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"@oashour Is this still WIP? If not, can you update the title?",
"@janosh done. The [WIP] tag was mainly because I'm a first-time contributor, and thought there might be some comments, but I have nothing to add to this unless someone spots a problem or possible improvement.",
"sorry this slipped. i forgot this ... | 2023-11-09T02:58:04 | 2024-09-22T00:15:55 | NONE | {
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} | ## Summary
Major changes:
- Add support for parsing orbital moments from OUTCAR
- Update the magnetization parsing test to check orbital moments from `OUTCAR.NiO_SOC.gz`.
## Todos
I opened this as a WIP since I have not contributed to `pymatgen` before, but it's technically complete. As far as I know, VASP... | {
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"There are good reasons to not use module scope in many instances. E.g., when a function is rarely used.",
"There are 2 more conditions for it to make sense to have function-scoped imports. The import must be expensive and not already in the import tree. I'm looking out for that in these refactors but those 3 con... | 2023-11-09T17:26:26 | 2023-11-09T20:05:24 | 2023-11-09T18:39:40Z | MEMBER | {
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"closing as no longer on my todo list. unlikely i'll pick this up again."
] | 2023-11-09T17:37:58 | 2024-09-04T14:08:55 | 2024-09-04T14:08:55Z | MEMBER | {
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} | Related to https://github.com/materialsproject/atomate2/pull/587 and https://github.com/materialsproject/emmet/pull/869.
Pinging @chiang-yuan in case you want to take this over. The tests are still WIP and I didn't do any real-life robustness testing yet. E.g. do we gracefully bail if running on HPC with no network ... | {
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} | ## Summary
Minor updates to the aims interface that I discovered were necessary when adapting the FHI-aims atomate2 interface to use it.
Major changes:
- feature 1: Default species directory from environment
- fix 1: Parser erroneously referred to atoms in one place
- fix 2: An error message did not use an f-s... | {
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"Yep, It's on my to-do list. I'll try to get the tests written by the end of the week.\n\nOn Nov 26, 2023, 5:16 PM, at 5:16 PM, Janosh Riebesell ***@***.***> wrote:\n>@janosh requested changes on this pull request.\n>\n>\n>\n>> @@ -2138,6 +2138,7 @@ def interpolate(\n> interpolate_lattices: bool = False,\n>... | 2023-11-10T00:28:13 | 2023-11-29T19:21:50 | 2023-11-29T19:21:50Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- added optional parameter to allow `Structure.interpolate()` to extrapolate beyond the `end_structure`. The parameter is the fractional amount of extrapolation beyond $q=1$ if $q$ is the normalized interpolation mode amplitude. Thus, `extrapolation=0.5` would produce structures spanning... | {
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Also thanks @BowenD-UCB for reporting. | {
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"Seems a new release is needed. It has been fixed I guess on the git repo already.",
"Fixed in #3468 and released in [v2023.11.12](https://github.com/materialsproject/pymatgen/releases/tag/v2023.11.12)."
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I recently update pymatgen using pip and then everything seems to be broken. The main reason is that there is a file missing under pymatgen.io.vasp
```
File "/Users/binouyang/miniconda3/envs/work3/lib/python3.9/site-packages/pymatgen/io/vasp/__init__.py", line 10, in <module>
from .inputs import I... | {
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"See attached mostly-complete POTCAR benchmark from PBE (2011 - 2022 Materials Project) to PBE_54 to PBE_64 (proposed).\r\n[POTCAR_analysis.xlsx](https://github.com/materialsproject/pymatgen/files/13369140/POTCAR_analysis.xlsx)\r\n\r\n",
"See https://github.com/materialsproject/pymatgen/discussions/3488 for ongoi... | 2023-11-12T18:16:39 | 2023-11-30T15:50:23 | 2023-11-15T20:02:36Z | MEMBER | {
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The only input set affected by this PR is `MatPESStaticSet` (#3254) which now inherits from `PBE64Base`. | {
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5945e95d5 refactor
723a56209 `Composition` add properties `charge` and `charge_balanced`
c5f8c7b71 Add `TestComposition.test_is_charge_balanced` | {
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## Checklist
- [ ] 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/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite`... | {
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"@janosh I use monkeypatch to mock the class method directly (rather than through module namespace) and add `fake_path` to `atomic_densities_path` to force the mock download function to be called. I think this work minimally already. Let me know what you think.\r\n\r\nhttps://github.com/materialsproject/pymatgen/bl... | 2023-11-15T04:59:35 | 2024-09-04T14:11:04 | 2024-09-04T14:11:03Z | CONTRIBUTOR | {
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## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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"Closing to remove irrelevant changes"
] | 2023-11-15T09:06:11 | 2023-11-15T09:06:49 | 2023-11-15T09:06:49Z | CONTRIBUTOR | {
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Major changes:
- fix 1: FHI-aims stress properties are now 3x3 matrices
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](htt... | {
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## Summary
Major changes:
- fix 1: all stresses are 3x3 now
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
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Just saw this inconsistency by chance. The doc string claims the input are structures but then `get_el_sp` is used on the object. | {
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cbb44a235 fix PhononDosPlotter.get_plot only ax.set_ylim if relevant_y is non-empty
77191b672 PhononDosPlotter.get_plot add legend keyword to customize legend
1cee2f5e4 Add alphabetical_formula property to SiteCollection class
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df68ddccc improve UX by preventing common user mistake in PhononDosPlotter passing DOS as 1st arg
42459489d Remove debug logging statements in PhononBSPlotter._make_ticks
a6df2a43c add class Kpoint type annos
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"The bond valence values are coupled to statistics related to the oxidation states. Even if the value might not be correct, we would need to keep it consistent with the model for the oxidation states. Thus, a potential solution would be much more complex.",
"In any case, thank you for pointing this out.",
"@shy... | 2023-11-19T16:39:11 | 2024-02-03T12:39:23 | NONE | {
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} | ### Problem
