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https://api.github.com/repos/materialsproject/pymatgen/issues/2201 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2201/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2201/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2201/events | https://github.com/materialsproject/pymatgen/issues/2201 | 942,046,369 | MDU6SXNzdWU5NDIwNDYzNjk= | 2,201 | `SpacegroupAnalyzer.get_symmetrized_structure()` weird results on structures with magnetic moments | {
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"would an `inc_magmoms` arg to `SpacegroupAnalyzer` be an acceptable addition `True` by default but can be turned off if all you care about is the structural spacegroup? ",
"> would an inc_magmoms arg to SpacegroupAnalyzer be an acceptable addition True by default but can be turned off if all you care about is th... | 2021-07-12T13:10:06 | 2021-07-14T04:46:48 | CONTRIBUTOR | {
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```
SymmetrizedStructure
Full Formula (Al12 Cr4 O24)
Reduced Formula: Al3CrO6
Spacegroup: R3 (146)
abc : 7.165227 7.166083 8.451375
angles: 1... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2202 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2202/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2202/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2202/events | https://github.com/materialsproject/pymatgen/pull/2202 | 944,258,023 | MDExOlB1bGxSZXF1ZXN0Njg5NzY2MTQ5 | 2,202 | [WIP - Needs Test] add include magmom toggle to `SpacegroupAnalyzer` #2201 | {
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"\n[](https://coveralls.io/builds/41358873)\n\nCoverage decreased (-0.6%) to 83.065% when pulling **8a05fcea91d96cea91a76e81ac8cd8e89d895f92 on CompRhys:magmom-toggle** into **5d600ca610d1a4d3e1532293e5f87062332b9a26 on materialsproject:master**.\n",
"... | 2021-07-14T10:02:08 | 2021-09-01T14:10:58 | 2021-09-01T14:10:32Z | CONTRIBUTOR | {
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add toggle on whether to include magmoms in spglib input in order to has equivalent sites correctly map to wyckoff positions without duplicates.
- [ ] Tests added for checking correct Wyckoff position multiplicities | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2203 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2203/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2203/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2203/events | https://github.com/materialsproject/pymatgen/issues/2203 | 946,548,760 | MDU6SXNzdWU5NDY1NDg3NjA= | 2,203 | `LocalStructOrderParams` is not translationally invariant when specifying neighbor indices | {
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"@nisse3000 do you have any thoughts on this issue?",
"@mkhorton, sure. That looks like a neighbor-finding/image-using \"issue\". \r\n\r\nIf you just print out the distances between the locations of the O neighbors from the V central atom using the \"low-fi\" index mechanism, you realize that 2 neighbors don't se... | 2021-07-16T19:36:04 | 2021-07-21T17:30:09 | 2021-07-21T17:30:09Z | NONE | {
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} | **Describe the bug**
Values of `LocalStructOrderParams` change after translating sites when specifying neighbor indices.
Also, IIUC, LSOP thinks this distorted octahedron is similar to a pentagonal pyramid.
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.analysis.local_env import LocalStruc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2204 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2204/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2204/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2204/events | https://github.com/materialsproject/pymatgen/issues/2204 | 951,806,585 | MDU6SXNzdWU5NTE4MDY1ODU= | 2,204 | Inconsistency between `formula` and `reduced_formula` for diatomic molecules and Ions | {
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"Overloading `Ion.get_reduced_formula_and_factor` would have the additional advantage of enabling special handling of important aqueous species like `OH[-]` (which otherwise shows up as `HO[-]`) and differentiating between `OH[-]` and hydrogen peroxide, `H2O2`. The fact that we can't distinguish these two species (... | 2021-07-23T18:24:41 | 2023-08-13T16:35:00 | 2023-08-13T16:35:00Z | CONTRIBUTOR | {
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} | **Describe the bug**
The output of `Composition.formula` and `Composition.reduced_formula` is counterintuitive for formulas listed in [`special_formulas`](https://github.com/materialsproject/pymatgen/blob/937eff5cc83febdea57258c0488a5b81cb550506/pymatgen/core/composition.py#L78), especially diatomic gases. In additi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2205 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2205/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2205/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2205/events | https://github.com/materialsproject/pymatgen/issues/2205 | 954,089,396 | MDU6SXNzdWU5NTQwODkzOTY= | 2,205 | Problems with saving figures | {
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} | I have been trying to save the output of plotter.get_pourbaix_plot. Earlier I could simply putthe pyplot object in a PDFPages objects like below to save the figure. However, due to changes in pymatgen get_pourbaix_plot returns a pyplot, which in theory should be the same as matplotlib.pyplot. The code below tries to sa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2206 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2206/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2206/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2206/events | https://github.com/materialsproject/pymatgen/issues/2206 | 956,056,926 | MDU6SXNzdWU5NTYwNTY5MjY= | 2,206 | BruteForceOrderMatching class in molecule_matcher module - very basic example - error | {
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"Thanks for the report @mhsiron.\r\n\r\n@fekad, do you have any thoughts on this one?",
"Thanks for the report @mhsiron.\r\n\r\nI have some notes:\r\n- Be careful to use `BruteForceOrderMatcher` with `SymmOp.from_rotation_and_translation`. This method also matches the indices of atoms so if you ignore them you ca... | 2021-07-29T17:27:54 | 2021-07-30T01:53:11 | CONTRIBUTOR | {
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} | **Describe the bug**
The BruteForceOrderMatching class in the molecule_matcher module appears to return erroneous results for simple molecule matching examples (ie with 2 molecule, with some simple transformations between them).
**To Reproduce**
Example 1:
```
from pymatgen.core import Molecule
from pymatgen.an... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2207 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2207/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2207/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2207/events | https://github.com/materialsproject/pymatgen/issues/2207 | 958,569,714 | MDU6SXNzdWU5NTg1Njk3MTQ= | 2,207 | KeyError when accessing PDOS via sites | {
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"This is not really the way this is meant to be used. The structure associated with the complete dos object is stored in the dos.structure attribute. So all you need to do is to replace vr.structures[-1] with dos.structure. vr.structures[-1] may not be exactly the same as the final structure since that is just the ... | 2021-08-02T23:00:56 | 2021-08-02T23:49:46 | 2021-08-02T23:49:46Z | CONTRIBUTOR | {
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} | **Describe the bug**
I cannot use `vasprun.complete_dos.get_site_orbital_dos()` in the snippet below because the site I pass in cannot be matched to any of the sites despite passing it a `PeriodicSite` directly from the structure.
My naive suspicion is that there is something going on with how the sites are compar... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2208 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2208/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2208/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2208/events | https://github.com/materialsproject/pymatgen/pull/2208 | 959,252,379 | MDExOlB1bGxSZXF1ZXN0NzAyMzk1Njgy | 2,208 | update MP2020 publication details | {
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"\n[](https://coveralls.io/builds/41870449)\n\nCoverage decreased (-0.6%) to 83.063% when pulling **c52889a41d0dfb23efe2cddefee3220435032654 on rkingsbury:master** into **3683e218cc512d15090927faf52794dbcea12322 on materialsproject:master**.\n"
] | 2021-08-03T15:45:26 | 2021-08-03T16:28:09 | 2021-08-03T15:48:41Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2209 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2209/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2209/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2209/events | https://github.com/materialsproject/pymatgen/issues/2209 | 961,582,858 | MDU6SXNzdWU5NjE1ODI4NTg= | 2,209 | import Lattice error in Anaconda | {
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"Lattice needs to be imported from either pymatgen.core or pymatgen.core.lattice. Convenient imports have been removed from v2022.0."
] | 2021-08-05T08:34:58 | 2021-08-05T14:26:46 | 2021-08-05T14:26:46Z | NONE | {
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} | **Describe the bug**
Steps to reproduce the behavior:
1. Install Anaconda3-2020.11-Linux-x86_64
2. install pymatgen by :
```
conda install --yes numpy scipy matplotlib
pip install pymatgen
```
3. run python and
`from pymatgen import Lattice `
4. See error
```
Python 3.8.8 (default, Apr 13 2021, 19:58... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2210 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2210/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2210/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2210/events | https://github.com/materialsproject/pymatgen/issues/2210 | 962,371,374 | MDU6SXNzdWU5NjIzNzEzNzQ= | 2,210 | Value ERROR: No Voronoi neighbours found for site - try increasing cutoff | {
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"> I'm trying to get condensed structure of stable materials from Materials Project using Robocrystellographer. But I'm getting this error `Value ERROR: No Voronoi neighbours found for site - try increasing cutoff` from line 892 of `C:\\Users\\...\\site-packages\\pymatgen\\analysis\\local_env.py`. Seems like it's c... | 2021-08-06T03:54:24 | 2023-10-29T05:53:30 | NONE | {
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} | I'm trying to get condensed structure of stable materials from Materials Project using Robocrystellographer. But I'm getting this error `Value ERROR: No Voronoi neighbours found for site - try increasing cutoff` from line 892 of `C:\Users\...\site-packages\pymatgen\analysis\local_env.py`. Seems like it's coming from th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2211 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2211/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2211/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2211/events | https://github.com/materialsproject/pymatgen/pull/2211 | 962,971,001 | MDExOlB1bGxSZXF1ZXN0NzA1NjgyODk0 | 2,211 | Abstract interface for Input classes | {
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"I am in favor of a more concrete API definition, but I am not sure about this implementation. \r\n1. Input conflicts with the Python built-in input method.\r\n2. I fail to see what the current Input offers beyond the VaspInputSet abstract class. Certainly we can abstract out parts of the VaspInputSet class to make... | 2021-08-06T18:52:58 | 2022-08-10T14:01:40 | 2022-03-14T14:05:10Z | CONTRIBUTOR | {
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} | After much discussion and feedback, here is a draft abstract interface for pymatgen I/O classes.
