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https://api.github.com/repos/materialsproject/pymatgen/issues/3254 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3254/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3254/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3254/events | https://github.com/materialsproject/pymatgen/pull/3254 | 1,857,411,067 | PR_kwDOACgets5YSUBy | 3,254 | Add VASP input set `MatPESStaticSet` | {
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"@SophiaRuan This looks good. But I would like @JiQi535 to go through it carefully and make sure everything is correct.",
"A few remarks given the updates to MP's GGA and r2SCAN WFs:\r\n- LREAL should be False for statics (consistent with how we do MP statics)\r\n- It says this is set is intended to r2SCAN, but t... | 2023-08-19T00:05:50 | 2023-08-28T15:53:44 | 2023-08-28T15:47:03Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- feature 1: add MatPESStaticSet class
## Todos
If this is work in progress, what else needs to be done?
1. make sure all the input set default settings are right.
2. write unit tests
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annot... | {
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} | All temporary test files should be written to temporary directories. This PR fixes the worst/most obvious offenders but probably many tests left writing to the current working or module directory.
f94f7a323 delete unused tests/files/chemenv/images/detailed_voronoi_container_coordination_numbers_1.png
bb4f4faf5 mv t... | {
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"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3256?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`100.00%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`5f... | 2023-08-19T03:04:38 | 2023-08-22T17:02:26 | 2023-08-22T16:52:50Z | CONTRIBUTOR | {
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} | ## Summary
I found a small bug inside the feff.inputs module. The absorbing_atom index is misused in the following sentence, which generated a bug.
```python
atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
```
When I created a cluster using ```inputs.Atoms```,there is an error, sin... | {
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} | 4276e4e90 delete analysis/solar/slme.py matrix_eigvals()
fcdd31188 fix whitespace
6d6026242 mv tests/io/lobster/test_{lobster,inputs}.py
89f454dd3 str concat to f-str
136590b4f use isinstance(x, Iterable) over hasattr(x, "__iter__")
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609cb75fc fix bad f-str conversion
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"Your import works for me. Try `pip uninstall pymatgen -y && pip install -U pymatgen` and then run your script again. Feel free to report back if that doesn't help."
] | 2023-08-21T11:26:45 | 2023-08-21T14:39:04 | 2023-08-21T14:38:37Z | NONE | {
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When I try to import
```py
from pymatgen.electronic_structure import dos
```
I get:
```py
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/pymatgen/electronic_structure/dos.py", line 625, in <module>
class Comple... | {
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"Hello @janosh,\r\nI have added the test code for get_projction_on_elements() when the structure have multiple ionic sites with the same elements. Please check if it meets the requirements."
] | 2023-08-22T01:30:31 | 2023-08-23T16:07:08 | 2023-08-23T16:06:41Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
Fixes a bug in the get_projection_on_elements function of Procar. In the current version, the code computes projections only for the final ion of each element when there are multiple ionic sites of the same element in the structure. To ensure projections are correctly computed and accumula... | {
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"`which` was removed from `monty` in favor of std lib `shutil.which` a while ago. Please update your `pymatgen` version or downgrade your `monty`.",
"Many thanks! I was able to resolve the issue by downgrading my monty package as follows:\r\n\r\n pip install 'monty==2022.4.26' --force-reinstall\r\n\r\nNow it seem... | 2023-08-22T16:12:45 | 2023-08-24T14:09:21 | 2023-08-23T22:30:30Z | NONE | {
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When running `from pymatgen.analysis.graphs import MoleculeGraph` , I get the error `ImportError: cannot import name 'which'`. Some googling suggests it is perhaps related to Python 2 compatibility? This system does not have Python 2 . I am using Python 3.6.8 from miniconda
#### Repro
```
[hus... | {
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"@henryiii More projects benefiting from https://learn.scientific-python.org/development/guides/repo-review/\r\n\r\nThanks again for such a useful tool!",
"@jarrodmillman Just curious if you guys have any tricks to suppress the \"Run cancelled\" email notifications from GitHub? Saw [this popular community discuss... | 2023-08-23T03:21:54 | 2023-08-23T14:46:20 | 2023-08-23T14:39:46Z | MEMBER | {
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As suggested by [https://scientific-python.github.io/repo-review](https://scientific-python.github.io/repo-rev... | {
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"Thanks @gpetretto for taking this on! Looks promising. 👍 \r\n\r\nI think we need better file IO support before merging. Right now, the properties are written to JSON\r\n\r\n```py\r\njson_str = struct_with_props.to(fmt=\"json\")\r\nassert '\"test_property\": 42' in json_str\r\n```\r\n\r\nbut they're not read back ... | 2023-08-23T08:01:45 | 2023-08-31T13:20:21 | 2023-08-24T18:41:48Z | CONTRIBUTOR | {
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This PR implements a `properties` attribute for `Structure` and `Molecule`. I also modified the `Poscar` object to store the `predictor_corrector_preamble` in the structure properties. | {
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#### Description
When modifying structures or molecules (e.g. with the replace_species method, but other modifications will likely be the same), some of the modified structures/molecules properties are wrong. Simple example for the number of electrons, it is defined in the __init__.
