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https://api.github.com/repos/materialsproject/pymatgen/issues/3565 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3565/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3565/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3565/events | https://github.com/materialsproject/pymatgen/issues/3565 | 2,091,954,188 | I_kwDOACgets58sLAM | 3,565 | Add alias `VaspInputGenerator` for `VaspInputSet` | {
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} | My decision is that I have no problems with having an alias called VaspInputGenerator. But VASPInputSet will not be deprecated. Let's be pragmatic - there are many things we probably want to rename. But deprecation of classes/methods creates headaches and unless there is an actual practical benefit, i.e.,... | {
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"Thanks @janosh !\r\nI would add the aliases to the subclasses too. For the base VaspInputSet, it's almost never used directly so it would not clarify things for the users. I can do that and make a PR to your vasp-input-gen-alias. I think it would be useful to add some explanations or note on this in the documentat... | 2024-01-20T07:59:28 | 2024-02-23T11:28:01 | 2024-02-23T10:52:37Z | MEMBER | {
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Closes #3565.
@utf @davidwaroquiers Let me know if this serves your purpose and if you think more changes along similar lines would make sense. | {
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"Hi @SteakEnthusiast, thanks for getting in touch. I have enabled [private vulnerability reporting](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing-information-about-vulnerabilities/privately-reporting-a-security-vulnerability) for this repo, which should allow you to ... | 2024-01-20T16:31:17 | 2024-01-21T00:38:35 | 2024-01-21T00:38:35Z | NONE | {
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I've identified a potential security issue that can arise from parsing arbitrary user input with the Pymatgen library. To securely address this, I am requesting that a [temporary private fork](https://docs.github.com/en/code-security/security-advisories/working-with-repository-security-advisories/c... | {
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9896133d3 fix highly-nested formula parsing in Composition
aca351cb4 add failure cases from gh-3559 as tests | {
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doesn't look like anything's actually broken in #3523 but still good to add a test. | {
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185711cd0 `test_remove_oxidation_states()` `assert struct_out is struct_specie` | {
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The ordering property of the CollinearMagneticStructureAnalyzer class is set depending on the `total_magnetization = abs(sum(magmoms))`. Due to floating point imprecision, the sum of magmoms can adapt values close to zero instead of zero. This can, for example, lead to collinear AFM structures being miscl... | {
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"Hi @utf, I have a quick question here: is there any particular reason for skipping `ENCUT` in INCAR (set as None) in `MITMDSet` and `MPMDSet`?\r\nhttps://github.com/materialsproject/pymatgen/blob/7e0c8f4ddea72367c2059865b0fa8cf8681663ea/pymatgen/io/vasp/sets.py#L2409\r\nhttps://github.com/materialsproject/pymatgen... | 2024-01-24T09:44:00 | 2024-01-31T19:08:30 | 2024-01-31T09:36:56Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- Follow #3484, add tests and clean up test_sets.py
## Todos
- Add more MD and NED-related tests
- Fix lints
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fi... | {
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"> They could also be affected by the error described in PR https://github.com/materialsproject/pymatgen/pull/3574 - do you think it's a good idea to add a threshold here as well?\r\n\r\nwhat would change based on the threshold? setting `self.total_magmoms` and `self.magnetization` to exactly 0 when below the thres... | 2024-01-24T13:47:58 | 2024-01-25T06:13:58 | 2024-01-25T06:13:58Z | CONTRIBUTOR | {
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A parameter threshold_ordering was added to CollinearMagneticStructureAnalyzer below which the total magnetization is treated as zero when defining the magnetic ordering.
@JaGeo @janosh `self.total_magmoms = sum(magmoms)` and `self.magnetization = sum(magmoms) / structure.volume` are defined before pro... | {
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} | ### Python version
Python 3.11.x
### Pymatgen version
2023.12.18
### Operating system version
_No response_
### Current behavior
The `QCOutput` file parser does not parse a lot of the data in Q-Chem 6.1.1 output files because various lines have been changed. For instance, the "final_energy" propert... | {
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"Feel free to use it. But pls acknowledge pymatgen and its development team. Also, I would just caution that we periodically update the json file to fix errors, add more properties, etc. "
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Thanks for all of your work on such an important library.
I'm currently working on a Rust project intended to be spiritually similar to pymatgen, but reimagined for a a different language and goals. (It's open-source as well.) I'd like to keep rough API compatibility where possible, though, and so if possi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3580 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3580/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3580/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3580/events | https://github.com/materialsproject/pymatgen/pull/3580 | 2,098,946,497 | PR_kwDOACgets5k_SU_ | 3,580 | Support parsing of "final_energy" in Q-Chem 6.1.1 | {
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} | ## Summary
This PR enables proper parsing of "final_energy" in Q-Chem 6.1.1 with `QCOutput` while maintaining backwards compatability. Partially addresses, but does not fully close, #3578.
CC: @samblau, @espottesmith, @rkingsbury
@janosh --- the error seems unrelated and is in `main`.
## Checklist
- [X]... | {
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} | ### Feature Requested
Right now, the Q-Chem `QCOutput` parser has a very rudimentary way of getting the version and only reports the major version, e.g. "6" instead of "6.1.1". It should report the full version. Note that 6.0 is reported as "6.0" and not "6.0.0".
```python
from pymatgen.io.qchem.outputs import Q... | {
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"when i first tried `StructureVis` 1-2 years ago i got the same behavior. not sure when it was last working. bug fix PRs welcome!",
"I've discovered that the issue is two-fold.\r\n\r\n1) I failed to read the documentation correctly and didn't realize that I needed to use the **set_structure** function on the newl... | 2024-01-25T01:19:50 | 2025-04-01T13:05:36 | 2024-01-25T23:58:09Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.11.0
### Pymatgen version
2023.12.18
### Operating system version
CentOS Linux 8
### Current behavior
I am attempting to visualize a crystal structure using the structure_vtk module. However, it just opens up a blank white window.
### Expected Behavior
I would like... | {
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"Thanks. Solution 2 has been implemented"
] | 2024-01-25T15:48:46 | 2024-01-25T15:55:51 | 2024-01-25T15:55:38Z | CONTRIBUTOR | {
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} | ### Feature Requested
Square brackets are used in formulas to denote coordination complexes, e.g. as in (NH4)2[FeCl5(H2O)].
