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https://api.github.com/repos/materialsproject/pymatgen/issues/1701 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1701/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1701/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1701/events | https://github.com/materialsproject/pymatgen/pull/1701 | 534,931,638 | MDExOlB1bGxSZXF1ZXN0MzUwNzE1MjEx | 1,701 | Bump tqdm from 4.40.0 to 4.40.1 | {
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"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [build (3.7)](https://developer.github.com/actions/)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-09T13:28:23 | 2019-12-09T14:23:15 | 2019-12-09T14:23:07Z | CONTRIBUTOR | {
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<details>
<summary>Commits</summary>
- [`4276147`](https://github.com/tqdm/tqdm/commit/42761473f9edf276937cc3a28a6fcabc59f5f97d) bump version, merge branch 'devel'
- [`ffb706e`](https://github.com/tqdm/tqdm/commit/ffb706ec9ecdadfb5cbaa826dfa48c22e04d58e... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1702 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1702/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1702/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1702/events | https://github.com/materialsproject/pymatgen/pull/1702 | 534,981,297 | MDExOlB1bGxSZXF1ZXN0MzUwNzU2MDIx | 1,702 | Fix bug in lobsterout | {
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I have fixed a bug in the Lobsterout class. Before this bug fix, "lobsterout" files which were created with only one thread could not be read and this bug led to an exception. I have included this option now and added an additional test to avoid this problem in the future. I ran into this bug by running Lobs... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1703 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1703/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1703/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1703/events | https://github.com/materialsproject/pymatgen/issues/1703 | 535,403,899 | MDU6SXNzdWU1MzU0MDM4OTk= | 1,703 | Illegal Instruction when importing find_points_in_spheres | {
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"I am not sure what's the issue with conda installation on Linux. But for linux, perhaps you can just try using `pip install pymatgen`. That usually forces a compile using whatever compiler you have on your system and works fine.",
"Thanks for the reply. The illegal instruction does not occur with Clang 9.0.0 and... | 2019-12-09T23:43:51 | 2019-12-10T01:38:16 | 2019-12-10T01:38:16Z | NONE | {
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} | An illegal instruction occurs when importing find_points_in_spheres from pymatgen.optimization.neighbors. The code was built with anaconda 5.2.0.
To reproduce:
$ conda create -n test_pymatgen -c conda-forge pymatgen
$ conda activate test_pymatgen
(test_pymatgen) $ python
Python 3.7.3 | packaged by conda-forge... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1704 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1704/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1704/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1704/events | https://github.com/materialsproject/pymatgen/pull/1704 | 536,106,044 | MDExOlB1bGxSZXF1ZXN0MzUxNjk2MjI2 | 1,704 | Add missing information to docstrings | {
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"Thanks!"
