatgen is not properly installed."
] | 2023-02-21T09:13:58 | 2023-02-21T23:33:18 | 2023-02-21T23:26:49Z | NONE | {
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} | Novice at pymatgen and using the matgenb notebooks [(http://matgenb.materialsvirtuallab.org/)](url) to get familiar with the workflow.
When trying to use the function pymatgen.core.surface.generate_all_slabs, the following AttributeError is raise:
![image](https://user-images.githubusercontent.com/124170375/220292334... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2856 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2856/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2856/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2856/events | https://github.com/materialsproject/pymatgen/pull/2856 | 1,594,164,937 | PR_kwDOACgets5KdxfY | 2,856 | Fix typo in OPTIMADE client: remove quotes in response fields | {
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} | ## Summary
One more fix related to #2852 -- response fields also should not have quotes around the entire field. This was caught by a test that directly queries MP, which was (also incorrectly) returning data that didn't quite match rather than an error, e.g.:
https://optimade.materialsproject.org/v1/structures?f... | {
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} | Prepare 2023.2.22 release of pymatgen. The 1st one with official python 3.11 support! 🎉
This PR also adds [`ubuntu-latest` back to the release job matrix strategy](https://github.com/materialsproject/pymatgen/blob/be80e438ac851eea7950313efb60bbdb78a66c99/.github/workflows/test.yml#L132) since it's unclear why it w... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2859 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2859/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2859/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2859/events | https://github.com/materialsproject/pymatgen/issues/2859 | 1,599,941,048 | I_kwDOACgets5fXSm4 | 2,859 | Return value for the method "periodic_table_heatmap" should change from "plt" to "fig, ax" | {
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If "plt" is returned, there is no object in it, only a class (`matplotlib.pyplot`) will be returned.
If we change the return to "fig, ax", then the periodic_table can be export by `fig.sa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2860 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2860/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2860/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2860/events | https://github.com/materialsproject/pymatgen/pull/2860 | 1,600,454,637 | PR_kwDOACgets5Kyx60 | 2,860 | del class AtomicFile, _maketemp(), ask_yesno() | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2861 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2861/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2861/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2861/events | https://github.com/materialsproject/pymatgen/pull/2861 | 1,601,640,352 | PR_kwDOACgets5K2yKy | 2,861 | Remove module pymatgen/command_line/gulp_caller.py | {
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"Why is this considered dead code? Though I don't use it, I was under the impression that it is working and some people actually use it.",
"My line of inquiry was following [this docs sentence](https://github.com/materialsproject/pymatgen/blob/40cbf1d7c47bb2eb75509780e356c9877ae9c2f7/docs_rst/installation.rst#opt... | 2023-02-27T17:42:12 | 2023-02-27T18:55:16 | 2023-02-27T18:55:10Z | MEMBER | {
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} | Don't want to step on anyone's feet so I'll leave this PR open for a while but looks like this might be dead code (based on not knowing anyone who still uses `gulp`).
@shyuep Let me know if this is a mistake. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2862 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2862/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2862/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2862/events | https://github.com/materialsproject/pymatgen/pull/2862 | 1,601,766,720 | PR_kwDOACgets5K3NoB | 2,862 | Enable flake8-simplify via ruff in pre-commit.ci | {
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"Seems to be fixed from commit https://github.com/materialsproject/pymatgen/commit/577b2cddf8d8cbad218d7285341ddf5869d2cdea\r\n\r\nWill be included in the next version.",
"@gVallverdu - great!\r\nSee also #2865 ",
"@ConradJohnston Yes, as you mentioned it is the same bug and I think the same commit fix both.\... | 2023-02-27T22:55:52 | 2023-05-19T20:20:06 | 2023-05-19T20:16:05Z | NONE | {
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} | **Describe the bug**
For the input generator class for Gaussian:
[pymatgen/io/gaussian.py : GaussianInput
](https://github.com/materialsproject/pymatgen/blob/0d2062a01bf0ccb36cb736c9a5d139787c55e4c1/pymatgen/io/gaussian.py#LL87C14-L87C14)
the `to_string()` method should produce a string consisting of a Gaussian in... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2864 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2864/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2864/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2864/events | https://github.com/materialsproject/pymatgen/pull/2864 | 1,602,165,167 | PR_kwDOACgets5K4ijZ | 2,864 | fix reduced formula in Ion | {
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"Thanks for catching this!"
