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https://api.github.com/repos/materialsproject/pymatgen/issues/4312 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4312/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4312/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4312/events | https://github.com/materialsproject/pymatgen/issues/4312 | 2,892,669,225 | I_kwDOACgets6saqEp | 4,312 | Selen having a way too low resistance | {
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"Hi thanks for asking this, looks like the periodic table JSON recording (with these \"Electrical resistivity\") has been there since the start of pymatgen: https://github.com/materialsproject/pymatgen/blob/24514dd132d371e0f6b9bfbf45faf22a1df427d3/pymatgen/core/periodictable.json\n\nI don't know where the data orig... | 2025-03-04T01:15:37 | 2025-04-01T15:27:31 | 2025-04-01T15:27:31Z | NONE | {
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} | ## Pymatgen version
Newest
### Current behavior
Resistance of selenium according to pymatgen: "high 10<sup>-8</sup> Ω m",
Resistance of silver according to pymatgen: "high 10<sup>-8</sup> Ω m",
### Expected Behavior
Resistance of selenium being higher or a source where the data is from
### Minimal exa... | {
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} | ### Feature Requested
More sources in the periodic table code or perhaps a site with all the sources, so you can put this python library and its sources as valid sources in your paper/essay. An idea would be like that: https://reference.wolfram.com/language/note/ElementDataSourceInformation.html
### Proposed Solution... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4314 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4314/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4314/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4314/events | https://github.com/materialsproject/pymatgen/issues/4314 | 2,900,087,816 | I_kwDOACgets6s29QI | 4,314 | Encoding issues in robocrystallographer output on the website | {
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"Hey @fxcoudert , this is probably better placed on the [robocrys](https://github.com/hackingmaterials/robocrystallographer) repo, it is an ongoing issue we're aware of at MP"
] | 2025-03-06T11:04:29 | 2025-03-10T17:15:49 | 2025-03-10T17:15:49Z | NONE | {
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} | ### Python version
Python 3.12.9
### Pymatgen version
2025.2.18
### Operating system version
macOS
### Current behavior
See https://next-gen.materialsproject.org/gnome/mp-3206242
which displays for me as:
### Expected Beh... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4315 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4315/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4315/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4315/events | https://github.com/materialsproject/pymatgen/pull/4315 | 2,901,312,968 | PR_kwDOACgets6NsBEr | 4,315 | patch to allow pyzeo to work | {
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"Great thanks. Can you add / enable some unittests to check that this is working? Thanks.",
"You would also need to add it as an [optional dependency](https://github.com/materialsproject/pymatgen/blob/master/pyproject.toml), thanks for the edit!",
"Note that even with the patch one would still need to manually ... | 2025-03-06T20:04:24 | 2025-03-10T14:23:48 | 2025-03-10T13:59:04Z | CONTRIBUTOR | {
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Pyzeo is a more maintained version of the cython but has different imports. This small patch allows users to swap out zeo++ with pyzeo.
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https://api.github.com/repos/materialsproject/pymatgen/issues/4316 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4316/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4316/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4316/events | https://github.com/materialsproject/pymatgen/issues/4316 | 2,902,277,876 | I_kwDOACgets6s_T70 | 4,316 | Error when using CifParser to read 0.220_Mn2SiO4.mcif | {
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"Thanks for reporting and I could recreate this. We globally enabled `strict` for `zip` at some point to ensure equal-length iterables and apparently test might be missing at certain spots :)",
"@Connor1y I just had a closer look and not sure if the cif file format is valid (**I could certainly be wrong here as I... | 2025-03-07T07:52:07 | 2025-03-10T10:07:07 | 2025-03-10T09:36:37Z | NONE | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
2025.2.18
### Operating system version
MacOS15.1 (24B2082)/CentOS Linux 7 (Core)
### Current behavior
when using CifParser to read 0.220_Mn2SiO4.mcif from [MAGNDATA](https://www.cryst.ehu.es/magndata/index.php?this_label=0.220),
we got this error
pymatgen/sr... | {
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} | ### Python version
3.12.4
### Pymatgen version
2024.10.3
### Operating system version
_No response_
### Current behavior
In the class EnumerateStructureTransformation (defined in pymatgen/transformations/advanced_transformations.py), the M3GNetCalculator is called like this:
m3gnet_model = M3GNetCalculator(pote... | {
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} | Parsing of the timer section has stopped working for the latest versions of Abinit. In addition the generation of a dataframe in the same set of objects is incompatible with pandas>2.
In this PR
* fixing these issues
* added a test file generated by latest abinit version (10.2.7)
* added tests for the abitimer m... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4320 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4320/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4320/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4320/events | https://github.com/materialsproject/pymatgen/issues/4320 | 2,908,951,034 | I_kwDOACgets6tYxH6 | 4,320 | `Molecule.from_ase_atoms()` does not pass kwargs appropriately | {
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"I'm happy to look into this :)"
] | 2025-03-11T03:17:37 | 2025-03-17T13:41:01 | 2025-03-17T13:41:01Z | MEMBER | {
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} | ### Python version
3.12
### Pymatgen version
2025.3.10
### Operating system version
_No response_
### Current behavior
The `Molecule.from_ase_atoms` method does not accept dedicated keyword arguments for the `Molecule` class. I demonstrate this below:
```python
from ase.build import molecule
from pymatgen.core ... | {
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"This looks good to me. I will give this through the end of the week for others to chime in, and if there's nothing I will do a final review and merge over the weekend.",
"Thanks, @DanielYang59! Merging. ",
"Ah, looks like I don't have permission to merge until the CI passes... ",
"> Ah, looks like I don't ha... | 2025-03-11T11:35:17 | 2025-03-17T13:46:04 | 2025-03-17T13:41:00Z | CONTRIBUTOR | {
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} | ### Summary
- Fix `from_ase_atoms` for `Molecule`, to close #4320
- [x] Add tests | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4323 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4323/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4323/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4323/events | https://github.com/materialsproject/pymatgen/pull/4323 | 2,918,065,003 | PR_kwDOACgets6Oj1fi | 4,323 | Tweak POSCAR / XDATCAR to accommodate malformed files | {
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"Thanks."