] | 2019-12-11T02:38:16 | 2019-12-11T02:43:16 | 2019-12-11T02:43:16Z | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1705 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1705/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1705/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1705/events | https://github.com/materialsproject/pymatgen/pull/1705 | 536,427,203 | MDExOlB1bGxSZXF1ZXN0MzUxOTU4NjMw | 1,705 | Fix bug of missing sp2 N-N bond data | {
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"Can you add a small unittest in the existing unittests to make sure this additional data works as intended? There are already tests there - so it is just copying and pasting one or two lines and changing it to the N-N bond. Thanks.",
"THanks!",
"Hi @kwaters4, please feel welcome to add your name to [this form]... | 2019-12-11T15:00:39 | 2020-01-13T22:07:15 | 2019-12-11T17:14:07Z | NONE | {
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} | Added data for an sp2 N-N bonds in bond_lengths.json
Use value of 1.25 from the following source
http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html
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"Thanks @guymoore13! One thing I noticed was missing is a test for the site property serialization fix. Doing a round-trip as_dict from_dict would probably be sufficient.",
"Sounds good @mkhorton, thank you for the tip!",
"@mkhorton should I add coordinate wrapping for all symmops? In other words, for translati... | 2019-12-11T15:27:38 | 2020-01-14T05:35:12 | 2020-01-14T05:35:12Z | CONTRIBUTOR | {
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} | ## Summary
* Added "Jones Faithful transformation" as an optional input for the MagneticSpaceGroup constructor, allowing the user to define the space-group in non-standard coordinates
* CIF file reader uses non-standard transformation in BNS setting as input to MagneticSpaceGroup constructor
* Fixed Monty deserial... | {
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"I would suggest we simply use have a different YAML setting file that specifies W instead of W_pv as the PSP.",
"We noticed this ourselves recently -- the immediate fix is simply to add `user_potcar_settings={\"W\":\"W_sv\"}` I believe. The _sv seems like the better pseudo potential anyway.\r\n\r\nMore broadly, ... | 2019-12-11T16:04:43 | 2023-06-01T00:41:02 | 2023-06-01T00:41:02Z | MEMBER | {
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} | **Describe the bug**
W_pv POTCAR does not exist in the newer POTCAR versions (PBE_54). Using the MVLScanRelaxSet or the LobsterSet for compounds including W will therefore result in an error:
**To Reproduce**
`from pymatgen.ext.matproj import MPRester`
`from pymatgen.io.vasp.sets import MVLScanRelaxSet`
`a = MPR... | {
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"Hmm... why don't you just edit the current input set rather than having yet another one?",
"Failing with `No library stub file for module 'pytest`",
"> Hmm... why don't you just edit the current input set rather than having yet another one?\r\n\r\n@shyuep my thought (informed by my experience as I've learned p... | 2019-12-11T17:47:17 | 2019-12-17T19:37:04 | 2019-12-17T19:37:04Z | CONTRIBUTOR | {
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} | ## Summary
This is a new VASP input set for the SCAN metaGGA functional. Compared to previous input sets, we have adjusted a number of INCAR tags based on internal benchmarking of energy convergence, and utilized some modernized features of VASP such as KSPACING.
This input set is utilized in a forthcoming atomat... | {
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> ## 5.3.2
> No release notes provided.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1715 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1715/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1715/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1715/events | https://github.com/materialsproject/pymatgen/pull/1715 | 538,591,685 | MDExOlB1bGxSZXF1ZXN0MzUzNzEwOTQz | 1,715 | Add fast `Structure.get_neighbor_list` method | {
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"Fantastic! Thanks @chc273 \r\n\r\nCould you comment a little on the change in the C++ compile args? Is this going to be any easier/more difficult to compile than previously?",
"@mkhorton `c++0x` is an older standard than `c++11`. Some supercomputer platforms (like tscc we are using) are still using the old gcc v... | 2019-12-16T18:56:40 | 2019-12-16T20:06:13 | 2019-12-16T20:06:13Z | CONTRIBUTOR | {
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} | ## Summary
Added a Structure method to construct neighbor list without using Neighbor class. Previously this is achieved by using `get_all_neighbors` method, which is much slower than the proposed methods. It may become a problem when the structure is very large, e.g., >10,000 atoms.
Here I am adding a new metho... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1716 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1716/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1716/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1716/events | https://github.com/materialsproject/pymatgen/pull/1716 | 539,390,021 | MDExOlB1bGxSZXF1ZXN0MzU0Mzc2MTAz | 1,716 | determine kspacing and smearing from bandgap in MPScanRelaxSet | {
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"@mkhorton @shyamd this is how E_gap maps to KSPACING. The VASP default value is 0.5. Should we cap the value at 0.5, or allow it to increase beyond that? (Would change the k-point density of materials with Egap > 6 eV)\r\n\r\n![image](https://user-images.githubusercontent.com/1908695/71046640-bdb03080-20ed-11ea-9... | 2019-12-18T00:52:52 | 2019-12-19T00:38:20 | 2019-12-19T00:38:02Z | CONTRIBUTOR | {
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} | This morning @mkhorton @shyamd @kristinpersson and I decided to compute the KSPACING value based on the bandgap of the input material in our SCAN workflow. At the time I thought this functionality would be part of atomate, but later learned it needs to be in MPScanRelaxSet.