] | 2023-02-28T00:22:46 | 2023-03-02T03:57:34 | 2023-02-28T21:11:30Z | MEMBER | {
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} | Fixed the handling of O-H containing compositions, where the string 'HO' was replaced by 'OH' directly in the reduced formula. This will cause certain materials, e.g. HSbO2, to have the wrong reduced formula of SbOH2.
This fix then adds a condition that the composition must have an equal number of H and O to be hand... | {
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"Duplicate of #2863 , by only a handful of hours. 😊 ",
"Thanks for linking these related issues. I wasn't aware of them when merging https://github.com/materialsproject/pymatgen/pull/2891. Closing this and #2863 now.",
"Thanks @janosh !\r\n"
] | 2023-02-28T11:47:29 | 2023-05-19T20:49:54 | 2023-05-19T20:15:34Z | NONE | {
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A clear and concise description of what the bug is.
When creating a GaussianInput object and calling `to_string(cart_coords=True)` method, it raises an error:
File "python3.10/site-packages/pymatgen/io/gaussian.py", line 423, in get_cart_coords
outs.append(" ".join(site.species_string, ... | {
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"Thanks for reporting!"
] | 2023-02-28T12:13:22 | 2023-03-24T03:34:01 | 2023-03-24T03:33:45Z | CONTRIBUTOR | {
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https://github.com/materialsproject/pymatgen/blob/40cbf1d7c47bb2eb75509780e356c9877ae9c2f7/pymatgen/electronic_structure/tests/test_dos.py#L285
uses equality to test a floating point number (`similarity_index`)
Inevitably that causes a failure, e.g. https://buildd.debia... | {
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- One small error parsing tweak and one change of @staticmethod to @classmethod | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
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<h2>v2.12.0</h2>
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
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<h2>Pandas 1.5.3</h2>
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.13.1</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.... | {
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<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
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<h1>SciPy 1.10.1 Release Notes</h1>
<p>SciPy <code>1.10.1</code> is a bug-fix release with no n... | {
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} | ## Summary
Include a summary of major changes in bullet points:
- Feature 1
- Feature 2
- Fix 1
- Fix 2
## Todo (if any)
If this is a work-in-progress, write something about what else needs to be done
- Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, ... | {
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"Nevermind; still impossible to do this properly and satisfy `mypy`."
] | 2023-03-05T20:29:28 | 2024-10-10T01:54:53 | 2023-03-05T21:09:55Z | CONTRIBUTOR | {
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Prompted by my review of https://github.com/materialsproject/pym... | {
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"I think the errors here should (mostly) disappear if you pull in `master` again.",
"Hi @janosh thx for looking into this :)\r\nMight be that people cannot use it right away because in the meantime we (+ @JaGeo ) found several problems in how LOBSTER outputs the NcICOBILIST.lobster file (but my test files are not... | 2023-03-06T17:26:17 | 2023-10-04T19:23:16 | 2023-10-04T19:22:01Z | CONTRIBUTOR | {
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} | ## Summary
Implemented a class to handle multi-center ICOBIs via NcICBILIST.lobster files with pymatgen in `pymatgen/io/lobster/outputs.py` and updated some comments. `Ncicobilist` is similar to `Icohplist` but not identical because of the different format styles of NcICOBILIST.lobster and ICO**LIST.lobster output f... | {
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updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.253 → v0.0.254](https://github.com/charliermarsh/ruff-pre-commit/compare/v0.0.253...v0.0.254)
- [github.com/MarcoGorelli/cython-lint: v0.12.4 → v0.12.5](https://github.com/MarcoGorelli/cython-lint/compare/v0.12.4...v0.12.5)
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"Thanks! Even if it's an edge case, always good to handle things correctly.\r\n\r\nCould you compress `test_files/OUTCAR.serial` and then load the zipped file in your test? Important to minimize file sizes for people cloning the repo.",
"Sure! Done now.",
"Thanks! 👍 "
] | 2023-03-07T09:43:20 | 2023-03-08T17:07:35 | 2023-03-08T17:07:35Z | CONTRIBUTOR | {
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} | ## Summary
When compiling VASP without MPI support, the OUTCAR has a few differences in some places compared to a compilation including MPI.