In the `pymatgen/pymatgen/analysis/bond_valence.py` module in the two functions `calculate_bv_sum `and `calculate_bv_sum_unordered` there is an error in the value of `b` parameter of the BV equation. In the two functions the BV for a given bond is calculated as `vij = exp((R - nn.nn_distance * scale_fact... | {
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### Part 1
https://github.com/materialsproject/pymatgen/blob/c8154cd5c1591734795232b1c7be581417f270b5/pymatgen/io/qchem/inputs.py#L178-L188
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https://api.github.com/repos/materialsproject/pymatgen/issues/3482 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3482/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3482/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3482/events | https://github.com/materialsproject/pymatgen/pull/3482 | 2,004,817,581 | PR_kwDOACgets5gDML6 | 3,482 | Aims input sets | {
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"Is there something I have to do in my personal fork to prevent the VASP errors when running the CI tests?",
"@tpurcell90 This error is genuinely yours:\r\n\r\n```py\r\n properties = (\"energy\", \"free_energy\", \"forces\")\r\n \r\n in_set = AimsInputSet(parameters, Si, properties)\r\n as... | 2023-11-21T17:38:34 | 2024-01-29T17:12:51 | 2024-01-29T16:50:57Z | CONTRIBUTOR | {
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} | ## Summary
Adds the `aims_input_set` from atomate2 into pymatgen
Major changes:
- feature 1: AimsInputSet is now here
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable... | {
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"@janosh: This should be ready for review. As I mentioned above, this code was largely written by @samblau --- I added some simple tests and cleaned up the linting errors. Longer term, it would probably make sense to create a new `QCScratch(MSONable)` class that parses scratch files in a directory. However, I have ... | 2023-11-26T06:16:40 | 2023-12-19T01:05:15 | 2023-12-02T21:57:42Z | MEMBER | {
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} | ## Summary
This PR adds function to `pymatgen.io.qchem.outputs` to parse (scratch) gradient, Hessian, and previous orbital coefficient files made by Q-Chem.
**Note**: 99% of the credit for this goes to @samblau. I am simply moving it into pymatgen where it belongs.
## Todos
I need to add tests. There are al... | {
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"Thanks, this is great stuff (as usual)!🥇 \r\n\r\n> Previously, respecting `user_incar_settings` was left down to specific input set implementations and there were a number of examples where this was not respected\r\n\r\nDo you think this needs better test coverage? In general, just having looked at the whole code... | 2023-11-26T22:54:21 | 2024-01-26T12:41:03 | 2024-01-20T07:12:39Z | MEMBER | {
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This PR refactors the VASP input sets to make them compatible with atomate2 and fixes some of the issues that have been raised previously.
**This PR does not introduce any breaking changes. The API for the input sets has not changed and pymatgen users can continue to use their existing code.**
The i... | {
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} | @janosh It looks like the issue from #2470 was reintroduced into pymatgen v2023.11.12
To Reproduce:
``` python
from pymatgen.symmetry.groups import SpaceGroup
```
The traceback:
``` python
Traceback (most recent call last):
Cell In[1], line 1
from pymatgen.symmetry.groups import SpaceGroup
Fil... | {
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} | Closes #3485.
Apologies! I broke this in https://github.com/materialsproject/pymatgen/pull/3464. | {
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} | ## Summary
I propose a few minor changes in the `Vasprun` object when parsing MD simulations and especially those produced with the ML option.
* the `converged_ionic` property was False for an MD simulation. But the check did not seems reasonable for an MD
* the number of steps for a simulation that involves ML MD... | {
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"How does this look, @janosh?",
"I think your most recent proposed changes (particularly the use of str.split() to form the key lists) save a small number of characters at the expense of increasing cognitive load.\r\n\r\nAs long as this gets merged, I don't really care, but at some point I'd love to chat with you... | 2023-12-04T21:01:05 | 2023-12-19T01:05:31 | 2023-12-05T17:06:58Z | CONTRIBUTOR | {
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Tests for relevant classes pass locally, black and ruff seem happy enough for the files I changes. Didn't check mypy, so here's praying. | {
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- Added fake POTCAR libraries to replace real POTCAR libraries in `tests/files` to stop infringing VASP copyright. Also added a PBE_64 fak... | {
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"@fraricci Thanks for pointing this out. Your fix needs to be accompanied by a new test so PRs welcome!\r\n\r\n@utf Good example for https://github.com/materialsproject/pymatgen/pull/3484#issuecomment-1826933582",
"Just to note that this was also fixed in #3484 \r\n\r\nhttps://github.com/materialsproject/pymatgen... | 2023-12-04T23:14:19 | 2023-12-06T03:00:52 | 2023-12-06T03:00:52Z | CONTRIBUTOR | {
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} | ```py
In [24]: MPHSEBSSet(structure,mode="Uniform",reciprocal_density=100).reciprocal_density
Out[24]: 50
In [25]: MPHSEBSSet(structure,mode="Uniform",user_kpoints_settings={"reciprocal_density":100}).reciprocal_density
Out[25]: 50
# the only way to get it right
In [26]: MPHSEBSSet(structure,mode="Uniform",user... | {
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"> Thanks @lbluque! 👍 \n> \n> Can we change this method to return the `ax` (`fig` for plotly)? Don't see a reason not to return. And add a test for the return type?\n\nThat looks like the `get_plot` method already does. This is for the `show` method to display the plot, in which the current implementation only wor... | 2023-12-05T04:44:01 | 2023-12-07T04:31:02 | 2023-12-06T22:31:36Z | CONTRIBUTOR | {
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} | ## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference re... | {
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"Just a general point, there are several approaches to adding interstitial atoms in the [pymatgen-analysis-defects](https://github.com/materialsproject/pymatgen-analysis-defects/) package, including\r\n\r\n- [Voronoi](https://github.com/materialsproject/pymatgen-analysis-defects/blob/aaa68e29ffa84599f306984b0f95eaa... | 2023-12-05T05:31:55 | 2023-12-05T23:21:24 | 2023-12-05T22:30:07Z | NONE | {
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} | ## Summary
Major changes:
- feature 1: add_interstitial() method
## Todos
Optimisation of the loops for larger structures.
