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"@chiang-yuan Yes, we definitely need a test for this.\r\n\r\nDo I understand correctly that your PR adds a `mag` key to any parsed `OSZICAR` even if that data is not present in the file? Will the value be `None` in that case?",
"Haven't tested different OSZICAR yet. Looks like OSZICAR test in test_ouptut.py does... | 2023-07-11T22:02:20 | 2023-08-18T16:46:19 | 2023-08-18T16:46:19Z | CONTRIBUTOR | {
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} | I tried to read `mag` from OSZICAR and found `mag` is not read from `ionic_MD_pattern`. Not sure if `mag` is available in all vasp md calculation.
@janosh should I add unit test for this? The OSZICAR in `test_files/OSZICAR` doesn't have all the available output fields like
```
2 T= 1239. E= 0.11712678E+03 F= -... | {
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"Thanks a lot @mcgalcode. This was a big chunk!"
] | 2023-07-11T22:41:14 | 2023-07-11T22:53:58 | 2023-07-11T22:53:40Z | NONE | {
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} | ## Summary
Fixes tests after compression of files in pymatgen/analysis.
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"This might well be true, but I expect this was written with reference to the [VASP docs](https://www.vasp.at/wiki/index.php/NBANDS). I'm not sure the appropriateness of referring to the source code here.",
"@mkhorton what do you mean? I thought that using the formula from the source code (which is distinct from ... | 2023-07-12T17:33:45 | 2023-07-20T22:16:27 | 2023-07-20T22:16:27Z | CONTRIBUTOR | {
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According to my version of the VASP source code, in `main.F`, the actual formula for NBANDS should be:
`max((valid_nelect+2)/2 + max(nions/2,3), valid_nelect*0.6)) + nmag`
with `nmag=0` alwa... | {
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"@matthewkuner Thanks for spotting this!\r\n\r\nWould be great if @aaron-kaplan or someone else more qualified than me could sign off on this.\r\n\r\nAlso, @matthewkuner we need a unit test in `pymatgen/io/vasp/tests/test_sets.py` for this change in behavior. It should pass with and fail without this change. Maybe ... | 2023-07-12T18:07:45 | 2023-08-05T13:50:32 | 2023-07-20T21:54:09Z | CONTRIBUTOR | {
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"thanks @arosen93 !",
"@janosh --- why does ruff hate me? :(",
"Looks like `ruff` just had a new release that finds new issues on `master`. So nothing to do with your changes. Does this still need testing?",
"Ah I see. No, this should be done! "
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} | Currently, the `.tags` property of the ASE `Atoms` object is lost when interconverting between ASE `Atoms` and Pymatgen `Structure`/`Molecule`. I adopted the solution by @brookwander in https://github.com/ulissigroup/catapalt/issues/2 to ensure the tags do not get lost. | {
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} | You can't set any type other than `str` using the `pmg` CLI at the moment.
```sh
pmg config --add PMG_POTCAR_CHECKS False
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# ~/.config/.pmgrc.yaml
PMG_POTCAR_CHECKS: 'False'
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which is truthy and so the opposite of expected behavior.
_Originally posted by @janosh in ht... | {
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} | Closes #3152
90a7c076d rename `PMG_DISABLE_POTCAR_CHECKS` to `PMG_POTCAR_CHECKS`
0729fc3f9 fix setting `bool` and `None` through `pmg` config CLI
0ef9ae7d2 document existence of `PMG_POTCAR_CHECKS` in all doc strings for `check_potcar: bool = True` | {
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"I think the fix is just to use el.symbol instead? Most of the time the compatibility is operated on MP entries. Most of which don't come with oxidation state decorated.",
"Yes, the fix is straightforward. Just baffled that it hasn't come up before."
] | 2023-07-13T21:25:55 | 2023-07-13T22:59:42 | 2023-07-13T22:59:42Z | MEMBER | {
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} | I'm surprised this didn't come up before. Opening this issue rather than quietly fixing to make sure I'm not missing something. It appears `MaterialsProject2020Compatibility` doesn't currently handle oxidation states.
