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https://api.github.com/repos/materialsproject/pymatgen/issues/2101 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2101/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2101/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2101/events | https://github.com/materialsproject/pymatgen/pull/2101 | 839,937,107 | MDExOlB1bGxSZXF1ZXN0NTk5ODcwODQ4 | 2,101 | small fix for insertion electrode | {
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"Thanks @jmmshn "
] | 2021-03-24T17:03:50 | 2021-03-25T23:18:43 | 2021-03-24T18:56:30Z | CONTRIBUTOR | {
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} | When the decomposition energy are missing the `get_max_instability` and `get_min_instability` functions all error out.
Now they will just return None
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https://api.github.com/repos/materialsproject/pymatgen/issues/2102 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2102/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2102/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2102/events | https://github.com/materialsproject/pymatgen/issues/2102 | 840,062,529 | MDU6SXNzdWU4NDAwNjI1Mjk= | 2,102 | Speed up SpacegroupAnalyzer().get_crystal_system() with bisect module | {
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"For reference, this is the result I'm getting with both functions:\r\n\r\n```py\r\nlog_gvrh.sg_number.apply(get_crystal_system).value_counts()\r\nlog_gvrh.sg_number.apply(new_get_crystal_system).value_counts()\r\n```\r\n\r\n```\r\ncubic 3847\r\ntetragonal 2056\r\northorhombic 1682\r\nhexagonal ... | 2021-03-24T19:01:17 | 2021-03-24T19:43:50 | 2021-03-24T19:43:50Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
`SpacegroupAnalyzer().get_crystal_system()` can be sped up with the [native `bisect` module](https://docs.python.org/3/library/bisect.html).
**Describe the solution you'd like**
I suggest to replace the current implementation of `get_crystal_sy... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2103 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2103/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2103/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2103/events | https://github.com/materialsproject/pymatgen/issues/2103 | 840,946,446 | MDU6SXNzdWU4NDA5NDY0NDY= | 2,103 | get_symmetrically_distinct_miller_indices gives wrong values for primitive fcc cell | {
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"I just realized that this is probably explained by the code not magically knowing the convention that for fcc people use conventional cell Miller indices instead of ones based on the reciprocal of the primitive cell lattice (combined with the fact that conventional 211 can be expressed with max index 1 in primitiv... | 2021-03-25T13:44:31 | 2021-03-25T15:33:07 | 2021-03-25T15:33:07Z | CONTRIBUTOR | {
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} | **Describe the bug**
When passed a primitive fcc cell and max index of 1, `get_symmetrically_distinct_miller_indices()` fails to find (1 0 0), but reports multiple equivalent copies of (110) and (111) differing by negative signs
**To Reproduce**
run the following python script
```
from ase.atoms import Atoms
fr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2104 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2104/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2104/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2104/events | https://github.com/materialsproject/pymatgen/pull/2104 | 841,272,371 | MDExOlB1bGxSZXF1ZXN0NjAxMDI4OTQ3 | 2,104 | Update mp2020 to v2021.03.22 DB release, without activating by default | {
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"Thanks @rkingsbury \r\n\r\n> There is one test in test_matproj.py that is failing, and I think this is a result of the new DB release rather than any changes in this PR.\r\n\r\nI'll handle this ..."
] | 2021-03-25T20:13:03 | 2021-03-26T04:30:12 | 2021-03-25T20:16:11Z | CONTRIBUTOR | {
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} | ## Summary
* Refit MP2020 corrections to the 2021.03.22 DB release using updated experimental data (see #2006 )
* Add the ability to point `MaterialsProject2020Compatibility` to an alternate configuration file
* Various docstring changes and updates ported from #2006
The purpose of this PR is to enable test bui... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2105 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2105/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2105/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2105/events | https://github.com/materialsproject/pymatgen/pull/2105 | 844,874,669 | MDExOlB1bGxSZXF1ZXN0NjA0MDc4NTI5 | 2,105 | Fix for correct bonds_broken in slab generation | {
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"Thanks for submitting this PR. Do you mind adding a unittest for the bug? You just need to add it to pymatgen/core/tests/test_surface.py. ",
"Just added a unit test. It is the first unit test I ever wrote so I hope I was able to pull it off :)",
"Looks good to me. Thanks!\r\n"
] | 2021-03-30T16:51:27 | 2021-04-01T23:21:59 | 2021-04-01T16:44:15Z | CONTRIBUTOR | {
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} | ## Summary
`SlabGenerator._get_c_ranges()` takes in a `bonds` dictionary and returns a set of tuples of fractional z-coordinates of neighboring (nearest) atoms if they have distinct z-coordinates. This set is then used in the `SlabGenerator.get_slabs()` method in order to calculate the total number of broken bonds. ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2106 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2106/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2106/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2106/events | https://github.com/materialsproject/pymatgen/pull/2106 | 859,111,254 | MDExOlB1bGxSZXF1ZXN0NjE2MjQ0NjEw | 2,106 | finalize MP2020 correction values | {
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"@mkhorton there seem to be some problems with the test environment - it complains about enumlib and openbabel not being installed / available",
"That message is just saying those tests have been skipped -- the actual error is that PMG_MAPI_KEY isn't set. I can look into it.",
"Thanks @rkingsbury :)"
] | 2021-04-15T17:49:05 | 2021-04-20T17:45:14 | 2021-04-20T17:44:53Z | CONTRIBUTOR | {
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} | ## Summary
Final correction fitting for `MaterialsProject2020Compatibility`
* Updates the fitted values to be fully consistent with the new `expt_formation_energy_kingsbury` dataset (see https://github.com/hackingmaterials/matminer/pull/602)
* Use `MaterialsProject2020Compatibility` by default in `get_pourbaix_e... | {
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"Using `None` instead of `np.nan` seems like a safe-enough change. PR incoming.",
"Looks like `uncertainty` isn't able to handle `None`:\r\n\r\n```py\r\n> if std_dev < 0 and not isinfinite(std_dev):\r\nE TypeError: '<' not supported between instances of 'NoneType' and 'int'\r\n```\r\n\r\n@jmmshn Would... | 2021-04-16T17:58:38 | 2023-05-30T22:55:47 | 2023-05-30T22:55:47Z | CONTRIBUTOR | {
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} | An example is shown here:
https://github.com/materialsproject/pymatgen/blob/04beca9af8e575005a40117f1779f1d464c0a697/pymatgen/entries/computed_entries.py#L49
I think these should be removed from any MSONable init function since they don't play well with database and model validation.
I'm currently just replacing... | {
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"\n[](https://coveralls.io/builds/39910127)\n\nCoverage decreased (-0.6%) to 83.014% when pulling **82c54470ab958cce369dd70f6cce4893a66f1f31 on nwinner:site-perturb-patch-2** into **5ba1d857cfe1867913e1d7981d2285e79a9233e0 on materialsproject:master**.\n... | 2021-04-16T19:46:35 | 2021-06-17T00:33:01 | 2021-06-17T00:33:01Z | CONTRIBUTOR | {
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} | ## Summary
* Feature 1: I've added a new site transformation called the RadialSiteDistortionTransformation which takes a selected site, and perturbs the atoms around it. The way I've written is that the first nearest neighbors are perturbed by the specified distance, and then subsequent sites follow a 1/r decay, whi... | {
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} | A simple fix. FermiDos at present uses 1 - f0(), which for very small numbers, causes python to collapse the result to 0. While such small numbers are within the noise of the dos, the function should be more stable. I moved the minus sign into the f0 function, which is equivalent, and has numpy handle all the precision... | {
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"Hi Shyue, \r\n\r\nIs there a reason you didn't add galore as a dependency? Galore only has numpy, Matplotlib and SciPy as dependencies (all of which are dependencies of pymatgen already), so it is not much bloat.\r\n\r\nIf there is something stopping you from using galore as a library (such as the issue you raised... | 2021-04-20T14:16:13 | 2021-04-21T14:37:05 | 2021-04-20T14:16:18Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2111 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2111/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2111/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2111/events | https://github.com/materialsproject/pymatgen/pull/2111 | 863,244,083 | MDExOlB1bGxSZXF1ZXN0NjE5Njg3OTg2 | 2,111 | rm spurious warnings filter from GibbsComputedStructureEntryTest | {
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"Thanks Ryan"
] | 2021-04-20T21:09:12 | 2021-04-20T21:35:49 | 2021-04-20T21:35:43Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2112 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2112/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2112/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2112/events | https://github.com/materialsproject/pymatgen/issues/2112 | 864,645,303 | MDU6SXNzdWU4NjQ2NDUzMDM= | 2,112 | Numpy numerical types in electronic_structure.bandstructure.Kpoint.as_dict result | {
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} | In the [`electronic_structure.bandstructure.Kpoint.as_dict` method](https://github.com/materialsproject/pymatgen/blob/6737f23caaf646cc58425561cf08339acf77b396/pymatgen/electronic_structure/bandstructure.py#L127), the numpy arrays `frac_coords` and `cart_coords` are converted to lists using `list()`, which leaves the co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2113 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2113/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2113/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2113/events | https://github.com/materialsproject/pymatgen/pull/2113 | 864,723,042 | MDExOlB1bGxSZXF1ZXN0NjIwOTA3MjYx | 2,113 | Use numpy tolist method in electronic_structure.bandstructure.Kpoint.as_dict | {
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"Pls add a unittest to check for this pls. Thanks.",
"> Pls add a unittest to check for this pls. Thanks.\r\n\r\nDone!",
"\n[](https://coveralls.io/builds/39046363)\n\nCoverage decreased (-0.7%) to 83.021% when pulling **49ac26104f98496915d4f2ee94543... | 2021-04-22T09:10:05 | 2021-04-22T14:12:20 | 2021-04-22T14:12:14Z | CONTRIBUTOR | {
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} | Use `np.ndarray.tolist()` method instead of python `list()` to convert k-point coordinates in `pymatgen.electronic_structure.bandstructure.Kpoint.as_dict()`.