## Checklist
- [x ] Google format doc strings added. Check with `ruff`.
- [x ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If ... | {
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"> Can you please add a test for this?\r\n\r\nSure, I have added a test for CombinedData."
] | 2023-12-05T10:24:12 | 2023-12-07T01:53:29 | 2023-12-06T17:28:41Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- feature 1: ...
- fix 1: Fix bug "TypeError: argument of type 'NoneType' is not iterable". Not all LammpsData in CombinedData should have attribute force_field, replace this `NoneType` attribute with `[]` to skip unexisting force_field.
## Todos
If this is work in progress, what ... | {
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"Thanks @janosh! Probably not worth adding tests for it. I'd suggest to either keep it in mind for any new `MPRester.request()` calls or to ensure that `MPRester.request()` always adds a trailing-slash."
] | 2023-12-05T22:21:53 | 2023-12-05T23:05:46 | 2023-12-05T23:02:50Z | MEMBER | {
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} | 5fe1c8e86f update ruff-pre-commit to v0.1.7
aa89d614e1 fic doc str indent
571f33e5c7 improve test_get_neighbor_list
0ffd0c9743 improve test_ebands_input
fd23063b88 improve asserts in test_get_feff_pot | {
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"@janosh is it really always an integer in VASP?",
"VASP manual states it is a REAL value: https://www.vasp.at/wiki/index.php/ZVAL",
"IIUC the issue here is about writing critic2 input files, not parsing of `ZVAL` from VASP files",
"Thanks. Yes, I have seen it now as well. "
] | 2023-12-06T05:44:41 | 2024-01-08T23:42:51 | 2024-01-08T10:10:35Z | CONTRIBUTOR | {
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} | ERROR: type should be string, got "https://github.com/materialsproject/pymatgen/blob/ebd776900edfc45bd3b9f045e1e04db1e2d2752b/pymatgen/command_line/critic2_caller.py#L198C1-L198C17\r\n\r\nMain issue:\r\n**formatting for zval is incorrect, causes failure when running .cri file**\r\n\r\nDefault behavior of the pmg Potcar object that is initialized by the Critic2Caller.from_path() method returns zval as a float rather than an int:\r\n\r\nSource from line 1640 in pymatgen.io.vasp\r\n```python\r\n parse_functions = dict(\r\n LULTRA=_parse_bool,\r\n LUNSCR=_parse_bool,\r\n LCOR=_parse_bool,\r\n LPAW=_parse_bool,\r\n EATOM=_parse_float,\r\n RPACOR=_parse_float,\r\n POMASS=_parse_float,\r\n ZVAL=_parse_float,\r\n```\r\n\r\nWhich causes an error because the float is not converted to int\r\n\r\n```python\r\n if not zpsp:\r\n potcar_path = get_filepath(\r\n \"POTCAR\",\r\n \"Could not find POTCAR, will not be able to calculate charge transfer.\",\r\n path,\r\n suffix,\r\n )\r\n\r\n if potcar_path:\r\n potcar = Potcar.from_file(potcar_path)\r\n zpsp = {p.element: p.zval for p in potcar}\r\n```\r\n\r\nFor anyone with the same issue, remove POTCAR from the directory and pass zpsp as an argument. \r\n\r\nOtherwise you will get a similar error in the output:\r\n\r\n```\r\n%% load int.CHGCAR id chg_int zpsp H 1.0 Au 11.0 C 4.0 S 6.0\r\n\r\nERROR : load int.CHGCAR id chg_int zpsp H 1.0 Au 11.0 C 4.0 S 6.0\r\nERROR (load): wrong syntax in ZPSP\r\n```\r\n\r\n\r\n" | {
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"Thanks a lot! We need a test for this fix."
] | 2023-12-06T05:53:38 | 2024-01-08T10:10:34 | 2024-01-08T10:10:34Z | CONTRIBUTOR | {
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} | Closes #3501.
Formatting for `zval` in Critic2Caller.from_path() method wrote `zval` as a `float` rather than an `int`, causing failure when running `.cri` file.
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"<b> Update </b>\r\nI noticed I had the same issue when trying to instantiate a Structure from a CONTCAR file... It seems that my compilation of VASP produces a CONTCAR file that features a slash after each element on the 6th line such as ```X/ Y/ Z/``` instead of the usual ```X Y Z```. It works as it should when I... | 2023-12-06T10:10:43 | 2023-12-08T15:25:49 | NONE | {
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} | <b> Problem </b>
When I try to instantiate a ```pymatgen.io.vasp.outputs.Locpot``` object from the file, I get an ```IndexError``` from the ```Species.from_str``` call. I am using pymatgen v2023.11.12.