At the moment, when instantiating a Composition object from a single string, _parse_formula() only searches for substrings in round brackets.
`match = re.search(r"\(([^\(\)]+)\)\s*([\.e\d]*)"... | {
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"I find it the `get_structure()` returns primitive cell, but the precision loss seems non-trivial"
] | 2024-01-26T02:00:57 | 2024-01-26T07:15:33 | 2024-01-26T07:15:33Z | NONE | {
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} | ### Python version
3.11.4
### Pymatgen version
2023.10.11
### Operating system version
Windows 11
### Current behavior
if I want to parse the "mp-13.cif" (whose content is attached at the end), I use:
```Python
parser = CifParser(fname)
lattice = parser.get_structures()[0].lattice
... | {
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e17322125 rename d|s vars | {
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"Thanks @Andrew-S-Rosen! If anyone else encounters this issue while using this release of pymatgen, please note that using `Vasprun(\"./vasprun.xml\")` should correctly parse the POTCAR in the current (relative) working directory.\r\n\r\nFixed (hopefully) in #3587 ",
"Thanks! As a note, this workaround isn't poss... | 2024-01-26T18:22:58 | 2024-01-28T18:51:30 | 2024-01-28T18:51:30Z | MEMBER | {
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} | ### Python version
3.11
### Pymatgen version
2024.1.26
### Operating system version
Ubuntu
### Current behavior
Do the following in a completed folder containing a VASP run.
```Python
from pymatgen.io.vasp.outputs import Vasprun
Vasprun('vasprun.xml')
```
```python
File /scratch/network... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3587 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3587/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3587/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3587/events | https://github.com/materialsproject/pymatgen/pull/3587 | 2,102,904,519 | PR_kwDOACgets5lMivG | 3,587 | Fix `Vasprun.get_potcars` search method; tweak fake POTCARs | {
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} | The main change here is to correct the `update_potcar_spec` method of `Vasprun` found by @Andrew-S-Rosen in issue #3586. Specifying `Vasprun("vasprun.xml")` would not find POTCARs, but specifying the leading `Vasprun("./vasprun.xml")` would. That has been corrected.
Other fixes:
- Add test for this behavior, `io/te... | {
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"A new version was released that should fix it. It is due to a bug introduced in monty."
] | 2024-01-27T01:04:19 | 2024-01-27T05:42:17 | 2024-01-27T05:42:17Z | MEMBER | {
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} | ### Python version
3.11.7
### Pymatgen version
2024.1.26
### Operating system version
Windows 11, Ubuntu
### Current behavior
```
conda create --name test python=3.11
pip install pymatgen
conda activate test
```
```Python
from pymatgen.io.vasp.outputs import Vasprun
```
Running the abov... | {
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"Changing the `__repr__` would be a safer option than changing `__str__` if we want something more readable."
] | 2024-01-27T04:54:12 | 2024-02-14T00:29:08 | CONTRIBUTOR | {
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} | Should the string representations for `Spin.up`/`Spin.down` be "up" and "down" respectively?
https://github.com/materialsproject/pymatgen/blob/ac8a7e9cd93ba9f7afeaced45dc28af6d4e151d4/pymatgen/electronic_structure/core.py#L29-L30
Similar to `OrbitalType`:
https://github.com/materialsproject/pymatgen/blob/ac8... | {
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"Thank @janosh! I was thinking of contributing myself and was waiting for comments from maintainers if this is a change that is required. No worries, I will try to fix the failed test here and open a PR to `fix-gh-3590` :)",
"thanks @R1j1t. i think this change makes sense which is why i wanted to make a PR to see... | 2024-01-28T07:56:48 | 2024-09-08T21:18:47 | 2024-02-26T14:59:07Z | MEMBER | {
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} | ## Summary
Adding the FHI-aims developers to the developers list
## 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://... | {
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"Hi @esoteric-ephemera, full support!\r\n\r\nThis is a very sensible addition, since it's in-line with existing transformation functionality. I would be happy to merge. The code itself looks fairly complete, is there anything left to be done?\r\n\r\nDon't forget to modify `setup.py`/`requirements-optional.txt` to a... | 2024-01-30T17:05:37 | 2024-02-29T19:12:01 | 2024-02-21T19:53:13Z | CONTRIBUTOR | {
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} | In a recent PR #3541, @mkhorton pointed out the existence of another SQS generation tool already natively in python, icet. This has nice features that complement the ATAT MCSQS interface already in PMG, namely generation of SQS by enumeration of all possible supercells.
This is possible for smaller supercells, and ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3594 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3594/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3594/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3594/events | https://github.com/materialsproject/pymatgen/issues/3594 | 2,108,878,919 | I_kwDOACgets59svBH | 3,594 | Issue when using pymatgen to plot dos | {
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"you can zip your `vasprun.xml` and upload the compressed version. without it, we can't repro your error.",
"i just realized your calling `python dos.ipynb`. I don't think that's supposed to work. You run the notebook through Jupyter, not with Python."
] | 2024-01-30T22:12:13 | 2024-01-31T10:51:48 | 2024-01-31T10:51:48Z | NONE | {
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} | ### Python version
Python 3.10.9
### Pymatgen version
2024.1.27
### Operating system version
linux? bridges2
### Current behavior
this is my `ipynb` file:
```py
from pymatgen.io.vasp import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
import matplotlib.pyplot as plt
v... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3595 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3595/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3595/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3595/events | https://github.com/materialsproject/pymatgen/issues/3595 | 2,109,304,901 | I_kwDOACgets59uXBF | 3,595 | tribchem: "Fixing" some issues in pymatgen. | {
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} | In [README.md](https://gitlab.com/triboteam/tribchem/-/blob/master/README.md?ref_type=heads) of tribchem, I noticed the following description [here](https://gitlab.com/triboteam/tribchem#fixing-some-issues-in-pymatgen):
> "Fixing" some issues in pymatgen
>
> In our installation, we encountered an error due to par... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3596 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3596/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3596/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3596/events | https://github.com/materialsproject/pymatgen/pull/3596 | 2,110,712,910 | PR_kwDOACgets5lmp1t | 3,596 | Switch macOS wheel building to new M1 runners | {
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} | This PR switches building the macOS wheel to [GitHub's just-announced free and much faster M1 hardware](https://github.blog/changelog/2024-01-30-github-actions-introducing-the-new-m1-macos-runner-available-to-open-source). My understanding is the compiled wheel will still be universal, i.e. run on M1 and Intel Macs. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3597 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3597/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3597/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3597/events | https://github.com/materialsproject/pymatgen/issues/3597 | 2,111,500,826 | I_kwDOACgets592vIa | 3,597 | Compare two descriptions of crystal structures to see if the have the same underlying structure. | {
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"It is called the StructureMatcher. We have had this since ages ago...",
"So, you mean that [my following code](https://github.com/romankempt/hetbuilder/issues/9#issuecomment-1920466398) is exactly for the purpose discussed here, am I right?\r\n\r\n```python\r\n$ cat pymatgen_compare_structures.py \r\nimport sys\... | 2024-02-01T04:12:29 | 2024-02-11T04:35:44 | 2024-02-01T04:53:01Z | CONTRIBUTOR | {
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} | I'm not sure if pymatgen can do the job as implemented in [XtalComp](https://github.com/allisonvacanti/XtalComp): Compare two descriptions of crystal structures to see if they have the same underlying structure.