This fixes issue #2112, where numpy numerical types (e.g. numpy.float64) exist in the result of `Kpoint.as_dict()`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2114 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2114/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2114/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2114/events | https://github.com/materialsproject/pymatgen/issues/2114 | 864,783,432 | MDU6SXNzdWU4NjQ3ODM0MzI= | 2,114 | Outdated BoltztrapRunner? | {
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"There is already a pymatgen.electronic_structure.boltztrap2 module (https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/boltztrap2.py).",
"Oops. But then how come `atomate` doesn't use it?\r\n\r\nhttps://github.com/hackingmaterials/atomate/blob/7bd29a52e5b6f965b73ec035e65fc6c55... | 2021-04-22T10:18:18 | 2021-04-22T13:27:59 | 2021-04-22T13:19:56Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
`BoltztrapRunner` requires `x_trans` to be in path (which appears to be outdated) and links to an [empty page](www.icams.de/content/research/software-development/boltztrap) to get it.
**Describe the solution you'd like**
https://github.com/mate... | {
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"\n[](https://coveralls.io/builds/39099092)\n\nCoverage decreased (-0.6%) to 83.032% when pulling **0f65f7b33e512f260fd29b75ff5deb5582974351 on nkeilbart:xdatcar_fix** into **8bb2dd5252909ee8bb54d045b7ab71b4648592fc on materialsproject:master**.\n",
"T... | 2021-04-23T21:24:41 | 2021-04-24T12:27:52 | 2021-04-24T12:27:48Z | CONTRIBUTOR | {
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} | ## Summary
* Updated Xdatcar class from pymatgen.io.vasp.outputs to update the lattice constants with each new step. Previously, only a single preamble was read in and used for the rest of the structures.
* Created a new XDATCAR test file named XDATCAR_6 to stay consistent with other filenames
* Added a test for X... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2116 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2116/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2116/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2116/events | https://github.com/materialsproject/pymatgen/issues/2116 | 869,231,920 | MDU6SXNzdWU4NjkyMzE5MjA= | 2,116 | MPRestError: REST query returned with error status code 403 | {
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} | **Describe the bug**
MPRestError: REST query returned with error status code 403
**To Reproduce**
Steps to reproduce the behavior:
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
#here I'm not using pymatgen.core since pourbaix_diagram is... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2117 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2117/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2117/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2117/events | https://github.com/materialsproject/pymatgen/pull/2117 | 869,241,071 | MDExOlB1bGxSZXF1ZXN0NjI0NjM4ODAw | 2,117 | Update bader_caller.py | {
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"Thanks @nwinner. For point 2, doesn’t the Bader binary already support this? (Ie getting volumes from the charge density, then integrating the spin density using those volumes) I seem to recall this feature was available in the Bader caller to do this automatically.",
"I hadn't seen that before, but after googli... | 2021-04-27T20:34:00 | 2021-05-03T21:56:33 | 2021-05-03T21:06:13Z | CONTRIBUTOR | {
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} | ## Summary
My last PR for the bader caller had some issues, which this PR resolves. (edited after discussion below)
* Fix 1: Previously, I had "self.nelects" for cube analysis created by looking for the site property with that name. It didn't occur to me that the self.structure object is not user-defined, but cre... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2118 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2118/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2118/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2118/events | https://github.com/materialsproject/pymatgen/issues/2118 | 869,673,036 | MDU6SXNzdWU4Njk2NzMwMzY= | 2,118 | Missing Hard-Coded path when using MontyEncoder/Decoder for MP2020Compat | {
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"Hi @CompRhys thanks for reporting this. The file `MP2020Compatibility.yaml` should be distributed with pymatgen and should be at the location listed in your error message. Is it possible that you serialized the entries using a newer version and are trying to open them with an old version? Basically, it's not clea... | 2021-04-28T08:29:00 | 2021-05-03T00:53:58 | 2021-05-03T00:53:58Z | CONTRIBUTOR | {
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} | Yesterday I pulled some ComputedStructureEntries using MPRester and saved them to a json file using the `MonthEncoder`, today I am trying to load that json on a google colab instance to do some EDA work. I used the MontyDecoder and I got a path missing error corresponding to my directory setup on the other machine.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2119 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2119/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2119/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2119/events | https://github.com/materialsproject/pymatgen/pull/2119 | 869,749,463 | MDExOlB1bGxSZXF1ZXN0NjI1MDYzMDAx | 2,119 | Use numpy tolist() in DOS-family object as_dict() methods | {
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"\n[](https://coveralls.io/builds/39184219)\n\nCoverage decreased (-0.6%) to 83.036% when pulling **ce0a5f14823fbd0d6a05a8e772dcef88a55c696c on zooks97:dos-asdict-patch** into **df0f9ba74f9b1ba54bb6ede88badb31b7cc1cdb4 on materialsproject:master**.\n",
... | 2021-04-28T09:41:33 | 2021-04-28T19:56:41 | 2021-04-28T19:56:35Z | CONTRIBUTOR | {
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} | Use `np.ndarray.tolist()` method instead of python `list()` to convert density of state (`Dos`, `FermiDos`, `CompleteDos`) energies and densities in their `as_dict()` methods.
This fixes an issue where numpy numerical types (e.g. numpy.float64) exist in the results of {`Dos`, `FermiDos`, `CompleteDos`}`.as_dict()`.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2120 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2120/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2120/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2120/events | https://github.com/materialsproject/pymatgen/issues/2120 | 869,771,333 | MDU6SXNzdWU4Njk3NzEzMzM= | 2,120 | Computed entry `__eq__` doesn't check class instance | {
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"closing as fixed by 56fa39fcd16e90489c24252e6b6a58520ea427ae "
] | 2021-04-28T10:04:43 | 2021-06-24T14:31:24 | 2021-06-24T14:31:24Z | CONTRIBUTOR | {
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} | I have a `PhaseDiagram` made with `PDEntry`'s and wanted to get some results for a `ComputedEntry` relative to that phase diagram. As `PDEntry` doesn't have an `entry_id` this causes an error.
```
cse.data["E_ps_per_at"] = phad.get_phase_separation_energy(cse)
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"\n[](https://coveralls.io/builds/39200231)\n\nCoverage decreased (-0.7%) to 82.995% when pulling **270e3d9d6ad1f77902861842866a3cfc5945a3bb on nwinner:patch-2** into **df0f9ba74f9b1ba54bb6ede88badb31b7cc1cdb4 on materialsproject:master**.\n",
"Thanks!... | 2021-04-28T18:26:19 | 2021-04-28T20:05:35 | 2021-04-28T19:55:59Z | CONTRIBUTOR | {
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} | ## Summary
* Feature 1: Spherical masks of the cube data is now supported
* Feature 2: Using spherical masks, atomic site averages and totals are now supported natively. These can be used, respectively, for getting the average electrostatic potential around a site using a V_HARTREE file from CP2K or the total spin... | {
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"Git does not seem well-equipped to diff `.json` files, so you can use this online tool to better see the changes:\r\n\r\nhttps://jsoncompare.com/#!/diff/id=6924b719277a2a2b7a630352828d155c&fullscreen/\r\n\r\nclick the 'lint' button on both panes and you will see each change nicely highlighted",
"\n[![Coverage St... | 2021-04-28T21:51:44 | 2021-04-29T00:23:50 | 2021-04-29T00:07:17Z | CONTRIBUTOR | {
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} | ## Summary
This PR updates the `van_der_waals_radius` data used by the `Element` class from Wikipedia data to the latest values in the in the CRC Handbook of Chemistry and Physics. Important changes from the previous values include:
- Revised the value for `H` down by 0.1 angstrom as recommended in a critical rev... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2123 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2123/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2123/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2123/events | https://github.com/materialsproject/pymatgen/pull/2123 | 870,442,941 | MDExOlB1bGxSZXF1ZXN0NjI1NjQzOTk4 | 2,123 | bug fix in SpacegroupAnalyzer | {
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"\n[](https://coveralls.io/builds/39322138)\n\nCoverage decreased (-0.6%) to 83.011% when pulling **381b843cc02ee839391f259066a1056586c0f3c5 on gpetretto:bugfix** into **ce2fb4ee48a864aa766742caeec4b99c74e54610 on materialsproject:master**.\n",
"Thanks... | 2021-04-28T22:20:43 | 2021-05-06T14:22:33 | 2021-05-06T14:22:32Z | CONTRIBUTOR | {
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} | There is a problem in the `get_conventional_standard_structure` method of the `SpacegroupAnalyzer`.
The code below demonstrates the issue:
```python
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.ext.matproj import MPRest... | {
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"\n[](https://coveralls.io/builds/39232927)\n\nCoverage decreased (-0.6%) to 83.013% when pulling **ce45ed36a71a9e27e825ff84f7d3868ff28f9974 on CompRhys:master** into **cb9854d5ba11f216aafd3c9a49c9fceca485f218 on materialsproject:master**.\n",
"Thanks ... | 2021-04-29T16:43:11 | 2021-05-03T00:53:59 | 2021-05-03T00:53:58Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2125 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2125/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2125/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2125/events | https://github.com/materialsproject/pymatgen/pull/2125 | 871,665,967 | MDExOlB1bGxSZXF1ZXN0NjI2NjcwNDIy | 2,125 | Small tweaks / fixes to Q-Chem parsing | {
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"\n[](https://coveralls.io/builds/39245138)\n\nCoverage decreased (-0.6%) to 83.012% when pulling **9760bc5ff8e350d49690502c164934db087481c4 on samblau:qchem** into **cb9854d5ba11f216aafd3c9a49c9fceca485f218 on materialsproject:master**.\n",
"Ready to ... | 2021-04-29T23:19:25 | 2021-05-03T00:55:55 | 2021-05-03T00:55:47Z | CONTRIBUTOR | {
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} | * Modified encoding to avoid errors when opening Q-Chem output files
* Fixed bug for reading force job outputs
* Removed two outdated warnings | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2126 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2126/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2126/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2126/events | https://github.com/materialsproject/pymatgen/issues/2126 | 872,209,877 | MDU6SXNzdWU4NzIyMDk4Nzc= | 2,126 | Source code link in documentation of surface module leads to 404 | {
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"I think this applies to every module in pymatgen.core as they appear to be linking to .../pymatgen/pymatgen/module.py rather than .../pymatgen/core/module.py"
] | 2021-04-30T09:20:15 | 2021-04-30T16:09:14 | 2021-04-30T16:09:14Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2127 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2127/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2127/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2127/events | https://github.com/materialsproject/pymatgen/pull/2127 | 872,663,388 | MDExOlB1bGxSZXF1ZXN0NjI3NTQ2Nzkw | 2,127 | [WIP] change the relative location of the filename for source code lookup. Fixes #2126 | {
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"Thanks.",
"\n[](https://coveralls.io/builds/39267023)\n\nCoverage decreased (-0.6%) to 83.013% when pulling **e2158fc553a238c73e9c61abc9192f46e81daa66 on adam-kerrigan:doc_conf** into **cb9854d5ba11f216aafd3c9a49c9fceca485f218 on materialsproject:mast... | 2021-04-30T14:57:58 | 2021-04-30T16:31:48 | 2021-04-30T16:09:15Z | CONTRIBUTOR | {
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} | ## Summary
* Generation of links to source code in the pymatgen.core have been fixed.