<b> Example </b>
```
Python 3.11.6 | packaged by conda-forge | (main, Oct 3 2023, 10:40:35) [GCC 12.3.0] on linux... | {
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"Oh dear, loss of symmetry in `__eq__` is pretty serious, esp. in the core `Structure` class.\r\n@bpuchala Thanks for reporting and thanks for finding the root cause! 🙏 \r\n\r\nI'm in favor of making `Structure.__eq__` more discriminative by promoting `Elements` to `Species` with oxi state 0 so that\r\n\r\n```py\r... | 2023-12-06T17:31:47 | 2023-12-08T18:51:16 | 2023-12-08T18:46:19Z | NONE | {
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```py
from pymatgen.core import IStructure
lattice_vectors = [[5.692, 0.0, 0.0], [0.0, 5.692, 0.0], [0.0, 0.0, 5.692]]
coords_frac = [
[0.0, 0.0, 0.0],
[0.0, 0.5, 0.5],
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"It appears to me that the `get_correction` method under `pymatgen.entries.compatibility` explicitly requires the `run_type` to be in `{\"GGA\", \"GGA+U\"}`, which in this case the `run_type` is `PBE`. However:https://github.com/materialsproject/pymatgen/blob/1dd74a8479ee700552accea770c3ceda85ef89c9/pymatgen/io/vas... | 2023-12-08T02:04:59 | 2024-01-08T16:06:42 | 2024-01-08T16:06:42Z | NONE | {
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```
from pymatgen.io.vasp import Vasprun
from pymatgen.entries.compatibility import MaterialsProjectCompatibility, AnionCorrection
vasprun1 = Vasprun("data/mp_1595_vasprun.xml")... | {
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} | 90a26c5bfd bump actions/setup-python to v5
4d739850b4 add **kwargs to get_plot_gs() to customize ax.plot()
6e56052f00 rename single-letter vars
4e08e01165 add label kwarg PhononBSPlotter and to plot_compare method to show in legend
fe3973805b fix PhononDosPlotter.get_plot dropping default font size when passing **k... | {
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"@janosh: I was looking to see if I could lower the numpy bound (i.e. see if the suite still passes)",
"The errors here are not from your `numpy` version change but would have also happened on `master`.\r\n\r\nI just fixed them in https://github.com/materialsproject/pymatgen/pull/3507.",
"@janosh: Yup, just not... | 2023-12-10T17:42:37 | 2023-12-10T19:00:46 | 2023-12-10T18:55:28Z | MEMBER | {
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"> i'm a bit concerned here that the tests pass even if you remove all attributes from\r\n> \r\n> ```python\r\n> @dataclass\r\n> class KpointOptProps:\r\n> \"\"\"Simple container class to store KPOINTS_OPT data in a separate namespace. Used by Vasprun.\"\"\"\r\n> \r\n> tdos: Dos | None = None\r\n> idos:... | 2023-12-10T23:04:22 | 2024-02-23T18:55:07 | 2024-02-23T11:23:19Z | CONTRIBUTOR | {
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} | ## Summary
This pull request resolves Issue #3455 , implementing parsing functionality for band structures generated using KPOINTS_OPT.
KPOINTS_OPT is a new VASP feature which provides an alternative method for specifying k-points for hybrid band structures.
The KPOINTS_OPT-related data is now read in by the Vaspr... | {
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314512682c add return type to `PhononDos` method doc strings
6072af8b2a define arithmetic dunder methods for `PhononDos` `__add__` `__sub__` `__mul__` `__neg__` `__eq__`
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"Thanks a lot! This is much appreciated! 👍 \n\nWe also need extensive tests for these three new features.",
"Hi, Janosh. I have made the modifications according to your feedback and further added comments. It is my first PR in github, I'm not familiar with this😂\r\n\r\nPlease check if there are any unreasonable... | 2023-12-13T05:22:45 | 2024-01-18T11:21:42 | 2024-01-18T11:21:42Z | CONTRIBUTOR | {
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PWmat is a GPU-accelerated first-principles calculation software developed under the leadership of Professor Lin-wang Wang. I am currently utilizing it for my research project, and in the course of this work, I have written some scripts. I hope to submit them to pymatgen to assist more people in convenien... | {
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"Unfortunately this is very old code that few people uses. You will need to contact the Zeo++ developers on this as we do not support Zeo++ directly.",
"However, the related description of `Zeo++` still appears in the current [document](https://pymatgen.org/installation.html):\r\n\r\n> Zeo++: For defect structure... | 2023-12-13T10:33:56 | 2024-02-03T06:07:55 | 2023-12-13T16:49:40Z | NONE | {
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I would like to use Zeo++ but I had some problems with the installation. The installation instruction seems to be missing from the documentation but is available from previous discussions (https://github.com/materialsproject/pymatgen/issues/290).
I had problems with this download command: svn checkout --us... | {
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Is it possible to update the conda build to track the latest github / `pip` releases?