See [here](https://github.com/romankempt/hetbuilder/issues/9#issuecomment-1920466398) for the related dis... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3598 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3598/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3598/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3598/events | https://github.com/materialsproject/pymatgen/pull/3598 | 2,112,935,188 | PR_kwDOACgets5luUMI | 3,598 | Rename `master` branch to `main` | {
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"I have said no to this before and I will not say it again. Do not merge this. ",
"there's no cost to being consistent with majority of repos but clear benefits by reducing mental burden",
"Agree with @janosh here, regardless of views on other factors, consistency has its benefits. 2 to 1?"
] | 2024-02-01T16:35:52 | 2024-02-01T21:49:51 | 2024-02-01T16:39:03Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3600 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3600/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3600/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3600/events | https://github.com/materialsproject/pymatgen/issues/3600 | 2,116,257,134 | I_kwDOACgets5-I4Vu | 3,600 | `PBE_64` configured via pmg doesn't work with pymatgen. | {
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"I noticed the following code snippet:\r\nhttps://github.com/materialsproject/pymatgen/blob/9ef132a9dcc3307ce2638b7b85aeef44abf08680/pymatgen/io/vasp/inputs.py#L1595-L1612\r\n\r\nIt indicates that in my example, the `psp_resources` directory must be populated as follows:\r\n```shell\r\n$ ls ~/Public/hpc/vasp/pot/ps... | 2024-02-03T05:37:49 | 2024-02-08T14:02:38 | 2024-02-06T03:18:27Z | CONTRIBUTOR | {
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} | I'm using the latest version of PAW potentials released by the VASP team but failed to let Pymatgen select them correctly. See my following configuration done via pmg:
```shell
$ cat ~/.pmgrc.yaml
PMG_DEFAULT_FUNCTIONAL: PBE_64
PMG_MAPI_KEY: <my-mapi-key>
PMG_VASP_PSP_DIR: /home/werner/Public/hpc/vasp/pot/psp_re... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3601 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3601/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3601/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3601/events | https://github.com/materialsproject/pymatgen/pull/3601 | 2,117,345,446 | PR_kwDOACgets5l9X9D | 3,601 | Minor update to avoid deprecation warning | {
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} | This is just a _tiny_ update to avoid the newly-added deprecation warnings for `get_vasp_input()`.
`get_vasp_input()` is still used in `DictSet.write_input()`, but should be changed to `get_input_set()` in line with the deprection warning (as implemented here).
PS: The recent updates to the VASP sets code is very n... | {
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"Thanks @janosh! Question for @shyuep: @janosh and I were discussing if it makes more sense to define the `self.copy` method for `MSONable` - do you think it makes more sense to define the `copy` method for specific classes that inherit from `MSONable`, or for `MSONable` itself?",
"Depends on how general the copy... | 2024-02-05T06:37:40 | 2024-02-08T09:36:06 | 2024-02-08T09:36:05Z | MEMBER | {
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} | as pointed out by @esoteric-ephemera, calling `.copy()` on VASP IO classes like `Incar` and `VaspInput` returns a dict rather than a new instance of the class as most users would expect. this PR adds explicit `copy()` methods to minimize user surprise.
@esoteric-ephemera that mixin snippet i sent doesn't work as the... | {
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updates:
- [github.com/kynan/nbstripout: 0.6.1 → 0.7.1](https://github.com/kynan/nbstripout/compare/0.6.1...0.7.1)
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"Thanks @bfield1, this is a duplicate of #3586, and should be fixed in #3587. Can you pip install from git and see if this issue is resolved (`pip install git+https://github.com/materialsproject/pymatgen.git`)?",
"@esoteric-ephemera Ah, yes, the latest development version of pymatgen fixes this. In my haste I mus... | 2024-02-05T21:34:50 | 2024-02-06T19:15:01 | 2024-02-06T18:59:51Z | CONTRIBUTOR | {
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} | ### Python version
3.9.18
### Pymatgen version
2024.1.27
### Operating system version
MacOS 13.6.4
### Current behavior
When loading a Vasprun using a 'vasprun.xml' file in the present working directory (i.e. `Vasprun('vasprun.xml')`), it throws a FileNotFoundError when it attempts to `get_potcar`.... | {
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} | ### Python version
Python 3.11.5
### Pymatgen version
2023.12.18
### Operating system version
_No response_
### Current behavior
Class DiscretizeOccupanciesTransformation in transformation/standard_transformation doesn't work correctly. discretize is not performed.