* Generation of links to source code where the line numbers cannot be found have been fixed.
This fixes #2126. I was unsure on the difference between conf-docset.py, conf-normal.py and conf.py so I only updated the ones with th... | {
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"\n[](https://coveralls.io/builds/39270514)\n\nCoverage decreased (-0.6%) to 83.011% when pulling **faed4eff372fe402613e4427715e66cc3c9882ef on rkingsbury:default_mp2020** into **af726e3b4f6c93b3faf78671e4a3908eb2ae3932 on materialsproject:master**.\n",
... | 2021-04-30T16:24:37 | 2021-05-03T00:53:20 | 2021-05-03T00:53:17Z | CONTRIBUTOR | {
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- Small update to the MP2020 correction values as we finalize for the upcoming database release. | {
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"\n[](https://coveralls.io/builds/39319301)\n\nCoverage decreased (-0.7%) to 82.996% when pulling **f1182e02fd0990268d2ad969202da9063cb4e6d3 on richardtran415:surfaces** into **af726e3b4f6c93b3faf78671e4a3908eb2ae3932 on materialsproject:master**.\n",
... | 2021-05-01T02:15:34 | 2021-05-05T22:26:12 | 2021-05-04T12:18:33Z | CONTRIBUTOR | {
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} | This pull request contains an improvement for analyzing surface symmetry of slabs. A slab now has symmetrically equivalent surfaces if (hkl) is a mirror plane, if [hkl] is a screw axis or if the slab has inversion symmetry.
Include a summary of major changes in bullet points:
* Modifications to is_symmetric() Sla... | {
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"\n[](https://coveralls.io/builds/39341111)\n\nCoverage decreased (-0.7%) to 83.008% when pulling **c63779000d0ee50b6b0ec863628e96bfd76be64f on rkingsbury:default_mp2020** into **12d6e2b1b6b49f7c6524dec2f834b959205f459b on materialsproject:master**.\n"
] | 2021-05-03T04:56:40 | 2021-07-15T14:32:32 | 2021-05-06T14:24:58Z | CONTRIBUTOR | {
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} | Ensures that energy corrections applied to each anion have unique names (e.g., N vs. Cl vs. Br).
If this is not the case, then in a compound with multiple corrected anions like `C2NCl`, `Compatibility` will apply a correction to the first anion, then think the second is a duplicate, warning
```
warnings.warn(
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"\n[](https://coveralls.io/builds/39320108)\n\nCoverage decreased (-0.6%) to 83.01% when pulling **03372b1b25a8d2eaf8091bc0bda11f12311c2bdc on samblau:qchem** into **ce2fb4ee48a864aa766742caeec4b99c74e54610 on materialsproject:master**.\n",
"@mkhorton ... | 2021-05-03T21:44:47 | 2021-05-04T01:03:54 | 2021-05-04T01:03:41Z | CONTRIBUTOR | {
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} | My last PR fixed one QChem parsing problem, but introduced a new one - the zopen call could no longer accommodate gzipped output files. I have fixed this problem and also gzipped one of my already present test output files to ensure that the ability to parse gzipped outputs is now tested. | {
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"\n[](https://coveralls.io/builds/39352112)\n\nCoverage decreased (-0.6%) to 83.018% when pulling **e11261e75ec5bfeef67d5afab6ddea0349197149 on htz1992213:master** into **ce2fb4ee48a864aa766742caeec4b99c74e54610 on materialsproject:master**.\n",
"Thank... | 2021-05-03T23:36:02 | 2021-05-05T12:24:44 | 2021-05-05T12:24:44Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Speedup LammpsData.as_string for non-hybrid data with large coeff sections
* Add as_lammpsdata method to CombinedData which allows CombinedData object to be converted to its superclass
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"I'm fine with it as-is. It's a little awkward, but it would also be a little awkward to shoehorn mode into the van_der_waals dict.",
"\n[](https://coveralls.io/builds/39345618)\n\nCoverage decreased (-0.6%) to 83.004% when pulling **c04c01c306e202c5e3... | 2021-05-04T16:32:45 | 2021-05-06T15:45:18 | 2021-05-06T14:23:10Z | CONTRIBUTOR | {
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} | ## Summary
Adds support for custom vdW radii to `QCInput` and `QChemDictSet`. These radii are used in the construction of PCM cavities and when calculating charges.
## TODO
- [x] Feedback requested from @samblau regarding the `vdw_mode` kwarg that I had to add. This construction is a little bit awkward. An alt... | {
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"I didn't add any new tests, but changed the existing tests to compressed files. Hope that's ok.",
"\n[](https://coveralls.io/builds/39413703)\n\nCoverage decreased (-0.7%) to 83.008% when pulling **419d9111910cea9f520dfddc29f1873024bbf0d4 on ab5424:la... | 2021-05-06T13:30:41 | 2021-05-10T08:22:01 | 2021-05-06T14:21:44Z | CONTRIBUTOR | {
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} | ## Summary
* Change parsing lammps logs to zopen
## 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. Start with running
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"\n[](https://coveralls.io/builds/40653175)\n\nCoverage decreased (-0.6%) to 83.103% when pulling **c0b5d4e23ac289d005ffcc2b24cc914a1d823fca on rkingsbury:qcinput-vdw** into **41d82c498900b6dffdd5c3c0db6de2564bdf75be on materialsproject:master**.\n",
"... | 2021-05-07T00:43:11 | 2021-07-15T14:33:03 | 2021-06-17T00:35:05Z | CONTRIBUTOR | {
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} | Follow up to #2133 , adds support for reading the `van_der_waals` block from a QChem output file.
This PR also refactors `test_write_file`. Previously, this test used `QCinput.from_file` to construct a dict, and then compared the contents of the dicts. The problem with this approach is that if `QCInput.from_file` ha... | {
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"Thanks ... | 2021-05-07T14:29:23 | 2021-05-23T23:11:02 | 2021-05-23T23:05:53Z | CONTRIBUTOR | {
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} | Add pymatgen `PBar` to applying compatibility settings to help impatient users like myself. I have by default suppressed the progress bar and added a boolean verbose flag to turn it on.
Changes made are superficial therefore no new tests added. | {
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"We have abandoned py36 support given that most of the underlying scientific python packages have abandoned py36. "
] | 2021-05-07T16:10:46 | 2021-05-07T16:33:38 | 2021-05-07T16:33:38Z | CONTRIBUTOR | {
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} | **Describe the bug**
Installation with Python 3.6 using Pip initially fails due to the lack of a compatible Numpy version.
The setup.py of Pymatgen reports that Python >= 3.6 is required, and Numpy >= 1.20 is required. However, Numpy version 1.20 [only supports Python 3.7-3.9](https://numpy.org/devdocs/release/1.20... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2138 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2138/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2138/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2138/events | https://github.com/materialsproject/pymatgen/issues/2138 | 883,265,004 | MDU6SXNzdWU4ODMyNjUwMDQ= | 2,138 | Structure.from_str reads from str(Structure) | {
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"Hi @goodwilling, we've had some requests for a Structure.from_str before, however I don't think this is in general a good approach. The string representation is lossy. It would be better if we could handle Pandas conversion natively. I know Pandas support extensions and custom data types but I'm not familiar with ... | 2021-05-10T03:23:26 | 2021-05-14T02:53:03 | 2021-05-14T02:53:03Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
It is necessary to convert str(Structure) to a Structure when a DataFrame contains column of structures and default_handler=str is set in DataFrame.to_json() in order to get rid of "OverflowError: Maximum recursion level reached".
**Describe the sol... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2139 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2139/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2139/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2139/events | https://github.com/materialsproject/pymatgen/pull/2139 | 883,808,871 | MDExOlB1bGxSZXF1ZXN0NjM3MjQ5OTMx | 2,139 | Add spacegroup details to SymmetrizedStructure string | {
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"Great, thanks @CompRhys!"