I also identified and corrected a potentia... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1717 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1717/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1717/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1717/events | https://github.com/materialsproject/pymatgen/issues/1717 | 539,988,010 | MDU6SXNzdWU1Mzk5ODgwMTA= | 1,717 | Reaction Calculator -- better stoichiometry coefficient balancing | {
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"Closed with commit #1718. "
] | 2019-12-18T23:46:21 | 2020-05-22T00:14:16 | 2020-05-22T00:14:16Z | MEMBER | {
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} | The current Reaction class’s stoichiometry/balancing code allows for the automatic shuffling of reactants/products to opposite sides -- or even deleting the reactants/products entirely. While this is occasionally a nice feature for underdetermined systems, it can lead to undesirable/unexpected solutions. For example, w... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1718 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1718/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1718/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1718/events | https://github.com/materialsproject/pymatgen/pull/1718 | 539,991,480 | MDExOlB1bGxSZXF1ZXN0MzU0ODc0Nzk1 | 1,718 | Reaction Calculator -- better stoichiometry/balancing | {
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"This looks excellent, thanks @mattmcdermott !\r\n\r\nBefore merging could you comment a little on the test changes, e.g. is `test_singular_case` still testing a singular case? It's not clear to me how the old test was correct in any case.",
"@mkhorton Yeah! All changes I made to the tests were because the previo... | 2019-12-18T23:58:14 | 2020-01-13T22:09:36 | 2019-12-20T22:22:34Z | MEMBER | {
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} | This PR references the issue described in #1717: i.e. that the stoichiometric coefficient solver in the _Reaction_ class often finds solutions which are unexpected/undesirable.
The fix adds tracking for the `num_errors`, which counts how many components flip sides or are deleted entirely. The `_balance_coeffs()` me... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1719 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1719/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1719/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1719/events | https://github.com/materialsproject/pymatgen/pull/1719 | 540,431,764 | MDExOlB1bGxSZXF1ZXN0MzU1MjQxODM5 | 1,719 | add missing docstring to symbol in PotcarSingle | {
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"Thanks!"
] | 2019-12-19T16:48:14 | 2019-12-19T16:58:01 | 2019-12-19T16:57:54Z | CONTRIBUTOR | {
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} | Adds a missing docstring to the 'symbol' property of 'PotcarSingle'. Also updates .gitignore to ignore VS code settings files. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1720 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1720/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1720/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1720/events | https://github.com/materialsproject/pymatgen/pull/1720 | 540,656,810 | MDExOlB1bGxSZXF1ZXN0MzU1NDM3NzUz | 1,720 | Bug fix: remove occasional blank line that makes CHGCAR unreadable | {
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"Thanks @LindaHung-TRI !",
"Hi @LindaHung-TRI, I forgot to mention, please do add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html). We want to make sure we credit all contributors, even if they're just small add... | 2019-12-20T00:15:12 | 2020-01-13T22:02:34 | 2019-12-20T01:01:25Z | CONTRIBUTOR | {
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* Fix 1: When writing CHGCAR files, if a full line is already output in the last step of the for loop, additional blank line is no longer added. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1721 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1721/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1721/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1721/events | https://github.com/materialsproject/pymatgen/issues/1721 | 541,054,710 | MDU6SXNzdWU1NDEwNTQ3MTA= | 1,721 | PhaseDiagram/PDPlotter may rotate endpoints when elements are not explicitly specified. | {
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"I don’t have a problem with this. I guess the simplest solution is to add a elements = sorted(elements) somewhere. Feel free to implement, with tests, and submit PR.",
"@JosephMontoya-TRI @montoyjh just checking, this issue is fixed with your PR from a couple of years ago and can be closed right?",
"Yep."