### Expected Behavior
It return the input str... | {
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"CI doesn't trigger on file changes in `docs/`"
] | 2024-02-06T03:37:24 | 2024-02-12T05:45:32 | 2024-02-12T05:45:07Z | CONTRIBUTOR | {
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} | Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.15.3 to 1.16.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/releases">nokogiri's releases</a>.</em></p>
<blockquote>
<h2>v1.16.2 / 2024-02-04</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] V... | {
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"Hi @fraricci, thanks for bringing this up. \r\n\r\nIn the older version of `MPHSEBSSet`, setting `user_kpoints_settings={\"reciprocal_density\":100}` wouldn't have any effect. It was simply ignored.\r\n\r\nIn the new version of the input sets, the `user_kpoints_settings` is strictly respected. In this case you are... | 2024-02-06T21:04:20 | 2024-02-08T17:29:21 | CONTRIBUTOR | {
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python 3.11
### Pymatgen version
2024.1.27
### Operating system version
_No response_
### Current behavior
In: `mpset = MPHSEBSSet(st, mode="Line",reciprocal_density=100)`
Out: Correct list of kpoints
In: `mpset = MPHSEBSSet(st, mode="Line",user_kpoints_settings={"reciprocal_density":100... | {
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Fixes: fix a funny typo that I encountered while working with the package
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```py
struct.composition.reduced_formula -> struct.reduced_formula
``` | {
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} | similar to #3610 but for `Entry`
4e094cb78 add properties formula and reduced_formula to Entry
b342ab1b6 refactor
86180a0d9 Add tests for formula and reduced formula properties
1bb9af8a9 composition.reduced_formula -> reduced_formula
115d45e65 composition.formula -> formula | {
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"this sounds interesting and i can see why you might want to allow only orientation-preserving rotations. but i don't have enough background to say why the current behavior was chosen in the first place. potentially there were reasons i'm unaware of. hoping others with more context can chime in",
"Is this the sam... | 2024-02-08T15:40:13 | 2024-02-22T12:20:19 | CONTRIBUTOR | {
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} | See my following testing:
```python
$ python ./pymatgenStructureMatcher.py 5/POSCAR 6/POSCAR -s0.53 -l 0.01 -a5
Structures are similar: True
Transformation Information:
(array([[ 1, 0, 0],
[ 0, -1, 0],
[ 0, 1, 1]]), array([-4.07660017e-17, -4.16198382e-01, 3.28125000e-01]), [3, 58, 59, 60, ... | {
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} | ## Summary
Major changes:
- fix 1:
- Fix URL joining in OptimadeRester. The original os.path.join function is not the correct function to use for joining URLs. It's designed for joining file paths, and its behavior depends on the operating system. On Windows, it uses a backslash (\) as the separator, while on... | {
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"@esoteric-ephemera --- I see the thumbs up. Does that mean this is good to go, or are you still planning to review this? ",
"Looks good to me. I think `ISMEAR` was probably omitted since this was intended to be set dynamically based on gap. I have no objection to include a default value.\r\n\r\nI believe there w... | 2024-02-09T05:18:52 | 2024-02-16T13:46:40 | 2024-02-16T13:40:33Z | MEMBER | {
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} | Tagging @esoteric-ephemera for review, @utf for context, and @shyuep & @mkhorton as code owners of the MP sets.
This PR ensures that the `MPSCANRelaxSet.yaml` in Pymatgen matches the [`BaseMPR2SCANRelaxSet.yaml`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/vasp/sets/BaseMPR2SCANRelaxSet.yaml)... | {
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"Ah, you beat me to making a comment, @shyuep. It looks like only those with write permissions to the repo are valid as `CODEOWNERS`, so it can't just me an arbitrary contributor. Feel free to remove my name under the ASE line.",
"I can grant you write permissions.",
"Sure, that works too. 👍 ",
"I was very e... | 2024-02-09T20:11:41 | 2024-02-21T08:06:12 | 2024-02-09T20:13:03Z | MEMBER | {
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"(`black` was updated recently to the 2024 stable style. We'll probably be seeing a bunch of these trivial changes across the repo unless someone decides to run `black .` on the whole thing)",
"@mjwen apologies for causing this bug and thanks for the fix! 👍 \r\n\r\nwe now have a test case to guard against this i... | 2024-02-09T21:03:44 | 2024-02-10T08:08:23 | 2024-02-10T07:40:57Z | MEMBER | {
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} | ## Summary
Fix a recursion bug when using TransformedStructure.final_structure. Revert it back it original implementation. See example bug here: https://github.com/materialsproject/atomate2/issues/707
Only the codes around line 90 of pymatgen/alchemy/materials.py are updated. Others are formatting by pre-commit.... | {
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"This is better for the discussion section of pymatgen, but I will leave some resources here and maybe someone (or yourself) could close this\r\n\r\nThe pymatgen [analysis.interfaces](https://pymatgen.org/pymatgen.analysis.interfaces.html) module could help you with input generation and structure matching (maybe), ... | 2024-02-12T11:38:04 | 2024-03-02T07:15:54 | 2024-03-02T07:15:54Z | CONTRIBUTOR | {
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I am currently exploring the theoretical aspects of heterostructures formed by two different single layers, each defined by specific Miller indices. A pivotal component of my study is identifying the stacking configuration between these layers that manifests the lowest energy, thereby... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3619 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3619/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3619/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3619/events | https://github.com/materialsproject/pymatgen/pull/3619 | 2,131,551,563 | PR_kwDOACgets5mtgDC | 3,619 | Adds support for an `MSONAtoms` class that's an `MSONable` form of an ASE `Atoms` object | {
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"MSONAbleAtoms is a mouthful.How about just call it AtomsM?",
"> MSONAbleAtoms is a mouthful.How about just call it AtomsM?\n\nMy personal opinion is that descriptive is better than concise. It's not immediately clear what an `AtomsM` means at a glance. Having it be unambiguous is particularly helpful with type h... | 2024-02-13T06:26:40 | 2024-02-22T14:26:57 | 2024-02-14T13:22:20Z | MEMBER | {
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Here, I introduce the `MSONAtoms` class, which is simply an `MSONable` version of the ASE `Atoms` object, introducing an `.as_dict()` and `from_dict()` method that uses ASE's JSON encode/decoder to do the serialization. By default, the object returned from `ASEAtomsAdaptor.get_atoms()` is now an `MSONable... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3620 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3620/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3620/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3620/events | https://github.com/materialsproject/pymatgen/pull/3620 | 2,131,860,077 | PR_kwDOACgets5mukNM | 3,620 | Refactors + types + fix doc string returns to use Google format | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3621 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3621/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3621/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3621/events | https://github.com/materialsproject/pymatgen/pull/3621 | 2,131,931,383 | PR_kwDOACgets5muzqb | 3,621 | Improve INCAR tag check | {
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"I did some research and found [typeguard](https://pypi.org/project/typeguard/) seems to be what we're looking for. \r\nFor example:\r\n```python\r\nfrom typeguard import check_type, CollectionCheckStrategy\r\n\r\n\r\ncheck_type(\r\n value=[1, \"hi\"], expected_type=list[int],\r\n collection_check_strategy=Co... | 2024-02-13T10:02:04 | 2024-02-24T15:01:09 | 2024-02-24T14:59:43Z | CONTRIBUTOR | {
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} | ## Summary
Some legacy from #3539.