```
Could not solve for environment specs
The following packages are incompa... | {
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**Before**
**After (with `bold=True`)**
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"Doesn't catch the \"NaN\" -> float(\"NaN\") edge case\r\n\r\n```py\r\n>>> Composition(float(\"NaN\"))\r\nTraceback (most recent call last):\r\n File \"<stdin>\", line 1, in <module>\r\n File \"pymatgen/pymatgen/core/composition.py\", line 127, in __init__\r\n elem_map = dict(*args, **kwargs) # type: ignore\r... | 2023-12-15T03:08:07 | 2023-12-15T18:00:27 | 2023-12-15T03:29:14Z | MEMBER | {
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```py
>>> Composition(float("NaN"))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pymatgen/pymatgen/core/composition.py", line 127, in __init__
elem_map = dict(*args, **kwargs) # type: ignore
TypeError: 'float' ob... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3519 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3519/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3519/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3519/events | https://github.com/materialsproject/pymatgen/pull/3519 | 2,044,171,011 | PR_kwDOACgets5iInXe | 3,519 | Raise `ValueError` for `float('NaN')` in `Composition` | {
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"Have you checked the tolerance in detail? I think it might be very tight. Similar for the overall tolerance",
"I just copied the `tol=1e-5` from the existing `has_imaginary_freq` method but use `tol=1e-3` in my own analysis. Should we increase to `tol=1e-3` by default?",
"> I just copied the `tol=1e-5` from th... | 2023-12-16T18:49:24 | 2023-12-16T19:58:30 | 2023-12-16T19:58:29Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3521 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3521/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3521/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3521/events | https://github.com/materialsproject/pymatgen/issues/3521 | 2,044,978,333 | I_kwDOACgets554-Sd | 3,521 | can't install pymatgen==2023.2.28 on Apple Silicon. | {
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"Any reason you need to install `2023.2.28`, an outdated version?",
"> Any reason you need to install `2023.2.28`, an outdated version?\n\nThe latest version of \"nomad-lab\" requires it.",
"@KatiGithub https://github.com/nomad-coe/nomad/pull/91 may solve that issue. Feel free to report back here if that's not ... | 2023-12-16T22:20:39 | 2023-12-20T18:25:41 | 2023-12-20T18:25:40Z | NONE | {
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Specs:
Apple M1 Pro
Python v3.10
The installation process keeps failing at the "building wheel" stage with this error output.
```py
Error compiling Cython file:
------------------------------------------------------------
...
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"Thanks @rkingsbury! 👍 "
] | 2023-12-17T15:08:43 | 2024-10-10T01:55:03 | 2023-12-17T15:47:55Z | CONTRIBUTOR | {
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Documents the `svp` and `pcm_nonels` kwargs of `QCInput`. Closes #3432 | {
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"Could you @Asif-Iqbal-Bhatti please include a minimal code snippet so that I could identify the issue more easily? Which module was used to produce this plot (is it `NEBAnalysis` under `pymatgen.analysis.transition_state`)? Thanks.\r\n\r\nI just looked into the [following code](https://github.com/materialsproject... | 2023-12-18T13:03:42 | 2024-01-22T19:49:32 | 2024-01-22T19:49:32Z | NONE | {
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I want to report that using the NEB analysis object to get the diffusion barrier, there is a label value error on the barrier height. I have attached one of the NEB plots. If you see the y-axis scale and barrier value, it does not make sense. It should be 20.4 meV, not 204 meV.
![Capture](https://github.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3524 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3524/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3524/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3524/events | https://github.com/materialsproject/pymatgen/pull/3524 | 2,047,218,368 | PR_kwDOACgets5iSyE9 | 3,524 | `PhononDos.get_smeared_densities` return unchanged for `sigma=0` | {
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} | 47fc96b6fd PhononDos.get_smeared_densities add special case for 0 Gaussian smearing
7079c6134c remove unnecessary assignment in test_dos.py
c3681eafa1 test sigma=0 in TestPhononDos.test_get_smeared_densities | {
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} | New method to find the last peak in the phonon DOS defined as the highest frequency with a DOS value at least `threshold` * height of the overall highest DOS peak. In case no peaks are high enough to match, the threshold is reset to half the height of the second-highest peak.
A peak is any local maximum of the DOS a... | {
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"This is a great idea that I'd love to see implemented.\r\nOn Mon, Dec 18, 2023, 6:34 PM Richard Tran ***@***.***> wrote:\r\n\r\n> Problem\r\n>\r\n> At the moment, all analysis in pourbaix_diagram.py assumes that we are\r\n> operating under room temperature. As a result, we assume all free energies\r\n> will have a... | 2023-12-19T02:34:00 | 2023-12-19T04:36:40 | CONTRIBUTOR | {
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} | ### Problem
At the moment, all analysis in pourbaix_diagram.py assumes that we are operating under room temperature. As a result, we assume all free energies will have a prefactor of 0.0591 for the pH variable i.e. pH * k_B * T * ln(10) (in eV) where T= 298K (RT) and k_B * T * ln(10) = 0.0591.
**Is there a (che... | {
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} | Hi all, another small PR that makes sure labels are passed when a `Symmetry.from_spacegroup` is used. This follows-up on an earlier PR: https://github.com/materialsproject/pymatgen/pull/3183
## Summary
Major changes:
- fix 1: Fix label propagation in `Symmetry.from_spacegroup`
## Checklist
- [x] Google f... | {
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"Changes made accordingly. Thanks for your explainations here.",
"@janosh Thanks for reviewing and the comments. Actually my first time PR, just started to working in the community and would try to keep working with you guys.",
"That sounds great! The more, the merry! 😄 "
] | 2023-12-20T03:20:17 | 2023-12-28T03:03:27 | 2023-12-20T03:48:37Z | CONTRIBUTOR | {
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} | # Summary
This pull request addresses suggestions to solve #3449 by adding two new issue templates.
Major changes:
- Added a new issue template for "Bug Report."
- Included an issue template for "Feature Request," aligning it with the original issue template format.