Thanks @utf @shyamd @arepstein @mkhorton and @computron for your thoughts so far, and feel free to add more here!
## Motivation
By defining a minimal interface for *all* `Input` classes in pymatgen, we can
1. Make i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2212 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2212/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2212/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2212/events | https://github.com/materialsproject/pymatgen/issues/2212 | 963,306,640 | MDU6SXNzdWU5NjMzMDY2NDA= | 2,212 | E-above-convex-hull equals 0 for structures with different energy | {
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"I am not sure what you mean. I ran your code and my output is:\r\n```\r\n##############################################################\r\nenergy Difference (eV): 0.19\r\nE-above-hull for structure Ca8As2 151: 0\r\nE-above-hull for structure Ca8As2 727: 0.0010000000002037268\r\n(mavrl) sp@Shyues-Mac-mini py % p... | 2021-08-07T21:25:47 | 2021-08-24T15:34:41 | 2021-08-24T15:34:41Z | NONE | {
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} | Dear ladies and gentlemen,
In my calculations it happens regularly that two `ComputedEntry`-instances with identical composition and sufficiently different total energies are both given an **energy-above-hull of 0** by `get_decomp_and_e_above_hull()`.
The total energy difference of the two compounds in question *... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2213 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2213/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2213/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2213/events | https://github.com/materialsproject/pymatgen/pull/2213 | 963,897,193 | MDExOlB1bGxSZXF1ZXN0NzA2NDM1NjI2 | 2,213 | Fix minor bug when reading Structure from a netcdf4 file with hdf5 groups | {
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"\n[](https://coveralls.io/builds/41998310)\n\nCoverage decreased (-0.6%) to 83.13% when pulling **fa70861ca4ce4bae19aa87f8103ba26063b9119b on gmatteo:master** into **e5fd7f5d460025a3f9311659eae722128aa43e67 on materialsproject:master**.\n",
"The [pyli... | 2021-08-09T11:24:21 | 2021-08-09T14:04:57 | 2021-08-09T14:04:57Z | CONTRIBUTOR | {
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} | ## Summary
* Fix minor bug when reading Structure from a netcdf4 file with hdf5 groups
* Move abiinspect module to abipy to facilitate new developments | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2214 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2214/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2214/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2214/events | https://github.com/materialsproject/pymatgen/issues/2214 | 965,955,010 | MDU6SXNzdWU5NjU5NTUwMTA= | 2,214 | get_entries_in_chemsys reports TypeError in the latest version (2022.0.11) | {
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"I used the exact code you paste and did not get any error. I suspect your install may be out of date. Can you remove pymatgen and reinstall and try again?",
"> I used the exact code you paste and did not get any error. I suspect your install may be out of date. Can you remove pymatgen and reinstall and try again... | 2021-08-11T05:29:40 | 2021-08-15T14:39:47 | 2021-08-15T14:39:47Z | NONE | {
"total": 0,
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} | **Describe the bug**
After upgrading to version 2022.0.11, I was trying to use `get_entries_in_chemsys` to obtain entries in a high dimentional chemical space. However a TypeError occurred, which pointed to the compatibility module under entries.
**To Reproduce**
The chemical system I demonstrated here is from pym... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2215 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2215/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2215/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2215/events | https://github.com/materialsproject/pymatgen/pull/2215 | 967,375,170 | MDExOlB1bGxSZXF1ZXN0NzA5NTUyODE1 | 2,215 | QChem: add CMIRS solvent model support | {
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"\n[](https://coveralls.io/builds/54037541)\n\nCoverage remained the same at 0.0% when pulling **df3a87952d3303699f05292ee04c3d6486b670dd on rkingsbury:cmirs** into **03691a8fdb8bc68db1f23a95930f71a07ffef4df on materialsproject:master**.\n",
"@samblau ... | 2021-08-11T20:07:42 | 2024-10-10T01:54:53 | 2022-11-22T19:57:08Z | CONTRIBUTOR | {
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} | ## Summary
Additions to `QCInput` and `QChemDictSet` needed to support the new CMIRS implicit solvent model and the isodensity implementation of SS(V)PE.
See relevant Q-Chem manual pages:
- https://manual.q-chem.com/latest/subsec_PCM_job_control.html
- https://manual.q-chem.com/latest/subsec_SS(V)PE.html
- htt... | {
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"Sorry it's my mistake, we can set `coords_are_cartesian` when construct the `Structure` object, so this is not a bug.\r\n"
] | 2021-08-15T05:52:40 | 2021-08-15T12:55:12 | 2021-08-15T12:55:12Z | CONTRIBUTOR | {
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} | **Describe the bug**
Hi, I was using Pymatgen `Structure` object to write a POSCAR and cif file using `to` method, but the files generated were wrong when using cartesian coordinates.
**To Reproduce**
Steps to reproduce the behavior:
1. generate a pymatgen `Structure` object using cartesian coordinates.
```
fro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2217 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2217/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2217/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2217/events | https://github.com/materialsproject/pymatgen/pull/2217 | 971,120,475 | MDExOlB1bGxSZXF1ZXN0NzEyOTI2MDk4 | 2,217 | fix issue #2216 | {
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"This is not a valid check. Fractional coordinations can also be less than 0 and greater than 1, even if they map to the unit cell. This is frequently used when you are working with trajectories. The reason why the coordinates are defaulted to fractional for crystals is because this is by far the most common way co... | 2021-08-15T12:16:38 | 2021-08-15T15:59:02 | 2021-08-15T12:20:31Z | CONTRIBUTOR | {
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} | ## Summary
Add a few lines code to exam the coords fed to `Structure` object are cartesian or not.
The setting of `coords_are_cartesian` was defaulted to `False` and problem may occur when feeding cartesian coords to `Structure`.
* Fix issue #2216
## Additional dependencies introduced (if any)
None
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https://api.github.com/repos/materialsproject/pymatgen/issues/2218 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2218/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2218/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2218/events | https://github.com/materialsproject/pymatgen/pull/2218 | 972,105,830 | MDExOlB1bGxSZXF1ZXN0NzEzNzUwMzA0 | 2,218 | Add `chempot_diagram` module for creation/plotting of chemical potential diagrams | {
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"\n[](https://coveralls.io/builds/42531927)\n\nCoverage decreased (-0.6%) to 83.156% when pulling **09d0397c323e3ef624c471a9721a2c986a5ad44e on mattmcdermott:chempot_diagrams** into **13d7c12a822fb64e47a44cc09bdf3b9dcaa0e76d on materialsproject:master**.... | 2021-08-16T21:14:02 | 2021-09-01T00:33:12 | 2021-09-01T00:33:12Z | MEMBER | {
"total": 0,
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} | ## Summary
* Added new module with class,`ChemicalPotentialDiagram`, for creating and plotting **chemical potential diagrams** for a list of entries with 2 or more elements. Chemical potential diagrams are like normal predominance diagrams (which are already implemented in pymatgen), but they also show the "extra" c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2219 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2219/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2219/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2219/events | https://github.com/materialsproject/pymatgen/issues/2219 | 972,141,270 | MDU6SXNzdWU5NzIxNDEyNzA= | 2,219 | Entry ID does not display on hovertext for plots of `CompoundPhaseDiagram` and `GrandPotentialPhaseDiagram` | {
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} | A phase's Entry ID does not display on the hovertext for Plotly-based plots of `CompoundPhaseDiagram` objects and `GrandPotentialPhaseDiagram` objects.
This has been a known issue and I will address it in a new PR.
Steps to reproduce the behavior:
1. Acquire any set of entry objects which contain an entry ID (e... | {
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"\n[](https://coveralls.io/builds/42187230)\n\nCoverage decreased (-0.6%) to 83.132% when pulling **234a4c1ca19797090ce11b235d62e14eceecf3ef on mattmcdermott:grand_pd_bug_fix** into **0f357e704c7c1a7ff98edba8c21c537114c61b29 on materialsproject:master**.... | 2021-08-16T22:53:39 | 2021-08-17T00:38:16 | 2021-08-17T00:38:16Z | MEMBER | {
"total": 0,
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} | ## Summary
* Bug fix for entry_ID phase diagram plotting bug described in this Issue: #2219
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Sta... | {
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"I plan to address this feature request in a new PR in the next week(s). \r\n\r\nThe Plotly viewer can also be used on the new MP website.",
"Closing this as this feature was added in #2233 "
] | 2021-08-18T17:46:39 | 2021-11-16T00:27:07 | 2021-11-16T00:27:07Z | MEMBER | {
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} | The current `InterfacialReactivity` module in `pymatgen.analysis.interface_reactions` is not user-friendly. To view the predicted reactions between two compositions, a user can call `InterfacialReactivity.plot()`, but they are unable to clearly tell which reactions are predicted, as there are no labels on the plot.