] | 2019-12-20T15:35:42 | 2022-02-25T21:34:54 | 2022-02-25T21:34:54Z | CONTRIBUTOR | {
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} | **Describe the bug**
PhaseDiagram/PDPlotter may rotate endpoints when elements are not explicitly specified.
**To Reproduce**
Steps to reproduce the behavior:
1. Make list of entries
2. PhaseDiagram(entries)
3. PhaseDiagram(entries.shuffle())
4. PDPlot both
5. One may be rotated relative to other
**Expecte... | {
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Sorts elements determined from entries, if elements are not explicitly specified. Adds test for to ensure that specified element order is respected and that unspecified element orderings result in the same ordering. Addresses #1721 . | {
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<details>
<summary>Changelog</summary>
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https://api.github.com/repos/materialsproject/pymatgen/issues/1724 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1724/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1724/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1724/events | https://github.com/materialsproject/pymatgen/pull/1724 | 541,756,108 | MDExOlB1bGxSZXF1ZXN0MzU2MzMwMDIy | 1,724 | Bump phonopy from 1.11.12.121 to 2.4.2 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1725 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1725/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1725/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1725/events | https://github.com/materialsproject/pymatgen/pull/1725 | 541,756,329 | MDExOlB1bGxSZXF1ZXN0MzU2MzMwMjE0 | 1,725 | Bump mypy from 0.750 to 0.761 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1726 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1726/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1726/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1726/events | https://github.com/materialsproject/pymatgen/pull/1726 | 541,756,596 | MDExOlB1bGxSZXF1ZXN0MzU2MzMwNDU1 | 1,726 | Bump ase from 3.18.2 to 3.19.0 | {
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<details>
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https://api.github.com/repos/materialsproject/pymatgen/issues/1727 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1727/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1727/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1727/events | https://github.com/materialsproject/pymatgen/pull/1727 | 541,756,624 | MDExOlB1bGxSZXF1ZXN0MzU2MzMwNDc4 | 1,727 | Bump tqdm from 4.40.2 to 4.41.0 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1728 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1728/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1728/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1728/events | https://github.com/materialsproject/pymatgen/pull/1728 | 541,756,942 | MDExOlB1bGxSZXF1ZXN0MzU2MzMwNzU4 | 1,728 | Bump scipy from 1.3.3 to 1.4.1 | {
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<summary>Release notes</summary>
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} | Bumps [numpy](https://github.com/numpy/numpy) from 1.17.4 to 1.18.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.18.0</h2>
<h1>NumPy NumPy 1.18.0 Release Notes</h1>
<p>In addition to the usual bug fix... | {
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"Thanks, I pushed a fix to include all renames of the \"e\" operation and added tests. Let me know if there are other issues."
] | 2019-12-29T18:32:38 | 2019-12-30T01:52:33 | 2019-12-30T01:51:56Z | MEMBER | {
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} | In `pymatgen/symmetry/symm_data.json`, there is the `Cmma` spacegroup (num. 67), but this spacegroup has [been renamed](https://hal.archives-ouvertes.fr/hal-00963925/document) (see top of page 00006-p.26) to `Cmme`, which is not found in the json file. Similarly, there is support for `Ccca` (num. 68), but this spacegro... | {
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"How about you remove the existing `write_spec` method (which hasn't been there long in any case) and add a `zip` flag to `write_input` also?\r\n\r\nThe `write_spec` was added to formalize some functionality that previously existed in Materials Project, but was only present in the website code, and since pymatgen h... | 2020-01-04T01:03:50 | 2020-01-07T17:42:26 | 2020-01-06T19:32:25Z | CONTRIBUTOR | {
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} | ## Summary
Adds a boolean `potcar_spec` option to the `write_input` method of a `VaspInputSet`. When this option is enabled, `write_input` generates a POTCAR.spec file rather than a POTCAR file (similar to the existing `write_spec` method, which outputs a .zip file containing all the inputs.) The purpose of this opt... | {
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Connectivity of environments. Allows to target specific environments in order e.g. to find isolated columns/planes of a given type of environment.