Please feel free to provide any suggesti... | {
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"Hi @janosh, I have added a test in pymatgen.tests.vis.test_plotters\r\n\r\nAlso, I added a line to check the given object has attributes x and y in SpectrumPlotter.add_spectrum. This can directly point out the problem that the given object has no x and y.\r\n\r\n```\r\nassert hasattr(spectrum, \"x\") and hasattr(\... | 2023-12-20T03:22:30 | 2023-12-20T17:43:30 | 2023-12-20T17:43:30Z | CONTRIBUTOR | {
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```python
def add_spectra(self, spectra_dict, key_sort_func=None):
"""
Add a dictionary of doses, with an optional sorting function for the
keys.
Args:
dos_dict: dict of {label: Dos}
key_sort_func: function used to sort ... | {
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} | 6087d5d90 PhononDos.get_last_peak reduce threshold value from 10% to 5%
8649e793a PhononBandStructure add max_freq() equivalent to min_freq() method
0dd35274e i->idx
d92f0e748 test_bandstructure.py add new test cases for (min|max)_freq
f77779c25 refactor symbol mapping in ExcitingInput and PhononBandStructure
dddd... | {
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"Good idea, thanks @DanielYang59!",
"Cheers! @janosh "
] | 2023-12-21T02:12:02 | 2023-12-21T02:25:21 | 2023-12-21T02:15:42Z | CONTRIBUTOR | {
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} | # Summary
Add default issue template labels, as I notice most recent issues are not assigned a label by the raiser, and also the prefix was removed as suggested by @janosh in #3528.
- Add default label "bug" for `Report a Bug`.
- Add default label "enhancement" for `Feature Request`. | {
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"@janosh Yes sure. I would try to get my hands on that ASAP. \r\n\r\nI adjusted the imports to alphabet order while I was fixing the run type issue, but that commit seems to have been reversed by workflow or something?",
"Imports are auto-sorted by `ruff`. No need to worry about that.",
"Thanks for clarifying @... | 2023-12-27T02:20:04 | 2024-01-09T01:48:53 | 2024-01-04T01:45:20Z | CONTRIBUTOR | {
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} | ## Summary
- Fixed inconsistent non-GGA run type handling, to fix #3506.
## Need suggestions from maintainer
As discussed in #3506, the run type of "PBE" is not treated as "GGA" which seems to be inconsistent with the defination in the following part: https://github.com/materialsproject/pymatgen/blob/1dd74a847... | {
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50d7c2e63 add TestPhononDos.test_r2_score
547cb669e better get_linear_interpolated_value err msg | {
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"also, could you rebase your branch onto pymatgen `master`?",
"I'm really sorry @janosh. I must have been messing with commits trying to rebase and combine my commit history. Should I close this PR and reopen a new one? "
] | 2023-12-31T13:34:01 | 2024-01-01T01:51:00 | 2024-01-01T01:51:00Z | CONTRIBUTOR | {
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- Added a codespace container configuration file.
- Added a brief guide to use codespace container for issue reproduction.
- Added link in issue template to encourage users to try this new workspace.
However I still need advice on handling user feedbacks, as I failed to identify a... | {
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"Also to answer your @janosh question in #3536 that:\r\n\r\n> Shouldn't this markdown be part of the issue template?\r\n\r\nMy idea is to keep the issue template clean (and it is not a tutorial at the end of the day), and make codespace optional (instead of \"pushing\" codespace to users). \r\n\r\nHowever it occurs... | 2024-01-01T03:05:36 | 2024-01-26T12:40:31 | 2024-01-08T08:55:23Z | CONTRIBUTOR | {
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- Added link in issue template to encourage users to try this new workspace.
However I still need advice on handling user feedbacks, as I... | {
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"An easy workaround for this issue is to use VASP version 6.4.0.\r\nIf using the newer VASP version 6.4.2, need to update INCAR with `LVTOT = \"False\"` (to not parse from LOCPOT file). This can be done by using `update_user_incar_settings` command.",
"So if I understand correctly, VASP 6.4.2 adds the extra `/` t... | 2024-01-01T17:37:26 | 2024-01-25T22:00:16 | 2024-01-22T19:39:30Z | CONTRIBUTOR | {
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} | atomate2 fails to create TaskDoc as it cannot parse the LOCPOT file generated after the VASP calculation. This happens if we use newer PBE 54 pseudopotential with hash or just using VASP version 6.4.2. The issue is where the element's name is printed in the LOCPOT file, which would be further used in the POSCAR file fo... | {
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updates:
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"Regarding the 1st POSCAR in the original issue. There is: https://github.com/materialsproject/pymatgen/blob/8aa1cf89a93e12c2ac16ddde517105e307a04b91/pymatgen/io/vasp/inputs.py#L121-L124\r\n\r\nMeaning selective dynamics array would only be written when there exists at least one degree of freedom (DOF) frozen. And ... | 2024-01-02T05:29:51 | 2024-02-23T02:26:13 | 2024-02-13T08:20:07Z | CONTRIBUTOR | {
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Major changes:
- Issue warning in `from_str` method when invalid selective dynamics info would found in POSCAR, to resolve #3008.
- Clean up INCAR tag checkings in `check_params` method.
- Fix missing type checkings in`test_check_params` of `tests/io/test_inputs.py`.