- In the preamble, the number of cores is not indicated with `running on 16 total cores` but `serial version`
- When reporting the number of plane waves for each k-point, ... | {
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} | ## Summary
I noticed SubstrateAnalyzer was perhaps a bit on the slow side. There are a few optimizations here: for a test set of 100 structures, these took the evaluation time down from ~43 minutes down to 193 seconds.
Optimizations include some caching, particularly of calls to spglib, since these are expensive ... | {
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"[I left a comment](https://github.com/materialsproject/pymatgen/pull/2836#issuecomment-1474312688) asking for a few changes."
] | 2023-03-08T16:43:43 | 2023-03-24T00:41:42 | 2023-03-24T00:41:00Z | CONTRIBUTOR | {
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"I don't see a big issue with it, but what is the difference with `structure.hello = \"world\"`? Unlike sites and Elements which are designed to be immutable for the most part, there are no restrictions with structure.",
"The only issue with setting properties like that is they won't be serialised through `struct... | 2023-03-09T11:12:34 | 2023-08-24T18:41:49 | 2023-08-24T18:41:49Z | MEMBER | {
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} | I'd like to add a `structure_property` attribute to the `Structure` class. Sometimes it is useful to have structure-wide properties that can be stored alongside the structure. One example is the `Poscar.predictor_corrector_preamble` which is necessary to write structures to continue MD simulations. Currently, only site... | {
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"What is the error message?",
"This is definitely a bug. I noticed it recently as well, and I am sorry -- I think it might be related to Plotly code I wrote a few years back. \r\n\r\nI have been meaning to fix and will try to address soon!",
"@mattmcdermott There's a strange swapping in the order of keys and va... | 2023-03-10T01:08:12 | 2023-03-24T01:28:27 | 2023-03-24T01:28:27Z | NONE | {
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} | **Describe the bug**
PDPlotter fails when there is no unstable entry.
This issue only occurs when using "plotly" as the backend. 'matplotlib' backend would work.
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.core import Composition
from pymatgen.analysis.phase_diagram import PhaseDiagra... | {
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"Since no concerns / comments have been raised, I'm going to move this out of WIP status.",
"@janosh soubds like this is ready to go. ",
"@arosen93 Thanks for the ping!\r\n\r\n@rkingsbury Thanks for adding tests! 👍 Merging now. "
] | 2023-03-10T01:25:15 | 2024-10-10T01:54:57 | 2023-06-02T14:08:36Z | CONTRIBUTOR | {
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} | ## Summary
Small change to the way `MaterialsProjectAqueousCompatibility` corrects energies for materials containing `H2O`.
As [described by a user on MatSci](https://matsci.org/t/mpaqueouscompatibility-applies-hydrate-correction-to-non-hydrate-materials/47360/2), the current way of detecting whether a material c... | {
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"Issue is resolved when defining pbc like:\r\npbc = np.array([1, 1, 1], dtype=int)\r\n\r\nRecommend revising docstring to specify this required typing",
"I'm no Cython expert but I think #2907 should fix this error."