] | 2025-03-13T18:22:51 | 2025-03-13T19:33:54 | 2025-03-13T19:33:49Z | CONTRIBUTOR | {
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} | Related to [this matsci.org issue](https://matsci.org/t/xdatcar-error-when-reading-xdatcar-could-not-convert-string-to-float/61831): sometimes the XDATCAR can be malformed because fortran uses fixed format floats when printing. In those cases, there's no space between coordinates:
```
Direct configuration= 2
-0.6326... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4324 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4324/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4324/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4324/events | https://github.com/materialsproject/pymatgen/pull/4324 | 2,918,852,819 | PR_kwDOACgets6OmbLV | 4,324 | GibbsComputedStructureEntry update to handle float temperature values | {
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"Thanks,."
] | 2025-03-14T02:37:46 | 2025-04-20T19:38:20 | 2025-04-20T19:38:20Z | CONTRIBUTOR | {
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} | ## Summary
Issue: when temperature %100==0 but is type float, you get KeyError because G_ELEMS has keys of integer values.
Major changes:
- feature 1: updated to handle float temperature values
- fix 1: G_ELEMS[str(self.temp)] is changed to G_ELEMS[str(int(self.temp))]
## Checklist
- [ ] Google forma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4325 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4325/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4325/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4325/events | https://github.com/materialsproject/pymatgen/issues/4325 | 2,919,949,962 | I_kwDOACgets6uCuaK | 4,325 | LATTICE_CONSTRAINTS tag not read properly for Incar | {
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"Hi @edansi thanks for reporting this. \n\nLooks like the type handling mechanism of INCAR tags has really been a pain and I assume it's time we really think about a more permanent solution other than having people reporting certain tag is not parsed correctly from time to time. \n\nUnfortuntately currently AFAIK t... | 2025-03-14T11:20:22 | 2025-04-03T17:23:53 | NONE | {
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} | ### Python version
3.11
### Pymatgen version
2025.1.9
### Operating system version
_No response_
### Current behavior
For the newer Vasp version, there's a new tag LATTICE_CONSTRAINT (list of three booleans) that allows the relaxation of only some of the lattice parameters. When reading an Incar file with this t... | {
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"Resolved by #4329 "
] | 2025-03-14T14:35:45 | 2025-03-25T22:00:57 | 2025-03-25T22:00:55Z | CONTRIBUTOR | {
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} | For my `wren` work I wrote several methods that use `spglib` to get prototype labels that follow the `aflow-sym` assignment scheme. These are generally more useful than just for the `wren` model, for example afaik @lbluque used them to help downselect materials to include in the OMAT dataset.
Installing my `aviary` pa... | {
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} | ## Summary
- Fix new `ruff` error in linting pipeline
- Avoid configuring the root logger | {
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"> ping @ml-evs for review?\r\n\r\nDon't think this is anything to do with me (nor does my review do anything on this repo), but generally looks fine...",
"Ooops sorry thought you're the owner of this module but thanks for looking into this in any case :) \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/... | 2025-03-15T13:02:12 | 2025-03-15T15:49:01 | 2025-03-15T15:40:52Z | CONTRIBUTOR | {
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} | ### Summary
Remove legacy MPRester tests from `TestMPResterNewBasic`, I believe some test methods (commented out previously, and recovered in #4027) are testing methods from the legacy MPRester (while being inside `TestMPResterNewBasic`), maybe we should remove them altogether?
ping @ml-evs for review?
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https://api.github.com/repos/materialsproject/pymatgen/issues/4329 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4329/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4329/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4329/events | https://github.com/materialsproject/pymatgen/pull/4329 | 2,923,475,721 | PR_kwDOACgets6O1x9E | 4,329 | Add protostructure and prototype functions from aviary | {
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"Closes https://github.com/materialsproject/pymatgen/issues/4326",
"@mkhorton "
] | 2025-03-17T01:10:48 | 2025-03-26T00:43:10 | 2025-03-22T15:48:51Z | CONTRIBUTOR | {
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} | ## Summary
Adds functions to get protostructure labels from spglib, moyo and aflow-sym. This avoids users who wish to use this functionality from needing to download `aviary` [to use these functions](https://github.com/CompRhys/aviary/blob/main/aviary/wren/utils.py).