] | 2021-05-10T09:22:19 | 2021-06-28T13:53:39 | 2021-05-11T20:04:53Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2140 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2140/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2140/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2140/events | https://github.com/materialsproject/pymatgen/pull/2140 | 887,586,357 | MDExOlB1bGxSZXF1ZXN0NjQwODA4ODQx | 2,140 | Update MPScanRelaxSet doc string | {
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"\n[](https://coveralls.io/builds/39579302)\n\nCoverage decreased (-0.6%) to 82.992% when pulling **4d3be5af32fed1edac61ae89a58ba22d3a3b41e1 on janosh:master** into **08aa5214a1b1a5fc6872de76b12cf97f5ceb03c9 on materialsproject:master**.\n"
] | 2021-05-11T15:11:45 | 2021-05-11T15:49:25 | 2021-05-11T15:49:25Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2141 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2141/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2141/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2141/events | https://github.com/materialsproject/pymatgen/pull/2141 | 891,453,763 | MDExOlB1bGxSZXF1ZXN0NjQ0MzIzMTE4 | 2,141 | MP2020 corrections post-release housekeeping | {
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"\n[](https://coveralls.io/builds/39820330)\n\nCoverage decreased (-0.6%) to 83.0% when pulling **daa95f3cdfaf131ef641614510f51f236c59ddba on rkingsbury:production_mp2020** into **9953bbe3431865bc637d7aff8a5199b21a3e7912 on materialsproject:master**.\n",... | 2021-05-13T23:16:18 | 2021-07-15T14:32:31 | 2021-05-21T17:12:38Z | CONTRIBUTOR | {
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} | ## Summary
Some housekeeping changes following up the MP2020 database release v2021.05.13
* Silence the oxidation states warning when using `MPRester`
* Update the Pourbaix Diagram tests to be less dependent on specific energy values from the database
* Add ChemRxiv link for MP2020 manuscript to the `MaterialsP... | {
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"@janosh: This can be closed as out of scope.",
"`flake8` was replaced with `ruff`."
] | 2021-05-14T11:41:27 | 2023-06-03T02:23:27 | 2023-06-03T02:23:16Z | NONE | {
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} | **Describe the bug**
Conflict between blake and flake8 settings.
**To Reproduce**
Steps to reproduce the behavior:
1. Commit changes with `git commit`
2. pre-commit is triggered
3. black (I think) changes all quotes to double "
4. flake8 complains about the double quotes with: Q000 Remove bad quotes
Recomm... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2143 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2143/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2143/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2143/events | https://github.com/materialsproject/pymatgen/pull/2143 | 891,969,192 | MDExOlB1bGxSZXF1ZXN0NjQ0NzUyMDI3 | 2,143 | Add new compact style for hkl annotations to peaks in diffraction patterns | {
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"Thanks. Feel free to make it the default!",
"Thanks!",
"Thank you for accepting this change!",
"We should be thanking you! The XRDs now look much better!"
] | 2021-05-14T14:27:53 | 2021-05-14T16:19:32 | 2021-05-14T15:12:31Z | NONE | {
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} | Introducing a new optional style for the hkl labels in diffraction patterns (see example figure below).
The default style was not changed. However, I would recommend making this new more-compact style the default because it prevents overlap of labels as in https://matgenb.materialsvirtuallab.org/2013/01/01/Calculat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2144 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2144/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2144/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2144/events | https://github.com/materialsproject/pymatgen/pull/2144 | 893,646,960 | MDExOlB1bGxSZXF1ZXN0NjQ2MTI3ODky | 2,144 | Bandstructure path name changes and Kpoint from_dict | {
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"\n[](https://coveralls.io/builds/39793806)\n\nCoverage decreased (-0.6%) to 82.996% when pulling **85583920bae3e045ca2ff593f3d21acb4621b72e on munrojm:bandstructure_fixes** into **37d8c1e4a94e79948bf2104d9b9caf61c05a603c on materialsproject:master**.\n"... | 2021-05-17T19:34:27 | 2021-05-21T17:12:21 | 2021-05-21T17:12:18Z | MEMBER | {
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} | ## Summary
* Path type names in `HighSymmKpath` changed from short form ('sc', 'hin', and 'lm') to long form ('setyawan_curtarolo', 'hinuma', 'latimer_munro').
* Proper `from_dict` method added to `Kpoint` class in `from pymatgen.electronic_structure.bandstructure`.
## Checklist
- [X] Code is in the [standar... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2145 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2145/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2145/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2145/events | https://github.com/materialsproject/pymatgen/issues/2145 | 893,717,264 | MDU6SXNzdWU4OTM3MTcyNjQ= | 2,145 | This looks like dead code since the class is redefined immediately after | {
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"nvm `Dos` not `DOS`",
"I think it is strange to have both though... I'm not sure that a work-in-progress replacement like this should be in the main branch since it causes confusion when a user goes to import the class. Maybe it's better to rename it `_DOS` or remove it until it's ready to be used?",
"Yes this... | 2021-05-17T21:10:45 | 2021-05-23T23:00:54 | 2021-05-17T21:11:07Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2146 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2146/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2146/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2146/events | https://github.com/materialsproject/pymatgen/issues/2146 | 893,803,258 | MDU6SXNzdWU4OTM4MDMyNTg= | 2,146 | from_dict in PourbaixEntry fails to read pbx entries with structure information | {
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} | **Describe the bug**
The from_dict method in PourbaixEntry fails to read a computed entry with structure information
**Expected behavior**
When reloading saved (dumpfn) pbx_entries using loadfn, it is expected pbx_entries still contain the structure information.
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https://api.github.com/repos/materialsproject/pymatgen/issues/2147 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2147/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2147/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2147/events | https://github.com/materialsproject/pymatgen/pull/2147 | 895,886,071 | MDExOlB1bGxSZXF1ZXN0NjQ4MDQ2ODYy | 2,147 | add basis_not_supported error to QCOutput | {
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} | Adds detection of basis set not supported error to `QCOutput`. This error will cause the calculation to fail before it even starts, so it is treated similarly to the existing `input_file_error`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2148 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2148/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2148/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2148/events | https://github.com/materialsproject/pymatgen/pull/2148 | 896,923,257 | MDExOlB1bGxSZXF1ZXN0NjQ4OTc3OTU3 | 2,148 | add test and fix for computed entries | {
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"Thanks"
] | 2021-05-20T14:43:14 | 2021-05-21T17:11:05 | 2021-05-21T17:11:00Z | CONTRIBUTOR | {
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} | ## Summary
* Updates PourbaixEntry.from_dict to invoke entries other than IonEntries using MontyDecoder, rather than hard-coding PDEntry.
* I initially had a bigger refactor which changed the ways Ions/IonEntries are invoked, but I'm a little worried about backwards compatibility of a core refactor, so I'm issuing ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2149 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2149/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2149/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2149/events | https://github.com/materialsproject/pymatgen/pull/2149 | 897,508,923 | MDExOlB1bGxSZXF1ZXN0NjQ5NTEwNzc4 | 2,149 | Overhaul interfaces | {
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"\n[](https://coveralls.io/builds/39901075)\n\nCoverage decreased (-0.6%) to 83.075% when pulling **0aa785d900801e9caa9cc782adfcec729e62eb98 on shyamd:interfaces** into **37d8c1e4a94e79948bf2104d9b9caf61c05a603c on materialsproject:master**.\n",
"Nice ... | 2021-05-20T22:15:47 | 2021-05-23T22:40:52 | 2021-05-22T06:29:01Z | NONE | {
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} | This PR overhauls all the interface code including the ZSL Generator and the substrate matcher:
- Creates a new `Interface` data class in core
- Moves interface algorithm to `analysis.interfaces`; imports and warnings in the old modules ensure they should still work
- Cleans up `ZSLGenerator` and `SubstrateAnalyze... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2150 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2150/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2150/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2150/events | https://github.com/materialsproject/pymatgen/pull/2150 | 897,644,914 | MDExOlB1bGxSZXF1ZXN0NjQ5NjI1NTkw | 2,150 | Python 3.6+ behavior of Exception.message | {
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"\n[](https://coveralls.io/builds/39878391)\n\nCoverage decreased (-0.7%) to 82.984% when pulling **83537c312cd4d0dd65beb8564cdc4937ea3d3fd4 on kmu:MPResterError-message** into **37d8c1e4a94e79948bf2104d9b9caf61c05a603c on materialsproject:master**.\n",
... | 2021-05-21T03:33:39 | 2021-05-21T16:56:49 | 2021-05-21T16:56:43Z | CONTRIBUTOR | {
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} | ## Summary
Hey guys,
Python 3.6+ seems to abolish `Exception.message`.
This PR addresses this problem.
It does not seem to be easy to write a unittest to reproduce this without imposing a large load on MP.
Here is a working example.
- Current implementation
```python
import re
from pymatgen.ext... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2151 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2151/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2151/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2151/events | https://github.com/materialsproject/pymatgen/issues/2151 | 897,758,428 | MDU6SXNzdWU4OTc3NTg0Mjg= | 2,151 | how to handle properties of tritium and deuterium? | {
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"I would actually go for option 1. I don't think it is that difficult to make it such that isotopes can be handled. The main problem, though, is that I don't have a source of compilation for all the other properties that most elements have (e.g., melting point, etc.) for isotopes.\r\n\r\nIf it is just D and T, I th... | 2021-05-21T07:11:24 | 2023-11-02T22:37:44 | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
In `cif`s (e.g., from the Cambridge Crystallographic Database) one sometimes finds symbols for common isotopes such as Tritium (`T`) or Deuterium (`D`). `pymatgen` parses them without issues, but it complains when one likes to access some properties li... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2152 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2152/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2152/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2152/events | https://github.com/materialsproject/pymatgen/pull/2152 | 899,733,183 | MDExOlB1bGxSZXF1ZXN0NjUxMzkzMTE5 | 2,152 | Ignore typical virtual environment file/directory names | {
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"The issue is that `mpr.get_structure_by_material_id` will download the primitive cell structure by default. This means that the [1, 0, 0] direction in your structure does not correspond to the [1, 0, 0] of the conventional cell but instead the [1, 1, 1] of the conventional cell.\r\n\r\nAsking for the conventional ... | 2021-05-24T19:42:14 | 2021-05-24T22:01:32 | 2021-05-24T21:02:26Z | NONE | {
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} | I am trying to generate some simulation diffraction pattern data using and got some patterns inconsistent with the real patterns. Wondering if I was doing this correctly. Here is the codes that I used (and the generated pattern is attached). mp-13 is Fe with cubic bcc structure so I am expecting the simulated pattern w... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2154 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2154/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2154/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2154/events | https://github.com/materialsproject/pymatgen/issues/2154 | 900,154,093 | MDU6SXNzdWU5MDAxNTQwOTM= | 2,154 | Surface slab visualization KeyError with oxidation states | {
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"I tried ```color = color_dict[sites[n].element.symbol]```\r\n\r\nbut I'm getting: ```[AttributeError: element]()```",
"Mhmm, I see. How about \r\n`color = color_dict[sites[n].species.elements[0].symbol]`\r\nor\r\n`color = color_dict[sites[n].species.remove_charges().elements[0].symbol]` ?",
"Thanks. I just pus... | 2021-05-25T01:14:51 | 2022-04-26T02:48:46 | 2022-04-19T14:20:06Z | NONE | {
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} | There seems to be a bug in displaying surface slabs when sites are decorated with oxidation states. Mentioned [here](https://matsci.org/t/is-it-a-bug-or-just-something-i-need-to-do-when-use-plot-slab-function/36521) and [here](https://matsci.org/t/surface-slab-visualization-key-error-o2/34557). I didn't have the time t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2155 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2155/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2155/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2155/events | https://github.com/materialsproject/pymatgen/issues/2155 | 903,389,596 | MDU6SXNzdWU5MDMzODk1OTY= | 2,155 | unexpected result of get_conventional_standard_structure() to mp-644693 | {
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"Thanks @lwk8891, this is almost certainly a serious bug. I will investigate.\r\n\r\nFor now, I suggest you use `.get_refined_structure()` which might work for your purposes.",
"Has this issue been resolved? I need to transform to the conventional setting and want to ensure I'm getting the correct results. Curren... | 2021-05-27T08:18:34 | 2023-09-03T19:43:23 | 2023-09-03T19:43:23Z | NONE | {
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} | **Describe the bug**
The get_conventional_standard_structure() method of pymatgen.symmetry.analyzer.SpacegroupAnalyzer class changes the atomic connection of mp-644693.