```py
from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
from pymatgen.... | {
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"Thanks for reporting this. @arosen93 The only sys.path that I noticed is in the io.ase. Did you add that? I am not sure of the purpose of it. Can you reverse it? @janosh \r\n",
"Nope, don't think that was me. @janosh, was that one you? Feel free to reverse. Otherwise, I'll take a look later today. ",
"Ah yes, ... | 2023-07-14T09:42:32 | 2023-07-15T07:58:33 | 2023-07-14T13:51:21Z | NONE | {
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} | Since [v2023.06.23](https://github.com/materialsproject/pymatgen/releases/tag/v2023.06.23) importing `pymatgen` manipulates [sys.path](https://github.com/materialsproject/pymatgen/blame/63bbd23b57ca2c68eaca07e4915a70ef66e13405/pymatgen/io/ase.py#L26). This is somewhat annoying if you have a more complicated site setup... | {
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"Thanks @mattmcdermott!"
] | 2023-07-14T23:58:35 | 2023-07-15T00:30:21 | 2023-07-15T00:30:20Z | MEMBER | {
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} | ## Summary
Fixes bug briefly mentioned in #3070, where recent spin property changes resulted in the `MagneticStructureEnumerator` failing. This is apparently due to creating structures where only some `Species.spin` properties are defined, causing `CollinearMagneticStructureEnumerator` to fail. For example, if you i... | {
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} | Some classes have static method `from_string` (`Poscar`, `CifParser`, ...), other's `from_str` (`Structure`, `Molecule`, ...).
`from_str` is shorter and clear enough, so rename methods to that and add deprecated `from_string` fallbacks for backwards compatibility. | {
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"Never mind, didn't realize [`pymatgen-io-fleur`](https://github.com/JuDFTteam/pymatgen-io-fleur) is an external namespace package (see https://github.com/materialsproject/pymatgen/pull/2610)."
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} | @shyuep `Structure.to()` imports from `pymatgen.io.fleur` which doesn't exist. Did you remove?
Either way, we should remove the `fmt == "fleur-inpgen" or fnmatch(filename, "*.in*")` option from `Structure.to()` since it would crash. | {
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"@shyuep ",
"This might be caused by https://github.com/materialsproject/pymatgen/pull/3137.\r\n\r\n@shwetaresearchsite Can you downgrade to `pip install pymatgen==2023.6.28` and see if the error disappears?",
"@stefsmeets In case it helps connect the dots, this issue might be related to #3166.",
"Are there a... | 2023-07-17T17:32:58 | 2023-07-20T15:37:49 | 2023-07-20T15:37:48Z | NONE | {
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} | Can anyone please suggest why I am unable to get structures from pymatgen?
```py
from pymatgen.core import Structure
from pymatgen.analysis.diffusion.neb.pathfinder import DistinctPathFinder
s = Structure.from_file("./system.vasp")
path_finder = DistinctPathFinder(symm_structure, "Ca", max_path_length=6.0)
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"It is a one-line fix. `cdef int n_pbc_im = 3 ** n_pbc` -> `cdef int n_pbc_im = int(round(3 ** n_pbc))`"
] | 2023-07-17T20:38:30 | 2023-07-17T23:18:49 | 2023-07-17T23:18:49Z | MEMBER | {
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} | [`cython` just released v3](https://cython.readthedocs.io/en/latest/src/changes.html#unified-release-notes) with a bunch of breaking changes that affect `pymatgen` installation.
This issue tracks migrating to `cython` v3 so we can remove the pin added in [e8d4917](https://github.com/materialsproject/pymatgen/commit/... | {
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"Just use https://github.com/pckroon/pysmiles ?"
] | 2023-07-18T21:08:12 | 2023-08-08T21:14:30 | MEMBER | {
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} | `openbabel` is difficult to install, esp. on Mac and apparently has been since 2012.
Current 1st party support in `Molecule.from_str()` is limited to `xyz`, `gjf`, `g03`, `json`.
SMILES is very widely used and warrants 1st party support. | {
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} | #### Description
A clear and concise bug description.