Unit tests and documentation for this connectivity analysis. | {
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* Added a horizontal line in DosPlotter. This is helpful when we have spin polarized DOS.
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"Thank you!",
"Thanks @uthpalah ! Make sure to add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html). We want to make sure we credit all contributors, even if it's just a small addition."
] | 2020-01-09T17:32:24 | 2020-01-10T23:35:20 | 2020-01-09T19:12:46Z | CONTRIBUTOR | {
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* Added a horizontal line at y=0 for the DOS plotter. This is helpful when we have spin polarized DOS plots.
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Bad check on a peculiar case (which in the latest version of the connected component code, could actually not occur anymore) that was actually wrong in other cases. => removed that check. | {
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This commit refactors 'write_input' so that 'get_vasp_input' is not called when `write_spec` is True. Avoiding the call to `get_vasp_input` is important for testing in systems where no POTCARs are installed. @utf was consulted on this fix as well. See https://github.com/hackingmaterials/atomate/pull/345 | {
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"While this is possible, but it would be highly inefficient since it is not possible to a priori know what r should be to get n neigbors. The easier way is simply to use `nn = get_all_neighbors(..)` with a reasonable r (say 5A), and then just take the first n neighbors. E.g., `nn[:n]`.",
"@shyuep we could add tha... | 2020-01-20T15:07:10 | 2020-01-21T00:51:20 | 2020-01-20T15:41:37Z | NONE | {
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} | Hello
As it stands there are many methods to get all sites within a radius r of some co-ordinates / site in a crystal. I notice that there is no way to specify 'n' instead where r is chosen to give exactly n sites. this functionality seems intuitive and I imagine fairly easy to add would it be possible to include th... | {
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} | **Describe the bug**
For Macos version at or than 10.15, the voronoi and zeo++ could be compiled successfully but could not be wrapped
**To Reproduce**
Steps to reproduce the behavior:
mkdir Voro++
mkdir Voro++/voro
cd Voro++/voro
svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk
cd trun... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1739 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1739/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1739/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1739/events | https://github.com/materialsproject/pymatgen/pull/1739 | 553,631,592 | MDExOlB1bGxSZXF1ZXN0MzY1OTI5Mjkx | 1,739 | automatic setting for NEDOS in MPNonSCFSet | {
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} | As discussed with @mkhorton, here an implemention of
an automatic setting for NEDOS for "uniform" mode in MPNonSCFSet.
It reads the max and min of eigenvalues from previous vasprun and use
a default energy step, called dedos, set at 0.005eV.
It works setting nedos=0 in from_prev_calc() method:
mpset = MPNonSCFSe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1740 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1740/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1740/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1740/events | https://github.com/materialsproject/pymatgen/pull/1740 | 553,637,061 | MDExOlB1bGxSZXF1ZXN0MzY1OTMzODc1 | 1,740 | Automatic setting for NEDOS in MPNonSCFSet | {
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"Many thanks @fraricci ",
"Seems there are failing tests.",
"Merging the master to my auto_nedos branch deleted my changes.\r\nI pushed back the new features in auto_nedos branch. \r\nTests were passing in my computer. They should pass here too now."
] | 2020-01-22T16:01:37 | 2020-01-29T00:41:23 | 2020-01-29T00:41:23Z | CONTRIBUTOR | {
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} | As discussed with @mkhorton, here an implemention of
an automatic setting for NEDOS for "uniform" mode in MPNonSCFSet.
It reads the max and min of eigenvalues from previous vasprun and use
a default energy step, called dedos, set at 0.005eV.