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"Hi Bin, just a note that at Materials Project we mostly now use the drone in [`atomate`](https://github.com/hackingmaterials/atomate/blob/main/atomate/vasp/drones.py) rather than the simple drone here. This is not directly relevant to your bug report but thought I would let you know in case you were looking for th... | 2021-08-20T22:04:25 | 2021-08-24T15:34:24 | 2021-08-24T15:34:24Z | NONE | {
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} | **Describe the bug**
At the assimilate method of SimpleVaspToComputedEntryDrone, it checks for existence of multiple INCAR POTCAR and DYNMAT with the following commands:
if len(files) == 1 or filename in ("INCAR", "POTCAR", "DYNMAT"):
files_to_parse[filename] = files[0]
If there is no DYNMAT file in the calculat... | {
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"My bad, I have been looping over a pandas dataframe of compositions when talking about multiple compositions, so the iteration over the Composition class should by default always go over the elements."
] | 2021-08-23T11:12:56 | 2021-08-23T11:17:49 | 2021-08-23T11:16:27Z | NONE | {
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I would like to point out a problem concerning the inconsistent return value of the __len__() method of the Composition class.
When an object contains one composition, the __len__() command returns the number of elements, whereas an object with multiple compositions returns the number of compositions. This is... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2224 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2224/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2224/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2224/events | https://github.com/materialsproject/pymatgen/pull/2224 | 977,556,706 | MDExOlB1bGxSZXF1ZXN0NzE4Mjg1OTA1 | 2,224 | Configured test files dir | {
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"\n[](https://coveralls.io/builds/42354378)\n\nCoverage decreased (-0.6%) to 83.136% when pulling **86f8981d6b1e38ed83c4dee5060a6536bef2faa6 on drew-parsons:configured_test_files_dir** into **e002969c12ca7e06cacb6984503d69114cb442ef on materialsproject:m... | 2021-08-23T23:15:49 | 2021-08-24T15:36:31 | 2021-08-23T23:39:56Z | CONTRIBUTOR | {
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} | ## Summary
* use PymatgenTest.TEST_FILES_DIR with all tests
Required to enable tests to run separately from the source, for instance for CI testing of packaging for Linux distributions,
see https://github.com/materialsproject/pymatgen/issues/2025
Before a pull request can be merged, the following items must b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2225 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2225/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2225/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2225/events | https://github.com/materialsproject/pymatgen/pull/2225 | 977,560,625 | MDExOlB1bGxSZXF1ZXN0NzE4Mjg5MzAx | 2,225 | update list of data files required for installation | {
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"\n[](https://coveralls.io/builds/42363078)\n\nCoverage decreased (-0.6%) to 83.134% when pulling **fd9004ddd600c6141a22aae485162720cbc4477e on drew-parsons:install_data_files** into **405a0b22c506077732ed0cabee82d2503ae9d0ce on materialsproject:master**... | 2021-08-23T23:25:13 | 2021-08-25T16:52:11 | 2021-08-24T15:29:24Z | CONTRIBUTOR | {
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## Summary
* update list of data files to be installed
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2226 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2226/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2226/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2226/events | https://github.com/materialsproject/pymatgen/issues/2226 | 978,572,671 | MDU6SXNzdWU5Nzg1NzI2NzE= | 2,226 | A bug in get_neighbors function? | {
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"@chc273 @shyuep I have tested the new fix. It worked."
] | 2021-08-25T00:00:00 | 2021-08-25T05:03:58 | 2021-08-25T05:03:58Z | NONE | {
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} | **Describe the bug**
I am trying to use the get_neighbors function to process some structures. However, it failed in some cases
**To Reproduce**
```Python
from pymatgen.core import Structure
poscar = '''POSCAR
1.0000000000000000
6.9082208665474800 0.0000000000000005 0.0000000000000011
-0.000... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2227 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2227/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2227/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2227/events | https://github.com/materialsproject/pymatgen/pull/2227 | 978,660,013 | MDExOlB1bGxSZXF1ZXN0NzE5MjEyODgy | 2,227 | Fix c mod in neighobrs | {
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"\n[](https://coveralls.io/builds/42390860)\n\nCoverage decreased (-0.6%) to 83.132% when pulling **c42bee17c8ee8cbd5d8fcbea0d96455d29563504 on chc273:fix_c_mod_in_neighobrs** into **40817cc97fe25bc027523a65aab528b59e22e78e on materialsproject:master**.\... | 2021-08-25T03:08:39 | 2021-08-25T03:31:53 | 2021-08-25T03:30:08Z | CONTRIBUTOR | {
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} | This PR fixes bug reported by #2226
In the previous implementation, I have turned on the c behavior for division in cython. In this case `-0.1 % 1 = -0.1` while I expected the result to be 0.9 as in python. This causes the atoms out of the unit cell in the negative direction not properly wrapped into the unit cell... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2228 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2228/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2228/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2228/events | https://github.com/materialsproject/pymatgen/pull/2228 | 980,116,570 | MDExOlB1bGxSZXF1ZXN0NzIwNDEyOTI1 | 2,228 | Changes due to new lobster version and changes to lobsterenv | {
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"I am working on it further. I will let you know once it is finished ... Found another inconsistency and had to make a few changes.\r\n\r\nJG",
"\n[](https://coveralls.io/builds/42448769)\n\nCoverage decreased (-0.7%) to 83.122% when pulling **f786a634... | 2021-08-26T11:06:05 | 2021-08-26T21:11:24 | 2021-08-26T21:02:25Z | MEMBER | {
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} | ## Summary
Hi all,
I have now fixed some problems due to the new Lobster versions. The Icohplist class can now at least handle orbitalwise ICOHPLIST.lobster files -it will ignore the orbitalwise information for now as it will probably take several days of work to think about a new data format for this additional i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2230 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2230/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2230/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2230/events | https://github.com/materialsproject/pymatgen/pull/2230 | 984,061,702 | MDExOlB1bGxSZXF1ZXN0NzIzNTQyNTYx | 2,230 | Update bader_caller.py | {
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"Thanks @nwinner",
"\n[](https://coveralls.io/builds/42550434)\n\nCoverage decreased (-0.6%) to 83.125% when pulling **aea737ffc405750d5a264fffb78edca1260d259b on nwinner:patch-1** into **48b031a44494b6452b9ca14619448e450bda7af9 on materialsproject:mas... | 2021-08-31T16:35:14 | 2021-09-01T01:10:46 | 2021-09-01T00:32:11Z | CONTRIBUTOR | {
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"Thanks @CompRhys !",
"\n[](https://coveralls.io/builds/42551120)\n\nCoverage decreased (-0.6%) to 83.125% when pulling **a88d4069e70048ef248ba91b013e0077687ce236 on CompRhys:master** into **48b031a44494b6452b9ca14619448e450bda7af9 on materialsproject:... | 2021-08-31T16:55:03 | 2021-09-01T01:15:08 | 2021-09-01T00:31:01Z | CONTRIBUTOR | {
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"Is there something I forgot to do for this PR to be checked? I notice that the workflows were never run here",
"Thanks. The reason why the CI did not run is because of new security features from Github. They need approval from a maintainer for first time contributors.\r\n\r\nThis looks good. Since it is an add-o... | 2021-09-01T09:27:54 | 2021-09-24T15:27:05 | 2021-09-24T15:27:05Z | CONTRIBUTOR | {
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} | This add-on (www.pypi.org/project/pymatgen-io-fleur) provides functionality for reading writing files used
by the FLEUR code (www.flapw.de)
## Summary
Include a summary of major changes in bullet points:
* Added entry for IO namespace package for the fleur code to the addons page
* Added the IO functionality... | {
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"@mkhorton My plan is to have this PR done by Wed, September 8, based on the previous timeline goal we set",
"Fantastic, thank you for the update @mattmcdermott !",
"@mkhorton Should be pretty much done. Seems like linting and tests are failing for recent changes related to Optimade.\r\n\r\nNote: you'll see I c... | 2021-09-02T22:16:18 | 2021-09-08T22:23:19 | 2021-09-08T22:22:56Z | MEMBER | {
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} | ## Summary
* Add: support for Plotly: calling `plot()` now provides a `backend` option for choosing matplotlib or Plotly.
* Add:`GrandPotentialInterfacialReactivity` class to separate code based on the use of grand potential phase diagrams (this greatly decreases the complexity of the `__init__` args) and is a more... | {
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"Honestly, even the current version of `__eq__` is not technically correct. There is no fixed reference direction in 3D space. E.g., if I rotate the basis vectors by a fixed angle, the lattices are technically still equivalent. The correct definition of `lattice.__eq__` should be that the lattice parameters (length... | 2021-09-03T12:42:04 | 2021-09-16T20:55:46 | 2021-09-16T15:39:35Z | CONTRIBUTOR | {
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} | In `Lattice.__eq__` the code uses the default tolerances for np.allclose which affects the strict equality of structures. Elsewhere the code pattern in `pymatgen` appears to be to have a `cls.blah_tol` for different objects i.e. `Site.position_atol = 1e-4`. The np.allclose defaults are quite strict for my use case and ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2235 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2235/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2235/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2235/events | https://github.com/materialsproject/pymatgen/issues/2235 | 988,025,876 | MDU6SXNzdWU5ODgwMjU4NzY= | 2,235 | hash of sites is not discriminate | {
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"Also a thought re: #2077 currently `Composition({\"Fe3+\": 2, \"O2-\":3})` and `Composition({\"Fe\": 2, \"O\":3})` have different hashes. I think this is okay but just want to check, I will make a PR to improve the docstring alongside and possible changes to `Site`'s hash",
"Differing hash methods for different ... | 2021-09-03T18:54:12 | 2021-09-13T16:26:59 | 2021-09-13T14:40:05Z | CONTRIBUTOR | {
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} | In #2077 we added a more discriminate hash from `Composition` individual `Site` are effectively `Composition` but they still use the old composition hash. Shall I update the `Site` hash to match composition? I haven't actually traced a slow-down to site matching like I did with compositions but was looking at `Site` co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2236 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2236/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2236/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2236/events | https://github.com/materialsproject/pymatgen/issues/2236 | 988,256,942 | MDU6SXNzdWU5ODgyNTY5NDI= | 2,236 | 🐞 Bug in parsing `bandOverlaps.lobster` file | {
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} | **Describe the bug**
Generated `bandOverlaps.lobster` file by `Lobster` (tested with `v4.0.0` and `v4.1.0`), writes spin as `spin 1` and `spin 2`. In the `self._read` method here, spins are parsed as `spin 0` and `spin 1` and therefore, it misses `spin 2` and fails.