#### Repro
Steps ... | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/rails/rails/releases">activesupport's releases</a>.</em></p>
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<h2>7.0.7.2 release</h2>
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86f03dec7 add `self.set` attribute to `InputSetTests` to make it harder to use the wrong `InputSet` in a test
Again, thanks for reporting @SophiaRuan. | {
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I briefly checked for other `Molecule` attributes that are currently static but might need to change when modifying in place but didn't find any. | {
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"I see you @shyuep! 👀😅\n\nI plan to finish this PR later today.",
"@janosh: When you're back on GitHub, would you mind helping me out with the `mypy` issue? I think it might be because `.properties` is not a `@property` attribute of `Structure` or `Molecule`, but I'm not 100% sure. Thank you 🙏 Not urgent!"
] | 2023-08-24T19:37:34 | 2023-09-28T01:49:42 | 2023-08-31T09:56:22Z | MEMBER | {
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Recent PR that added `properties`: #3264
Breaking because `IMolecule.__eq__` and `IStructure.__eq__` were changed to check `self.properties == other.properties`. See https://github.com/materialsproject/pymat... | {
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This prevents you from getting a symmetrized structure that does not check the occupancy. | {
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321c04914 test_repr()
6c0267aaf ruff . --fix
77056eeb3 delete repeated words | {
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07b1256f4 `TestLibxcFunc` add `test_repr`
03dc9318b use python behavior that `__str__` falls back to `__repr__` if not defined | {
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"@materialsproject/pymatgen-maintainers there are a handful of test failures here that seem unrelated to the changes in this PR. I believe I am up to date with the latest `master` branch; please advise if further changes are needed. Thanks!"
] | 2023-08-28T14:02:53 | 2023-08-28T15:32:25 | 2023-08-28T15:32:25Z | CONTRIBUTOR | {
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} | ## Summary
`Ion.reduced_formula` does not correctly handle dissolved gas molecules, such as `O2`, for example:
```
>>> Ion.from_formula('O2').get_reduced_formula_and_factor()
('O', 2)
>>> Ion.from_formula('O2').formula
'O2 (aq)'
>>> Ion.from_formula('O2').reduced_formula
'O(aq)'
```
This PR modifies `I... | {
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} | 0d86dd110 psps->PSPs in doc strings
798953cfd fix typo
0323c473b try fix test_valid_magmom_struct() err msg regex | {
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"@janosh \r\nEverything on this pull request looks good from my end. Let me know if there are any changes you want me to make.",
"@janosh \r\nI got the tests to work with just one cif that is already in the test files directory. Please let me know if there are other changes you would like.",
"@jonathanjdenney T... | 2023-08-28T17:20:17 | 2024-11-13T17:53:23 | CONTRIBUTOR | {
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} | I have written code that takes a list of symmetrized structure objects and generates an f* diagram automatically with the plotly library.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] If... | {
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"I was not able to directly commit to this PR, so I opened #3280 ",
"> I was not able to directly commit to this PR, so I opened #3280\r\n\r\nYou can push directly to this PR after @SophiaRuan adds you as a collaborator to her fork."