- Clean up INCAR parameters recording file `incar_parameters.json` to separate types and values.
- Clean up INCAR checking mechanism accordingly.
## TODOs
Enable checking of more complex type annotations like `LATTICE_CONSTRAINTS : Sequence[bool, bool, bool])` suggested b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3622 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3622/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3622/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3622/events | https://github.com/materialsproject/pymatgen/issues/3622 | 2,132,331,257 | I_kwDOACgets5_GMr5 | 3,622 | Error when initializing Vasprun when LDAUL/J or MAGMOM exception triggers | {
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} | ### Python version
Python 3.10.13
### Pymatgen version
2023.12.18
### Operating system version
Mint 20
### Current behavior
I wasn't sure where to post this as it triggered when `VasprunXMLValidator` from `custodian` checked a job and found issues with the LDAU parameters in the `vasprun.xml`. I fe... | {
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} | Non-breaking change but makes for a more functional API since modification methods can now be chained.
E.g. frequent use case of loading a file from disk/memory and directly applying an in-place modification previously required 2 lines:
```py
struct = Structure.from_file("path/to/file")
struct.add_oxidation_sta... | {
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"@JaGeo , Tagging you here. Let us know if you have any suggestions on this change 😃 ",
"From my side, this is fine. A breaking change is probably okay here as not many people are using LobsterEnv directly"
] | 2024-02-14T12:56:55 | 2024-04-10T05:58:22 | 2024-02-18T05:49:25Z | CONTRIBUTOR | {
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- [x] Adapt LobsterNeighbours to work using pymatgen objects instead of file path
- [x] Rename args to use lowercase
- [x] Add test for new functionality of working with pymatgen objects
- [ ] Align lightstructure environment output to match other types
- [ ] Add test for adapted lightstructure environme... | {
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} | Fixed Incar object to allow for ML_MODE vasp tag which does not want to have capitalized values (train, run, ...). By default, pymatgen capitalizes the values of the INCAR tags (e.g. "ALGO = Fast", even if you set incar["ALGO"] = "fast"). This is not working for the ML_MODE tag.
Also fixed (i.e. ignored specific mypy ... | {
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"Mentioned this in PR #3628"
] | 2024-02-14T14:55:17 | 2024-02-23T10:37:39 | 2024-02-23T10:37:39Z | CONTRIBUTOR | {
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} | ### Python version
3.10.0
### Pymatgen version
2024.2.8 or master
### Operating system version
_No response_
### Current behavior
The check() method of the CifParser class performs checks on the compositions reported in both cif and Structure object parsed from cif. Besides other things, it is checked if the rel... | {
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"Hi @JaGeo , I made this changes as per our prep to update our schema in atomate2.",
"Thank you!\r\n\r\n@naik-aakash , could you add tests for from_dict as well? And, doesn't monty already implement as_dict. Why do you need to implement this yourself?",
"Just to add @naik-aakash and I will discuss this and then... | 2024-02-14T16:16:38 | 2024-02-21T08:07:55 | 2024-02-15T15:25:44Z | CONTRIBUTOR | {
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} | # Todo
Make MSONable
- [x] Charge
- [x] Sitepotential
- [x] Grosspop
- [x] Bandoverlap
- [x] MadelungEngeries
- [x] Icohplist
- [x] Update tests | {
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"~~If you are okay with this approach i could adapt the 2 cif tests that are failing now (and for example add a formula key so the checks are not skipped).~~ (Modifying the tests no longer necessary as other checks than for relative stoichiometry were reincluded in case of missing formula keys)",
"Thanks @kaueltz... | 2024-02-16T13:40:31 | 2024-02-23T10:49:43 | 2024-02-22T18:09:32Z | CONTRIBUTOR | {
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} | closes #3626. `CifParser.check()` raises a `UserWarning: Incorrect stoichiometry` for a cif, if
- the keys `_chemical_formula_sum` and `_chemical_formula_structural` are missing and
- crystallographic sites have different multiplicities
For the relative stoichiometry to be checked correctly, the site multiplicitie... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3629 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3629/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3629/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3629/events | https://github.com/materialsproject/pymatgen/issues/3629 | 2,139,491,065 | I_kwDOACgets5_hgr5 | 3,629 | POTCAR setup instructions should be made clearer | {
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"I imagine this is covered in the [POTCAR setup](https://pymatgen.org/installation.html#potcar-setup) section of the docs, but it is not written clearly enough for me to understand.\r\n\r\n- What is `<MY_PSP>`? It is not defined anywhere.\r\n- Why should there need to be reconfiguring of my POTCAR directory anyway?... | 2024-02-16T21:08:53 | 2024-02-17T05:04:38 | 2024-02-17T05:04:37Z | MEMBER | {
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} | ### Python version
3.10+
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
Currently, when Pymatgen searches for a pseudopotential, it has a default set of paths it looks in. For instance, if we look for the PBE_54 pseudos and symbol Al, Pymatgen will sea... | {
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} | Closes #3629. I have always found the POTCAR setup instructions to be incredibly confusing, in part because some parts were never defined (e.g. `<MY_PSP>`) and in other parts because things are quite out-of-sync with the POTCAR structure offered by VASP as of the last several years. This is an attempt to make it cleare... | {
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"Thanks a lot for the fast and clean fix! @janosh "
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} | I'm quite sure that this PR is causing the "bader_analysis_from_path" method to fail for any of its usage. I'm confused how could this PR pass the tests without failing.