**To Reproduce**
1. get the structure of mp-644693 by calling s=get_structure_by_materials_id('mp-644693') of pymatgen.ext.matproj.MPRestrer class... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2156 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2156/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2156/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2156/events | https://github.com/materialsproject/pymatgen/pull/2156 | 906,452,691 | MDExOlB1bGxSZXF1ZXN0NjU3NDUzODU3 | 2,156 | Update usage.rst | {
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"Thanks.",
"\n[](https://coveralls.io/builds/40140538)\n\nCoverage decreased (-0.6%) to 83.078% when pulling **3183ae8fbb036c116c3c909c98e3d306c054b967 on 755452800:master** into **1d0471d5232f19dfb3eff2d988d0f82460d0a832 on materialsproject:master**.\... | 2021-05-29T11:48:53 | 2021-05-29T12:12:03 | 2021-05-29T11:50:18Z | CONTRIBUTOR | {
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## Summary
I think there is a typo in line 189:
`w = CifWriter(p.struct)`
should be:
`w = CifWriter(p.structure)`
or else error **AttributeError: 'Poscar' object has no attribute 'struct'** will occur.
Include a summary of major changes in bullet points:
* fix a typo in usage.rst line 189
## Additional de... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2157 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2157/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2157/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2157/events | https://github.com/materialsproject/pymatgen/pull/2157 | 906,554,635 | MDExOlB1bGxSZXF1ZXN0NjU3NTMxOTcy | 2,157 | Support combining data with multiple mol-id | {
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"\n[](https://coveralls.io/builds/40215177)\n\nCoverage decreased (-0.6%) to 83.078% when pulling **3a90f50895f128fabcdeb30687552f531decf612 on htz1992213:master** into **37da2710fc3e23c901f6e6a275adf4ee540cd1f3 on materialsproject:master**.\n",
"Thank... | 2021-05-29T20:36:53 | 2021-06-01T20:56:45 | 2021-06-01T20:56:45Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Feature 1: Support combining data files that have multiple molecules (mol id) in a single data object
* Feature 2: Added restriction to LAMMPS data name list for easier parsing.
* Fix 1: Changed maintainer
* Fix 2: Linting errors in other modul... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2158 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2158/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2158/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2158/events | https://github.com/materialsproject/pymatgen/issues/2158 | 909,518,842 | MDU6SXNzdWU5MDk1MTg4NDI= | 2,158 | typo | {
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"Hi @ddopplereffekt, thanks for reporting, I've fixed this now. In future, you can also suggest edits to files directly by clicking the \"Edit\" button on GitHub for small typos like this, and then we can merge the change in with one-click."
] | 2021-06-02T13:43:49 | 2021-06-02T19:24:10 | 2021-06-02T19:24:10Z | NONE | {
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} | **Describe the bug**
in pymatgen/entries/compatebility.py line 1031 is a type: the enclosing bracket for the formular is missing
**Expected behavior**
f"({entry.composition.reduced_formula}). Assigning anion correction to "
instead of
f"({entry.composition.reduced_formula}. Assigning anion correction to "
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https://api.github.com/repos/materialsproject/pymatgen/issues/2159 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2159/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2159/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2159/events | https://github.com/materialsproject/pymatgen/issues/2159 | 909,691,268 | MDU6SXNzdWU5MDk2OTEyNjg= | 2,159 | Support for ASE-style "extended XYZ" with Lattice parameters | {
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"I think the would be a welcome inclusion, I know this format (or a similar one) is used in AtomEye too. Would you be interested in preparing a PR?",
"I can't promise I can support everything - since it seems \"Properties\" can include a lot. But the Lattice extension IMHO is easy and IMHO the big first piece.\r\... | 2021-06-02T16:42:50 | 2021-06-02T19:57:17 | NONE | {
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} | As far as I can tell, the current versions of `pymatgen` support the traditional non-lattice XYZ from Open Babel.
I just implemented initial support for "extended XYZ" in Avogadro2 - the first layer is pretty easy. The second line (for comments / title) now have the lattice vectors and optionally additional properti... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2160 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2160/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2160/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2160/events | https://github.com/materialsproject/pymatgen/pull/2160 | 909,801,582 | MDExOlB1bGxSZXF1ZXN0NjYwMzIxNzIx | 2,160 | fix another CombinedData bug | {
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"\n[](https://coveralls.io/builds/40429423)\n\nCoverage decreased (-0.6%) to 83.082% when pulling **8a30eab02d056fc51b6af18475a0c0ddc3cfca6b on htz1992213:master** into **c724e7b679581783dcdb4690a83c374a57437ae6 on materialsproject:master**.\n",
"Thank... | 2021-06-02T19:02:49 | 2021-06-09T20:07:31 | 2021-06-09T20:07:30Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Include a summary of major changes in bullet points:
* Fix 1: The CombinedData constructor previously creates new ff dict only according to the keys in the first mol in the mols llist, which may cause the ff information in the remaining mols lost. The new implementation create the ff dict using a set o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2161 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2161/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2161/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2161/events | https://github.com/materialsproject/pymatgen/issues/2161 | 910,202,173 | MDU6SXNzdWU5MTAyMDIxNzM= | 2,161 | Cleave a (111) surface that alpha=beta=90 degree | {
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"set the max_normal_search=1 can resolve the problem. "
] | 2021-06-03T07:32:38 | 2021-06-03T07:46:03 | 2021-06-03T07:43:31Z | NONE | {
"total": 0,
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} | **Describe the bug**
When I try to cleave a CeO2(111) surface, I found that the lattice matrix is not similar with the Material Studio produced, that is the alpha=85 degree not the 90 degree,How can I get the same result with the Material studio.
**To Reproduce**
The following code I used in this issue:
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https://api.github.com/repos/materialsproject/pymatgen/issues/2162 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2162/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2162/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2162/events | https://github.com/materialsproject/pymatgen/issues/2162 | 910,381,028 | MDU6SXNzdWU5MTAzODEwMjg= | 2,162 | Inefficient k-point generation for NiO (and possibly other structures) | {
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"You didn't use the default `grid_density`, so you're getting a k-point mesh commensurate with that. If you want a smaller k-point mesh, then set `grid_density` to a smaller number. \r\n\r\nAlso, that is an example calculation from the VASP manual. It is not in any way a recommendation on k-point density. That you ... | 2021-06-03T11:04:37 | 2021-07-06T10:23:57 | 2021-07-06T10:23:57Z | CONTRIBUTOR | {
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} | **Describe the bug**
When using the NiO structure (mp-19009) from the MP, the generation of k-points in VASP is inefficient.
**To Reproduce**
Using
```
with MPRester() as a:
struct = a.get_structure_by_material_id('mp-19009')
relax = MPRelaxSet(structure=struct,
user_kpoints_settings... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2163 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2163/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2163/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2163/events | https://github.com/materialsproject/pymatgen/pull/2163 | 911,825,066 | MDExOlB1bGxSZXF1ZXN0NjYyMDQyMzA2 | 2,163 | Fix KSPACING formula in MPScanRelaxSet | {
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"FYI @rkingsbury, can I ask for your review?",
"Thanks for the catch @ab5424 ",
"\n[](https://coveralls.io/builds/40323647)\n\nCoverage decreased (-0.6%) to 83.077% when pulling **bb1de613d938ea89e4eecc96227d8a849c5b62fc on ab5424:kspacing** into **4... | 2021-06-04T20:46:24 | 2021-06-07T19:25:32 | 2021-06-07T19:25:24Z | CONTRIBUTOR | {
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} | ## Summary
Change rmin formula to match Eq. 25 from the paper. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2164 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2164/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2164/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2164/events | https://github.com/materialsproject/pymatgen/pull/2164 | 912,656,269 | MDExOlB1bGxSZXF1ZXN0NjYyNzk4NzY5 | 2,164 | reorder SETTINGS load priority | {
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"\n[](https://coveralls.io/builds/40337082)\n\nCoverage decreased (-0.6%) to 83.078% when pulling **ea9c9e54431280223f9f2c70435fad256f463245 on ardunn:master** into **463e4f1b577287c593e493b2b1138320418f0bc7 on materialsproject:master**.\n",
"Thanks @a... | 2021-06-06T06:13:29 | 2021-06-07T18:21:57 | 2021-06-07T18:21:57Z | CONTRIBUTOR | {
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} | ## Summary
When both a .pmgrc.yaml and environment variables are specified, any pmg environment variable will not be read into `pymatgen.core.__init__`'s `SETTINGS`.