#### Repro
Steps to reproduce the behavior:
1. Go to 'https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/analysis/graphs.py#L73'
2. the code is supposed to compare the edge information of two molecules provided as arguments but instea... | {
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"@njzjz Thanks for reporting. This is not intended.\r\n\r\nThis was caused by #3135. @stefsmeets Could you take a look? `label` should still be `H` here.",
"Thanks for pinging me!\r\n\r\nI added `Site.label` is a new attribute (default `None`), so it was never 'H' to begin with unless explicitly set by the user o... | 2023-07-19T19:21:16 | 2023-07-20T15:37:48 | 2023-07-20T15:37:48Z | CONTRIBUTOR | {
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} | #### Description
The latest version gives the `'label': None` in `Structure.as_dict()`. I want to confirm if it is expected, as it breaks the tests in our downstream package.
#### Repro
```py
from pymatgen.core import Structure
import numpy as np
s = Structure(np.eye(3), ["H"], np.zeros((1, 3)), coords_are_... | {
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"There are two possible solutions:\r\n1, Redefine the getattr of Species as the following:\r\n```python\r\ndef __getattr__(self, attr):\r\n if attr == \"_el\":\r\n raise AttributeError\r\n return getattr(self._el, attr)\r\n```\r\n2, Add\r\n```python\r\nself._el = None\r\n```\r\nto the __init__ function... | 2023-07-19T21:47:19 | 2023-07-19T22:12:21 | 2023-07-19T22:12:21Z | NONE | {
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} | #### Description
After pymatgen update v2023.6.28, a recursion issue happens when using DummySpecies in pytest fixtures.
Here is the fixture initialization error:
```bash
collecting ...
test_cofe/test_domain.py:None (test_cofe/test_domain.py)
..\..\venv\lib\site-packages\pluggy\_hooks.py:265: in __call__
r... | {
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} | ## Summary
This PR fixes some issues with labels and adds new tests for previously unspecified behaviour.
Major changes:
- `Site.label` (and derivatives) defaults to `.species_string` instead of `None`
- Add label attribute to `Neighbor` and `PeriodicNeighbor`
Closes #3166
Closes #3160
## Checklist
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"@emayMTK https://github.com/materialsproject/pymatgen/pull/3140 was a recent breaking change that renamed some of the `ParseError` subclasses. `AbinitTimerParserError` is now `AbinitTimerParseError` (note the dropped `r`). Looks like this was already addressed in https://github.com/abinit/abipy/commit/704f4eb0b02f... | 2023-07-20T14:33:11 | 2023-07-20T18:11:18 | 2023-07-20T16:58:14Z | NONE | {
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} | I'm encountering an issue when trying to use `abicheck.py` with the `abipy` and `pymatgen` libraries in my `abienv` conda environment. Here's the command I'm running and the error I'm facing:
**Command:**
```bash
(abienv) mtk@mtk-HP-EliteBook-x360-1030-G2:~/abipy$ abicheck.py --with-flow
```
**Error :**
`... | {
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"Nice test, thanks @pablogalaviz! 👍 "
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} | ## Summary
The proc_val function modifies the value of string variables (changes 'd' for 'e'). For example, smearing = 'cold' becomes smearing = 'cole'. It is solved by using a local variable.
Major changes:
Added a local variable
```
val_replace = val.replace("d", "e")
return smart_int_or_float(va... | {
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"The error message says\r\n\r\n> The current occupancy_tolerance is set to: 1.0. Species occupancies sum to more than 1!\r\n\r\nIf you increase `occupancy_tolerance=10`, the file parses fine.\r\n\r\n```py\r\nfrom pymatgen.io.cif import CifParser\r\n\r\nparser = CifParser(\"Mn-Zn-Im.cif\", occupancy_tolerance=10)\r\... | 2023-07-21T13:39:58 | 2023-07-25T16:58:06 | 2023-07-22T03:23:25Z | NONE | {
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} | The `cif` file opens without any issue in VESTA, indicating that it is not broken. However, when the same file is loaded using the `pymatgen` library, it throws an error. The file in question is attached: Mn-Zn-Im.txt (GitHub does not accept the `.cif` file extension).