## TODO
* ~~should `pyxtal` be added to the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4330 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4330/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4330/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4330/events | https://github.com/materialsproject/pymatgen/pull/4330 | 2,923,692,717 | PR_kwDOACgets6O2fbY | 4,330 | Update type-hinting for `pymatgen.io.qchem.outputs` | {
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"I guess we have a type alias `PathLike` which might be preferred to annotate such \"pathlike\" things: https://github.com/materialsproject/pymatgen/blob/168999dc7acac4f4dda6296b5cef1ca512ed33a6/src/pymatgen/util/typing.py#L28\r\n\r\n```python\r\nfrom pymatgen.util.typing import PathLike\r\n```"
] | 2025-03-17T04:12:00 | 2025-03-17T13:38:34 | 2025-03-17T13:38:32Z | MEMBER | {
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I updated several I/O parsers in `pymatgen.io.qchem.outputs` such that they are properly type-hinted with `str | Path` arguments rather than just `str`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4331 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4331/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4331/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4331/events | https://github.com/materialsproject/pymatgen/pull/4331 | 2,937,135,237 | PR_kwDOACgets6PjbBv | 4,331 | Optimized cube file parsing in from_cube for improved speed | {
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"Nice! Thanks a lot!"
] | 2025-03-21T03:07:49 | 2025-03-22T16:35:11 | 2025-03-22T16:35:11Z | CONTRIBUTOR | {
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} | # **Summary**
### **Major Changes:**
This PR enhances the `from_cube` function in `io.common.VolumetricData` to significantly improve performance. When processing large `.cube` files, the original implementation took minutes to read and set Pymatgen objects. The optimized version incorporates several key improvemen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4332 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4332/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4332/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4332/events | https://github.com/materialsproject/pymatgen/pull/4332 | 2,939,780,203 | PR_kwDOACgets6PsVTb | 4,332 | Bump nokogiri from 1.18.3 to 1.18.4 in /docs | {
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} | Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.18.3 to 1.18.4.
<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>v1.18.4 / 2025-03-14</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] V... | {
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"I would use the extract_cluster method. Just extract, iterate, extract until all sites are bundled into separate clusters. I personally think this is always the easiest way rather than trying to do complicated graph-based algorithms."
] | 2025-03-22T17:17:50 | 2025-04-20T19:59:07 | 2025-04-20T19:59:07Z | NONE | {
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} | I want to sort a molecular crystal supercell cif so the atoms are printed one molecule after the other in any file either cif or pdb. I was trying with a neighbor search. If you could suggest a better way to sort the molecules?
```
from pymatgen.core.structure import Structure, Molecule
from pymatgen.analysis.graphs im... | {
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"Thanks very much. Can you add some tests to test_feff.py for the updated functionality? ",
"I've added a test, and I've changed the behavior of the Potentials class to be able to handle situations where the radius is not defined (in which case it will revert to the old behavior of defining a potential for every ... | 2025-03-25T17:57:35 | 2025-03-28T19:35:05 | 2025-03-28T19:02:10Z | CONTRIBUTOR | {
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} | Changed the Potentials class to consider the same radius that is used in
the Atoms class. This is necessary to avoid a situation where the radius is small enough to only have a subset of the unique elements in a structure, but all the elements have potentials defined, which causes FEFF to fail when run.
## Summary
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} | ### Python version
Python 3.13.2
### Pymatgen version
2024.10.3
### Operating system version
Ubuntu 24.04
### Current behavior
When adding magnetic moments to a structure, `MPStaticSet` produces different `MAGMOM` values in the INCAR depending on whether `add_site_property()` or `add_spin_by_site()` is used. The... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4336 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4336/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4336/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4336/events | https://github.com/materialsproject/pymatgen/issues/4336 | 2,956,270,161 | I_kwDOACgets6wNRpR | 4,336 | [Proposal] Better periodic table dev recording (`periodic_table.yaml`)- One property per file? | {
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"Maintenance is not done on the json, but on the yaml (which is a lot easier to read and modify). That file is in dev scripts. \nI am not opposed to splitting up by element but I suspect 100 file open calls will be more expensive than loading one big file. If you can prove to me that loading multiple element data f... | 2025-03-28T14:02:43 | 2025-04-01T10:39:36 | 2025-04-01T10:39:36Z | CONTRIBUTOR | {
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- It's simply too large and monolithic as a single file, and as such maintaining it (and track git history) is quite hard.