The problematic line is line 455 in this PR and now line 451 in the latest pymatgen. The method is now looking for CHGCAR in the "Co... | {
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} | ### Python version
3.10+
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
In [this part](https://github.com/materialsproject/pymatgen/blob/ff45527caf5de3bc76ed859bab0d978cab38972d/pymatgen/io/vasp/sets.py#L746-L753) of `pymatgen.io.vasp.sets.py`, a `BadInputSetWarning... | {
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} | Closes #3633. Relaxing a metal with ISMEAR = 0 is fine, as noted in the VASP manual, provided SIGMA is sufficiently small (< 0.05 is the recommendation in the VASP manual).
> If you have no a priori knowledge of your system, for instance, if you do not know whether your system is an insulator, semiconductor or metal... | {
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"Awesome. Thanks! I recently tried the minimum distance method for an amorphous structure 😅... \r\nAnd it took forever. ",
"@ftherrien thanks, much appreciated! the failing test here looks like maybe this doesn't handle translations correctly? shifting the `I` atom by a full $a$ lattice vector shouldn't make a d... | 2024-02-19T20:41:25 | 2024-02-20T18:23:08 | 2024-02-20T17:49:16Z | CONTRIBUTOR | {
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} | `_get_image` and `_get_original_site` do not need to recompute site and index when `site` is a `PeriodicNeighbor` which has them as attributes.
When there are several sites, this makes a significant difference on speed for `get_nn_info`
Alternative implementation would have been `try/except` and `hasattr`. `try/e... | {
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"pinging @stefsmeets in case you know a good fix (of course no obligation to respond)",
"Sure, I can have a look at this next week."
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} | ### Python version
Python 3.10.8
### Pymatgen version
2023.11.12
### Operating system version
_No response_
### Current behavior
When there is nothing in REMS, a blank line appears between the blank line TITL and CELL.
### Expected Behavior
When there is nothing in REMS, CELL must come after ... | {
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"Thanks! Can you add a test to catch future regressions?",
"> Thanks! Can you add a test to catch future mistakes?\r\n\r\nYes, just added one now",
"Hi @janosh , can a new release of Pymatgen be made please? As this is bug breaks our LobsterPy package https://github.com/JaGeo/LobsterPy/pull/232 \r\n\r\nSorry fo... | 2024-02-21T13:22:45 | 2024-03-13T18:02:01 | 2024-02-21T15:04:38Z | CONTRIBUTOR | {
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The charges read from file are not assigned
# Fix
Fix the erroneous if else condition introduced during #3624
# Todo
- [x] Add test | {
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I am quite new to using Lammps for my MDs and I am struggling to load my MD data into a pymatgen trajectory. I am studying diffusion in a crystal. Currently I have my MD trajectory in an xyz file but it would be possible for me to use other common outputs from LAMMPS if that's easier.
Thanks in ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3639 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3639/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3639/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3639/events | https://github.com/materialsproject/pymatgen/pull/3639 | 2,147,281,275 | PR_kwDOACgets5njTqw | 3,639 | [BugFix] Subclass Construction Locpot<:VolumetricData | {
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"No problem! The test I added passes with the new code but not the old code."
] | 2024-02-21T17:15:06 | 2024-02-23T11:28:26 | 2024-02-21T19:43:13Z | CONTRIBUTOR | {
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} | ## Subclass Construction Locpot<:VolumetricData
The constructor signature for `Locpot` is different from the parent.
This makes it hard to write general code to handle different kinds of `VolumetricData` objects.
Just adding a `**kwarg` there should work. | {
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"No errors were found after commenting out the following lines (starting at 4345)\r\n\r\n```python\r\n if len(self.Gpoints[ink]) != nplane and 2 * len(self.Gpoints[ink]) != nplane:\r\n raise ValueError(\r\n f\"Incorrect {vasp_type=}. Please open a... | 2024-02-22T08:30:34 | 2024-02-22T08:34:03 | CONTRIBUTOR | {
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} | ### Python version
Python 3.11.7
### Pymatgen version
Version: 2023.11.12
### Operating system version
Red Hat Enterprise Linux 8.8
### Current behavior
similar to #1995
```
vsh wavecar WAVECAR -k 130 -b 84 85 -S CONTCAR -o both_bands_gamma.vasp -p --vasp-type ncl --prec accurate
Traceback (most recent call... | {
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"I support the gzipping effort @DanielYang59!",
"I guess someone just needs to go ahead and do it. We discussed it before. I compressed some cohp files a while ago but one can surely do more. \r\n",
"Everyone, we don't need to revisit this again. Gzipping can be done. But it is not going to help because Git alr... | 2024-02-22T08:30:48 | 2024-02-23T01:33:02 | 2024-02-22T16:55:40Z | CONTRIBUTOR | {
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} | ### Feature Requested
During a recent clone I noticed the total repo size is pretty big at around 1.9 GB in total, where (sorted and only show the largest several)
```bash
959M tests
868M .git
49M docs
16M pymatgen
11M cmd_line
9.4M dev_scripts
```
While in `tests`:
```bash
898M ... | {
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"we can make a new release once this and #3645 is merged."
] | 2024-02-22T08:43:36 | 2024-02-23T10:31:08 | 2024-02-23T10:31:08Z | CONTRIBUTOR | {
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as this bug breaks the interface with Abinit? Thanks | {
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"See #3644 (if you want a quick workaround just `pip install ase`)",
"Thank you for the workaround suggestion!\r\n\r\nClosing this as duplicate of #3644 "
] | 2024-02-22T13:57:44 | 2024-02-23T07:01:34 | 2024-02-23T07:01:33Z | CONTRIBUTOR | {
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} | ### Python version
3.11
### Pymatgen version
2024.2.20
### Operating system version
Any Linux
### Current behavior
Importing gives a NameError:
```
from pymatgen.core.trajectory import Trajectory as PymatgenTrajectory
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"Also just a comment that I would've expected this to be picked up by a linter; for me `Atoms is possible unbound` is flagged up by pyright but perhaps mypy is less picky as configured?",
"I noticed the same issue while trying to export XRD pattern for example [here](https://next-gen.materialsproject.org/material... | 2024-02-22T14:04:10 | 2024-02-23T10:18:21 | 2024-02-23T10:18:21Z | CONTRIBUTOR | {
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3.11.7
### Pymatgen version
2024.2.20
### Operating system version
Any
### Current behavior
I observed this in a fresh virtual environment when trying to install and use `mp_api`. Before #3619 (or related follow-up commits, can't tell) you were able to import the AseAtomsAdaptor ... | {
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"> It would be nice to add a test or linter rule that would have caught the initial issue.\r\n\r\nthat 👍 ",
"> > It would be nice to add a test or linter rule that would have caught the initial issue.\r\n> \r\n> that 👍\r\n\r\nAs opposed to a linter rule that only catches my fix ;)\r\n\r\n```\r\npymatgen/io/ase.... | 2024-02-22T14:24:40 | 2024-02-23T11:27:50 | 2024-02-23T10:18:20Z | CONTRIBUTOR | {
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Hopefully closes #3644. Not sure if this is the approach you want to take.