You can find the file here: [Mn-Zn-Im.txt](http... | {
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Doesn't actually change the default behavior of `CifParser.get_structures()`. That seemed too breaking. Instead adds a new kwarg
```py
on_error: Literal["ignore", "warn", "raise"] = "warn"
```
which is a step towards better error messages on parse errors when set to "error". | {
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} | ## Summary
Fix a bug introduced in #3158. A lot of `from_string` methods should be `classmethod`.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/mo... | {
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"Do you mind adding a unittest for one mag structure to check for this? I am worried that someone might make changes in future that breaks this again.",
"Thanks!"
] | 2023-07-23T18:58:20 | 2023-07-24T16:36:05 | 2023-07-24T16:36:04Z | CONTRIBUTOR | {
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} | ## Summary
With the new changes that set the default `Sepcies.spin` to `None`, I fixed the logic for setting zero magmoms in `SpacegroupAnalyzer` to check for `None` values as well.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X... | {
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"Why keep both, if we’re referring people to functionality in pymatviz? We should probably have a strategy here.\r\n\r\nSimilar issue with plotting functionality in crystal toolkit; generally, plotting changes there have been upstreamed to pymatgen, but only for plotters that already existed within pymatgen, becaus... | 2023-07-24T16:44:58 | 2023-08-13T22:28:33 | 2023-07-25T18:52:32Z | MEMBER | {
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"Another example [mp-18767](https://materialsproject.org/materials/mp-18767):\r\n\r\n```py\r\nComposition('Li+:2 Mn3+:2 O2-:4')\r\n```\r\n\r\nBefore\r\n\r\n```py\r\nComp: Li2 Mn2 O4\r\n```",
"This is a good proposal, but what if in the future we consider even more detailed information like partial charge, would i... | 2023-07-25T01:46:34 | 2023-07-25T19:10:33 | 2023-07-25T19:10:33Z | MEMBER | {
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```py
from pymatgen.core import Composition
from pymatgen.core.periodic_table import Species
comp1 = Composition({Species("Fe2+"): 2})
comp2 = Composition({"Fe2+": 2})
comp3 = Composition({"Fe": 2})
```
These 3 compositions all print
```
Comp: Fe2
```
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} | Closes #3181.
1d3ff8467 include oxidation states in `Composition.__repr__`
26b3b5b98 delete unused `doctest.testmod() if __name__ == "__main__"`
d2aed40d1 add tests for `Composition.__repr__` and `__str__` | {
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"Thank you very much @stefsmeets, this is great! 🙏 \r\n\r\nJust to get an overview, are there more structure operations that are known to drop the site labels? Supercells, inserting/deleting sites, applying translations/rotations are all very important. Just want to leave a record here of what else might need doin... | 2023-07-25T12:21:18 | 2024-04-16T18:15:06 | 2023-07-31T15:36:11Z | CONTRIBUTOR | {
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This PR follows up from #3137 and makes sure that labels are propagated correctly throughout structure, for example, when making supercells, inserting/deleting sites, applying translations/rotations, etc.
This PR also fixes a bug where the labels were incorrectly assigned when the CIF contains multiple... | {
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"Yikes, this is a pretty significant bug. So if I understand #3185 correctly, _if_ one applies `MP2020Compatibility` to an entry that has been pre-processed such that the structure is decorated with oxidation states (as opposed to just carrying `oxi_states` in the `.data` attribute, then the oxide (or other) correc... | 2023-07-25T21:01:40 | 2023-07-27T18:14:51 | 2023-07-27T14:37:45Z | MEMBER | {
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`Element in Composition` is currently `False` if that `Element` appears in `Composition` as a `Species` with an oxidation state.
This PR changes the `__contains__` method to return `True` for `x in Composition` if
1. `x` exactly matches a `Species` (both element symbol and oxidation state) in the c... | {
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"The problem is on this line which uses `Composition.__contains__` to check for `oxygen` in the entry composition. `Composition` doesn't currently contain an `Element` if that `Element` appears as a `Species` with an oxidation state.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/5c5f271ad1d6ca2e51146db4d... | 2023-07-25T21:27:42 | 2023-07-27T14:37:46 | 2023-07-27T14:37:46Z | MEMBER | {
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} | This minimal example of mp-18767 (LiMnO2) currently doesn't receive an oxide correction.