] | 2023-03-10T20:59:10 | 2023-03-24T00:25:44 | 2023-03-24T00:19:31Z | NONE | {
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"TypeError: a bytes-like object is required, not 'list'" is thrown when passing the appropriate types.
The doc string reads: "pbc: (list of bool) whether to set periodic boundaries" and I am passing a list of bools.
All other dtypes align with the requested types.
## To Reproduce
Steps to... | {
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"@munrojm I think this is for you.",
"@zifengdexiatian which version of `mp-api` are you running with? I don't see this issue on my end with the most up to date client. Try updating with `pip install mp-api --upgrade` and see if the problem persists.",
"> @zifengdexiatian which version of `mp-api` are you runni... | 2023-03-12T13:39:42 | 2023-03-13T01:49:00 | 2023-03-13T01:49:00Z | NONE | {
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When I use
from pymatgen.ext.matproj import MPRester
with MPRester('new_API_KEY') as mpr:
entries=mpr.get_entries_in_chemsys('Cs-Pb-I')
to return all the entries, it contains obviously incorrect energy information, e.g. mp-540839-R2SCAN ComputedStructureEntry - Cs4 Pb4 I12 (CsPbI3) Energy (U... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2889 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2889/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2889/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2889/events | https://github.com/materialsproject/pymatgen/pull/2889 | 1,620,515,414 | PR_kwDOACgets5L1-V7 | 2,889 | Replace `codecs.open` with `io.open` for reading `PotcarSingle` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2891 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2891/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2891/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2891/events | https://github.com/materialsproject/pymatgen/pull/2891 | 1,621,327,086 | PR_kwDOACgets5L4rUU | 2,891 | Read input parameters for both internal and cartesian coordinates | {
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"This is causing some test failures. Could you take a look?\r\n\r\n```py\r\n ind = toks.pop(0)\r\n data = toks.pop(0)\r\n try:\r\n nn.append(int(ind))\r\n except ValueError:\r\n ... | 2023-03-13T11:50:13 | 2023-05-19T20:13:53 | 2023-03-15T14:29:23Z | CONTRIBUTOR | {
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} | Closes #2863, closes #2865.
If there is only one blank line between `coord_lines` and `input_lines`, `input_params` will be ignored. So set `spaces` as 1 to avoid this case.
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"Test failure here is unrelated. Let me know if this is ready to go.",
"@janosh good to go"
] | 2023-03-13T20:24:38 | 2023-03-14T02:41:40 | 2023-03-14T02:41:40Z | CONTRIBUTOR | {
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- Switch multiple_outputs_from_file to staticmethod to play nicely with Atomate
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"I believe this was already fixed in https://github.com/materialsproject/pymatgen/pull/2891.\r\n\r\nBut the code could still be improved. There's no reason to use join in the first place if it's just 2 items.\r\n\r\n",
"@janosh yes , it could be just a string concatenation."
] | 2023-03-14T15:49:07 | 2023-03-23T15:06:34 | 2023-03-23T13:52:38Z | NONE | {
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```py
TypeError: str.join() takes eactly one argument (2 given)
```
I am gettting this error while trying to run "Gaussian_input.write_file(paramset=paramset, mol=mol)" where both the paramset and mol are correct inputs. Paramset includes the route parameters, and none otherwise, and the mol ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2894 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2894/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2894/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2894/events | https://github.com/materialsproject/pymatgen/pull/2894 | 1,625,640,139 | PR_kwDOACgets5MHMki | 2,894 | Breaking: Rename `gen_sl_transform_matricies->gen_sl_transform_matrices` | {
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"This is not fixed yet (2023.9.25).\r\n\r\n```\r\n~/.local/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1806: UnknownPotcarWarning: POTCAR data with symbol O does not match any VASP POTCAR known to pymatgen. There is a possibility your POTCAR is corrupted or that the pymatgen database is incomplete.\r\n ... | 2023-03-15T17:33:42 | 2023-10-03T02:03:43 | 2023-03-15T17:40:58Z | CONTRIBUTOR | {
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Since commit e4bde8e400d28095425d0b1e7f0b1c8923ddc13a it seems that loading is broken if any but the first POTCAR in the file has a sha256 hash.