## Todo
It would be nice to add a test or linter rule that would have caught the initial issue.
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"wow, that's way more possibly unbound variables than expected... 😅 ",
"@coderabbitai ignore",
"my impression is coderabbitai is too verbose. if it has useful suggestions, they are buried in a lot of boilerplate language that you don't want to read",
"Here I come! Giving you a hand on all those `pyright` fix... | 2024-02-22T14:31:11 | 2024-04-13T10:25:56 | 2024-04-13T10:18:52Z | CONTRIBUTOR | {
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} | Hopefully all tests have been written in such a way that they will be skipped if the underlying required package is not found... this would hopefully catch issues like #3645 ahead of time (although better linting would do the same too and avoid the potential need to update tests to skip if packages are missing -- only ... | {
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} | This line has been changed in #2862:
https://github.com/materialsproject/pymatgen/blame/38b9b58f16a9528cb2c8f0bc0c7889955687ae8e/pymatgen/electronic_structure/plotter.py#L1740
and the replacement of the `intersection` function with a `&` brakes the code since the second item is not a set but a list.
Solutions:
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"Meanwhile I noticed there are `vasprun.xml.lobster.spin` and `vasprun.xml.lobster.nonspin` in `pymatgen/tests/files`. I did a global search and didn't see them being used anywhere. Do you have any idea? @JaGeo Thanks!",
"> Meanwhile I noticed there are `vasprun.xml.lobster.spin` and `vasprun.xml.lobster.nonspin`... | 2024-02-23T03:48:19 | 2024-02-23T09:01:31 | 2024-02-23T08:15:56Z | CONTRIBUTOR | {
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} | Compressed (`gzip`) test vasprun.xml files.
### Summary:
Total vasprun.xml file size reduced by 78.67% (361 MB -> 77 MB), with test runtime largely unaffected (increased by 1.05% but could be random error)
### Before compression:
Total vasprun.xml file size:
```bash
> find . -type f -name 'vasprun*' -exec du ... | {
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1. Make Lobsterout class MSONABLE
2. Add test | {
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} | 2231ec528c plotter.py and phonon band structure: improve doc strings + refactor
7c47053e32 Add Kpoint.__eq__ method
50efc02308 Add test for Kpoint equality
8b63b10640 Add PhononBandStructureSymmLine.__eq__ method | {
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slightly improve `BSPlotterProjected` test coverage | {
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"thanks for reporting! the whole `bader` is very brittle atm. i was hoping we could transition to [`pybader`](https://github.com/adam-kerrigan/pybader/issues/1) at some point in the future to have less install and subprocess shenanigans but development there seems to have stalled.\r\n\r\nif you could fix the curren... | 2024-02-24T02:54:23 | 2024-03-15T03:47:51 | 2024-02-26T08:50:42Z | CONTRIBUTOR | {
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Noticed two `Bader` related issues:
- GitHub test workflow doesn't download Bader properly
- Tests for Bader fails
### Test workflow not running properly
While trying to clean up test files for VASP, I noticed tests for `Bader` in (tests/command_line/test_bader_caller.py) (apparently depends on VASP ... | {
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"Do you have any comments so far before I proceed? @janosh \r\n\r\n### Test file naming\r\n\r\nRegarding the test file naming conventions, I would like to hear about your suggestions. Taking `vasprun.xml` for example, I'm thinking of:\r\n- Keep `vasprun` as the header so that they could be listed and grouped proper... | 2024-02-24T06:04:00 | 2024-03-07T07:39:31 | 2024-03-07T07:34:28Z | CONTRIBUTOR | {
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This is the first step of cleaning up test files: VASP outputs, relocate VASP output files to a dedicated dir (`vasp/outputs`) under `tests` dir to tidy up the `files` dir.
With the aim to clean up test files so that future developers could easily find and reuse existing test... | {
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"Hi @JaGeo,@janosh this change in doc-string got leftout with small changes done before merging. So would be great if this could be merged as well 😄 ",
"@janosh I merged it as it was a tiny doc change. "
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"Meanwhile this PR only fixes the second half of #3652.\r\n\r\nFirst half of the GitHub workflow run still needs to be fixed (`wget` failed with `403 Forbidden` error) @janosh .",
"Test setup for `Bader` seems to have been fixed using `https` instead of `http`. Then every test workflow would get the following err... | 2024-02-26T02:37:17 | 2024-03-15T02:29:34 | 2024-02-26T08:48:23Z | CONTRIBUTOR | {
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- Clean up `__init__` of `BaderAnalysis`
- Mark `parse_atomic_densities` in `BaderAnalysis` as deprecated, to be removed on 26 Feb 2025, as discussed in #3652. | {
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Major changes:
- fix 1: I found a bug at `pymatgen/core/lattice.py::Lattice::get_niggli_reduced_lattice`.
- After updating lattice parameters at A1, variables `A, B, ...` also need to be updated.
- Otherwise, condition checking would be wrong at A2 or later.
- Therefore, I added a line for upd... | {
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"Proposed solution in https://github.com/materialsproject/pymatgen/pull/3183#issuecomment-1959355057: update the label to `Composition({\"Au\": 0.5, \"Cu\": 0.5}).formula`"
] | 2024-02-26T12:09:19 | 2024-03-05T19:12:24 | 2024-03-05T19:12:24Z | CONTRIBUTOR | {
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} | > I noticed that performing a `Structure.replace_species` operation leaves the label intact, leading to a misleading label or a confusing end-user experience (for example, replacing `Au` with `{"Au": 0.5, "Cu": 0.5}` will leave the label as `Au`). Do you have any thoughts on this @stefsmeets?