- It doesn't carry enough metadata, for example we don't know the "source/reference" of each data entry, also some informat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4337 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4337/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4337/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4337/events | https://github.com/materialsproject/pymatgen/issues/4337 | 2,956,710,229 | I_kwDOACgets6wO9FV | 4,337 | Simple correction proposal for CifFile to handle properly CifBlock with same header | {
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As from 11/10/2023, the from_str() method of the CifFile class is annotated as:
"# TODO (@janosh, 2023-10-11) multiple CIF blocks with equal header will overwrite each other,"
"# latest taking precedence. maybe something to fix and test e.g. in test_cif_writer_write_file"
This class not suppor... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4338 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4338/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4338/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4338/events | https://github.com/materialsproject/pymatgen/pull/4338 | 2,956,778,338 | PR_kwDOACgets6Ql7rD | 4,338 | [DEV] `ptable_table.json` generate with unified interface | {
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"I want to point out that ChatGPT can make this extremely easy. I passed ChatGPT the yaml and prompted it to \"separate out the units of each property for each element from the value, keeping the dictionary schema consistent\". Below is the result. \r\n\r\n```\r\nBelow is a Python script that reads your existing YA... | 2025-03-28T17:35:55 | 2025-04-21T11:40:29 | 2025-04-20T19:45:37Z | CONTRIBUTOR | {
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} | ## Summary
- Clean up development resources for `ptable_table.json` generation, #4336
- Allow sources/reference, #4313
- Remove seemingly unused `bvparm2011` (1d9ab4d276aaf8e46fca3c2925928f6fd12f5537) and `periodic_table.db`(benchmark from c80afb5d483ca3cc43ce0c155e7184eb8eb9e7b6)
### JSON/YAML generation direct... | {
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} | ### Python version
3.11.11
### Pymatgen version
2025.1.9
### Operating system version
_No response_
### Current behavior
When one uses Atoms -> AseAtomsAdaptor -> Structure -> to(fmt="json") the following error is raised:
`TypeError: Object of type bool_ is not JSON serializable`
### Expected Behavior
atoms = ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4340 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4340/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4340/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4340/events | https://github.com/materialsproject/pymatgen/issues/4340 | 2,962,037,355 | I_kwDOACgets6wjRpr | 4,340 | Monthly issue metrics report | {
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| Metric | Average | Median | 90th percentile |
| --- | --- | --- | ---: |
| Time to first response | 5 days, 20:06:06 | 2 days, 7:09:02 | 15 days, 4:49:57 |
| Time to close | 8 days, 3:53:51 | 6 days, 10:23:24 | 13 days, 23:12:57 |
| Time to answer | None | None | None |
| Metric | Count |
| --- | --... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4341 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4341/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4341/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4341/events | https://github.com/materialsproject/pymatgen/pull/4341 | 2,962,965,109 | PR_kwDOACgets6Q6HIM | 4,341 | Remove "Electrical resistivity" for Se as "high" | {
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} | ### Summary
- Remove "Electrical resistivity" for Se as "high", to fix #4312
Current the data for Electrical resistivity of Se is "high" (with `10<sup>-8</sup> Ω m` as the unit), and our parser would interpret it to:
```python
from pymatgen.core import Element
print(Element.Se.electrical_resistivity)... | {
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} | ## Summary
- Correct Mn "ionic radii" in `core.periodic_table.json`
Our csv parser should copy the high spin ionic radii to the base entry:
<img width="858" alt="image" src="https://github.com/user-attachments/assets/00f3ecff-3c78-4583-90b8-106ed362b78b" />
https://github.com/materialsproject/pymatgen/blob/4c... | {
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- Drop duplicate `iupac_ordering` entries in `core.periodic_table.json`
If I understand correctly, the `Element.iupac_ordering` should access the other "IUPAC ordering" instead:
https://github.com/materialsproject/pymatgen/blob/4c7892f5c9dcc51a1389b3ad2ada77632989a13e/src/pymatgen/core/periodic_tabl... | {
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"This one we need to be careful about. I am unclear where the old values come from. I believe it is the official Pauling definition. It might be old but it is what people have been using all this while. This can potentially cause havoc since MP uses the electronegativity in generating the formula.",
"Yes can neve... | 2025-04-01T11:56:51 | 2025-04-20T19:38:50 | 2025-04-20T19:36:56Z | CONTRIBUTOR | {
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} | ## Summary
Looks like some [data entries from Wikipedia](https://en.wikipedia.org/wiki/Electron_affinity_(data_page)) changed quite dramatically (some are just flucations), not sure if we want to update them?
https://github.com/materialsproject/pymatgen/blob/4c7892f5c9dcc51a1389b3ad2ada77632989a13e/dev_scripts/up... | {
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"I asked ChatGPT to do some validation. See below. Of course, ChatGPT notoriously can hallucinate. So you might want to just quickly check the discrepancies.\r\n\r\n```\r\nI have cross-referenced the van der Waals and metallic radii in your table with authoritative public sources, including Bondi’s 1964 compilation... | 2025-04-01T13:07:15 | 2025-04-17T17:14:17 | 2025-04-17T16:04:34Z | CONTRIBUTOR | {
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} | ## Summary
- Fix inconsistent "Van der waals radius" and "Metallic radius" in `core.periodic_table.json`
Currently some of the radii from JSON is different from our CSV (the YAML is the same):
After this PR:
```
Element | Van der waals radius | Metallic radius
-------------------------------------------... | {
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"Can you first upgrade your version of pymatgen by running `pip install --upgrade pymatgen`? A version from 2023 is likely missing updates to VASP parsing functionality"
] | 2025-04-02T17:37:44 | 2025-04-14T15:55:33 | NONE | {
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} | ### Python version
Python 3.11.10
### Pymatgen version
2023.10.11
### Operating system version
Ubuntu 22.04
### Current behavior
My WAVECAR file for a PBEsol+U calculation is not being read.
I have also tried setting vasp... | {
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} | - ~~Skip `BoltzTraP2` in pipeline for now, now sure why it's failing (build works on my Ubuntu 22.04/24.04 local machine) but I would open an issue on their side~~
- Merge `ZEO++` install into optional Ubuntu pipeline (also add macos to this optional, never hurt to get more test coverage?)