It works setting nedos=0 in from_prev_calc() method:
mpset = MPNonSCFSe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1741 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1741/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1741/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1741/events | https://github.com/materialsproject/pymatgen/pull/1741 | 553,641,266 | MDExOlB1bGxSZXF1ZXN0MzY1OTM3NDIw | 1,741 | Isym uniform bug fix | {
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"Thanks @fraricci! Can we use ISYM = 2 as this should be more efficient. See https://www.vasp.at/wiki/index.php/ISYM",
"I am fine with this, but please implement tests.",
"@utf , thanks for the suggestion, that's preferable indeed.\r\n@shyuep test on isym added as well.",
"Thanks @fraricci !"
] | 2020-01-22T16:08:21 | 2020-01-23T21:30:48 | 2020-01-23T21:30:47Z | CONTRIBUTOR | {
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} | As discussed in issue #1453, ISYM has to be set to 1 in case of uniform mode in MPNonSCFSet.
This pull request should fix the problem.
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"Thanks @davidwaroquiers "
] | 2020-01-24T14:53:49 | 2020-01-24T21:46:38 | 2020-01-24T21:46:33Z | CONTRIBUTOR | {
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"Thanks @yimingchen95 !\r\n\r\n@shyamd is there anything else you need from this for the builders/api?",
"I don't think we need separate classes for XANES and EXAFS, since both have the same init. I think you can add a name arg to the XAS to allow you to specify whether it is K,L XANES or EXAFS.\r\n\r\nThen, what... | 2020-01-26T21:49:17 | 2020-01-29T00:34:13 | 2020-01-29T00:34:07Z | CONTRIBUTOR | {
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} | ## Summary
Update XAS module with EXAFS module and stitching code
* Add EXAFS module
* Add stitching method for XANES and EXAFS
* Add stitching method for L2 and L3 edge XANES
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that... | {
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"Hi @gVallverdu,\r\n\r\nThis is certainly something we’ve (@shyuep) talked about but have not reached a decision on yet.\r\n\r\nI will note that the situation is not quite as bad as it might seem: the large repo size is due to extensive test files, the actual source distribution on PyPI is just 2.6 MB. Also, the de... | 2020-01-27T08:55:56 | 2023-06-05T18:13:24 | 2023-06-05T18:13:01Z | CONTRIBUTOR | {
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I wonder if it could be possible in any way to distribute a kind of small/min/light version of pymatgen including only core classes ? Now pymatgen is a quite large python packages (git repo is about 1.5 Go). All different modules are really interesting but sometimes, if you want to develop a new application, wh... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1745 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1745/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1745/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1745/events | https://github.com/materialsproject/pymatgen/issues/1745 | 556,009,037 | MDU6SXNzdWU1NTYwMDkwMzc= | 1,745 | Numerical error produces lattice with values close to 0, but negative | {
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"Thanks for the report @felentovic, Negative values are not intrinsically incorrect and somewhat inevitable given the nature of floating point arithmetic -- can you give a specific example of error accumulation leading to a bug?\r\n\r\nThis said, I agree it's unfortunate there are these small-non-zero values in thi... | 2020-01-28T06:27:23 | 2020-01-28T14:08:51 | 2020-01-28T14:08:51Z | NONE | {
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In the class `Lattice` the method `from parameters` in some cases creates lattice vectors which have a value close to zero, but negative. E.g [5.61018515, 0.0, 3.435247643285757e-16]. This accumulates errors later in calculations.