**Expected corrections**
> Energy Adjustments:
> MP2020 anion correction (oxide): -2.7480 eV (-0.3435 eV/atom)
> MP2020 GGA/GGA+U mixing correction (Mn): -3.3360 eV (-0.4170 eV/atom)
**Actual**
> Energy Adju... | {
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} | This is a feature enhancement to add an interface with [Metalwalls](https://gitlab.com/ampere2/metalwalls). As stated in their repo:
> MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a ... | {
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"@stefsmeets Could this be caused by the recent changes to `Site.label`?",
"@matthewcarbone what is the last known version that this is working?\r\n\r\nI did a git bisect to way before we added labels, and it seems to be broken since a couple of months from what I can tell.\r\n\r\n```\r\nc62f8a05f4607d0d75f34c9f1... | 2023-07-26T16:14:17 | 2023-09-18T15:37:08 | 2023-08-10T15:36:21Z | CONTRIBUTOR | {
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} | #### Description
I've found what appears to be a strange edge case when using the `FEFFDictSet`, which does not appear in older versions of Pymatgen.
```python
print(struct) # this is mp-2664
```
```
Full Formula (Ti1 O1)
Reduced Formula: TiO
abc : 3.033043 3.033043 3.033043
angles: 60.000000 ... | {
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"Beats me. I think you need to ping @arosen93 or @esoteric-ephemera. And if they don't know we're screwed. 😄 ",
"I think this would be within the wheelhouse of @mvenetos97. ",
"I think it's ok - caveat, this is not my area of expertise. The name of this set \"cs\" suggests computation of chemical shifts via NM... | 2023-07-27T20:09:18 | 2023-08-01T15:22:24 | 2023-08-01T15:22:24Z | CONTRIBUTOR | {
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However, why is this even desired? | {
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} | You can now use
```py
BaderAnalysis(bader_exe_path="/abs/path/to/bader")
```
to run `bader` anywhere on your system without any `PATH` modification shenanigans.
TODO: Promote `atomate2.SETTINGS.VASP_RUN_BADER: bool` to accept a string so users only need to specify `bader_exe_path` once in their `atomate2` c... | {
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"Thank you so much for doing this! It has been on my backlog for a very long time.",
"You don't need to add it in this PR (unless you're feeling ambitious!), but it's likely that an analogous fix will solve similar issues with the [`chargemol_caller`](https://github.com/materialsproject/pymatgen/blob/master/pymat... | 2023-07-29T00:01:06 | 2023-08-08T19:59:32 | 2023-08-08T19:14:53Z | CONTRIBUTOR | {
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} | In the original implementation, CHGCAR is copied into temporary folder by `monty.zopen`. Since CHGCAR is usually very large, this makes bader analysis calling from pymatgen extremely slow.
this might close #2487
- fix 1: use `monty.tempfiie.ScratchdDr` context manager
- fix 2: do not copy large files like CHGC... | {
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} | > MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials.
This is the same PR but without dirty commit from other branch. The input classes a... | {
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"@naik-aakash [v2023.8.10](https://github.com/materialsproject/pymatgen/releases/tag/v2023.8.10) will be on PyPI in ~1h.",
"Thank you both!",
"@shyuep and @janosh , Thank you 😃 "
] | 2023-07-31T12:30:42 | 2023-08-11T06:35:53 | 2023-08-08T15:24:07Z | CONTRIBUTOR | {
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} | # Issue
The recent feature added to `pymatgen.io.lobster.lobsterenv.LobsterNeighbors` class to handle cobis and coops via PR #3050 is necessary for our Lobsterpy package to extend its functionality.
It would be great if a new release is made available soon. | {
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} | 60ff0cbb3 don't use tempfile.TemporaryDirectory() in tests, prefer PymatgenTest.tmp_path auto-used fixture
b8a0f633c fix broken test_files paths in TestPackmolSet
2013d15b4 skip failing TestPackmolSet.test_random_seed due to openbabel not installed
b3c6150c3 only skip pymatgen/io/tests/test_packmol.py if packmol not... | {
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13ef1f80d del unused w_area_has_intersection_smoothstep | {
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a70f4c4c5 add `Structure/Molecule.sites` setter, move `@property` to SiteCollection
7f510ca35 don't use implementation detail `(Structure|Molecule)._sites`
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"Pls add a test for this.",
"Actually, I was able to find the bug in atomate2 that caused this.\r\nhttps://github.com/materialsproject/atomate2/pull/460"
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Recent changes resulted in some of the structures in my atomate2 workflow that had `[None, ...]` for all the `Magmom` values. I'm still looking into where these `[None, ...]` values came from (not 100% sure it's related to #3179) but this fix:
- Skips writing Magmom completely if all... | {
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Major changes:
- Fixes a bug updating the charges from POTCAR while reading a vasprun.xml file in the case of a chemical shift calculation
- Slight update to the splitting of POTCARs when reading from file.