- [ ] Waiting for response ... | {
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} | - Remove deprecated grain boundary analysis https://github.com/materialsproject/pymatgen/blob/55798119194076fd28cb28b539423779905c6ff9/src/pymatgen/analysis/gb/grain.py#L7-L12 | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
2025.3.10
### Operating system version
Ubuntu 24.04.2 LTS
### Current behavior
When using LOBSTER version 5.1.1, the generated ICOHPLIST.lobster file may not include a trailing newline. This causes the Icohplist parser in pymatgen’s outputs module to miscount... | {
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"Thanks, @alibh95, for raising this fix. Can you please also adapt the failing test in the PR?",
"Please provide a unittest to check for this issue. Thanks.",
"Hi @alibh95 , it would be great if you can fix the newly added test that is failing and also adapt the existing failing test to reflect correct number o... | 2025-04-04T08:46:28 | 2025-05-01T21:17:12 | 2025-05-01T21:17:06Z | CONTRIBUTOR | {
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} | LOBSTER 5.1.1 sometimes produces an ICOHPLIST.lobster file without a trailing newline, which causes the Icohplist parser to miscount bond entries (e.g., 1079 vs. 1080). This commit updates the file-reading logic in Icohplist.__init__ to use splitlines() and filters out any blank lines, ensuring that only valid, non-emp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4351 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4351/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4351/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4351/events | https://github.com/materialsproject/pymatgen/issues/4351 | 2,972,000,048 | I_kwDOACgets6xJR8w | 4,351 | Consistent serialization method naming (`as_dict` preferred over `to_dict`?) | {
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"Please contact the jdftx PR submitter on this. Since htis is relatively new, we can potentially just modify it without keeping backwards compaitbility. But it is trivial to add a to_dict = as_dict to maintain backwards compatibility anyway,.\n",
"Thanks for the input, I could do that (just to confirm I wasn't ge... | 2025-04-04T10:49:53 | 2025-04-10T15:44:29 | 2025-04-10T15:44:28Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4352 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4352/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4352/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4352/events | https://github.com/materialsproject/pymatgen/pull/4352 | 2,972,798,730 | PR_kwDOACgets6Rbj4T | 4,352 | Replace `to_dict` with `as_dict` | {
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"Only as dict. Pls leave the rest as is. There is no good reason to break everything for this. ",
"> Only as dict. Pls leave the rest as is. There is no good reason to break everything for this.\r\n\r\nOkay sure",
"BTW, I noticed there're two `contributing.md`? https://github.com/materialsproject/pymatgen/blob/... | 2025-04-04T15:54:31 | 2025-04-10T15:48:26 | 2025-04-10T15:44:27Z | CONTRIBUTOR | {
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} | - Deprecate `to_dict` with `as_dict`, to close #4351
- Updated `contributing.md` to note preferred naming convention
- [x] Regenerate `docs`
The recent additional of JDFTx IOs have a relatively short grace period of 6 months, and others have one year
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https://api.github.com/repos/materialsproject/pymatgen/issues/4353 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4353/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4353/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4353/events | https://github.com/materialsproject/pymatgen/pull/4353 | 2,977,710,609 | PR_kwDOACgets6RrbWa | 4,353 | pre-commit autoupdate | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.9 → v0.11.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.9...v0.11.4)
- [github.com/RobertCraigie/pyright-python: v1.1.396 → v1.1.398](https://github.com/RobertCraigie/pyright-python/compare/v1.1.396...v1.1.398)
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"It was indeed my commit that broke things. Thanks for reporting!\nYour example should be working with my new commit."
] | 2025-04-09T19:34:01 | 2025-04-10T17:59:42 | 2025-04-10T17:59:42Z | NONE | {
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} | ### Python version
3.11.5
### Pymatgen version
2025.3.10
### Operating system version
Ubuntu 22.04 LTS
### Current behavior
Converting the structure back and forth between ase atoms and structure, the constraints will change in the latest versions. (2025.3.10), but it works correct with the old version (2024.11.... | {
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"> In your comment, can you please link to the prior PR where this bug was introduced?\r\n\r\nThe original PR is #4229. (I am not 100% sure which comment you are referring to: here, in the bug report, or in the commit message).",
"Thanks, @yantar92! That's the one. I wanted to make sure it was linked to this iss... | 2025-04-10T16:35:29 | 2025-04-10T17:59:41 | 2025-04-10T17:59:41Z | CONTRIBUTOR | {
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} | * src/pymatgen/io/ase.py (AseAtomsAdaptor.get_structure): When no explicit constraint is given for a site in ASE Atoms object, use "T T T" selective dynamics (no constraint). The old code is plain wrong.
* tests/io/test_ase.py (test_back_forth): Add new test case.
Fixes #4354.
Thanks to @yaoyi92 for reporting!
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- `core.Lattice` cast `pbc` to `bool` (possibly `np.bool_`), to close #4339 | {
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"No that was an import I used for debugging and forgot to delete, apologies for leaving it in there.",
"No worries at all, it simply means we're missing a test for this :D"
] | 2025-04-10T19:46:12 | 2025-04-10T20:16:03 | 2025-04-10T20:15:30Z | CONTRIBUTOR | {
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- Fix circular import of `SymmOp`, to close #4309
Looks like the import of `SymmOp` was added in #4177, @tpurcell90 do we have a reason to import `SymmOp` at runtime? https://github.com/materialsproject/pymatgen/blob/482ffd01312e7607c58bdd3ed285bf8a45e405bf/src/pymatgen/symmetry/groups.py#L24-L33 | {
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} | - Make `pybtex` optional, to close #4285
Rationale (see details in #4285):
- It's only used in two places across the code base: `cif.CifParser.get_bibtex_string` and `util.provenance.StructureNL`
- `pybtex` hasn't got any release since Jan 2021, and doesn't support Python 3.13 yet
I'm not entirely sure if this ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4359 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4359/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4359/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4359/events | https://github.com/materialsproject/pymatgen/pull/4359 | 2,996,919,557 | PR_kwDOACgets6SshXc | 4,359 | Avoid repeated `Incar.get()` calls which slow down vasprun parsing by ~20-50% | {
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"Thanks!"