] | 2023-08-28T21:42:55 | 2023-08-29T15:20:35 | 2023-08-29T13:41:16Z | CONTRIBUTOR | {
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} | ## Summary
Related PR: #3254
Major changes:
- feature 1: Revise MatPESStaticSet, inherit from DictSet
## Todos
Check if the previous Incar will override the default MatPESStaticSet Incar.
Check if the new settings added by Custodian will be updated.
## Checklist
- [ ] Google format doc strings a... | {
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"Pls report this to the mpapi repo. Pymatgen maintainers are not responsible for mpapi. "
] | 2023-08-29T00:11:12 | 2023-08-29T00:20:41 | 2023-08-29T00:20:41Z | NONE | {
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} | #### Description
When I run the following code under home internet
```
from mp_api.client import MPRester
USER_API_KEY='XXXX'
mpr = MPRester(USER_API_KEY)
mp_entries = mpr.get_entries_in_chemsys(['Li','Mn','O'])
```
The following message shows up:
```
MPRestError: REST query returned with error status c... | {
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"Linting and test workflows are failing. When you add a new input set, the hash test needs to be updated. The linting errors are easy to fix. Fix both first.",
"New PR #3281 was opened as the superset of the PR #3280 , so this #3280 can be closed."
] | 2023-08-29T05:12:08 | 2023-08-30T02:44:36 | 2023-08-30T02:44:36Z | CONTRIBUTOR | {
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} | Related PR: #3278 #3254
Tests now covers all MatPESStaticSet parameters.
Remaining question: While the default setting of MatPESStaticSet is without Hubbard U, when +U is enabled, the Hubbard U related parameters will be the same as MPRelaxSet. As I have noticed that MITRelaxSet and MPRelaxSet have different de... | {
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"The relevant tests pass. I merged."
] | 2023-08-29T21:31:05 | 2023-08-30T15:05:46 | 2023-08-30T15:05:38Z | CONTRIBUTOR | {
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} | ## Summary
Related: #3280
Major changes:
- fix 1: fix test_sets.py
## Todos
Check if all the incar, kpoints and potcars are tested.
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests ad... | {
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"In general, we recommend serialization and deserialization with the MontyJSONEncoder and MontyJSONDecoder, which support more types than just python primitives. The as_dict function is not meant to return a json serializable dict directly since there are many situations where we merely want a dictionary representa... | 2023-08-30T15:21:10 | 2023-08-30T15:31:39 | 2023-08-30T15:30:46Z | NONE | {
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} | #### Description
Calling the as_dict() method on a structure loaded in from a POSCAR returns a dictionary that can't be serialized. It appears the issue is with the selective dynamics that are stored as a numpy array.
#### Repro
I included my example script and the POSCAR I initialized the structure from in a zi... | {
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Major changes:
- feature 1: incar will update custodian added incar settings but will not change default incar settings
Problem:
I cannot update the incar settings with a new incar() method overriding DictSet incar. The test will all fail.
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Context [here](https://matsci.org/t/varying-results-with-get-primitive-structure/41663). I finally took some time to figure out why this was happening and it turned out to be the check that compares the lattice parameters of the primitive structures found against the constraints. The equivalency check in ... | {
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6decb99da add `test_bandgap_tol()` to `TestMPScanRelaxSet` | {
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9d6ee83cb add MatPESStaticSet init type hints
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<p><em>Sourced from <a href="https://github.com/joblib/joblib/releases">joblib's releases</a>.</em></p>
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<h2>Joblib 1.3.2</h2>
<p>Bug fix release</p>
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42b7451e1 deprecate overlooked `from/as_..._string` methods (these were missed in https://github.com/materialsproject/pymatgen/issues/3230 and https://github.com/materialsproject/pymatgen/pull/3158 due to extra characters between `from_..._str`. | {
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"The warning still comes when the incar and POTCARs are generated. I think it is fine. ",
"Actually, I'm wrong. This line\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/49083cc93f5d2bb5633aabab094f025b047d591c/pymatgen/io/vasp/sets.py#L376-L377\r\n\r\ncalls the structure `@setter` and so all that logic ... | 2023-09-02T04:30:10 | 2023-09-02T05:09:34 | 2023-09-02T05:09:23Z | MEMBER | {
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"I would assume properties must be something that can be handled by MontyEncoder. This can be made explicit in the doc."