_Originally posted by @... | {
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"Please review @janosh. Thanks.\r\n\r\nMaybe relocate the utility function to a more general accessible location (as I notice there are other tests seem to alter compressed file in place as well, cannot remember which one at the moment, would tag them in the future once I find any)?\r\n\r\nTests for `test_cod` seem... | 2024-02-28T04:13:20 | 2024-03-04T02:14:22 | 2024-03-01T14:17:44Z | CONTRIBUTOR | {
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} | ### Summary: Avoid bader_caller from altering compressed file in place
- Prevent `bader_caller` from altering compressed test in place, see https://github.com/materialsproject/pymatgen/pull/3656#issuecomment-1963538547
- Removed `bader_exe_path` to encourage users to add `Bader` executable to PATH for simplicity
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There was a missing ```, making the public docs look awful. I was the culprit. Oops. All patched! | {
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"Just came across this PR randomly... I guess I added this warning in #3539. I just had another look and I think this PR is right and I misunderstood the implementation. This https://github.com/materialsproject/pymatgen/blob/d07164fd27b955010ad411033d262ef3d935d09c/pymatgen/io/vasp/inputs.py#L259-L267\r\nis nested ... | 2024-02-29T19:27:11 | 2024-03-08T20:29:09 | 2024-02-29T19:49:22Z | CONTRIBUTOR | {
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} | A `BadPoscarWarning` was recently added to `pymatgen.io.vasp.inputs.Poscar` when the elements in the POSCAR are identified by the order of elements in the POTCAR file. Reading in the element names from POTCAR is valid VASP input, and it's [even permitted to omit the species names in POSCAR](https://www.vasp.at/wiki/ind... | {
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"could this be related to https://github.com/materialsproject/pymatgen/pull/3664?\r\n\r\nwhat do you get for `os.getenv(\"CI\")`?",
"Thanks for the response. I'm unaware what CI is though. After importing `os`, `os.getenv(\"CI\")` returns `None`, both before and after importing pymatgen",
"Good. Just wanted to... | 2024-02-29T21:00:03 | 2024-03-01T19:43:27 | 2024-03-01T19:43:27Z | NONE | {
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} | ### Python version
3.9.18
### Pymatgen version
2024.2.23
### Operating system version
MacOS 14.2.1 (M2 chip)
### Current behavior
I'm new to pymatgen, but my python kernel keeps dying when I import CifParser using the following command:
`from pymatgen.io.cif import CifParser`
It happens when both in the termin... | {
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"Has this issue been fixed? It looks like I am still seeing this error in my CI test.\r\n\r\nhttps://github.com/qzhu2017/PyXtal/actions/runs/8304091691/job/22729255439",
"this was released 2 weeks ago in [v2024.3.1](https://github.com/materialsproject/pymatgen/releases/tag/v2024.3.1). your errors should disappea... | 2024-03-01T09:20:59 | 2024-03-16T06:15:44 | 2024-03-01T10:04:43Z | MEMBER | {
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} | we have a major problem with how deprecation removal reminders are currently setup for CI causing other package CI runs to fail. [in this case with](https://github.com/CederGroupHub/chgnet/actions/runs/8105153971/job/22153023416)
```py
E RuntimeError: remove the change of default primitive=True to False made on 2... | {
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"It seems you started with an empty first line, which should be the comment line. And therefore the `Lu3` line is treated as the `scaling factor` line thus the error.\r\n\r\nThis should work:\r\n```python\r\nfrom pymatgen.io.vasp.inputs import Poscar\r\n\r\nposcar_text = \"\"\"Lu3\r\n1.0\r\n8.212068 -1.711729 -0.00... | 2024-03-02T19:59:22 | 2024-03-05T02:40:24 | 2024-03-04T16:50:20Z | MEMBER | {
"total": 0,
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} | ### Python version
3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
When using the various Pymatgen input parsing utilities on the POSCAR below, a `BadPoscarWarning` is raised even though it is seemingly valid. I've drilled down to the root cause be... | {
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"I just had a quick look (quite busy this week sorry) and found this seems not specific to `METAGGA`, \r\nfor example `print(vr.parameters[\"ALGO\"])` would also trigger `KeyError: 'ALGO'`. Not sure about the reason though.\r\n\r\nMeanwhile `Vasprun` indeed got these tags as `.incar` but not into `.parameters` (hav... | 2024-03-02T20:22:48 | 2024-03-05T02:40:56 | 2024-03-05T02:40:55Z | MEMBER | {
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3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
The `Vasprun` parser is not properly parsing the METAGGA flag, which can introduce some painful downstream effects related to MP (see my original report in emmet https://github.com/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3668 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3668/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3668/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3668/events | https://github.com/materialsproject/pymatgen/issues/3668 | 2,165,509,591 | I_kwDOACgets6BEw3X | 3,668 | `MSONAtoms` may not serialize appropriately if the `.info` flag is populated | {
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"I don't actually know that this one is readily solvable since people can dump whatever they want into `.info`, and the logic for the (de)serialization is in `monty`.\r\n\r\nI'll close this as a result but wanted to report it anyway. "
] | 2024-03-03T19:04:47 | 2024-03-04T21:31:43 | 2024-03-04T21:31:43Z | MEMBER | {
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} | ### Python version
3.9+
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
The recently introduced `MSONAtoms` class in https://github.com/materialsproject/pymatgen/pull/3619 gives Pymatgen additional flexibility in making ASE `Atoms` objects `MSONable`, h... | {
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"Hey @lihaojie87, it looks like VASP is now distributing these (from the portal) as \"PAW POTCAR files: LDA & PW91 & PBE (outdated)\" with the description:\r\n> The LDA, PW91 and PBE PAW datasets (snapshot: 05-05-2010, 19-09-2006 and 06-05-2010, respectively). These files are outdated, not supported and only distr... | 2024-03-04T04:52:41 | 2024-03-11T17:17:48 | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ### Python version
Python 3.12.0
### Pymatgen version
2024.3.1
### Operating system version
Windows
### Current behavior
I have already downloaded the POTCAR into D:\DFT\POTCAR\origin and the folder contents is
```
> ls
Directory: D:\DFT\POTCAR\origin
Mode LastWriteTime ... | {
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