] | 2025-04-15T16:00:35 | 2025-04-15T16:10:48 | 2025-04-15T16:10:41Z | CONTRIBUTOR | {
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https://github.com/materialsproject/pymatgen/blob/31aa2148f85fcd3f01461e269a06b0186f82a22b/src/pymatgen/io/vasp/inputs.py#L847
This can be slow when called many times because of the `... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4360 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4360/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4360/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4360/events | https://github.com/materialsproject/pymatgen/pull/4360 | 2,997,022,650 | PR_kwDOACgets6Ss3zA | 4,360 | Speed up `Vasprun` parsing some more | {
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"Thanks. but I don't think we need to use string concat? I believe np.loadtxt would be able to handle the text without concat.",
"Example:\r\n```\r\nIn [1]: import numpy as np\r\n\r\nIn [3]: np.loadtxt([\"1 2\", \"3 4\"])\r\nOut[3]:\r\narray([[1., 2.],\r\n [3., 4.]])\r\n```",
"Even better, no reshaping ne... | 2025-04-15T16:40:35 | 2025-04-15T21:25:19 | 2025-04-15T21:25:19Z | CONTRIBUTOR | {
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From further profiling and playing around, I found I could speed up `_parse_vasp_array` (one of the main bottlenecks when using `parse_dos = True` (default), `parse_eigen = True` (default) and/or `parse_projected_eigen = True` (False by default)), using `numpy`'s parse from string function.
e.g. parsing a S... | {
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"I cannot say I'm a bibtex expert, at least all tests seem to pass (both for `cif` and `StructureNL`), anyone experienced with bibtex please free feel to review and comment :D"
] | 2025-04-15T18:07:51 | 2025-04-18T06:07:58 | 2025-04-18T02:59:39Z | CONTRIBUTOR | {
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} | ## Summary
- Replace `pybtex` with `bibtexparser`
- [x] Add `bibtexparser` lower bound
- [x] Update requirements.txt (or any other lock file)
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"\nAdd a unit test pls. "
] | 2025-04-17T17:52:20 | 2025-04-18T02:59:07 | 2025-04-18T02:59:07Z | CONTRIBUTOR | {
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When `auto_dipole=True`, `MVLSlabSet` was passing a NumPy array into the INCAR’s DIPOL tag, causing pymatgen to serialize it with brackets (e.g. `DIPOL = [0.1 0.2 0.3]`). VASP expects three space‑separated floats without any brackets: https://www.vasp.at/wiki/index.php/DIPOL.
This PR converts the comput... | {
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} | Just a minor fix; after #4360 the format of `actual_kpoints_weights` was changed from `list[float]` to `list[np.ndarray[float]]` (where these were `np.ndarray[float]` with a single value). Minor thing but this changes the format back to what it was before, and adds a quick test for this. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4364 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4364/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4364/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4364/events | https://github.com/materialsproject/pymatgen/issues/4364 | 3,003,642,205 | I_kwDOACgets6zB_Fd | 4,364 | The strange display style of bar (-) on next-gen.materialsproject.org. | {
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"This is not a pymatgen issue. Pls report to Materials Project.",
"I have reposted at https://matsci.org/t/the-strange-display-style-of-bar-on-next-gen-materialsproject-org/63076."
] | 2025-04-17T23:57:51 | 2025-04-18T13:24:27 | 2025-04-18T02:32:39Z | CONTRIBUTOR | {
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See below as shown [here](https://next-gen.materialsproject.org/materials?formula=TiN):
As you can see, the bar (-) on 3 is displayed with a bizarre and blurred style.
Regards,
Zhao | {
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"I would mark this PR as ready, but noticed [NP1 seems to fail on Python 3.13 on Windows](https://github.com/materialsproject/pymatgen/actions/runs/14532459539/job/40774628811) but I cannot recreate this locally. I would add a follow up PR/issue if I could find a recreation."
] | 2025-04-18T08:28:35 | 2025-04-20T20:31:40 | 2025-04-20T19:35:32Z | CONTRIBUTOR | {
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- Python 3.13 support (previously #4100), to close #4284
- [ ] fix vampire install: https://github.com/richard-evans/vampire/issues/122
```
wget https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
--2025-04-18 10:45:13-- https://vampire.york.ac.uk/resources/release-5/vampire-5.0... | {
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"Also just to check, should developers of downstream packages consider the dropping of `mp-api` and new `MPRester` semantics/formats to be stable from now on, or are other breaking changes likely in the near future?",
"I will address these changes in a day or two. Feel free to report any further changes. Note th... | 2025-04-18T22:06:47 | 2025-04-19T02:04:03 | 2025-04-19T02:04:02Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12
### Pymatgen version
2025.4.17
### Operating system version
MacOS
### Current behavior
There seems to be some issues with the updated `MPRester` behavior, after the dropping of `mp-api`.
- `property_data` does not appear to be used in `get_entries`, but is in the docstring. It woul... | {
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"Thanks for fixing this. "
] | 2025-04-19T06:23:31 | 2025-04-20T03:13:45 | 2025-04-19T14:24:42Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- fix 1: If I'm not mistaken, #4270 added a random seed parameter to Structure.perturb() but ended up setting the same random vector for all atoms. This should probably be fixed by pulling the seed-setting line out of the get_rand_vec() function.