I really appreciate the effort by @shyuep to clean up the code and get rid of the regex stuff and unicode handling. However, a small mistake appears ... | {
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"FYI @janosh, there was no need to use m3gnet's custom `TrajectoryObserver`. ASE's native `Trajectory` object stores all the desired properties (e.g. positions, energies, forces, cells, stresses). I'm going to use ASE's `Trajectory` object in #3044 so that the user doesn't have to install `m3gnet` just to have a tr... | 2023-03-18T03:34:23 | 2023-06-07T21:23:56 | 2023-03-18T04:13:10Z | MEMBER | {
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} | 813019427e add `return_trajectory` option to `Structure.relax()`
64dee2a8ba test new option in `test_relax_with_observer()`
db0871a327 convert vars to snake case | {
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"Maybe our resident VASP expert @arosen93 can chime in?",
"@janosh: This looks fine to me. The `len(final_esteps) < self.parameters[\"NELM\"]` check is the check for the SCF convergence and is unrelated to the \"ionic loop\" (i.e. relaxation trajectory). The line highlighted is indeed correct for checking that th... | 2023-03-18T15:39:33 | 2023-05-15T07:06:05 | 2023-05-14T22:54:12Z | NONE | {
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https://github.com/materialsproject/pymatgen/blob/89fc2d6f37dd4677e8f861f3227985daf6d3f812/pymatgen/io/vasp/outputs.py#L626
but this is wrong. many times it is possible to stop the ionic loop based i.e. on walltime us... | {
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"Good catch and thanks for the new test! 👍 "
] | 2023-03-19T22:48:17 | 2023-03-21T03:43:14 | 2023-03-21T03:43:02Z | CONTRIBUTOR | {
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"Bug confirmed.\r\n\r\n@CifLord Are you familiar with this code? If you have time, maybe you could take look?",
"Yeah I can take a look, thanks for letting me know!",
"Made a pull request to fix this. @cedenoruel do you know what version of matplotlib you're using? If its 3.6.0 or higher, its not compatible wit... | 2023-03-20T14:28:08 | 2023-04-26T12:33:15 | 2023-04-22T02:02:48Z | NONE | {
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} | **The Bug**
The wulff.show() function which normally gives a static plot no longer works.
Instead, it returns `<Figure size 576x576 with 0 Axes> `
However, wulff.get_plotly() works (which gives an interactive plot).
**To Reproduce**
```
!pip install pymatgen
# Import the neccesary tools to generate surfa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2901 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2901/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2901/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2901/events | https://github.com/materialsproject/pymatgen/pull/2901 | 1,632,768,915 | PR_kwDOACgets5MfFLw | 2,901 | Cp2k patch | {
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"Thanks! 👍 ",
"Why protect only `ELEMENT` and not `KIND`? When defining basis sets and pseudopotentials per element, wouldn't `SUBSYS` include something like this?\r\n\r\n```\r\n &KIND F\r\n BASIS_SET some_basis_set\r\n POTENTIAL some_ecp\r\n &END KIND\r\n```",
"@svandenhaute It never... | 2023-03-20T19:57:21 | 2023-12-08T19:22:40 | 2023-03-21T03:41:19Z | CONTRIBUTOR | {
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} | ## Summary
Patch for cp2k module.
- Fix 1: Postprocessor typecasts Element "F" to "False". Add a workaround.