Minor changes:
- Issue warn... | {
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"@materialsproject/pymatgen-maintainers is something amiss with the CI tests? They are all failing with\r\n\r\n```\r\n × Getting requirements to build wheel did not run successfully.\r\n │ exit code: 1\r\n ╰─> [20 lines of output]\r\n Traceback (most recent call last):\r\n File \"/opt/hostedtoolcache... | 2024-01-03T19:06:33 | 2024-10-10T01:55:04 | 2024-01-08T16:06:41Z | CONTRIBUTOR | {
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} | Fixes #3506
See discussion in #3534 which settled on moving the run type check and `raise` statement to `get_adjustments` itself and remove the other statements, as illustrated [here](https://github.com/materialsproject/pymatgen/pull/3540/files) as the cleanest fix.
The logic is the following:
- when `process_en... | {
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"Thanks Aaron!",
"Also noting another (Pythonic) SQS generator in `icet` although I have not tried it myself."
] | 2024-01-03T20:56:21 | 2024-01-25T16:38:29 | 2024-01-05T19:33:51Z | CONTRIBUTOR | {
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} | The `SQSTransformation` class in `pymatgen.transformations.advanced_transformations` has a `return_ranked_list` kwarg in `apply_transformation`.
Because this can be either boolean (return all best SQS structures from parallel runs) or an int (return only the `return_ranked_list` best SQS structures) and `bool` subc... | {
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"Thanks for these nice improvements @esoteric-ephemera \r\n\r\nSince you’re looking at this part of the code, do you have a view of how H2O or OH sites should be handled? It’s one remaining weakness of the CIF parser I think.",
"Also adding a note that the `mp` prefix has been registered with the IUCr, if we want... | 2024-01-05T20:25:09 | 2024-01-29T19:27:11 | 2024-01-17T08:50:58Z | CONTRIBUTOR | {
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- `pymatgen.io.cif.CifParser` now checks that the composition reported in a CIF matches that of the resulting `pymatgen` `Structure` and if not, warns the user what elements are missing (most often Hydrogens in experimental CIFs which are hard to locate without using neutron scattering), or ... | {
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} | I commented out BoltzTraP2 in `setup.py` util broken install is fixed, hopefully following merge of https://gitlab.com/sousaw/BoltzTraP2/-/merge_requests/18.
Pinging @esoteric-ephemera who helped troubleshoot this issue.
<details><summary>Install logs</summary>
```python
Collecting BoltzTraP2>=22.3.2 (from py... | {
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4c651752d `test_convenience_imports()` | {
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"Note added: the bug persists in pymatgen version 2023.12.18. ",
"Hi @deecadance, can you explain why you expect to get space group 12 here? The space group of the POSCAR you attached is 8, and you're not directly symmetrizating the structure.\r\n\r\n`symprec` and `angprec` control the tolerance with which pymatg... | 2024-01-09T13:34:45 | 2024-02-01T10:40:46 | NONE | {
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} | ### Python version
Python 3.10.13
### Pymatgen version
Version: 2023.11.12
### Operating system version
Mac OSX 13.2.1
### Current behavior
```Python
I try to symmetrize a POSCAR file. The symmetrization is successful but the structure produced is wrong: space group is 8 and the atoms are clearly overlapping. Us... | {
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"Hi @janosh , This PR can be reviewed",
"@JaGeo , just tagging you here incase you have comments on this.",
"> lgtm! 👍\r\n\r\nThanks! I missed adding it as decorator so did not seem to work. Good to know how to correctly use it 😃 "
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"It seems some other unit tests (for example `tests/io/vasp/test_outputs.py`) are broken as well? (Or something with my environment?) Can you please look into this? @janosh ",
"Closed as everything seems to work just fine in my home PC. Might be something wrong with my office PC. I would double check from my side... | 2024-01-12T03:20:28 | 2024-01-12T05:08:44 | 2024-01-12T05:07:13Z | CONTRIBUTOR | {
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Python 3.10.13
### Pymatgen version
Version: 2023.12.18
### Operating system version
Ubuntu 20.04.6 LTS (Codespace Container)
### Current behavior
Not sure if I'm missing anything, the unit test of `tests/io/vasp/test_inputs.py` seems broken? I tried to run the unittest in a br... | {
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Right now, there is not too much flexibility with the `CifWriter` when it comes to what fields can be written out to the resulting CIF. It does have a keyword argument for writing out magnetic moments, but that's really it. It would be ideal to support a more generic option where the user can w... | {
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"Hey @hongyi-zhao, sorry for the slow response. This issue may have been recently fixed by PR #3542, see also (potentially duplicate) issue #3571\r\n\r\nIf you're still having issues parsing VASP I/O after upgrading PMG (the latest release should have these fixes), please let me know!",
"closing this as assumed f... | 2024-01-13T13:14:49 | 2024-01-31T12:57:12 | 2024-01-31T12:57:11Z | CONTRIBUTOR | {
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While using vasp.6.4.2 compiled with HDF5 support, I've encountered an issue while working with pymatgen for handling some of the output files, aka, CONTCAR/CHGCAR/CHG, where I found some strings in these files that I hadn't seen before, as shown below:
```
$ ug -a Re/5e0f28cc669
CONTCAR: R... | {
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"@janosh: This is ready for review!\r\n\r\nEdited because I solved the issue."
] | 2024-01-13T23:11:32 | 2024-01-26T12:41:55 | 2024-01-14T15:51:16Z | MEMBER | {
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Closes #3548 by adding a `write_site_properties: bool = False` keyword argument to `CifWriter`. Existing behavior is unchanged, but if `write_site_properties = True`, then the `Structure` object's site properties will be written out to the CIF file as atom site entries.