**To Reproduce**
I have attached two following ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2237 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2237/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2237/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2237/events | https://github.com/materialsproject/pymatgen/pull/2237 | 988,258,021 | MDExOlB1bGxSZXF1ZXN0NzI3MjE0Mjc2 | 2,237 | 🛠 fixes the issue in parsing `bandOverlaps.lobster` file | {
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"Thank you for finding this. ",
"Thanks @pzarabadip! Ideally there would have a minimal test added with the fix, could you add one?",
"I'll do it @mkhorton. I'm having a little bit of issue running tests on M1 Mac but should be fixed soon. I'll updated the available `BandoverlapsTest` test class to reflect this... | 2021-09-04T09:59:21 | 2021-09-10T16:35:49 | 2021-09-10T16:11:54Z | CONTRIBUTOR | {
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} | ## Summary
* Fix #2236
## Additional dependencies introduced (if any)
None.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python st... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2238 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2238/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2238/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2238/events | https://github.com/materialsproject/pymatgen/pull/2238 | 988,381,016 | MDExOlB1bGxSZXF1ZXN0NzI3MzA2ODA3 | 2,238 | Updates to OPTIMADE REST interface | {
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"\n[](https://coveralls.io/builds/42662827)\n\nCoverage decreased (-0.01%) to 83.773% when pulling **f94e8d5c32dc3671ca5aeee3066ac5a2401ecd73 on optimade-updates** into **e9760e2799a1d05805bbdb9971faa39fd541c1ea on master**.\n"
] | 2021-09-04T22:40:57 | 2022-10-10T17:54:17 | 2021-09-05T20:44:01Z | MEMBER | {
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} | ## Summary
Preparing new features in advance of OPTIMADE lesson on Tuesday.
The main feature added in this PR is for `pymatgen.ext.optimade.OptimadeRester` to allow querying multiple providers simultaneously. It also adds more logging and reporting/user experience improvements.
## TODO (if any)
There are se... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2239 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2239/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2239/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2239/events | https://github.com/materialsproject/pymatgen/pull/2239 | 989,467,819 | MDExOlB1bGxSZXF1ZXN0NzI4MjA1ODEx | 2,239 | Speed up nearest-neighbor routines & structure graph generation | {
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"\n[](https://coveralls.io/builds/42699463)\n\nCoverage decreased (-0.6%) to 83.143% when pulling **30a1b6f1198aa42bb413bad686c9412c10db6aef on ltalirz:speedup-cutoff-dict** into **1ea090680ce34ca944cd7671032fa274bf035192 on materialsproject:master**.\n"... | 2021-09-06T22:50:14 | 2021-10-23T22:21:00 | 2021-09-07T13:59:43Z | CONTRIBUTOR | {
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} | ## Summary
The `get_nn_info` routines of many nearest-neighbor flavors in `pymatgen.analysis.local_env` recomputed the original periodic image of sites although this information was already stored on the `PeriodicNeighbor` objects (at least it seems so to me - correct me if I'm wrong).
This resulted in O(N^2) inste... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2240 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2240/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2240/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2240/events | https://github.com/materialsproject/pymatgen/issues/2240 | 989,491,820 | MDU6SXNzdWU5ODk0OTE4MjA= | 2,240 | io.lammps.data.LammpsData does not read charge from structure | {
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"It seems that the `oxidation_states` should have been considered as \"charge\" in the `site_properties` of a structure."
] | 2021-09-07T00:13:00 | 2021-09-07T00:46:33 | CONTRIBUTOR | {
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} | **Describe the bug**
For a `structure` with decorated atomic charges, I would expect `LammpsData.from_structure(structure, atom_style='charge')` to read the atom charges from the `structure`. However, this is not the case and the charges are all assigned zero.
**To Reproduce**
```
from pymatgen.core import S... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2241 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2241/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2241/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2241/events | https://github.com/materialsproject/pymatgen/pull/2241 | 989,754,153 | MDExOlB1bGxSZXF1ZXN0NzI4NDQ0NzA2 | 2,241 | improve Structure.from_str fmt doc string and type hint | {
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"Sorry about this hasty PR. I'd never looked into [contravariance](https://www.python.org/dev/peps/pep-0483/#covariance-and-contravariance) before. I still think there would be some value in having a more restrictive type hint (same for docs) but seems that would require use of `# type: ignore` on [line 2338](https... | 2021-09-07T08:56:45 | 2021-10-06T19:15:01 | 2021-10-06T19:12:59Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2242 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2242/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2242/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2242/events | https://github.com/materialsproject/pymatgen/pull/2242 | 990,007,621 | MDExOlB1bGxSZXF1ZXN0NzI4NjYyNTA4 | 2,242 | Add two more pre-defined Optimade aliases | {
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"Thanks @blokhin!"
] | 2021-09-07T13:50:23 | 2021-09-07T16:06:59 | 2021-09-07T15:57:01Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2243 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2243/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2243/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2243/events | https://github.com/materialsproject/pymatgen/issues/2243 | 990,049,615 | MDU6SXNzdWU5OTAwNDk2MTU= | 2,243 | Extraneous parameter in OPTIMADE extension when using raw filters (plus a missing dependency) | {
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"Hi @ml-evs,\r\n\r\nThanks for the write-up. I will address 1. myself, but if you're willing to make a PR for the latter, that would be of course welcome!",
"Great!\r\n\r\nre: `retrying`, I ran into it in a fresh binder env that I used for your tutorial: https://mybinder.org/v2/gh/Materials-Consortia/optimade-tut... | 2021-09-07T14:30:57 | 2021-09-15T21:06:49 | 2021-09-15T21:06:49Z | CONTRIBUTOR | {
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} | **Describe the bug**
Some minor bugs arising from today's OPTIMADE NOMAD tutorial:
1. The library [`retrying`](https://pypi.org/project/retrying/) is used in the [OPTIMADE extension](https://github.com/materialsproject/pymatgen/blob/f72963b038be33c058c844f93ec2392f1613fffe/pymatgen/ext/optimade.py#L13) but it is ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2244 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2244/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2244/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2244/events | https://github.com/materialsproject/pymatgen/pull/2244 | 990,143,321 | MDExOlB1bGxSZXF1ZXN0NzI4Nzc2Mzk1 | 2,244 | Remove bad param when setting OPTIMADE response fields | {
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"Thanks @ml-evs! Since you're a first time contributor, I had to manually approve the CI, but will merge once it's run.\r\n\r\nBtw, (also since you're a first time contributor), please make sure to fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can acknowledge you appropriately on our [development ... | 2021-09-07T16:12:56 | 2021-09-15T21:06:49 | 2021-09-15T21:06:49Z | CONTRIBUTOR | {
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} | ## Summary
OPTIMADE uses the `response_fields` URL parameter to select the response fields, this PR removes an extraneous URL parameter that is added when using a raw OPTIMADE filter through `OptimadeRester`.