- Added a test for the chemical shift vasprun.xml parsing with a POTCAR
- Re-added a test for... | {
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a63aa2f23 cover edge cases in class XYZTest | {
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} | e0768d5c1 test_computed_entries.py rename single-letter vars
b4f4e7c3f google-style doc str
c199bb95d fix EnergyAdjustment.__repr__ when used by mp-api MPRester
c8e2f340a add test_energy_adjustment_repr()
Fixes
```py
print(entries['R2SCAN'].energy_adjustments)
File "pymatgen/pymatgen/entries/computed_entri... | {
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"Duplicate of https://github.com/materialsproject/pymatgen/issues/3170. See https://github.com/materialsproject/pymatgen/issues/3170#issuecomment-1644272034 for the fix."
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While I have been using pymatgen for a while, I recently wanted to try using abipy to do some calculations in abinit. Using one of the example jupyter notebooks, there is an import line
`pymatgen.io.abinit.abitimer import AbinitTimerParserError
`
The import fails. Investigation of the modules a... | {
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} | Now that we use markdown for docs, let's start adopting some of the tooling around it. Running https://github.com/igorshubovych/markdownlint-cli in pre-commit is a good start. `blacken-docs` should be next.
a4db1e352 pre-commit exclude tests/files (prev .*test_files) (fixes currently failing CI)
2c826b340 add pre-c... | {
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} | 937a435f4 fix .gitattributes outdated test_files/**/* linguist-vendored causing wrong language detection
70ee6e452 test.yml fix --durations-path (test_files->tests/files)/.pytest-split-durations
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"I don't think a final_structure even makes sense in a GW_BSE calculation isn't it? It only makes sense in a relaxation. This is not a bug. It simply means the calculation does not change the position of the atoms.",
"In any case, I have just pushed a fix that makes sure Vasprun.final_structure == Vasprun.initial... | 2023-08-04T00:37:29 | 2023-08-07T14:42:35 | 2023-08-07T14:42:34Z | CONTRIBUTOR | {
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https://github.com/materialsproject/pymatgen/blob/6d1ffa40123f4f714323f4308418b4062d422d65/pymatgen/io/vasp/outputs.py#L475
So if... | {
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824296fff `BalancedReaction` don't create unnecessary lists
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Should say 100% Python. GH linguist misclassifies our test files. This PR ignores test ... | {
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"Looks like a simple oversight in https://github.com/materialsproject/pymatgen/commit/8648d50f746486e194c2355d3c12e6dce8f6dea1. @arosen93 Could you confirm that line 1334 should be deleted?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/inputs.py#L... | 2023-08-04T17:15:28 | 2023-08-04T19:26:41 | 2023-08-04T19:26:40Z | CONTRIBUTOR | {
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What is the point of this when you always set the style to gamma a few lines later? | {
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"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`50.00%`** and project coverage change: **`-0.01%`** :warning:\n> Comparison is base [(`bda... | 2023-08-04T18:48:15 | 2023-08-04T19:26:40 | 2023-08-04T19:26:39Z | MEMBER | {
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"Tagging @arosen93 as the author.",
"Just to copy over part of my discussion with Matthew here: if a Monkhorst-Pack grid doesn't break the symmetry of the lattice, then everything should be OK. I did check the \"gold-standard\" MP entry, mp-149 / cubic diamond Si, and the input for the task document has a Monkhor... | 2023-08-04T20:37:12 | 2023-08-18T14:23:34 | 2023-08-18T14:23:33Z | CONTRIBUTOR | {
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Currently, this code could use Monkhorst-pack schemes for FCC and Face-centered orthorhombic cells. According to the [vasp wiki](https://www.vasp.at/wiki/index.php/KPOINTS#Symmetry_reduction_of... | {
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"I've been moving `from_string -> from_str`. But it shouldn't have broken anything during the ongoing deprecation period. I made that change in #3158 but looks like I forgot to add the fallback `from_string` on `InputFile`. Fix incoming.\r\n\r\nGood catch on the `from_str` vs `get_string` inconsistency. Let's go wi... | 2023-08-07T19:40:01 | 2024-04-17T04:07:30 | 2023-08-09T20:25:03Z | CONTRIBUTOR | {
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The `from_string` method in `pymatgen.io.core.InputFile` was recently changed to `from_str`. I am fine with either convention (though it did break pymatgen.io.openmm downstream) but there is now internal inconsistency between the [InputFile.from_str](https://github.com/materialsproject/pymatgen/blob/1fa... | {
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} | Closes #3230.