- Fix 2: Site properties are set to "None" by default, which can cause problems if user doesn't set magnetization or ghost properly. Add a check for this. Long term it might be nice to have a pydantic (o... | {
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} | 8c2fda6646 os.environ.get() -> os.getenv()
a82d23326d dict.get(key, None) -> dict.get(key)
de4b02a36e remove repeated copyright notice in every source file (not needed, license applies to whole code base) | {
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"@janosh This should be good to go"
] | 2023-03-21T17:06:55 | 2023-03-21T19:19:11 | 2023-03-21T19:19:11Z | CONTRIBUTOR | {
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} | ## Summary
OpenBabelNN() will miss molecular O-C or O-H bonds if oxygen is forming three bonds, e.g. in H3O+ or XOH2+. In order to remedy this, I have implemented pymatgen.analysis.local_env.oxygen_edge_extender in a similar vein as pymatgen.analysis.local_env.metal_edge_extender, but simpler. I have also written a ... | {
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"Yes, this was intentional, but I'm adding a note here to explain: the magCIF standard was a working standard, with many magCIF files \"in the wild\" prior to the standard being finalised. During this process, some of the keys changed, so there are two supported notations for this field, and the current pymatgen pa... | 2023-03-22T01:07:27 | 2023-08-15T16:26:58 | 2023-08-15T16:26:58Z | NONE | {
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- `_atom_site_moment_label`
- `_atom_site_moment_crystalaxis_x`
to parse atomic magnetic moments.
But the mcif files in MAGNDATA(<http://webbdcrista1.ehu.es/magndata/>), a large database with more than 2000 published magnetic str... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2905 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2905/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2905/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2905/events | https://github.com/materialsproject/pymatgen/issues/2905 | 1,635,287,285 | I_kwDOACgets5heID1 | 2,905 | refined/conventional structure retaining properties not working as expected | {
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"I recently ran into the same issue, with magnetic moments this time. After querying FeNi (mp-2213) and calling `SpaceGroupAnalyzer(struct).get_conventional_standard_structure(keep_site_properties=True)` on it, the magnetic moments on Ni sites are incorrect. Taking a closer look, the culprit seems to be the `get_re... | 2023-03-22T08:35:26 | 2023-06-07T10:14:11 | NONE | {
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} | When converting a primitive cell to a conventional one with `keep_site_properties=True` (https://github.com/materialsproject/pymatgen/pull/2349), the resulting properties are incorrect.
**To Reproduce**
In this example I mark each site with a different label to find where the corresponding cite is in the resulting ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2906 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2906/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2906/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2906/events | https://github.com/materialsproject/pymatgen/issues/2906 | 1,637,393,180 | I_kwDOACgets5hmKMc | 2,906 | New release? | {
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"Done. v2023.3.23.",
"Thanks."
] | 2023-03-23T11:55:04 | 2023-03-23T14:42:56 | 2023-03-23T14:38:18Z | CONTRIBUTOR | {
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I wonder if it's possible to release a new version of pymatgen that contains the bug fix merged in #2899.
so that I can release a new version of abipy that is required for the implementation of the ABINIT workflows in atomate2.
Best regards,
Matteo | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2907 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2907/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2907/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2907/events | https://github.com/materialsproject/pymatgen/pull/2907 | 1,638,507,360 | PR_kwDOACgets5MyX8I | 2,907 | Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to `find_points_in_spheres()` `pbc` kwarg | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2908 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2908/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2908/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2908/events | https://github.com/materialsproject/pymatgen/pull/2908 | 1,638,536,369 | PR_kwDOACgets5MyeO6 | 2,908 | Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD | {
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933d3eb2e4 fix ValueError: not enough values to unpack (expected 2, got 0)
f654d9f32c add test to prevent regression | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2909 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2909/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2909/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2909/events | https://github.com/materialsproject/pymatgen/pull/2909 | 1,638,681,877 | PR_kwDOACgets5My9DH | 2,909 | Fix `VolumetricData.to_cube()` not preserving structure dimensions | {
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697e73ad61 VolumetricData.to_cube() doesn't preserve structure dimensions
f2d89233e1 create pymatgen/io/tests/test_common.py with test_cube_io_faithful() to prevent future regression | {
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"@janosh @shyuep, I think I have tests are failing due to some hash mismatches.\r\nI'm not familiar with the hashing setup but since I'm only removing blank lines I think it should have been OK.\r\n",
"> I'm not familiar with the hashing setup but since I'm only removing blank lines I think it should have been OK... | 2023-03-25T21:39:26 | 2023-04-04T02:48:43 | 2023-04-04T01:33:41Z | CONTRIBUTOR | {
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} | ## bug fix for potcar parsing
2023.3.10 rewrote the `PotcarSingle.from_file` function slightly.