Addresses and closes #2243 (cc @mkhorton)
~Haven't added any tests as I don't think this extension is ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2245 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2245/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2245/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2245/events | https://github.com/materialsproject/pymatgen/issues/2245 | 993,147,749 | MDU6SXNzdWU5OTMxNDc3NDk= | 2,245 | cannot import name 'coord_cython' from 'pymatgen.util' | {
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When I run 'import pymatgen.core.structure import Molecule' to check whether it works well, something wrong happens like this:
Is there any reason or ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2246 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2246/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2246/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2246/events | https://github.com/materialsproject/pymatgen/issues/2246 | 993,149,388 | MDU6SXNzdWU5OTMxNDkzODg= | 2,246 | cannot import name 'coord_cython' from 'pymatgen.util' | {
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"Pls reinstall pymatgen. Try pip install --update pymatgen.",
"> Pls reinstall pymatgen. Try pip install --update pymatgen.\r\n\r\nIt works, thank you so much for your help!",
"I've tried upgrade it but it didn't work. There is no coord_cython.py but a coord_cython.cp39-win_amd64.pyd in pymatgen/util/.\r\nAnd s... | 2021-09-10T11:33:53 | 2023-09-21T03:26:43 | 2021-09-16T15:38:52Z | NONE | {
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When I run 'from pymatgen.core.structure import Molecule' to check whether it works well, something wrong happens like this:
Is there any reason or solut... | {
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"\n[](https://coveralls.io/builds/43286494)\n\nCoverage decreased (-0.6%) to 83.134% when pulling **069a01ae5d36ef04776d09b92a933195baf2dca2 on janosh:literal-types** into **2926a20ccdf5c41a17eb4bd79fe76f1d6ae0afc8 on materialsproject:master**.\n",
"I ... | 2021-09-11T18:58:52 | 2021-10-06T19:41:31 | 2021-10-06T19:41:03Z | MEMBER | {
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} | Follow up to #2241. Here are a few more examples where `Literal` type hints make sense. I think there are ~80 more places throughout pymatgen. Happy to address more of them in this PR if you guys will accept. | {
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"Definitely not desired behaviour!\r\n\r\nThat was my code so mea culpa. Was there a reason you closed this issue?",
"It was related to much hash concerns about `Site` and there the takeaway for me was that because two compositions are not equal if they have assigned charges then it doesn't matter that the hashes... | 2021-09-13T11:55:21 | 2021-10-07T07:28:22 | 2021-10-07T07:28:22Z | CONTRIBUTOR | {
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} | ```python
>>> from pymatgen.core.composition import Composition
>>> Composition({"Fe3+": 2, "O2-":3}).chemical_system
'Fe3+-O2-'
>>> Composition({"Fe": 2, "O":3}).chemical_system
'Fe-O'
>>> Composition({"Fe3+": 2, "Fe2+": 1, "O2-":4}).chemical_system
'Fe2+-Fe3+-O2-'
```
Not sure if this is a bug or not, it n... | {
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"\n[](https://coveralls.io/builds/42858314)\n\nCoverage decreased (-0.6%) to 83.161% when pulling **6c571fc272554b0e8f07e77099f92e90a7085a02 on CompRhys:chemsystem** into **b8b27c6fa3236f032581aa82f668b25a78aa3b57 on materialsproject:master**.\n",
"Tha... | 2021-09-14T11:26:10 | 2021-10-13T08:59:44 | 2021-10-06T19:39:26Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2250 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2250/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2250/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2250/events | https://github.com/materialsproject/pymatgen/issues/2250 | 996,205,727 | I_kwDOACgets47YOSf | 2,250 | A bug in pointgroupanalyzer? | {
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"The relevant tolerance in this case is the `eigen_tolerance`, which determines whether it is classified as a symmetric top or not. Setting `eigen_tolerance=1e-3` gives C2 as expected. "
] | 2021-09-14T16:22:50 | 2021-09-14T16:32:15 | 2021-09-14T16:32:15Z | NONE | {
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} | **Describe the bug**
I am trying to use the `PointGroupAnalyzer` to perform some symmetry analysis on some cluster. However, it does not work as I expected for some cases.
**To Reproduce**
```python
from pymatgen.core import Molecule
from pymatgen.symmetry.analyzer import PointGroupAnalyzer
xyz = """15
C7 N8... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2251 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2251/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2251/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2251/events | https://github.com/materialsproject/pymatgen/issues/2251 | 996,392,593 | I_kwDOACgets47Y76R | 2,251 | Outcar parsing error from pymatgen | {
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} | **Describe the bug**
I am relaxing an oxide slab e.g. IrO2 with ISPIN=2 LORBIT=11 and with the WalltimeHandler from Custodian switched on. The vasp command that I am using is mpirun --map-by core -np 32 /opt/vasp.5.4.4.pl2/bin/vasp_std. Sometimes I will receive a parsing error from pymatgen when it is trying to parse ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2252 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2252/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2252/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2252/events | https://github.com/materialsproject/pymatgen/issues/2252 | 997,719,116 | I_kwDOACgets47d_xM | 2,252 | convert from pymatgen Molecule/Structure into SMILES/SELFIES and vice versa | {
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"Converting to SMILES is already possible. That can be done via the babel interface in pymatgen.io.babel. As for SELFIES, I am happy for it to be included if someone implements it.",
"Hi, could you give a small example of how to use pymatgen.io.babel to convert `pymatgen` Structure/Molecule to SMILES?\r\n\r\nI am... | 2021-09-16T03:28:41 | 2021-09-16T15:36:01 | 2021-09-16T15:36:01Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
It would be a useful feature to have, especially if this could be done for [SELFIES](https://github.com/aspuru-guzik-group/selfies). SELFIES is a new more robust version of SMILES. It is useful because it might be good to explore machine learning on st... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2253 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2253/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2253/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2253/events | https://github.com/materialsproject/pymatgen/issues/2253 | 998,194,624 | I_kwDOACgets47fz3A | 2,253 | get_pointgroup function takes long time? | {
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"This can be resolved by setting matrix_tolerance=0.2 in your PointGroupAnalyzer. Unfortunately, if too small a tolerance is set, the code just goes on... I will add a warning message."
] | 2021-09-16T13:08:42 | 2021-10-27T15:52:19 | 2021-10-27T15:52:19Z | NONE | {
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} | **Describe the bug**
I am trying to use the PointGroupAnalyzer to parse the molecular symmetry. It works well in general. However, I sometimes encounter some cases in which the get_pointgroup function takes forever.
**To Reproduce**
```python
from pymatgen.symmetry.analyzer import PointGroupAnalyzer
from pymat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2254 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2254/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2254/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2254/events | https://github.com/materialsproject/pymatgen/issues/2254 | 1,011,029,712 | I_kwDOACgets48QxbQ | 2,254 | Update AFLOW prototype library | {
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"I reached out to the AFLOW team, and they don't want archives of the full library unless you purchase through them ([here's the thread](https://groups.io/g/aflow/topic/85959008)). \r\n\r\nI'll close this request because these prototypes cannot be updated to the full library😢",
"Hahahaha"
] | 2021-09-29T14:21:51 | 2021-09-29T22:25:00 | 2021-09-29T22:22:26Z | CONTRIBUTOR | {
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} | Would someone be able to update the `aflow_prototypes.json` in the `pymatgen.analysis` module?
Currently it only includes 288 prototypes (so Part 1 of their library), but they are now at 1,100 prototypes (thanks to Parts 2 and 3).
I don't use the aflow software, so I'm not sure how to download these structures an... | {
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"Zeo++ and its related tools have moved around a bit over time. The current version of Zeo++ can be found [here](http://www.zeoplusplus.org/download.html) and Voro++ [here](https://github.com/chr1shr/voro.git). However, I'm pretty sure that Zeo++ ships with everything needed for installation, including a compatible... | 2021-10-01T16:18:08 | 2023-06-03T02:25:52 | 2023-06-03T02:25:52Z | NONE | {
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} | I am following the directions on the pymatgen documentation site on installing and setting up Zeo++ and Voro++ (https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps). When I do the svn chackout command I get an "Access denied" error. I found an older Bug back from 2016 that offered a solution but when I t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2256 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2256/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2256/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2256/events | https://github.com/materialsproject/pymatgen/pull/2256 | 1,015,808,197 | PR_kwDOACgets4sq6qF | 2,256 | Type hint and correct documentation of Structure.remove_site_properties | {
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"\n[](https://coveralls.io/builds/43268100)\n\nCoverage decreased (-0.6%) to 83.134% when pulling **27ce06b72049a2e76e3e206a3c4e99c5d0029a34 on kmu:master** into **5011c0a6e1dc48380ed2d7a29ec6b0561f60be3b on materialsproject:master**.\n",
"Thanks."
] | 2021-10-05T02:12:18 | 2021-10-05T13:39:43 | 2021-10-05T13:39:39Z | CONTRIBUTOR | {
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} | ## Summary
Type hint and correct documentation of `Structure.remove_site_properties`
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
* Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2257 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2257/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2257/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2257/events | https://github.com/materialsproject/pymatgen/pull/2257 | 1,021,509,739 | PR_kwDOACgets4s9tpW | 2,257 | InsertionElectrode bug fix & doc clarification | {
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"\n[](https://coveralls.io/builds/44306257)\n\nCoverage decreased (-0.6%) to 83.111% when pulling **59f1b2e7439f20588bee501aa96c711ef59d1c30 on acrutt:master** into **9276567df1bf01eea473933688975003449dc5e5 on materialsproject:master**.\n",
"Note for ... | 2021-10-08T22:24:26 | 2021-11-16T17:37:14 | 2021-11-16T17:36:50Z | CONTRIBUTOR | {
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} | The InsertionElectrode.from_entries() method can use either ComputedEntries or ComputedStructureEntries - this has been added to the documentation. Setting strip_structures=True only works with ComputedStructureEntries so this has also been clarified.
In constructing the PhaseDiagram to compare the energies of the p... | {
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"Just trying to give some insight here:\r\nI believe this is because in Pandas, NaN (in `coeff6` here) will automatically upscale the rest of the data in that column to float. \r\nThe `NaN` is from when we don't have a coefficient (the first 3 rows here)\r\n\r\nA proposed solution to this issue would be to use `fil... | 2021-10-08T23:11:12 | 2021-11-15T22:25:35 | 2021-11-15T22:25:35Z | CONTRIBUTOR | {
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} | **Describe the bug**
When reading a file containing a `Dihedral Coeffs` section, `LammpsData.from_file` sometimes change the datatype of the `coeff6` column from `int` to `float`. This is a problem because LAMMPS is very particular about the data types for dihedral coefficients. Having a float instead of an int can re... | {
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"@yang-ruoxi: You've done XAS calculations before, right? Do you think this issue is still relevant?\r\n\r\n@janosh ",
"Hi @pjf295, VAPS can't do XANES calculation as far as I know. the IO for XANES in pymatgen is for the code FEFF. \r\nThanks, @arosen93 for keeping track of the issue! ",
"Oops, sorry 'bout tha... | 2021-10-12T04:44:01 | 2024-03-18T14:08:47 | NONE | {
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} | The current version of Pymatgen (2022.0.14) does not recognize XANES output from VASP 6.