] | 2023-09-02T18:42:51 | 2023-09-05T21:47:29 | 2023-09-05T21:47:29Z | MEMBER | {
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} | Recently, a `.properties` attribute was added to the `Structure`/`Molecule` objects in #3264. However, since the user can provide any data they want here, it has the potential to break serialization (same thing with the pre-existing `.site_properties`, technically, but `.properties` is more open-ended).
We should th... | {
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} | ## Summary
The function `Kpoints.automatic_density_by_length()` takes in a sequence of values, e.g. `[50, 50, 1]`, to set the k-point density for each dimension. However, the function does not raise any kind of error if a sequence of dimensions != 3 is supplied.
This PR adds a `ValueError` if the `len` is != 3, a... | {
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updates:
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} | This is simply to track when Pydantic 2+ is supported by Pymatgen. I know this depends on upstream dependencies.
Related:
- https://github.com/materialsvirtuallab/monty/pull/548
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Is the first 'unbreakable' rule for sets no longer true / should this be updated? | {
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} | d3dbd5097 fix typo matricies -> matrices
ebad8c2d0 fix `TestVaspInput.test_write()` polluting repo dir
58925e5a9 `def setup()` -> `def setUp()` | {
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_No response_
### What happened?
Error when parsing the Hessian from a frequency job. Finding number of coordinates / atoms by using wrong structure list (`input_structures `instead of `std_structures`). Error can be circumvented by a simple check:
```
if len(input_structures):
ndf = 3 ... | {
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"Since the goal is to add type hints all across `pymatgen` (although some areas still fall short), I moved the `py.typed` into the package root."
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> Skipping analyzing "pymatgen.io.vasp.inputs": module is installed, but missing library stubs or py.typed marker
Since `pymatgen.io` is such a commonly used module, let's add a `py.typed` there unless there's a reason to avoid... | {
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} | Closes #3306.
013a1da58 add _parse_hessian method to GaussianOutput
55031490b snake_case vars
35c952e86 fix typo in test name: paramaters->parameters | {
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} | New release as requested by @Andrew-S-Rosen to propagate `pydantic<2` pin removal across MP stack.
Also thanks @utf for the inspiration to add `.github/release.yml`.
7ec6221b1 add .github/release.yml
83701e2f1 remove @dependabot PRs from changelogs
3712380dc fix doc str indent
285655146 add release note catego... | {
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"Unit test pls. Thanks.",
"of course @shyuep , was already on it before your comment!",
"@shyuep ready for merging"
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Thank you @trachote. | {
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"Hi Bin (@Jeff-oakley),\r\n\r\nThis issue is caused by `MPRester.get_entries`, not pymatgen. This function returns entries of different thermo_types. This has been clarified in the latest release of mp-api (https://github.com/materialsproject/api/commit/83b27a0899101f5d0cb73fa16352e082adb264a3). Thanks @munrojm!\r\... | 2023-09-13T01:12:04 | 2023-09-28T00:54:16 | 2023-09-28T00:54:15Z | NONE | {
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} | ### Email (Optional)
bouyang@fsu.edu
### Version
2023.7.17
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
Not sure this is because of pymatgen, new api of MP or my incorrect understanding . Below is the sample code.