E.g., I have a `PMG_MAPI_KEY` as an environment variable and my .pmgrc.yaml does not contain that key - it looks like
```
#.pmgrc.yaml
MAPI_DB_... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2165 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2165/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2165/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2165/events | https://github.com/materialsproject/pymatgen/pull/2165 | 912,855,849 | MDExOlB1bGxSZXF1ZXN0NjYyOTc0NjUz | 2,165 | QChem: detect NLebdevPts error in QCOutput | {
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"Note that there seems to be a new pylint error causing linting to fail on all PRs\r\n```\r\n************* Module pymatgen.entries.computed_entries\r\npymatgen/entries/computed_entries.py:700:8: E1101: Instance of 'ComputedStructureEntry' has no '_composition' member (no-member)\r\n```",
"\n[![Coverage Status](ht... | 2021-06-06T15:01:08 | 2021-07-15T14:33:04 | 2021-06-17T00:37:19Z | CONTRIBUTOR | {
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} | ## Summary
Detect `need to increase the array of NLebdevPts` error in `QCOutput` that can occur when computing RESP charges. Detecting this error is necessary to enable a handler in custodian. See [custodian #170](https://github.com/materialsproject/custodian/pull/170)
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https://api.github.com/repos/materialsproject/pymatgen/issues/2166 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2166/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2166/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2166/events | https://github.com/materialsproject/pymatgen/issues/2166 | 914,064,642 | MDU6SXNzdWU5MTQwNjQ2NDI= | 2,166 | typing_extensions dependency | {
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"This is an issue in `pymatgen.io.qchem.inputs` not in `setup.py`, typing_extensions is not required for Python >= 3.8 since the relevant type hints are built-in. Fixed with https://github.com/materialsproject/pymatgen/commit/73783005ce1e9030f06d50125abd87e4071183f3.\r\n\r\nThanks @htz1992213 for reporting, fyi @es... | 2021-06-07T23:55:21 | 2021-06-08T00:25:15 | 2021-06-08T00:25:14Z | CONTRIBUTOR | {
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} | **Describe the bug**
Dependency requirements for `typing-extensions` should apply for any python versions, not just python<3.8. Current version:
https://github.com/materialsproject/pymatgen/blob/dfc90b07d6362848442ce611ebe1c3a3e1ca2926/requirements.txt#L17
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https://api.github.com/repos/materialsproject/pymatgen/issues/2167 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2167/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2167/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2167/events | https://github.com/materialsproject/pymatgen/issues/2167 | 914,977,545 | MDU6SXNzdWU5MTQ5Nzc1NDU= | 2,167 | Could it manually enter high symmetry point information when I draw energy band? | {
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} | Could it manually enter high symmetry point information when I draw energy band?In fact I have Dirac points (k and k') inside the input KPOINTS file, which prevents my energy band diagram from showing the horizontal coordinates.Hope for reply,thanks!
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https://api.github.com/repos/materialsproject/pymatgen/issues/2168 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2168/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2168/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2168/events | https://github.com/materialsproject/pymatgen/issues/2168 | 916,127,970 | MDU6SXNzdWU5MTYxMjc5NzA= | 2,168 | [Improvment] duplicated data selection from `exterema_df` | {
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I have been using the `ChargeInsertionAnalyzer` class and realized that within the `get_label` function, we first select the desired data with average charge density below the maximum threshold from `extrema_df`:
https://github.com/materialsproject/pymatgen/blob/c724e7b679581783dcdb4690a83c374a57437ae6/pymatg... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2169 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2169/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2169/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2169/events | https://github.com/materialsproject/pymatgen/issues/2169 | 916,803,036 | MDU6SXNzdWU5MTY4MDMwMzY= | 2,169 | None radius for He Ne | {
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"This is just that there is no provided radius in the data source, https://github.com/materialsproject/pymatgen/blob/master/pymatgen/core/periodic_table.json\r\n\r\ne.g. for He\r\n\r\n```json\r\n \"He\":{\r\n \"Atomic mass\":4.002602,\r\n \"Atomic no\":2,\r\n \"Atomic orbitals\":{\r\n \"1s\... | 2021-06-10T01:38:29 | 2023-05-30T02:31:46 | 2023-05-30T02:31:46Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2170 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2170/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2170/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2170/events | https://github.com/materialsproject/pymatgen/issues/2170 | 917,087,551 | MDU6SXNzdWU5MTcwODc1NTE= | 2,170 | Adding alternative symmetry finding backends to pymatgen | {
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"It depends on how it's implemented, and how easy it is to switch backends. We would not want any core code that requires installing packages outside pip, and would not want to add clutter within the existing classes. A more general coupling between pymatgen and the symmetry-finding code might result in the pymatge... | 2021-06-10T08:51:38 | 2021-06-11T00:03:36 | 2021-06-10T17:32:23Z | CONTRIBUTOR | {
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} | Would a PR be welcomed adding alternative symmetry finding backends to pymatgen?
Currently pymatgen uses `spglib` which should definitely remain the default due to speed and the fact that it's a pip-installable package but alternative finders such as find-sym and aflow-sym trade can produce better results - https://... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2171 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2171/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2171/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2171/events | https://github.com/materialsproject/pymatgen/pull/2171 | 917,238,212 | MDExOlB1bGxSZXF1ZXN0NjY2ODAwMTY1 | 2,171 | Avoid error exit for ALGO=CHI | {
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"Can you add a simple unittest for this? Thanks.",
"\n[](https://coveralls.io/builds/40537438)\n\nCoverage decreased (-0.6%) to 83.083% when pulling **180153deaf7da2d6bfbd016c20d78c305bb273a2 on KazMorita:master** into **afa2cb9ba4111b4488933692d14f3c4... | 2021-06-10T11:32:11 | 2021-06-13T02:31:24 | 2021-06-13T02:27:57Z | CONTRIBUTOR | {
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} | ## Summary
* Added ALGO=CHI in place of ALGO=BSE to avoid the code from error exiting.
* This change is minor, so no change to the document is required.
## Additional dependencies introduced (if any)
* non
## TODO (if any)
* non
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https://api.github.com/repos/materialsproject/pymatgen/issues/2172 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2172/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2172/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2172/events | https://github.com/materialsproject/pymatgen/pull/2172 | 917,544,118 | MDExOlB1bGxSZXF1ZXN0NjY3MDYzODg0 | 2,172 | Use tighter EDIFF for DFPT calculations | {
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"test pls.",
"Done.",
"\n[](https://coveralls.io/builds/40484767)\n\nCoverage decreased (-0.6%) to 83.082% when pulling **d1ee3c77f84dd68ad30dd93d74cbd63d74f8ec60 on utf:dfpt** into **77c6dd669e159ca5fc5b2605b5a07b0bd3e500f9 on materialsproject:maste... | 2021-06-10T16:24:36 | 2021-06-11T16:49:47 | 2021-06-11T16:49:47Z | MEMBER | {
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} | ## Summary
Set EDIFF = 1e-5 when `lepsilon = True` in `MPStaticSet`. Note that this is [already used in atomate](https://github.com/hackingmaterials/atomate/blob/128a754000533029ce2b3d1faf3eb06aabe6f88b/atomate/vasp/firetasks/write_inputs.py#L378), I'm just moving the configuration to the input set itself. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2173 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2173/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2173/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2173/events | https://github.com/materialsproject/pymatgen/issues/2173 | 919,202,513 | MDU6SXNzdWU5MTkyMDI1MTM= | 2,173 | Significantly different Pourbaix diagrams somewhere between 2020.3.13 and 2022.0.8 | {
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"Hi @mwitman1, please see the Materials Project database release notes here for more information: https://matsci.org/t/materials-project-database-release-log/1609/18\r\n\r\n@rkingsbury can comment further (though he's not available this week, so may take some time for a response)",
"Hi @rkingsbury thanks for look... | 2021-06-11T20:51:49 | 2021-06-20T23:12:59 | 2021-06-20T23:12:59Z | NONE | {
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} | **Describe the bug**
There seems to significant difference in the Pourbaix diagrams generated in 2022.0.08 and those up to at least v2020.3.13. I’m referencing v2020.3.13 because it’s the last version in the Change Log that makes a mention of “pourbaix”. Ultimately it seems to come down to the computed energies for ea... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2174 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2174/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2174/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2174/events | https://github.com/materialsproject/pymatgen/pull/2174 | 919,313,541 | MDExOlB1bGxSZXF1ZXN0NjY4NjUxNzky | 2,174 | Q-Chem NBO | {
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"\n[](https://coveralls.io/builds/40715205)\n\nCoverage decreased (-0.6%) to 83.141% when pulling **7f07cc4693489915ce953b7546ece9b30bccdd8d on samblau:qchem** into **df22c1a523eee198ad6381dad585ac9b851dc9b3 on materialsproject:master**.\n",
"@mkhorton... | 2021-06-11T23:51:00 | 2021-06-19T00:06:23 | 2021-06-19T00:06:21Z | CONTRIBUTOR | {
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} | ## Summary
Add Q-Chem NBO functionality, whereby the NBO package can be called from within Q-Chem
* Input reading/writing in QCInput and corresponding testing
* Output parsing in QCOutput and corresponding testing
* NBO functionality in Q-Chem sets and corresponding testing
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https://api.github.com/repos/materialsproject/pymatgen/issues/2175 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2175/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2175/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2175/events | https://github.com/materialsproject/pymatgen/issues/2175 | 921,836,006 | MDU6SXNzdWU5MjE4MzYwMDY= | 2,175 | SpacegroupAnalyzer setting _space_group_data to None | {
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"This is not a problem with pymatgen but rather with the CIF file itself. Some of the atoms generated are too near each other, resulting in atomic collisions in the symmetry finding algorithm.\r\n\r\nUsing your second CIF file as an example,\r\n\r\n```python\r\nfrom pymatgen.core import Structure\r\ns = Structure.f... | 2021-06-15T21:57:37 | 2021-06-16T16:02:03 | 2021-06-16T12:27:33Z | CONTRIBUTOR | {
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} | **Describe the bug**
When attempting to fetch the spacegroup info for structures parsed from certain cifs (provided), an exception is thrown about the space group data being None.