**Proposed Solution:** Enable Pymatgen to read VASP 6 XANES output from either the `vasprun.xml` file or the `OUTCAR` file. Additionally, consider supporting electron-phonon coupling results. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2260 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2260/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2260/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2260/events | https://github.com/materialsproject/pymatgen/issues/2260 | 1,024,889,793 | I_kwDOACgets49FpPB | 2,260 | defects test_generators fails on non-amd64 architecture | {
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} | **Describe the bug**
The test suite includes VoronoiInterstitialGeneratorTest.test_int_gen in pymatgen/analysis/defects/tests/test_generators.py,
https://github.com/materialsproject/pymatgen/blob/fffcc6d3edf95132fbf910ddc520d00309f1b448/pymatgen/analysis/defects/tests/test_generators.py#L107
This test run at bu... | {
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"You can install `typing_extensions`, which is actually already a requirement of pymatgen if you're running in Python 3.7.\r\n\r\nThe correct way of resolving this is following this example:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/f97868791cb8f01aadf1eb3620d1df63fb0ff49a/pymatgen/io/qchem/inputs.py... | 2021-10-13T10:53:42 | 2021-10-14T19:51:45 | 2021-10-14T16:57:29Z | MEMBER | {
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@CompRhys informed me that due to #2247, Pymatgen is no longer installable in Google Colab which is locked to Python 3.7 while `typing.Literal` was only added in Python 3.8.
There's a relatively recent but quiet issue tracking the ability to select different Python versions in Colab: https://githu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2262 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2262/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2262/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2262/events | https://github.com/materialsproject/pymatgen/pull/2262 | 1,027,949,105 | PR_kwDOACgets4tRnQ- | 2,262 | removed _ from beginning of arguments | {
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"Thanks @jmmshn!"
] | 2021-10-16T04:30:45 | 2021-10-18T22:15:55 | 2021-10-18T22:15:49Z | CONTRIBUTOR | {
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"> I have several small QOL changes like this on that branch and think it would be easier if they are merged separately first \r\n\r\nThanks @CompRhys -- are you planning on submitting these as separate PRs? i.e. should I merge this one, or wait?",
"These two PRs are the only two not in phase diagram relevant fil... | 2021-10-16T08:56:10 | 2021-10-19T09:15:18 | 2021-10-18T22:14:38Z | CONTRIBUTOR | {
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I am making this PR as I am looking at trying to get my `PatchedPhaseDiagram` ready to be merged in near future, I have several small QOL changes like this on that branch and think it would be easier if they are merged... | {
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"Thanks!"
] | 2021-10-16T09:17:09 | 2021-10-19T09:14:57 | 2021-10-18T22:15:29Z | CONTRIBUTOR | {
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} | Previously when dealing with entry equality we wrote these function to do a robust eq check. After these changes didn't fix the results @mkhorton and @mattmcdermott came up with a better solution for the `__hash__` and `__eq__` but these functions were not removed. They are not referenced in `pymatgen` beyond their def... | {
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"Thanks for the contribution. However, I think this is too specific an analysis to be added to pymatgen and it can be done with the existing get_distance_matrix coupled with the elemental information. Can you provide more details on where such an analysis would be useful that it justifies the creation of this metho... | 2021-10-18T07:58:54 | 2023-02-03T17:52:36 | 2023-02-03T17:52:35Z | NONE | {
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} | ## Summary
Added a new get_element_distance() method to the pymatgen.core.structure.Structure class that:
* Calculates the minimum element-element distance for one element or between two different elements.
* Automatically calculates with a supercell if any element in the input structure occupies only one site o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2266 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2266/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2266/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2266/events | https://github.com/materialsproject/pymatgen/issues/2266 | 1,029,871,315 | I_kwDOACgets49YpbT | 2,266 | Should the called processes be terminated automatically when the execution of pymatgen script is stopped? | {
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"For general purposes, it is desired to stop the execution of mcsqs when the python script calling \r\nSQSTransformation is terminated. Therefore, I added the following lines (in bold) to \r\npymatgen/command_line/mcsqs_caller.py and all mcsqs processes can be stopped when the execution of \r\npython script is term... | 2021-10-19T05:17:53 | 2021-10-26T16:01:10 | NONE | {
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} | I am using SQSTransformation to generate SQS in RHEL 8.3 by using the command
python test_sqs.py &
where test_sqs.py is just a copy from pymatgen/transformation/tests.
Since it takes time, the execution of the python script is stopped by
pkill -f test_sqs.py
However, many mcsqs processes s... | {
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"I think the reason for this is simply that the hash database is incomplete.\r\n\r\nThere are two sets of hashes, a \"file\" hash (checks the POTCAR is byte-to-byte identical) and a \"data\" hash (which is a bit more permissive, e.g. if there are changes in comment strings etc.)\r\n\r\nThe data hash matches, but th... | 2021-10-19T16:42:05 | 2021-10-20T23:32:09 | CONTRIBUTOR | {
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} | **Describe the bug**
Round trip Potcar parsing results in a warning that's not present when writing input.
**To Reproduce**
```
import unittest
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.io.vasp.inputs import VaspInput
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure impo... | {
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"Thanks."
] | 2021-10-19T21:07:44 | 2021-10-20T13:59:59 | 2021-10-20T13:54:46Z | CONTRIBUTOR | {
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} | Added google docstrings to fit `pymatgen` style guide and whitespace line changes for better readability. Several typos/whitespaces. Slightly adjusted the function of `_get_slsqp_decomp()` to make it more useful as a stand alone function. Added a few ease of use methods for intermediary calculations that help in the `P... | {
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"thanks\r\n"
] | 2021-10-20T02:46:04 | 2021-10-20T13:38:39 | 2021-10-20T13:38:32Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Fix 1: allowed pmg.io.babel.BabelMolAdaptor to accept pybel.Molecule
## Checklist
Before a pull request can be merged, the following items must be checked:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-00... | {
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"I have no problem changing the name, and agree re. the private method call, but I believe the class itself exists for a good reason.\r\n\r\nIf I remember correctly, the _reason_ for this class was to make PhaseDiagram itself MSONable without breaking backwards compatibility, but I would have to check.",
"No. The... | 2021-10-20T14:12:11 | 2021-10-27T15:58:19 | 2021-10-27T15:42:17Z | MEMBER | {
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} | I am not sure when this class was introduced. But whatever it is, the naming is not good. A new user coming to pymatgen will be wondering what the heck is a BasePhaseDiagram. It has the connotations of an abstract base class but is actually not one. Then the original PhaseDiagram class inherits from BasePhaseDiagram bu... | {
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"They're debug calls anyway, presumably were useful to whoever was writing that class.",
"happy for me to remove? the git blame it 4 years ago so I am sure that they're finished debugging by now?",
"It's more a philosophical point -- I think `logger.debug()` statements are useful for whoever develops the code n... | 2021-10-20T16:12:55 | 2021-10-21T17:54:14 | 2021-10-21T17:54:14Z | CONTRIBUTOR | {
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@shyuep are these logging calls still needed in the code? I can't trace anywhere where they might be used and was wondering if I should clean them up? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2272 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2272/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2272/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2272/events | https://github.com/materialsproject/pymatgen/pull/2272 | 1,031,664,689 | PR_kwDOACgets4tc-Nq | 2,272 | Make the appearance of periodic_table_heatmap changeable. | {
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"\n[](https://coveralls.io/builds/43671060)\n\nCoverage decreased (-0.6%) to 83.131% when pulling **30af0330ecdd2d6c70bc979ce771058269d13268 on penicillin0:add-option-periodic_table_heatmap** into **b40ae2d962936a2ad8c2a024a3c0b2efc503e8e8 on materialspr... | 2021-10-20T17:37:49 | 2021-10-21T15:26:28 | 2021-10-21T15:26:22Z | CONTRIBUTOR | {
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} | ## Summary
I found the current periodic table difficult to read because of the color and the size of the letters, so I made it partially changeable.
* The color of the periodic table border can be changed.
* The font size of value and symbol on the periodic table can be changed.