By running the code below, it will s... | {
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"I have fixed some of the obvious ValueErrors. But there are some things which are not worth the time to fix. For example, the data on the artificial elements like Og, Lv, etc. are sparse (they exist for fractions of a second). None of these elements are used in any usual sense of the world. Quite simply, they are ... | 2023-09-13T12:55:01 | 2023-09-13T16:03:01 | 2023-09-13T16:01:58Z | CONTRIBUTOR | {
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_No response_
### Version
v2023.2.28
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
- There are about 80 ValueErrors, 400 TypeError(s), 120 KeyError(s) and 10 IndexError(s) when Trying to access the specific attributes of the Elements... | {
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"Thanks. I have no problems with most of this, but I would point out a few issues. \r\n\r\nThe MPRelaxSet is generally used as the *first* calculation for a new structure. So the assumptions are (a) we do not know whether it is a metal or not, and (b) too strict criteria result in extremely long ionic convergence. ... | 2023-09-13T18:57:53 | 2023-10-27T00:38:19 | CONTRIBUTOR | {
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} | There have been internal talks with @munrojm @Janosh @esoteric-ephemera, among others, about changing the MP Input Sets. We want to open the discussion up before moving forward with such changes.
Currently, we are in favor of the following changes:
For **all** MP sets:
- Set LMAXMIX = 6 for all structures. This... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3323 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3323/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3323/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3323/events | https://github.com/materialsproject/pymatgen/pull/3323 | 1,896,133,172 | PR_kwDOACgets5aUeaK | 3,323 | More Google-style class attribute doc strings | {
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} | Missed some in #3320.
819b65771 rename variables: d->dct
47f1ed7f3 :param to google-style
46d4aba4c fix typos
a6c0569c8 staticmethod to classmethod
19f89bdf7 more class attribute doc strings to google style
f72ac9a31 fix doc str indentation | {
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"Looks like oxidation state of 0 for diatomic molecules isn't specified in `Element.icsd_oxidation_states` or `Element.oxidation_states` here\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/047ce69fe111d53fd6776f8773216bd9a042f987/pymatgen/core/composition.py#L912-L916\r\n\r\nNot sure if the better solutio... | 2023-09-14T20:44:46 | 2023-09-18T17:36:59 | 2023-09-18T16:21:41Z | CONTRIBUTOR | {
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_No response_
### Version
latest from git as of 2023.09.14
### Which OS(es) are you using?
- [ ] MacOS
- [X] Windows
- [X] Linux
### What happened?
1. I was using `Ion.oxi_state_guesses` to determine oxidation states of elements in aqueous species. This method inherits from `... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3325 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3325/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3325/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3325/events | https://github.com/materialsproject/pymatgen/pull/3325 | 1,897,821,579 | PR_kwDOACgets5aaKtl | 3,325 | Readme notice regarding updated pymatgen publication | {
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"And thanks @janosh! :)"
] | 2023-09-15T06:52:05 | 2023-09-15T17:53:14 | 2023-09-15T06:52:34Z | MEMBER | {
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} | > It would potentially break 100s of projects, scripts. (😬) Mine included.
Sorry to open this issue again. In our project updated to latest pymatgen, we encounter unexpected errors in various scripts customizing the window title and size after using get_plot(). After updating all the scripts accordin... | {
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"According to the following URL, it seems to be solved by the replacement of \r\n ax = axes3d.Axes3D(fig) \r\nwith\r\n ax = fig.add_subplot(projection='3d')\r\n\r\nin pymatgen/utils/plotting.py.\r\n\r\nmatplotlib and Axes3D give a blank picture\r\nhttps://stackoverflow.com/questions/76069849/matplotlib-and-axes... | 2023-09-15T12:02:19 | 2023-09-16T14:45:04 | 2023-09-16T14:45:04Z | MEMBER | {
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from pymatgen.ext.matproj import MPRester
mpr = MPRester("32-digit key")
bs = mpr.get_bandstructure_by_material_id("mp-3748")
plotter = BSPlotter(bs)
plotter.plot_brillouin()
```
Result: an empty window comes out.