e703c43f0 restore accidentally deleted io.core.InputFile.from_string (fixes #3230)
2b52712f8 add io.core type hints
ded857431 deprecate get_string methods in favor of get_str | {
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} | d3176316b fix ruff PYI041 (redundant-numeric-union)
2faafa2d2 ruff ignore PYI024
4b756d068 remove over-engineered _attr_desc = namedtuple
ca70565ba fix CI AttributeError: 'NoneType' object has no attribute 'split' | {
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"I think this is something you have to experiment with the Wavecar class and see if it meets your needs."
] | 2023-08-09T01:53:41 | 2023-08-17T14:08:04 | 2023-08-17T14:08:04Z | CONTRIBUTOR | {
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} | Suppose I would like to achieve the following purposes based on the wavefunction analysis from WAVRCAR:
1. Calculate the topological number based on the exact form of wavefunction, aka, an n*1 array under plane wave basis.
2. Compute the traces of matrix presentations and determines the corresponding irreducible r... | {
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"1. Pls use the new API.\r\n2. This is actually not a good way to use this method. You can easily get all the mpids AND formulas/chemical systems in one shot and just postprocess that data to get the mpids of the specific systems.\r\n3. Even if you prefer to use this method, having two wild cards makes it very diff... | 2023-08-09T15:30:49 | 2023-08-10T18:00:06 | 2023-08-10T15:04:27Z | CONTRIBUTOR | {
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} | #### Description
When attempting to pull a "large" amount of data via the MPRester `get_data()` method, even just getting Materials Project IDs consistent with a pattern, e.g.
```python
pattern = "Ti-O-*-*-*" # All titanium oxides with 5 unique atom types
with MPRester(api_key) as mpr:
result = mpr.get_da... | {
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"This all depends on how you download the structures from MP. If you are choosing the symmetrized or conventional CIF, then the cooridnates will shift. Pls contact the mp-api repo if you believe this to be a bug,."
] | 2023-08-10T17:15:08 | 2023-10-18T11:50:45 | 2023-08-13T16:32:15Z | NONE | {
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} | **(Updated 18/Oct/2023) The answer:** The structure downloaded from MPRester is of a **primitive** crystallographic structure, whereas the symmetrized CIF downloaded from the Materials Project is of a **conventional** crysallographic structure. There lies the discrepancy between the crystal coordinates.
<br>
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} | Previously if `filename` was passed, `Structure/Molecule.to(filename="some/file.json|cif|yaml|poscar|...")` would return `None`. No performance cost from always returning the same string that was written to file. Simplifies implementation and testing, and can be useful in rare cases.
96f7084f5 fix some ruff PERF401
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"If I can chime in here, I noticed a bug potentially introduced by this pull request.\r\nAs mentioned [here](https://matsci.org/t/bsplotterprojected-get-elt-projecte-plots-method-broken/51434/4?u=fraricci), there is a \"ax =\" missing [here](https://github.com/materialsproject/pymatgen/blob/3ee84ead10675be75239129b... | 2023-08-13T19:49:56 | 2023-11-02T19:34:20 | 2023-08-17T22:35:33Z | MEMBER | {
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} | Closes #3138.