* Added the option to change the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2273 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2273/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2273/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2273/events | https://github.com/materialsproject/pymatgen/pull/2273 | 1,031,913,827 | PR_kwDOACgets4tdyZw | 2,273 | Correct POTCAR hash warnings | {
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"\n[](https://coveralls.io/builds/43657330)\n\nCoverage decreased (-0.02%) to 83.745% when pulling **21f23fbb471aa4f5249978a71fe3b255623273a7 on potcar-warning** into **6f73449fd8cc7da094505a7bceaacda24386875c on master**.\n"
] | 2021-10-20T23:35:15 | 2022-10-10T17:54:05 | 2021-10-21T16:41:29Z | MEMBER | {
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} | ## Summary
Fix for #2267 | {
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} | **Describe the bug**
I have found that when reading in a cif file of a doped structure, where hydrogen and another element share the same lattice site, the hydrogen is not shown in the structure, except as 'implicit_hydrogens' in structure.site_properties. If however the lattice site of the hydrogen is not shared with... | {
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"You need to provide more details. That one liner does not give any information about your installation and there is no way we can diagnose where the problem lies. ",
"Build [log](https://people.freebsd.org/~yuri/py-pymatgen.log).\r\n\r\n[List](https://people.freebsd.org/~yuri/py-pymatgen-plist.txt) of installed ... | 2021-10-22T15:51:38 | 2022-04-27T08:42:50 | 2021-10-22T19:19:19Z | NONE | {
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} | **Describe the bug**
```python-3.8 -m pytest``` fails:
```
===> py38-pymatgen-2022.0.15 depends on file: /usr/local/bin/python3.8 - found
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/usr/local/lib/python3.8/site-packages/_pytest/main.py", line 206, in wrap_session
INTERNALERROR> ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2276 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2276/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2276/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2276/events | https://github.com/materialsproject/pymatgen/pull/2276 | 1,033,862,162 | PR_kwDOACgets4tkGBS | 2,276 | Make `Simplex` `MSONable` | {
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"I think there should be a test for this MSONable for Simplex.",
"Yes, this PR is not complete",
"\n[](https://coveralls.io/builds/43711331)\n\nCoverage increased (+0.001%) to 83.748% when pulling **7899caf4efbd3fc42004444eaa6cd5846f283c15 on simplex... | 2021-10-22T18:52:09 | 2022-10-10T17:53:58 | 2021-10-22T20:30:25Z | MEMBER | {
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"\n[](https://coveralls.io/builds/43719978)\n\nCoverage decreased (-0.6%) to 83.101% when pulling **00ecc46d9242e4a92cf6438abf8bd41bbc2b5505 on chc273:fix_small_cutoff_neighbor** into **71c8ab8da6369970d5766113d9f688db78cba899 on materialsproject:master*... | 2021-10-23T16:59:38 | 2021-10-26T16:01:27 | 2021-10-26T16:01:27Z | CONTRIBUTOR | {
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} | ## Summary
In the current cell list implementation for finding neighbors, the space is divided into ~O((cell length / cutoff)^3) cubes for fast neighbor finding. This causes issues when the user chooses unrealistic small or even zero cutoffs.
In this PR, I am doing the following:
1) For reasonable cutoff (def... | {
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"\n[](https://coveralls.io/builds/43721197)\n\nCoverage decreased (-0.6%) to 83.101% when pulling **09ac6172c9606ebaa99fa05294ff6d57ba7187e0 on ltalirz:update-cutoff-docs** into **71c8ab8da6369970d5766113d9f688db78cba899 on materialsproject:master**.\n",... | 2021-10-23T22:03:44 | 2021-11-08T23:58:38 | 2021-11-08T23:58:08Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2279 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2279/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2279/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2279/events | https://github.com/materialsproject/pymatgen/issues/2279 | 1,035,296,191 | I_kwDOACgets49tV2_ | 2,279 | Support for FPLO lattice convention | {
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"The link doesn't work. Not sure what FLPO is. But in general, the lattice vectors should not have any impact on any analysis.",
"[FPLO is a major DFT code](https://www.fplo.de/). Lattice vectors do have impact on analysis, e.g. if you use the cartesian k-vectors output by the DFT code, they will make no sense in... | 2021-10-25T15:45:55 | 2021-10-25T16:31:45 | CONTRIBUTOR | {
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It would be great if pymatgen also supported FPLO conventions on lattice generation from parameters.
They are as follows: https://www.listserv.dfn.de/sympa/arc/fplo-users/2020-01/msg00002.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2280 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2280/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2280/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2280/events | https://github.com/materialsproject/pymatgen/issues/2280 | 1,037,382,411 | I_kwDOACgets491TML | 2,280 | 🪛 [RFC] Returning index of vbm and cbm | {
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"I have no objections to this really, but I would ask that you add a kwarg such as \"include_kpoint_and_index=False\". By default, the return will still be the same. If that kwarg is set to true, the kpoint and index will be returned as per your suggestion. That will ensure that the method itself retains backward c... | 2021-10-27T12:49:44 | 2021-10-27T15:59:30 | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
Currently, [`eigenvalue_band_properties`](https://github.com/materialsproject/pymatgen/blob/fcb84a1e129da3a3010b9f6b9cf18beddf39f245/pymatgen/io/vasp/outputs.py#L958) does not return the kpoint and eigenvalue index for `vbm` and `cbm`. The former one i... | {
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} | Ion.from_formula should correctly recognize formulae in which the `+` or `-` sign precede the charge number. See also #2204
**Describe the bug**
```
>>> ion = Ion.from_formula('La[3+]')
>>> ion.charge
3.0
```
```
>>> ion = Ion.from_formula('La[+3]')
>>> ion.charge
1.0
```
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https://api.github.com/repos/materialsproject/pymatgen/issues/2282 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2282/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2282/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2282/events | https://github.com/materialsproject/pymatgen/issues/2282 | 1,038,920,381 | I_kwDOACgets497Kq9 | 2,282 | Add Composition.replace() | {
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"Composition is meant to be immutable. Which is why it inherits Mapping and Hashable and not dict or MutableMapping. Composition objects are probably the one of the most used keys in dictionaries and sets. So in place modifications are *not* allowed. FYI, the above can be easily done using `Composition({(k if k.sym... | 2021-10-28T20:19:45 | 2021-10-28T20:54:30 | 2021-10-28T20:52:54Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
`Composition` does not support elemental substitutions.
**Describe the solution you'd like**
New method `Composition("Fe2O3").replace({"Fe": "Mg"})` similar to [`Structure.replace_species()`](https://github.com/materialsproject/pymatgen/blob/v2... | {
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"```\r\ne_h = np.array(e_h)\r\ne_h_mp = np.array(e_h_mp)\r\nidx = np.argwhere(np.invert(np.isclose(e_h, e_h_mp)))\r\nprint(len(idx))\r\nprint(e_h[idx][2:3])\r\nprint(e_h_mp[idx][2:3])\r\nprint([ppd.get_decomp_and_e_above_hull(mp_data[i]) for i in idx[2:3, 0]])\r\nprint([mp_data[i] in ppd.stable_entries for i in idx... | 2021-10-28T21:22:26 | 2022-08-11T03:46:17 | 2022-07-21T00:54:29Z | CONTRIBUTOR | {
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Handler Class to allow for thermodynamic properties to be calculated across large chemically diverse phase diagrams whilst only generating relevant phase diagrams once.
Designed to inherit as much as possible and be modular to allow additional functionality to be approximated if solutions can be devis... | {
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I originally attempted to handle `SpeciesLike` rather than just `str` as input, i.e.
```py
elem_map: Dict[SpeciesLike, Union[SpeciesLike, Dict[SpeciesLike, float]]]
```
instead of the current
```py
elem_map: Dict[str, Union[str, Dict[str, float]]]
```
but it turned into much more of ... | {
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"Dropped some unused variables that `flake8` pre-commit hook was complaining about.",
"\n[](https://coveralls.io/builds/43882122)\n\nCoverage decreased (-0.6%) to 83.104% when pulling **b180cac685a432ed62ea0a80926ce4bb61ef0651 on janosh:str-fixes** int... | 2021-10-29T13:38:24 | 2021-11-09T19:34:48 | 2021-11-09T19:32:19Z | MEMBER | {
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"\n[](https://coveralls.io/builds/43983158)\n\nCoverage decreased (-0.6%) to 83.102% when pulling **85898a64447e5103c1e5dc0c256d5b07e0991bbd on janosh:silence-elem-x** into **acfe5899ee50add1e2a0dd6385ee4fba78122e0f on materialsproject:master**.\n",
"N... | 2021-10-30T18:24:20 | 2021-11-18T19:29:04 | 2021-11-03T13:44:52Z | MEMBER | {
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} | The warning about missing electronegativities is by far the most prevalent one in my use of pymatgen and it has never once been useful. Would be great to get rid of it.
It comes up all the time and usually repeated a dozen times or so when iterating over a dataframe column involving creation of new `Elements()`. | {
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"\n[](https://coveralls.io/builds/43894854)\n\nCoverage decreased (-0.6%) to 83.115% when pulling **d378d277e70ef8b9d6b48ebb4ba0b82b9b3f7ee1 on rkingsbury:ion_fixes** into **acfe5899ee50add1e2a0dd6385ee4fba78122e0f on materialsproject:master**.\n",
"Th... | 2021-10-31T01:01:26 | 2022-06-08T22:25:54 | 2021-11-09T19:30:58Z | CONTRIBUTOR | {
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} | ## Summary
This PR contains some miscellaneous bugfixes and enhancements for the `Ion` class.
* Fixes #2281
* Partially address #2204 by overloading `get_reduced_formula_and_factor` to provide special formula handling for ions. The `reduced_formula` for hydroxide, hydrogen peroxide, acetate, acetic acid, and sm... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2288 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2288/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2288/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2288/events | https://github.com/materialsproject/pymatgen/issues/2288 | 1,040,378,938 | I_kwDOACgets4-Auw6 | 2,288 | How to install and use zeopp modules | {
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"Please refer to pymatgen.org's instructions. But honestly, these questions should be posed to the Zeo+ developers rather than to pymatgen since we only provide an interface to it."