_Originally posted by @goodwilling in https://github.com/materialsproject/pymatgen/i... | {
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cd7567481 breaking: same for get_ax_fig_plt->get_ax_fig
0a58b782b remove :class:`SomeObject` from doc strings
bf1a65e3c simplify doc strings: pymatgen.core.(lattice.->'')Lattice
0f4214013 blank line before all Args: and R... | {
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} | Closes #3328.
As suggested by @goodwilling in https://github.com/materialsproject/pymatgen/issues/3328#issuecomment-1722076836. Thanks! 👍
Applies to `BSPlotter.plot_brillouin()` and `WulffShape.get_plot()`. | {
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"This is due to #3253. Should be easy to fix by reinstating explicit `atol=1e-08`. Thanks for reporting!"
] | 2023-09-17T07:20:29 | 2023-09-17T20:04:14 | 2023-09-17T20:04:14Z | NONE | {
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} | #### Issue: Coherent Interface Builder Fails in pymatgen 2023.9.10 on Windows 10
##### Description
When building Si(100)/Au(100) interfaces using `coherent_interface_builder` on Windows 10, we encounter an `AssertionError` in pymatgen version 2023.9.10. The issue didn't exist in previous versions. We're using `mp... | {
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} | Closes #3334.
Fix accidental breaking change introduced in https://github.com/materialsproject/pymatgen/pull/3253 by reinstating explicit `atol=1e-08` (default for `np.allclose` whereas `np.testing.assert_allclose` sets this to 0). | {
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"Adding a note that, while reviewing this, I noticed a lot of methods on `SiteCollection` reference a \"structure\", even though these methods are also used by `IMolecule`/`Molecule`. Might cause some confusion. "
] | 2023-09-17T19:33:31 | 2023-09-17T23:26:27 | 2023-09-17T23:22:53Z | MEMBER | {
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} | Addendum to #3264, notifying @gpetretto, @janosh.
Two things I think we missed in #3264:
* A formal `@property` so that we get a docstring for the new `IStructure.properties`
* An edge-case for backwards compatibility. While I strongly recommend people _do not_ use pickle as an archival format, nevertheless this... | {
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"Hi @kavanase! It seems that your supercell is quite large and if you are saving it as a `POSCAR` with default settings you may be running into numerical precision issues. I suggest you look into either (1) increasing export accuracy or (2) playing with the `SpacegroupAnalyzer`'s `symprec` parameter, to allow for l... | 2023-09-18T11:21:28 | 2024-09-20T19:34:30 | CONTRIBUTOR | {
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} | ### Email (Optional)
sean.kavanagh.19@ucl.ac.uk
### Version
v2023.9.2
### Which OS(es) are you using?
- [X] MacOS
- [ ] Windows
- [ ] Linux
### What happened?
When using `SpacegroupAnalyzer.get_symmetrized_structure()`, I noticed some odd behavior.
If the input structure is a non-diagonal supercell of the primi... | {
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"I agree this is misleading behavior. A PR that modifies `converged_ionic` to also check `EDIFFG` sounds like an improvement.\r\n\r\nThough as @Andrew-S-Rosen pointed out, some calculations keep some atoms fixed in which case you may end up with large forces even though VASP is done. @shyuep @esoteric-ephemera curi... | 2023-09-19T17:33:06 | 2023-09-21T20:21:44 | CONTRIBUTOR | {
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_No response_
### Version
v2023.6.28
### Which OS(es) are you using?
- [ ] MacOS
- [ ] Windows
- [X] Linux
### What happened?
I have a long VASP calculation and I use `STOPCAR` to stop the calculation early before reaching wall time limit. Once the vasp finishes, I use the `pymatgen.io.vasp.... | {
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"Besides adding new POTCAR hashes (or whatever future validation technique we migrate to), are we expecting additional TODOs?",
"Here are a few questions:\r\n\r\n- Everything works as-expected with the `pmg config` command-line utility? \r\n- Parsing of the POTCAR spec in the `Potcar` class fetches all the metada... | 2023-09-20T17:59:29 | 2023-10-20T19:22:28 | 2023-10-20T19:21:11Z | MEMBER | {
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} | ### Email (Optional)
_No response_
### Problem
VASP has now released v64 pseudopotentials (PBE and LDA). This is an issue tracker to monitor progress related to ensuring that Pymatgen plays nicely with them.