`pymatgen` plotting methods using the `matplotlib` backend return the `matplotlib.pyplot` module (`plt`), rather than an object related to the plot itself, such as the `Figure` or `Axes`. This is suboptimal API design and inconsistent with the `plotly` backend which returns `go.Figure`.
This PR chan... | {
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"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`96.87%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`d9f... | 2023-08-13T23:08:18 | 2023-08-14T16:48:37 | 2023-08-14T16:38:53Z | CONTRIBUTOR | {
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Added a method `from_boundary_distance` to `SupercellTransformation`, which can automatically find a `SupercellTransformation` that guarantee minimum distance periodic boundaries to be larger than a desired value (`min_boundary_dist`). This method allows high throughput generation of supercells for all 154,... | {
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"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?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: **`-0.01%`** :warning:\n> Comparison is base [(`18... | 2023-08-13T23:32:59 | 2023-08-14T00:14:08 | 2023-08-14T00:14:07Z | MEMBER | {
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} | 16be0518e add `Lattice` property `params_dict`
47699ef57 use new prop in `Lattice.as_dict`
069852f6d test keys in `TestLattice.test_to_from_dict`
41a424db4 add `TestLattice.test_parameters` | {
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"What's the bug you encountered?",
"Hi Janosh,\r\nI found a small bug inside the feff.inputs module.\r\n\r\natom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]\r\n\r\nThe argument 'absorbing_atom' is misused, which generated bugs. Based on my understanding, this \"absorbing_atom\" is the ... | 2023-08-14T18:28:48 | 2023-08-19T01:59:27 | 2023-08-19T01:59:27Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- features: fix the bug in the feff.inputs
- fix 1: .delete atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
- fix 2: change the argument: self.pot_dict = get_atom_map(self._cluster, self.absorbing_atom)
## Todos
If this is work in progress, what ... | {
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"Also running into this issue, with this traceback:\r\n```\r\nImportError while loading conftest '/home/runner/work/PyTASER/PyTASER/tests/conftest.py'.\r\ntests/conftest.py:6: in <module>\r\n from pytaser.generator import TASGenerator\r\npytaser/generator.py:8: in <module>\r\n from pymatgen.ext.matproj import... | 2023-08-15T08:58:19 | 2023-08-15T18:15:52 | 2023-08-15T14:51:20Z | NONE | {
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} | #### Description
Error of **ModuleNotFoundError: No module named 'boto3'** with latest version (pymatgen>=v2023.7.20). BTW the __version__ isn't updated for those versions.
#### Fixed by
`pip install boto3`
#### Environment
Relevant versions and platform info:
- OS: Mac, Linux
- Version>=v2023.07.20)... | {
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"@janosh seems like the tests that are failing are unrelated? Not 100% sure. If they are indeed unrelated, this should be ready for merging",
"Tests were fine on `master`. Looks like something you changed turned `magmons` from `tuple` to `list`. I pushed a fix.\r\n\r\n```py\r\nself._cell\r\n>>> (((...), (...), (.... | 2023-08-16T23:34:37 | 2023-10-12T18:19:49 | 2023-08-18T14:23:16Z | CONTRIBUTOR | {
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"I have no idea what you mean by partial occupancy. Does it mean that some Wyckoff sites are occupied or do you mean all sites are occupied by a partial occupied composition. Either case, this is already implemented in pymatgen. You can refer to the matgenb examples.",
"So what I meant is:\r\nAs an example, Li6PS... | 2023-08-17T07:07:11 | 2023-08-17T15:42:56 | 2023-08-17T14:05:34Z | NONE | {
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Is there a module in Pymatgen that can construct supercells based on partial occupancy or Wyckoff position?
A supercell with partial occupancy would be a great feature. If that is already implemented, that would be great.
Asif | {
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https://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/outputs.py#L608 | {
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eb9cc3ec3 fix doc str return type indentation
572f67c1e reformat long unpackings | {
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} | Reason: significantly more helpful error messages on failed tests.
Example before with `assert np.allclose`:
```py
tests/analysis/gb/test_grain.py:100: AssertionError
def test_as_dict_and_from_dict(self):
d1 = self.Cu_GB1.as_dict()
d2 = self.Cu_GB2.as_dict()
Cu_GB1_new = GrainBo... | {
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