] | 2021-10-31T05:17:06 | 2021-10-31T15:07:12 | 2021-10-31T15:07:12Z | NONE | {
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} | when I open the address in http://zeoplusplus.org/, it was a cpp source and I can not using it. could you tell me how to install it in the py? thank you for your patience. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2289 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2289/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2289/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2289/events | https://github.com/materialsproject/pymatgen/issues/2289 | 1,044,308,093 | I_kwDOACgets4-PuB9 | 2,289 | Load bonds from .cif to make StructureGraph | {
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"That would be nice. Can you point to the CIF specification? Last time I looked into it, it was unclear to me how CIF defined bonds that crossed periodic boundaries.\r\n\r\nIf we do add, I think StructureGraph -> CIF export would also be useful.",
"The bond information in CIF files is defined by the [GEOM_BOND](h... | 2021-11-04T02:46:37 | 2022-06-04T19:41:34 | NONE | {
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"This suggests that your enum.x and makeStr.x are incorrectly compiled. I suggest you compile from the enumlib source. ",
"Thanks @shyuep for the quick reply. I followed the description in the readme https://github.com/msg-byu/enumlib and compiled it again. The error still occurs",
"What OS are you using? Also,... | 2021-11-05T13:25:24 | 2023-12-06T12:57:12 | 2023-12-06T12:57:11Z | NONE | {
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} | I tried to use the `MagOrderingTransformation` module https://github.com/materialsproject/pymatgen/blob/50f51443b118d1f72dd8c9e3269ad1969eba5fb9/pymatgen/transformations/advanced_transformations.py#L621
Code snippet:
```ruby
magnetic_species = {"Ni": 1.0, "O": 0.0}
MagOrder = MagOrderingTransformation(mag_s... | {
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"\n[](https://coveralls.io/builds/44171744)\n\nCoverage decreased (-0.6%) to 83.115% when pulling **d1d01d6d166191a203dca6ad02642de08bcbdea6 on janosh:replace-species** into **9276567df1bf01eea473933688975003449dc5e5 on materialsproject:master**.\n",
"... | 2021-11-05T17:00:09 | 2021-11-18T18:34:06 | 2021-11-18T18:32:41Z | MEMBER | {
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"Fixed in #2293."
] | 2021-11-07T09:26:13 | 2021-11-15T01:49:12 | 2021-11-15T01:49:12Z | MEMBER | {
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} | In the [docs](https://pymatgen.org/pymatgen.electronic_structure.dos.html) for `pymatgen.electronic_structure.dos`, many of the docstrings are cutoff because of ":" characters not playing well with the doc generator. For instance, see the `Returns` entries [here](https://pymatgen.org/pymatgen.electronic_structure.dos.h... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2293 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2293/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2293/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2293/events | https://github.com/materialsproject/pymatgen/pull/2293 | 1,046,689,912 | PR_kwDOACgets4uMHrJ | 2,293 | Docstring updates: Fix missing Outcar attributes and update elemental_dos_dos string | {
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"\n[](https://coveralls.io/builds/44069430)\n\nCoverage decreased (-0.6%) to 83.103% when pulling **105253d538a972a09f06e5383f41c11a95f2a8ad on arosen93:rosen-docs** into **50f51443b118d1f72dd8c9e3269ad1969eba5fb9 on materialsproject:master**.\n",
"Tha... | 2021-11-07T09:30:12 | 2021-11-15T05:47:51 | 2021-11-08T13:12:27Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
* The docs for `pymatgen.io.vasp.outputs.Outcar` are missing many of the attributes. For instance, it wasn't clear to me until I read the code that the `Outcar()` object has a `total_mag` keyword. I've update the docstring to include the missing attributes.
* The docs for `pymatgen.electronic_structure... | {
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"\n[](https://coveralls.io/builds/44425206)\n\nCoverage decreased (-0.6%) to 83.114% when pulling **b587d68a2877f90bb9c051f9628cab52439b119e on janosh:pyupgrade** into **8fd02cf3a7d33059a62200c12dd48a15be21a8a3 on materialsproject:master**.\n",
"Thanks... | 2021-11-10T17:57:04 | 2021-12-04T17:46:09 | 2021-12-03T20:35:15Z | MEMBER | {
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} | Lots of automatic updates to use newer language features by running
```sh
pyupgrade --py37-plus **/*.py
```
across the whole code base. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2295 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2295/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2295/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2295/events | https://github.com/materialsproject/pymatgen/pull/2295 | 1,051,188,850 | PR_kwDOACgets4uauCP | 2,295 | Update DOI URLs | {
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"Thank you @e-kwsm!",
"\n[](https://coveralls.io/builds/44381135)\n\nCoverage decreased (-0.6%) to 83.112% when pulling **d7044eb809f1b8b0c96caab8f52061ee23542bad on e-kwsm:doi** into **9276567df1bf01eea473933688975003449dc5e5 on materialsproject:maste... | 2021-11-11T17:08:07 | 2021-11-19T00:42:42 | 2021-11-18T19:07:00Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Include a summary of major changes in bullet points:
* URLs are changed to https://doi.org/ in accordance with https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding.
<!--
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https://api.github.com/repos/materialsproject/pymatgen/issues/2296 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2296/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2296/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2296/events | https://github.com/materialsproject/pymatgen/pull/2296 | 1,052,804,666 | PR_kwDOACgets4ufa3h | 2,296 | Remove accidentally tracked files and unset executable flag | {
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"Good catch @e-kwsm, thank you",
"\n[](https://coveralls.io/builds/44289132)\n\nCoverage decreased (-0.6%) to 83.112% when pulling **23c0e07833ea5ef1054186617f4d1e4083722afd on e-kwsm:chmod-x** into **9276567df1bf01eea473933688975003449dc5e5 on materia... | 2021-11-13T23:52:39 | 2021-11-19T00:41:35 | 2021-11-18T18:30:59Z | CONTRIBUTOR | {
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} | ## Summary
<!--Include a summary of major changes in bullet points:-->
Subject says it all.
<!--
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"\n[](https://coveralls.io/builds/44468724)\n\nCoverage decreased (-0.6%) to 83.117% when pulling **debcc753d732d2d0db0bf09c248e6a659ac7b4fe on arosen93:rosen-mixing** into **9276567df1bf01eea473933688975003449dc5e5 on materialsproject:master**.\n",
"T... | 2021-11-14T22:31:27 | 2021-11-24T03:30:02 | 2021-11-24T01:56:48Z | MEMBER | {
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} | This PR implements a simple `BadInputSetWarning` if `LASPH = False` (or is not set) yet the user is running a meta-GGA/hybrid/DFT+U/vdW-DF calculation. | {
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"\n[](https://coveralls.io/builds/44468633)\n\nCoverage decreased (-0.6%) to 83.116% when pulling **e0f7d28c14b22740ea59ff0986771d83b061490f on arosen93:rosen-lhfcalc** into **9276567df1bf01eea473933688975003449dc5e5 on materialsproject:master**.\n",
"... | 2021-11-15T09:46:33 | 2021-11-23T18:58:06 | 2021-11-23T16:14:00Z | MEMBER | {
"total": 0,
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} | Per the VASP manual (https://www.vasp.at/wiki/index.php/LHFCALC), hybrid calculations should only be run with ALGO = All, Damped, or Normal (never Fast or VeryFast despite no clear error written in the output). This PR implements a `BadInputSetWarning` if LHFCALC = True and Algo is not one of the three supported option... | {
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"\n[](https://coveralls.io/builds/44358398)\n\nCoverage decreased (-0.6%) to 83.112% when pulling **a0dcaf93c9325aa2cbf09791af5e69060fb94c98 on rkingsbury:pourbaix_updates** into **e084ec1383aa7006f9e4c9f6781bd9199043e05a on materialsproject:master**.\n"... | 2021-11-18T04:19:49 | 2024-10-10T01:54:44 | 2024-10-10T01:54:43Z | CONTRIBUTOR | {
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} | ## Summary
The eventual goal of this PR is to provide some additional methods that make `PourbaixDiagram` more easily customizable within pymatgen. This is a WIP motivated by requests and challenges faced by several users that I've interacted with.
Part of the goal here is to provide similar functionality to [MPR... | {
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"This should be an option, but not forced. You can modify the kwargs of the method to provide an option called to_unit_cell.",
"I don't think we can add a kwarg for `__mul__` and I would argue that this kind of folding is the \"expect\" behavior when we construct supercells. \r\n\r\nIf we really can't change it m... | 2021-11-20T02:00:04 | 2021-11-23T20:14:56 | 2021-11-23T16:59:46Z | CONTRIBUTOR | {
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} | When you create supercell I think the expected behavior should be that the sites in the SC sit in the unit-cell.
Currently, the behavior is:
```
# Si unit cell
Full Formula (Si2)
Reduced Formula: Si
abc : 3.866974 3.866975 3.866975
angles: 60.000006 60.000002 60.000010
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"Thanks @arosen93!\r\n\r\nFor the PR itself, if WIP, please either put [WIP] in the title or you can explicitly \"convert to draft\" in the top-right.\r\n\r\nFor the proposed changes, this looks like an important thing to clarify, and the PR looks good.\r\n\r\nI did also want to make sure you knew about the [`Magmo... | 2021-11-20T20:29:13 | 2021-11-23T18:57:18 | 2021-11-23T17:00:46Z | MEMBER | {
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} | Currently, the handling of the MAGMOM INCAR flag in `pymatgen.io.vasp.sets` could be made clearer. This became apparent to me when trying to modify MAGMOM in an atomate workflow, which did not at all do what I expected it to do (and led to some confusing errors). This PR does not change how magnetic moments are handled... | {
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