**To Reproduce**
Copy in cifs provided at the bottom (sorry, I can't upload .cif files to these issues), run the code below.
```
fro... | {
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"Babel has its own bonding algorithm. You would use this to get what Babel thinks should be bonded, so it's not surprising that it disagrees with what you put in. If you put in the resulting babel bonded-molecule and it changed again, then there would be a bug. ",
"Your answer was helpful for me. Thank you, shyam... | 2021-06-18T15:15:45 | 2021-06-25T16:54:11 | 2021-06-25T16:54:00Z | NONE | {
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} | Hello. I'm a newbie of pymatgen.
BabelMolAdaptor(mol) seems that a bridge between pymatgen_mol and openbabel_mol.
But if I try to convert pymatgen_mol to openbabel_mol with the following codes:
`openbabel_mol = BabelMolAdaptor(pymatgen_mol).openbabel_mol`
the number of bonds in openbabel_mol is different ... | {
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"I think it was more intended to include single entries that one might want to inspect and use for analysis post serial/deserialization in the multi-entry case, but I think it's probably overly complex and misnamed, so I'm in support of getting rid of it.",
"Thanks @rkingsbury, @shyamd, including discussion in ht... | 2021-06-19T09:39:59 | 2021-06-20T23:13:58 | 2021-06-20T23:12:59Z | CONTRIBUTOR | {
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} | ## Summary
Default `PourbaixDiagram` to use `filter_solids=True` for consistency with the MP website and discussion in #2173.
In addition:
* Fix a bug in `MaterialsProjectAqueousCompatibility` introduced by e8028b0cfe783f8628c9090da07ff6e435244f6c
* add type hinting to `PourbaixDiagram` and make a few type hin... | {
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"Can you add a simple unittest pls?\r\n",
"> Can you add a simple unittest pls?\r\n@shyuep I uploaded a simple unittest here. Thanks!\r\n\r\n",
"Hi there, you do not need to send it as a zip file. All you need to do is to edit pymatgen/io/tests/test_pwscf.py to add this test to it. Then the checks will automa... | 2021-06-20T04:12:00 | 2021-08-11T22:28:59 | 2021-08-11T22:28:59Z | CONTRIBUTOR | {
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} | Allow to distinguish same element with different oxidation state, which might have different pseudopotentials.
## Summary
The only change I made is at line 153 of pwscf.py file:
out.append(" %s %.6f %.6f %.6f" % (site.specie.symbol, site.a, site.b, site.c))
-> out.append(" %s %.6f %.6f %.6f" % (site.spec... | {
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"\n[](https://coveralls.io/builds/40766573)\n\nCoverage decreased (-0.6%) to 83.149% when pulling **9f113be5cfe4156aefe0964dd81f9ed6e0c4adb5 on rkingsbury:kspacing-guard** into **33844780c5f735a18d6d28d788f5fc22f208b646 on materialsproject:master**.\n"
] | 2021-06-22T04:44:45 | 2021-07-15T14:32:57 | 2021-06-22T16:03:14Z | CONTRIBUTOR | {
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} | ## Summary
Add a guard statement and a test to ensure that the KSPACING value calculated by `MPScanRelaxSet` never exceeds the range 0.22 - 0.44.
This is a follow up to #2163. After that PR was merged I noticed from our atomate tests of the SCAN workflow that if a material's bandgap was sufficiently large >9 eV ... | {
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"Hi @VictorPullzz, since this is not a bug, you would be better off asking for help at our discussion forum: matsci.org/pymatgen\r\n\r\nIn brief, the CIF format is a crystallographic format, meaning it also defines a periodic lattice. XYZ files typically describe molecules, although some have a header with lattice ... | 2021-06-22T22:31:31 | 2021-06-23T20:36:33 | 2021-06-23T19:16:07Z | NONE | {
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} | **Describe the bug**
Hello I have a question. How I can convert XYZ file to cif format?
For ex:
I have some XYZ file
I need convert this to cif format file.
How I can doing this?
Pelase help me)
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"Thanks for reporting this. Can you provide an actual profile code showing this is indeed the offending line? I would assume a quick search through stable entries would be faster than doing the actual decomp computation for stable entries. Of course, if you have 100000 unstable entries and only 10 stable entries, t... | 2021-06-24T13:38:25 | 2021-06-28T16:22:19 | 2021-06-28T14:46:32Z | CONTRIBUTOR | {
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In `PhaseDiagram.get_decomp_and_e_above_hull` the current code first checks if an entry is in the stable entries. This wastes a large amount of compute to ensure that the decomp is ... | {
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"\n[](https://coveralls.io/builds/40858948)\n\nCoverage decreased (-0.6%) to 83.149% when pulling **5420e901364090346f3174e7125ba155eb568bc2 on CompRhys:3daxes** into **f4d2b6a53061074ccebba5bf0e75afa9fed15281 on materialsproject:master**.\n"
] | 2021-06-24T17:00:45 | 2021-06-28T12:42:40 | 2021-06-28T12:41:46Z | CONTRIBUTOR | {
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} | matplotlib is deprecating the old way to setup 3d plots used by the "matplotlib" backend in PDPlotter. This was giving me deprecation warnings in the testing scripts so I've replaced the calls with the more up to date api usage. I have tested the backend and it still works as before for 4d gibbs simplicies. | {
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"Thanks @gVallverdu, fixed with https://github.com/materialsproject/pymatgen/commit/8c96e7a395a2c5894d9d7d6d3094873b7e172741"
] | 2021-06-24T23:06:01 | 2021-06-24T23:37:42 | 2021-06-24T23:37:42Z | CONTRIBUTOR | {
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} | Hi,
There is an inconsistency between the definition of the `append()` function of the `Molecule` class and the documentation.
The `validate_proximity` is set to `False` by default but in the docstring of the function it is said that the default value is `True`.
Here is the link to the `append()` method in the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2184 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2184/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2184/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2184/events | https://github.com/materialsproject/pymatgen/issues/2184 | 931,466,729 | MDU6SXNzdWU5MzE0NjY3Mjk= | 2,184 | Lattice object should not be hashable | {
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"Strictly speaking, yes. Practically, this is normal practice and sometimes, there are cases where you want to hash a Lattice or some other mutable object in a dict. The default Python Object is hashable. "
] | 2021-06-28T11:24:14 | 2021-06-28T12:41:32 | 2021-06-28T12:41:32Z | NONE | {
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} | The lattice object (pymatgen/pymatgen/core/lattice.py) implements the hash-function as follows:
```
def __hash__(self):
return 7
```
I think that this is not a good way to implement the hash-function and that lattice should not be hashable because it is mutable. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2185 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2185/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2185/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2185/events | https://github.com/materialsproject/pymatgen/issues/2185 | 932,225,519 | MDU6SXNzdWU5MzIyMjU1MTk= | 2,185 | eigenvalue_band_properties based on separate spin channels | {
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"Addressed in #2187."
] | 2021-06-29T05:24:31 | 2021-07-01T04:45:31 | 2021-07-01T04:45:31Z | MEMBER | {
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} | **Is your feature request related to a problem? Please describe.**
Currently, the band gaps computed using the `eigenvalue_band_properties` function in `pymatgen.io.vasp.outputs` (e.g. for the `Vasprun` or `Eigenval` classes) are based on the VBM and CBM independent of spin. For some spin-polarized systems, this might... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2186 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2186/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2186/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2186/events | https://github.com/materialsproject/pymatgen/pull/2186 | 932,274,036 | MDExOlB1bGxSZXF1ZXN0Njc5NjQyMjQ4 | 2,186 | Revise #2164 - Make SETTINGS loading more robust | {
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"\n[](https://coveralls.io/builds/40957332)\n\nCoverage decreased (-0.6%) to 83.148% when pulling **be53de0347d21b5fbd55512316dee670fcd6b0e5 on ardunn:master** into **0e3181fe3bd2553267340dcb8b8afd19332387a7 on materialsproject:master**.\n",
"Thanks @a... | 2021-06-29T06:47:59 | 2021-06-30T18:04:51 | 2021-06-30T18:04:50Z | CONTRIBUTOR | {
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} | ## Summary
Changes in SETTINGS load priority from #2164 can sometimes cause the loaded SETTINGS dictionary to be empty, leading to the following kind of error:
```
File "/home/runner/work/matminer/matminer/test_env/lib/python3.8/site-packages/pymatgen/ext/matproj.py", line 202, in __init__
if "MAPI_DB_VER... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2187 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2187/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2187/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2187/events | https://github.com/materialsproject/pymatgen/pull/2187 | 932,820,349 | MDExOlB1bGxSZXF1ZXN0NjgwMTIwNjcy | 2,187 | Add support for spin-dependent eig band props | {
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"\n[](https://coveralls.io/builds/41009700)\n\nCoverage decreased (-0.6%) to 83.158% when pulling **9c748d3a87c4593b83a9e51eb6c30751d1db1884 on arosen93:master** into **0e3181fe3bd2553267340dcb8b8afd19332387a7 on materialsproject:master**.\n",
"Thanks ... | 2021-06-29T15:19:47 | 2021-07-01T04:46:19 | 2021-07-01T04:43:47Z | MEMBER | {
"total": 0,
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} | ## Summary
PR to address #2185 (please refer to this Issue for additional context). This PR allows for the band gap, CBM, VBM, and is_direct_band_gap to be computed for each individual spin channel in a spin-polarized calculation when using the VASP Eigenval or Vasprun parsers via a new `separate_spins` keyword argu... | {
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"FYI @htz1992213 @orioncohen",
"Per a side discussion with @mkhorton , we might want to consider adding `DataFrame` support to `monty` so that we don't have to implement custom `as_dict` / `from_dict`. If we do that, just inheriting from `MSONable` and making sure that all kwargs are stored as class attributes s... | 2021-06-29T20:21:36 | 2023-11-05T22:19:54 | CONTRIBUTOR | {
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} | **Describe the bug**
I am unable to serialize and deserialize a `CombinedData` object using `loadfn` / `dumpfn`. I believe this occurs because `CombinedData` inherits `from_dict` from `LammpsData`, but `CombinedData.init()` takes different kwargs.