In principle, it would be nice t... | {
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} | ### Python version
Python 3.11.7
### Pymatgen version
Version: 2023.12.18
### Operating system version
Ubuntu
### Current behavior
```Python
Version: 2023.12.18
```
### Expected Behavior
When using a `Path` as the `filename` in `Structure.to()`, a file should be written. Instead, the foll... | {
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4cd59493a test_structure.py add self.struct.properties["foo"] = "bar" for test_to_from_abivars() | {
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1a39d626f accept Path objects as filename in IStructure.to()
5afdf01c7 add test case for saving structure to pathlib.Path | {
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"Tagging @JonathanSchmidt1 as I have seen a similar fix in one of his atomate2 branches. ",
"@JaGeo My solution basically was the same as here.\r\n Maybe sth relevant for you is that when I added magnetic moments it broke sth in atomate2 because some of the functionalities of phonopy did not work with magnetic ... | 2024-01-15T11:03:32 | 2024-01-15T14:09:14 | 2024-01-15T14:08:43Z | CONTRIBUTOR | {
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Phonopy needs magnetic moments to calculate the symmetry etc, currently pymatgen does not send it.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
python -m pytest tests/io/test_... | {
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"Oof thanks for reporting this @kuwabara74 and @janosh! Yes I've made this a private attr in #3491, which hopefully fixes the docs issue. Huge oversight on my part!",
"> Huge oversight on my part!\r\n\r\nNo worries. I didn't even know it would end up as 10k lines in the docs as a non-private attribute.\r\n\r\nAny... | 2024-01-15T13:52:06 | 2024-01-17T08:33:12 | 2024-01-17T08:33:12Z | MEMBER | {
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<div type='discussions-op-text'>
<sup>Originally posted by **kuwabara74** January 15, 2024</sup>
Hello,
The documentation web page of pymatgen.io.vasp package (https://pymatgen.org/pymatgen.io.vasp.html) is too heavy to open immedi... | {
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02593cd21 test_structure.py cover fmt='yml' in test_to_from_file_string | {
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"I am not a pymatgen developer, but I am working on a class that does basically this. \r\n\r\nMy two cents are that I would discourage crystal_sg as the amount of handpicked information you need to correctly provide the coordinates in terms of Wyckoff positions to QE is too large, and also you don't get the informa... | 2024-01-16T14:37:00 | 2024-01-22T16:48:41 | NONE | {
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} | ### Feature Requested
Hi! When would the pymatgen.io.pwscf support for symmetry be added? It would greatly reduce the computational complexity of the input files generated.
### Proposed Solution
Implementing a function to read symmetrised CIFs, and using the crystal_sg tag in quantum espresso
### Relevant Informati... | {
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"thanks for the detailed bug report! should be a straightforward fix by turning the `if match` statement in `_parse_formula()` into a `while` loop to keep unpacking nested parens\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/20475b6e2ba9f7304f9cc2094b9fa4685c094c58/pymatgen/core/composition.py#L561-L571"... | 2024-01-17T06:37:10 | 2024-01-22T16:27:53 | 2024-01-22T16:27:53Z | NONE | {
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} | ### Python version
Python 3.10.12
### Pymatgen version
2023.12.18
### Operating system version
Ubuntu 22.04.3 LTS
### Current behavior
The `Composition` class in `pymatgen` fails to correctly parse strings containing complex chemical formulas, resulting in a `ValueError`. An example of such a formu... | {
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```diff
- with open(path, "w") as file:
+ with open(path, mode="w") as file
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"Hi @janosh, thanks for keeping on top of deprecation notices. I think we may have been a bit premature here:\r\n\r\n* There was no notice on the [compatibility](https://pymatgen.org/compatibility.html) page.\r\n* An updated atomate2 has not been released yet. I see your PR https://github.com/materialsproject/atom... | 2024-01-17T12:17:46 | 2024-02-15T11:34:45 | 2024-01-17T13:42:07Z | MEMBER | {
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Migration to the new API in all cases is to replace `(to|from|as|get)_string` with `(to|from|as|get)_str`. | {
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8b893efb0 fix structure_to_abivars() for non-hexagonal structures | {
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"@mturiansky thanks for profiling! such analysis is hugely appreciated!\r\n\r\nlazy-loading seems like a good UX improvement here. PR incoming",
"Actually, I'm not sure this solves the problem. Sorry, I probably could have been more clear in my description.\r\n\r\nThe reason this doesn't work is because the impor... | 2024-01-18T06:52:15 | 2024-01-25T00:41:06 | 2024-01-22T16:13:29Z | CONTRIBUTOR | {
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} | ### Feature Requested
I noticed that pymatgen can have quite an overhead when importing relatively simple pieces of code from within. From a computing point of view, it's a rather small cost (and something inherent to python), but from a UX perspective, it can be quite noticeable. Take the simple example of importing ... | {
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"Hi @janosh, I found some bugs on Ruff when it recently upgraded to `0.1.14`.\r\nWhen I firstly run `ruff format --check .` locally, it has the warning of \"The following rules may cause conflicts when used with the formatter: `ISC001`.\"\r\nThus I added the conflict formatter `ISC001` into `pyproject.toml` ignore ... | 2024-01-20T07:43:33 | 2024-01-24T10:05:55 | 2024-01-20T14:32:08Z | MEMBER | {
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} | 47b91ebc9 fix ruff SIM300 Yoda asserts
2d8571f4c fix ruff F841 local var assigned but never used
6c278aa33 fix ruff SIM113 use enumerate() for index variable
c9d67d973 fix ruff RUF021 parenthesize `a and b` when chaining `and` and `or` together
386b969ec fix likely unintentional operator precedence in LobsterEnv._f... | {
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