This caused a parsing error in the tests for `pymatgen-analysis-defects`.
I think this small change gives the intended behavior.
Otherwise, the POTCAR in this folder cannot be parsed.
https://github.com/materialsp... | {
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"I think the error message is quite clear that you do not have vasprun.xml file?",
"But if I have it, what happens is that I don't know where to put it. A Now that file is in a subfolder of pymatgen, test_files",
"> I think the error message is quite clear that you do not have vasprun.xml file?\r\nBut if I have... | 2023-03-26T01:25:37 | 2023-03-28T21:25:19 | 2023-03-28T21:25:19Z | NONE | {
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run = BSVasprun("vasprun.xml", parse_projected_eigen=True)
of notebook 2013-01-01-Bandstructure of NiO
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```py
if dos:
```
change to
```py
if isinstance(dos, CompleteDos): # Dos obj has no structure
```
The DOS object has no structure property, which causes error if parsing DOS data without projection.
This modification allows user to plot BS and TDOS at the same time, while keeping the BS+PDO... | {
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} | 3f353862e3 de-duplicate `docs/_static/(examples|phase_diagram).png`
1d0a89d85e add link to personal homepage in `docs_rst/team.rst`
4d0947eb12 absolufy imports in `pymatgen/core/__init__.py`
7566e92138 rename var `nndata` -> `nn_data` | {
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"Thanks @kavanase for the clear explanation and screenshots. Very helpful!",
"No problem @janosh, thanks for the speedy merge!",
"Just wanted to second, this was a great change. Thanks @kavanase!",
"No problem @mkhorton! 😃 \r\nJust curious, do you know if/when this will be reflected in the `Phase Diagram Exp... | 2023-03-28T11:00:16 | 2023-05-15T18:59:57 | 2023-03-28T21:13:37Z | CONTRIBUTOR | {
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} | The `ChemicalPotentialDiagram` object for which the (very useful! 🙌) `pymatgen.analysis.chempot_diagram` module is written, plots the chemical potential diagram using the absolute DFT energies, rather than the actual (formal) chemical potentials (aka. reference potentials) of the elements, which are the meaningful val... | {
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"Hey! The xyz file you attached seems more complex than the simple format the Molecule.from_file() can read.\r\nI see two extra columns containing M,V30,index. There are also some extra lines, sections.\r\n\r\nYou could remove that extra info if not needed either manually or with some sort of converter.\r\n\r\nThou... | 2023-03-28T16:53:57 | 2023-04-21T15:39:39 | 2023-04-21T15:39:39Z | NONE | {
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} | I have a .xyz file generated by stk and when I try and create a molecule from it I get the following error:
IndexError: list index out of range
Maybe stk writes .xyz files in a format that isn't quite standard?
Input code:
test_mof=Molecule.from_file("test.xyz")
Full error messages:
File "test.py", lin... | {
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} | Create a Pourbaix diagram object:
```py
pd = PourbaixDiagram(entries)
>>> Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_18612\515482332.py in <module>
1 # Create the Pourbaix diagram object
----> 2 pd = PourbaixDiagram(entries)
D:\Install\anaconda\lib\site-packages\pymatgen\analysis\... | {
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} | I am getting the below error while running MPrester from pymatgen. I have updated pymatgen as well. Help me.