**To Reproduce**
Steps to reproduce the behavior:
Create a la... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1746 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1746/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1746/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1746/events | https://github.com/materialsproject/pymatgen/issues/1746 | 556,138,269 | MDU6SXNzdWU1NTYxMzgyNjk= | 1,746 | POTCAR file hashes appear to be incorrect | {
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"Thanks for reporting this.\r\n@mkhorton @shyamd I honestly dislike the file hash approach to dealing with POTCARs. Should we just do away with this? I think basic checks such as the functional, date and parameters would suffice?",
"These aren't supposed to be file hashes, but rather data hashes, so this is the e... | 2020-01-28T11:10:47 | 2020-01-30T00:25:16 | 2020-01-30T00:25:16Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1747 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1747/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1747/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1747/events | https://github.com/materialsproject/pymatgen/issues/1747 | 556,320,986 | MDU6SXNzdWU1NTYzMjA5ODY= | 1,747 | Fail to build python bindings to Zeo++ with Cython | {
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"Pls contact the developers of Zeo++ as we do not maintain that code. "
] | 2020-01-28T16:23:10 | 2020-01-28T16:26:48 | 2020-01-28T16:26:47Z | NONE | {
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Successful compilation of Zeo++ but fail to build the python bindings , the return error is ''command 'gcc' failed with exit status 1'', I am not sure whether it is the problem for the gcc or something else. I successfully do it only once in a cluster but failed in my Macbook (Macos.10.15.2) and o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1748 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1748/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1748/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1748/events | https://github.com/materialsproject/pymatgen/pull/1748 | 556,341,253 | MDExOlB1bGxSZXF1ZXN0MzY4MTIzNTY2 | 1,748 | XYZ reader | {
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} | I just change two characters in the regex used to read XYZ files in order to allow more flexibility (again).
For example, I got some files such as:
```
32
C32-C2-1
C 2.70450 1.16090 -0.14630 1 3 23 2
C 1.6193... | {
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"thanks @rkingsbury, can you double-check that *all* the potcar hash in the .json file I provided way back are now included in this? because that should have been almost complete"
] | 2020-01-28T18:00:11 | 2020-01-29T01:03:28 | 2020-01-29T01:03:28Z | CONTRIBUTOR | {
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Hashes have been recomputed using the complete set of POTCARs distributed with VASP 5.4.4 on Cori. | {
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"[[*site.coords, site.specie.symbol, site.specie.oxi_state] for site in structure]\r\n\r\nI don’t think there is a need to use the as_dict method.",
"I had tried this I believe but I didn't want the 'sites' for partial occupancies I wanted a raw list of atoms which I struggled to achieve without hacky list compr... | 2020-01-29T05:05:01 | 2020-01-29T23:32:55 | 2020-01-29T22:55:52Z | NONE | {
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} | In order to get a raw point cloud from a pymatgen structure I've found I've had to use the as dict method and list comprehensions which is computationally expensive, a quick command to extract a 2d list of every species in the from [x,y,z,element, oxidation,occupancy] or something similar would be invaluable for geomet... | {
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"@mkhorton ",
"Discussing this in the lab, thanks -- @rkingsbury will be implementing a further update to this",
"Good catch @bjmorgan , thank you for reporting!"