**To Reproduce**
Create a `CombinedData` object called `data`
``... | {
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"Try 2019.12.31",
"Thanks for your suggestion. Pymatgen 2020.12.31 worked for me. In colab, it worked fine. In conda, there was module not found error for ruamel.yaml. But `import ruamel_yaml` worked. It was resolved by following steps:\r\n\r\n1. `cd anaconda3/lib/python3.8/site-packages/pymatgen`\r\n2. `find . -... | 2021-07-02T01:56:44 | 2021-07-04T02:03:06 | 2021-07-02T14:13:46Z | NONE | {
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} | The latest version of tensorflow and pymatgen are incompatible due to dependency errors. Tensorflow depends on older version of numpy (1.19.1) while pymatgen uses numpy 1.20.1.
When installing pymatgen in a new conda environment or in colab containing tensorflow, installation errors with exit status 1. Maybe it will... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2190 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2190/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2190/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2190/events | https://github.com/materialsproject/pymatgen/pull/2190 | 935,914,897 | MDExOlB1bGxSZXF1ZXN0NjgyNzUxMjYx | 2,190 | Gruneisen classes | {
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"Will fix the rest of the problems on Monday... (sorry)",
"Looking at the logs, it's unclear why so many linting issues are coming up for classes that are not touched by this PR -- only linting issues associated with the files modified by this PR need to be addressed.\r\n\r\nOne request is that when a new plotter... | 2021-07-02T16:30:37 | 2021-07-09T17:21:21 | 2021-07-09T16:41:53Z | MEMBER | {
"total": 0,
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} | ## Summary
@ab5424 , @gpetretto and I have worked on classes to handle Grüneisen parametrs in pymatgen. We have added a module phonopy.phonon.gruneisen.py and also plotter classes. The parameters can also be imported from phonopy.
Please let me know if we can do anything further to get this pull request merged s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2191 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2191/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2191/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2191/events | https://github.com/materialsproject/pymatgen/pull/2191 | 936,138,980 | MDExOlB1bGxSZXF1ZXN0NjgyOTQxODc3 | 2,191 | CombinedData.as_dict/from_dict and other methods overwrite; CombinedData.as_lammpsdata deepcopied | {
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"Fixes #2188 ",
"\n[](https://coveralls.io/builds/42396886)\n\nCoverage decreased (-0.6%) to 83.143% when pulling **cab0331c70be487ee9b8edbdd8e8d98b888a6cba on htz1992213:master** into **40817cc97fe25bc027523a65aab528b59e22e78e on materialsproject:mast... | 2021-07-03T01:19:59 | 2021-08-26T18:00:19 | 2021-08-25T16:45:55Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Include a summary of major changes in bullet points:
* Add `as_dict`, `from_dict` for CombinedData to overwrite superclass methods
* Overwrite `structure`, `disassemble`, `from_ff_and_topologie`, `from_structur` methods for CombinedData
* Rewrite `as_lammpsdata` method for CombinedData so that each a... | {
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"Also tagging @shyamd here. A recent PR #2149 cleaned up a lot of the interface functionality and added new features.",
"Yup. Dumb bug on my part. Already opened a PR to fix it in #2198 ",
"Thanks!"
] | 2021-07-05T20:44:12 | 2021-09-13T08:39:12 | 2021-09-13T08:39:12Z | NONE | {
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} | **Describe the bug**
pymatgen.analysis.interfaces.substrate_analyzer returns None objects rather than SubstrateMatch objects.
**To Reproduce**
Code to run:
from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer
from pymatgen.ext.matproj import MPRester
mpr = MPRester("API_KEY")
subst... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2193 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2193/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2193/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2193/events | https://github.com/materialsproject/pymatgen/pull/2193 | 939,111,891 | MDExOlB1bGxSZXF1ZXN0Njg1MzgzMTAw | 2,193 | Bugfix for defect BandFillingCorrection | {
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"\n[](https://coveralls.io/builds/41191123)\n\nCoverage decreased (-0.6%) to 83.191% when pulling **6c69bc4c6b6657b60883ecc892885a1882f9bf4a on kavanase:master** into **3855d50c857fc61e70a0a4497e194a819d617a64 on materialsproject:master**.\n",
"Thanks ... | 2021-07-07T17:33:20 | 2021-07-12T19:11:56 | 2021-07-08T19:51:21Z | CONTRIBUTOR | {
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} | ## Summary
This is a bugfix for two significant errors in the BandFillingCorrection class for defects.
I have attached a PDF, notebook and corresponding data to demonstrate the errors, and how these are now fixed with this PR. I have changed the value in the BandFillingCorrection test to match the correct value as we... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2194 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2194/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2194/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2194/events | https://github.com/materialsproject/pymatgen/issues/2194 | 939,419,843 | MDU6SXNzdWU5Mzk0MTk4NDM= | 2,194 | ZSLGenerator not returning all inequivalent transformations | {
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"I just noticed the undocumented `bidirectional` argument for the `ZSLGenerator` constructor, but it's not clear to me how exactly it relates to this behavior. It would be nice if it could be explained in the docstring.",
"I just updated to 2022.0.10, and I'm running into a new bug. I've modified my code for th... | 2021-07-08T03:00:57 | 2021-09-13T08:39:41 | CONTRIBUTOR | {
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} | **Describe the bug**
`ZSLGenerator` doesn't return some expected mappings between two low symmetry lattices.
**To Reproduce**
run
```
from pymatgen.analysis.substrate_analyzer import ZSLGenerator
# find in-plane supercell lattice pairs that are compatible
zsl = ZSLGenerator(max_area=4.5, max_length_tol = 0... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2195 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2195/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2195/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2195/events | https://github.com/materialsproject/pymatgen/issues/2195 | 939,460,311 | MDU6SXNzdWU5Mzk0NjAzMTE= | 2,195 | Inconsistent use of output file path in Structure.to() method | {
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"Thanks for the report. I didn't see your issue at the time but this was fixed in 6a6056cd417f1310d6810cf3ebdd2d2126fe4d41 and released in [v2022.11.1](https://github.com/materialsproject/pymatgen/releases/tag/v2022.11.1)."
] | 2021-07-08T04:36:58 | 2023-05-30T16:53:47 | 2023-05-30T16:53:47Z | NONE | {
"total": 0,
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} | **Describe the bug**
Structure.to() method ignores the parent path of filename for certain file formats, say, .xsf format.
For example, in the following scenario,
```python
struct = Structure(...)
struct.to(filename="/path/to/struct.ext")
```
the output file is correctly written to /path/to/struct.ext when .ext... | {
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} | **Describe the bug**
core/__init__.py tries to import ruamal, which results in an error, rather than ruamel, which I think is the proper import statement.
**To Reproduce**
Steps to reproduce the behavior:
import pymatgen.core
Provide any example files that are needed to reproduce the error,
especially if the... | {
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"Thanks for the feedback. but I need a bit more context about where this is causing problems. In general, data files that are packaged are meant to be defaults. If alternatives are allowed, those code should be implemented with an argument to allow other files to be supplied. So pls provide a specific scenario wher... | 2021-07-08T18:50:52 | 2021-08-24T15:35:27 | 2021-08-24T15:35:27Z | MEMBER | {
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The current implementation of pymatgen is difficult to adapt/use in environments where data files are packaged separately from source code. In these cases, the actual file name of the resource, such as `pymatgen/analysis/op_params.yaml` won't necessa... | {
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"\n[](https://coveralls.io/builds/41228307)\n\nCoverage decreased (-0.6%) to 83.187% when pulling **33c9032ca48e98c119d13b20b2db96bd9386cc2a on shyamd:fix_sub_analyzer** into **ec611b9f0fc04c49de003132a53ff4df4b2a3f7f on materialsproject:master**.\n",
... | 2021-07-08T20:07:19 | 2023-05-30T16:49:34 | 2021-07-09T22:45:15Z | NONE | {
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} | This should fix #2198 , which was a bug introduced in the interfaces reorganization where the substrate analyzer was constructing matches to return, but not actually returning them... DOH!
I've added a test to check for this in the future. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2199 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2199/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2199/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2199/events | https://github.com/materialsproject/pymatgen/issues/2199 | 940,199,792 | MDU6SXNzdWU5NDAxOTk3OTI= | 2,199 | Outdated costdb_elements.csv, active elemental price updates for CostAnalysis? | {
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"If there is an API that you can use to use latest prices, by all means implement an interface to it. I think there is an XML feed that can be used quite easily."
] | 2021-07-08T20:33:10 | 2021-07-08T21:17:53 | CONTRIBUTOR | {
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} | The costdb_elements.csv is vastly outdated, especially for metal prices. If we look at Rh today, its currently at $600000/kg compared to the $20000/kg price obtained from WolframAlpha in 2013, about a 3000% increase. However even if we update all the elements with the most recent costs, there's still a lot of volatilit... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2200 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2200/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2200/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2200/events | https://github.com/materialsproject/pymatgen/issues/2200 | 940,234,112 | MDU6SXNzdWU5NDAyMzQxMTI= | 2,200 | V+2 and V+3 do not appear in Pourbaix Diagrams | {
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} | **Describe the bug**
V+2 and V+3 species do not appear on our `PourbaixDiagram` for vanadium, even though several credible sources indicate that they should. This shortcoming was reported by an external user.
I've included below the pymatgen / Materials Project Pourbaix Diagram and several other points of reference... | {
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