## Checklist
- [x] Google format do... | {
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} | ## Summary
This PR is part of an effort to include workflows for running LAMMPS via atomate2. A concurrent PR will be opened in atomate2 that has the flows, while this PR aims to update the input set generators to match the inputs required there.
These changes are based on initial work here: https://github.com/Matg... | {
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"@DanielYang59 \n",
"Thanks for pinging me, I guess it has been fixed by 212af7f85b622c93dbc4db36a9586698cc4a8433? \n\n>[v2.21.2](https://github.com/pypa/cibuildwheel/releases/tag/v2.21.2)\n> ✨ Adds official support for running on Python 3.13 (https://github.com/pypa/cibuildwheel/pull/2026)",
"Let me try runnin... | 2025-04-20T20:35:25 | 2025-04-20T22:13:16 | 2025-04-20T21:07:53Z | MEMBER | {
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} | ### Python version
Python 3.13
### Pymatgen version
current
### Operating system version
_No response_
### Current behavior
See CI release workflow run. 3.13 builds do not work.
### Expected Behavior
3.13 wheels are built and uploaded.
### Minimal example
```Python
```
### Relevant files to reproduce this ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4370 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4370/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4370/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4370/events | https://github.com/materialsproject/pymatgen/issues/4370 | 3,007,232,051 | I_kwDOACgets6zPrgz | 4,370 | [DEV] Update CSV source for vdw/metallic radii data of `core.periodic_table.json` with CRC Handbook | {
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"Looks like some values are manually updated/added directly to JSON in #2122 (and CSV not updated), so likely #4345 might have reverted some changes made in #2122, I would re-apply the update directly to the CSV (and automatically to the JSON) perhaps from a latest version of CRC Handbook \n\ncc @rkingsbury @mkhort... | 2025-04-20T21:14:57 | 2025-04-21T19:47:49 | 2025-04-21T19:47:49Z | CONTRIBUTOR | {
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} | #4345 only corrected inconsistency when data exists in BOTH the CSV and JSON, however I noticed some more issues are not corrected **when the data only exist in JSON but not the CSV** (meaning the data source is likely unknown or at least not from the CSV...)
Note the parent hash of #4338 is 4a3d06780cf32fdd8ad38f480a... | {
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"Would close this now, now that the new JSON generator uses the one with extra info",
"Ah I see it was updated in #3902"
] | 2025-04-20T22:02:01 | 2025-04-20T22:15:25 | 2025-04-20T22:06:23Z | CONTRIBUTOR | {
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} | repost from #4338 for visibility, "Electronic structure" in ptable YAML (for dev) and JSON (production) are quite different. The hash for the parent of #4338 is 4a3d06780cf32fdd8ad38f480ad588a82860e0e6
For example the electronic structure for Ac in YAML is: https://github.com/materialsproject/pymatgen/blob/4a3d06780c... | {
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"@rkingsbury I believe this PR has reverted #4345 and updated the [radii.csv](https://github.com/materialsproject/pymatgen/blob/master/dev_scripts/periodic_table_resources/radii.csv) accordingly. Would appreciate it if you could help me double check as I currently don't have access to a CRC handbook (we could/shoul... | 2025-04-21T08:40:01 | 2025-04-22T08:13:37 | 2025-04-21T19:47:48Z | CONTRIBUTOR | {
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} | ## Summary
- Update ptable vdw radii CSV source, to fix #4370
- [x] Revert #4345 and apply changes to CSV
vdw radii data source:
> John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 105th Edition (Internet Version 2024), CRC Press/Taylor & Francis, Boca Raton, FL.
> If a specific table is cited, use... | {
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"link #4374"
] | 2025-04-21T11:40:19 | 2025-04-21T12:01:27 | 2025-04-21T12:01:27Z | CONTRIBUTOR | {
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} | Repost from #4338, it looks like ["Ground level"](https://github.com/materialsproject/pymatgen/blob/ac95b80fc914d237bc31b0e3cd74c1d95f85e135/dev_scripts/update_pt_data.py#L258-L279) (also from `ionization_energies_nist.html`) and ["NMR Quadrupole Moment"](https://github.com/materialsproject/pymatgen/pull/1099) are dire... | {
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"close, just do this in #4376"
] | 2025-04-21T11:49:57 | 2025-04-22T18:25:23 | 2025-04-22T18:23:43Z | CONTRIBUTOR | {
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- [x] Add "NMR Quadrupole Moment" as a separate YAML source
- [x] "ground level" seems to be generated from the same NIST source as ionization energies | {
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} | Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.18.4 to 1.18.8.
<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>v1.18.8 / 2025-04-21</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] V... | {
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"Is this ready for merging?",
"Yes I believe so as far as I could tell. Tested both consistency of the values and performance, and nothing stands out (except for some changes which I consider to be fixes and have been highlighted as comments).\r\n\r\nCan we merge #4380 first? This PR would automatically drop thos... | 2025-04-22T14:53:50 | 2025-05-01T21:21:46 | 2025-05-01T21:15:55Z | CONTRIBUTOR | {
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} | Follow up #4338
- JSON would carry a unit for each property (previously unit would be carried together with the value like `"1.0 kPa"`)
- [x] Avoid hard-coded units in `core.periodic_table.py`
- [x] Avoid post-process values/units on the fly now that it's a static local copy (and store already processed values ins... | {
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} | ### Python version
Python 3.11.11
### Pymatgen version
2025.4.17
### Operating system version
Mac OS X 15.3.2
### Current behavior
When plotting 2D ternary (and 3D quaternary) phase diagrams with `PDPlotter`, if there are multiple above-hull entries for a non-hull composition, the plot will typically show the hi... | {
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"Thanks."