```py
from pymatgen.ext.matproj import MPRester
import numpy as np
import pandas as pd
# Load SAXS data
data = load_data('SCOOH_Au10_1to4_NH2_Au5_HCl_1mM_20.0C_00133.avg') # replace with your own data ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2924 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2924/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2924/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2924/events | https://github.com/materialsproject/pymatgen/issues/2924 | 1,648,206,713 | I_kwDOACgets5iPaN5 | 2,924 | frac_tolerance argument in Structure.from_file() function fails when input file is POSCAR | {
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"That's because `Poscar.from_string()` doesn't have a `frac_tolerance` kwarg. \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/713740f5b8bf27990d9d0c92ca154fae4164ec59/pymatgen/io/vasp/inputs.py#L247-L280\r\n\r\nThat functionality currently only exists in `CifParser`:\r\n\r\nhttps://github.com/materialspro... | 2023-03-30T19:41:56 | 2023-08-15T16:26:17 | 2023-08-15T16:26:16Z | NONE | {
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} | **Describe the bug**
`frac_tolerance` argument in `Structure.from_file()` function fails when input file is `POSCAR`. Error message is:
```py
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
~\AppData\Local\Tem... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2925 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2925/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2925/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2925/events | https://github.com/materialsproject/pymatgen/pull/2925 | 1,648,375,809 | PR_kwDOACgets5NTScj | 2,925 | auto version | {
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"I think forks just need to merge from the main master branch for versioning to be correct? The versions are updated when the release happens.",
"So merging from the upstream master did no work.\r\nThe following setting in the `pyproject.toml` breaks because the setuptools thinks the `pymatgen` version is too old... | 2023-03-30T21:52:20 | 2023-03-31T03:02:05 | 2023-03-31T03:02:05Z | CONTRIBUTOR | {
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} | ## Allow proper versioning for forked repos
I'm not 100% sure how the current version numbering is updated for `pymatgen` but it's not able to update the number properly for forks. The forks seem to keep a much older version number (from before the forking)
This creates problems if you have the forked repo as a de... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2926 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2926/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2926/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2926/events | https://github.com/materialsproject/pymatgen/pull/2926 | 1,650,082,150 | PR_kwDOACgets5NY8qJ | 2,926 | Plotting of Multicenter COBIs | {
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"Just as a warning that this might sit here for a longer time. I discovered an issue for the multi-center COBI computations in Lobster for the spin-polarized case during the plotting implementation. I will wait until there is a new Lobster version that can generate useful test data.",
"Will try to finalize a firs... | 2023-03-31T21:47:02 | 2024-03-16T13:44:32 | 2024-03-16T13:44:31Z | MEMBER | {
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} | ## Summary
Lobster now also has options to compute multi-center interactions. This leads to a different format of the COBICAR.lobster (e.g., no average COBI is included) and the labels of the bonds are different. At this stage, I can already plot this different format but no tests are included so far. Bond lengths a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2927 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2927/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2927/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2927/events | https://github.com/materialsproject/pymatgen/pull/2927 | 1,650,233,359 | PR_kwDOACgets5NZb-W | 2,927 | add kwarg to MoleculeGraph method and fix PackmolSet bug | {
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"Thanks @orionarcher! 👍 ",
"Thank you @janosh!"
] | 2023-04-01T01:36:43 | 2023-04-04T15:13:19 | 2023-04-04T15:13:19Z | CONTRIBUTOR | {
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} | ## Summary
The get_disconnected_fragments method returns a new graph with reordered indices but provides no way to get the mapping from new to original indices. This PR reconstructs that map and adds an optional keyword argument to return it. This will not affect current functionality.
Additionally, I found an er... | {
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major... | 2023-04-01T12:57:41 | 2023-04-04T16:31:30 | 2023-04-04T16:31:18Z | CONTRIBUTOR | {
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} | Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.12.1</h2>
<ul>
<li>🐛 Fix a bug that prevented the ... | {
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