### Proposed Solution
N/A
### Alternatives
_No response_
### Code of Conduct
- [X] I agree to follow th... | {
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"tag @tschaume you might be interested to comment since I mentioned this bug to you 😄 ",
"The error I received is \r\n```\r\n-> 3585 f.write(\"\".join(self.data_aug.get(data_type, [])))\r\n\r\nTypeError: can only join an iterable\r\n```\r\n@janosh this is a file output bug, so do you want me to check if the file... | 2023-09-20T20:33:45 | 2023-09-30T20:30:32 | 2023-09-30T20:30:32Z | CONTRIBUTOR | {
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} | Context: I was trying to download `AECCAR`s from aws and save them locally as vasp compatible format. `CHGCAR`s can pass successfully but `AECCAR` will yield error when `aeccar.write_file` like following
```python
mp_id = 'mp-1523380'
prefix = 'aeccar0s'
suffix = prefix.rstrip("s")
fpath = f'{mp_id}-{suffix}.... | {
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"> I'm also happy to use this PR to help make the other codes consistent. Thoughts?\r\n\r\nThanks @matthewcarbone. Which other codes are you referring to?",
"@janosh \r\n\r\n> Thanks @matthewcarbone. Which other codes are you referring to?\r\n\r\nWell, selfishly the ones I use [here](https://github.com/AI-multimo... | 2023-09-21T16:50:01 | 2024-03-03T18:26:41 | 2024-02-26T09:11:31Z | CONTRIBUTOR | {
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} | `pymatgen/io/feff/inputs.py` lines 504-506 rounded the FEFF geometry to 6 decimal places by default. This also occurs in 518-520. Other writers (such as the one for EXCITING) do not appear to do this. This commit makes a simple change and removes the `":f"` from the string representation in the lines formatting. Thus F... | {
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"was this accidentally left in draft mode?"
] | 2023-09-21T21:34:59 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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Still need to add a test to go along with it | {
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20c8b1693 fix TestPotcar.test_write polluting git repo on failure | {
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"Hmm... the error suggests it is a problem with your gcc and not pymatgen? I just installed it on my mac and there were no issues. Also, your numpy seems to be really old. I would upgrade numpy first using `pip install --upgrade numpy`.",
"The above occurred with numpy-1.26.0-cp39-cp39-macosx_10_9_x86_64, from a ... | 2023-09-25T18:53:02 | 2023-09-26T18:19:11 | 2023-09-26T18:19:11Z | CONTRIBUTOR | {
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} | Hi! I noticed that the just-released pymatgen `v2023.9.25` [in this specific configuration cannot `pip install` correctly on **MacOS X86_64 GitHub runner**](https://github.com/amkrajewski/pqam-dparamhu2021/actions/runs/6302862819/job/17112125672) for Python 3.9 and Python 3.10, but can for Python 3.11.