] | 2025-04-23T13:50:05 | 2025-04-23T14:11:45 | 2025-04-23T14:11:41Z | CONTRIBUTOR | {
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} | ## Summary
This PR fixes an error that occurs when calling `merge_sites` on a structure with only one site. For example:
```python
from pymatgen.core import Structure, Lattice
cu = Structure(Lattice.from_parameters(2.5, 2.5, 2.5, 60, 60, 60), species=["Cu"], coords=[[0.0, 0.0, 0.0]])
cu.merge_sites(mode="delet... | {
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"I think I know what is happening. Basically, I was getting property_data from the summary interface, which is the so-called \"best\" data available. In many cases, this is the r2scan data. That's why there is a mismatch.\n\nI have modified the code to just get it from the thermo interface to be consistent. There a... | 2025-04-23T18:22:11 | 2025-04-23T19:28:48 | 2025-04-23T19:28:48Z | CONTRIBUTOR | {
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} | ### Python version
3.10
### Pymatgen version
2025.4.20
### Operating system version
_No response_
### Current behavior
Related to https://github.com/materialsproject/pymatgen/issues/4366
I have tested and those issues have now been resolved. However, I have seen some remaining issues:
The `(uncorrected)_energy_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4380 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4380/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4380/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4380/events | https://github.com/materialsproject/pymatgen/pull/4380 | 3,020,271,104 | PR_kwDOACgets6T7Pm7 | 4,380 | Drop unknown source metallic radius from ptable JSON | {
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"close as already included in #4376"
] | 2025-04-25T14:45:29 | 2025-05-01T21:21:41 | 2025-05-01T21:21:23Z | CONTRIBUTOR | {
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} | ### Summary
Follow up #4345, drop unknown source metallic radius from ptable JSON for the following elements:
```
[metallic_radius][Ac]: 1.878 → None
[metallic_radius][Bi]: 1.82 → None
[metallic_radius][Br]: 1.14 → None
[metallic_radius][Ge]: 1.39 → None
[metallic_radius][Pb]: 1.75 → None
[metallic_radius][... | {
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"## 👋 Hello from RepoBird.ai!\n\nI'm the founder of **RepoBird.ai**, an AI Software Engineer Agent that integrates seamlessly as a GitHub App.\n\nThis Pull Request was automatically generated by our agent, **RepoBirdBot**, to address issue #3940. This issue was marked as a `good first issue` and appeared to be una... | 2025-04-27T21:13:02 | 2025-04-29T15:10:23 | 2025-04-29T15:10:23Z | NONE | {
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} | This PR simplifies the serialization process in the `PhaseDiagram` class by removing the redundant commented-out code for the `all_entries` key in the dictionary returned by `as_dict()`. Previously, the code left a commented-out line that serialized `all_entries` which was redundant and caused confusion.
The changes ... | {
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"Though I am not responsible for the magnetisation part of the code, as a UK-educated man, I must just say that Americans butcher the English language. :-) \n\n@mkhorton I think you might want to fix these? Probably just a rename with an additonal property method where appropriate to maintain backwards compatibilit... | 2025-04-27T21:20:28 | 2025-04-28T17:47:05 | CONTRIBUTOR | {
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} | Just flagging, obviously a very minor thing, but for most parts of the code; "magnetization" (US english) is used, but there are a small minority of cases which use "magnetisation", such as:
https://github.com/materialsproject/pymatgen/blob/93be6fb1ae3c5066164526e9f487c0b4114169e9/src/pymatgen/io/vasp/outputs.py#L390 | {
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"Thanks for reporting this. I just pushed a fix.",
"Great, thank you! I've confirmed it's all now working as expected, and passing all our tests."
] | 2025-04-27T21:37:38 | 2025-04-27T23:29:29 | 2025-04-27T22:53:29Z | CONTRIBUTOR | {
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} | Thank you very much for the recent updates @shyuep -- `MPRester()` is now mostly working as before for our target use cases. There are two remaining issues we have been running into:
- When using `summary_data` with systems with wide chemical systems, a URl error is returned. e.g. when looking for potential competing ... | {
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| Time to first response | 1 day, 9:59:31 | 2:47:08 | 1 day, 23:31:55 |
| Time to close | 2 days, 0:11:47 | 2:34:48 | 6 days, 4:54:35 |
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"After posting this \"proposal\", I realized two issues:\n- The saving/loading process is more or less detatched from the serialization (`as_dict`), so one could always install `orjson` locally without any change needed from pymatgen's side.\n- For some processes where the `json.dumps` is integrated, very likely a ... | 2025-05-01T09:39:38 | 2025-05-02T18:16:27 | CONTRIBUTOR | {
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A quick line profiling reveals two significant bottlenecks:
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} | ### Python version
Python 3.10-3.12
### Pymatgen version
2025.5.2
### Operating system version
_No response_
### Current behavior
From running our `doped` tests with the latest `pymatgen` release, we get many of these warnings (which breaks tests):
```
Using UFloat objects with std_dev==0 may give unexpected res... | {
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