**Notes:**
-... | {
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"What is your MPRester version? Also, this should be reported to the mp-api package since it has nothing to do with pymatgen. ",
"@yuxin-chang I thought this was an issue in `Ion.reduced_formula`, but I'm not able to reproduce:\r\n\r\n```\r\n>>> from pymatgen.core.ion import Ion\r\n>>> i=Ion.from_formula('SnHO2+'... | 2023-09-25T20:50:03 | 2023-09-26T13:28:36 | 2023-09-25T20:59:06Z | NONE | {
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} | The ion entry of Sn was in a wrong name:
the ion entry with composition Sn1 O2 H1 has name SnOH2[+1]
the ion entry with composition H1 Sn1 O2 has name SnOH2[-1]
As printed out, the number of O and H are opposite
```
mpr = MPRester()
entries = mpr.get_pourbaix_entries([ "Sn"])
for entry in entries:
print(e... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3350 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3350/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3350/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3350/events | https://github.com/materialsproject/pymatgen/pull/3350 | 1,913,723,811 | PR_kwDOACgets5bPiXk | 3,350 | Ion: default hydrates=False in reduced_formula | {
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"@rkingsbury Is this intentionally in draft mode?",
"@janosh it was intentional, but I think it's good to go. All tests pass, but I wanted to make sure that this didn't mess up anything on the API side. When we re-did the [Pourbaix ion data](https://next-gen.materialsproject.org/contribs/projects/ion_ref_data?_li... | 2023-09-26T15:03:42 | 2024-10-10T01:55:02 | 2023-10-09T14:41:58Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- default to `hydrates=False` in `Ion.get_reduced_formula_and_factor()`
- explicitly use `Ion.get_reduced_formula_and_factor()` rather than `super().get_reduced_formula_and_factor()` in `reduced_formula
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] ... | {
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"Thanks for taking a fresh look at this problem @esoteric-ephemera, it's been unsatisfactory for a while. These warnings frequently confuse or alarm people unnecessarily, but the underlying motivation of rigorously checking pseudopotential compatibility is of course very important.\r\n\r\n> However FORTRAN is space... | 2023-09-26T16:57:20 | 2023-09-30T01:53:23 | 2023-09-30T00:03:15Z | CONTRIBUTOR | {
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**Issues:**
current method of POTCAR validation is too brittle to work well in high-throughput calculations. For example, hashes are sensitive to subtle changes in spaces (addition/deletion). However FORTRAN is space-insensitive, thus two POTCARs that differ by spaces are read identically by VASP.
**... | {
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} | Thanks @munrojm for reporting. [This change](https://github.com/materialsproject/pymatgen/blame/4bff21d33625bc9f7077c7b4eb06098d1f50277c/pymatgen/analysis/molecule_matcher.py#L146) (although it improved code readability) caused errors in emmet CI. | {
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"Sorry but we cannot do this. Whatever the merits of the renaming, this will cause all other packages that depends on pymatgen to break. Writing out files is probably one of the main uses. At best, we can allow write_file as an alias for to so that we preserve backwards compatibility. ",
"> Sorry but we cannot do... | 2023-09-27T09:16:22 | 2023-09-27T17:15:26 | 2023-09-27T17:15:25Z | CONTRIBUTOR | {
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I have noticed that many beginners (including myself a while ago) find it very unintuitive to write e.g. structures to a file by using `.to()`, especially with the `.from_file()` method counterpart. That's why I refactored each instance/occurrence using the [pycharm](https://www.jetbrains.com/pycharm/) bu... | {
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"Thanks"
] | 2023-09-27T14:16:12 | 2023-10-03T23:06:28 | 2023-09-27T14:41:46Z | CONTRIBUTOR | {
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} | ## Summary
Small bugfix for the MPMD vasp input set. The input parameter `time_step` was added in fabdd276497493f87f72348a3573bbe8a6c38f26 (it was in the docstring before that), but it was not added as a class attribute, leading to an `NotImplementedError` raised when trying to convert the object to a dict:
~~~
... | {
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"You don't actually need to write it this way. All that needs to be done is to add `to_file = to` and `write_file = to` in SiteCollection. That will create the aliases without so much code.",
"> You don't actually need to write it this way. All that needs to be done is to add `to_file = to` and `write_file = to` ... | 2023-09-27T17:40:49 | 2023-10-03T23:07:57 | 2023-09-30T17:17:06Z | CONTRIBUTOR | {
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I have noticed that many beginners (including myself a while ago) find it very unintuitive to write e.g. structures to a file by using .to(), especially with the .from_file() method counterpart. That's why I added aliases `to_file` for structures and molecules.
PS: This is the second attempt of #3354 a... | {
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