] | 2020-01-30T11:11:22 | 2020-02-02T21:57:54 | 2020-02-02T21:57:54Z | CONTRIBUTOR | {
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} | The `validate_poscar` function [https://github.com/materialsproject/pymatgen/blob/4d9bfd9915b818cf61113e9402112c302a958aae/pymatgen/io/vasp/sets.py#L2860](here) contains a `for/else` construction, that looks like it is supposed to be indented differently to give `if/else`:
```python
for psingle in potcar:
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1753 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1753/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1753/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1753/events | https://github.com/materialsproject/pymatgen/pull/1753 | 557,681,060 | MDExOlB1bGxSZXF1ZXN0MzY5MjI4NDk5 | 1,753 | Update OpenBabel; Fix NN classes, graph classes | {
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"Thanks for the quick fix @espottesmith ",
"Once tests pass, will merge",
"Thanks @espottesmith , have made a note of the pandas issue to re-visit once pandas 1.0 has settled down",
"Got a tonne of linter errors on this: https://circleci.com/gh/materialsproject/pymatgen/9592?utm_campaign=vcs-integration-link&... | 2020-01-30T18:45:23 | 2020-01-31T04:31:36 | 2020-01-31T03:38:43Z | CONTRIBUTOR | {
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} | ## Summary
This PR addresses two major issues:
* The recent OpenBabel release 3.0.0 breaks the previous API in several ways, most notably in how the Python interface is imported
* A bug was found in which certain NearNeighbors classes failed to approrpriately detect bonds in molecules
With respect to the seco... | {
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"Thanks"
] | 2020-01-31T17:54:50 | 2020-01-31T18:02:01 | 2020-01-31T18:01:54Z | CONTRIBUTOR | {
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} | ## Summary
Extremely small change - just adds docstrings in pymatgen/analysis/local_env.py | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1755 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1755/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1755/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1755/events | https://github.com/materialsproject/pymatgen/pull/1755 | 558,309,029 | MDExOlB1bGxSZXF1ZXN0MzY5NzIyODI4 | 1,755 | Bugfix for validate_potcar_hashes | {
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"Hi @paulneves77,\r\n\r\nNot all materials have band structures associated with them. If you visit this [materials details page](https://materialsproject.org/materials/mp-756234) you can see there is no band structure supplied, which is why you have the error. The error message could be more useful however! Later i... | 2020-02-02T00:48:40 | 2023-08-10T15:00:33 | 2023-08-10T15:00:06Z | NONE | {
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} | **Description:**
I get an error when calling **get_bandstructure_by_material_id** on material **mp-769885**. I do not know if this error is also present in other materials, nor whether the error is due to the get_bandstructure_by_material_id function or in the material itself. I have been able to use get_bandstructure... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1757 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1757/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1757/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1757/events | https://github.com/materialsproject/pymatgen/pull/1757 | 558,764,000 | MDExOlB1bGxSZXF1ZXN0MzcwMDYwNDI5 | 1,757 | Parse NPLWV, NPLWVs at kpoints from OUTCAR-files into Outcar.data dictionary. | {
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"Pls add a unittest for the new functionality. Thanks.",
"Thanks",
"Hi @stichri, thanks for this PR. Could you fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can acknowledge your contribution appropriately in the [pymatgen documentation](https://pymatgen.org/team.html)? I have been checking our... | 2020-02-02T21:51:03 | 2020-08-05T06:09:53 | 2020-02-03T04:06:02Z | CONTRIBUTOR | {
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} | ## Summary
* Parse NPLWV from OUTCAR file using the read_pattern method of Outcar class
* Parse numbers of plane waves at each kpoint from OUTCAR file using the read_table_pattern method of Outcar class
## Checklist
Before a pull request can be merged, the following items must be checked:
- [x] Code is in ... | {
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"I don't understand why the travis-ci failed here."
] | 2020-02-04T14:57:35 | 2020-02-05T13:04:45 | 2020-02-05T13:04:45Z | CONTRIBUTOR | {
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* Fixed as_dict/from_dict of StructureConnectivity
* Computation of Coordination sequences in connected components. | {
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"Thanks @lbluque !",
"If this is your first contribution to pymatgen, please also fill out our [developer's form](https://forms.gle/JnisFb38QDR8QTFTA) so we can [credit you appropriately](https://pymatgen.org/team.html), thanks!"
] | 2020-02-04T19:03:03 | 2020-02-12T04:11:32 | 2020-02-12T04:08:59Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Allow to use a list/tuple of species as the supercell_size kwarg for StructureMatcher. This allows to use 'sublattices' (for example a anion sublattice in a cathode material) to determine the formula units in a supercell.
Before a pull request ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1760 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1760/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1760/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1760/events | https://github.com/materialsproject/pymatgen/pull/1760 | 561,948,342 | MDExOlB1bGxSZXF1ZXN0MzcyNjYzNDA4 | 1,760 | Revise POTCAR hash checking | {
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"@mkhorton the only test failure left arises in `MPNonSCFSet`. Can you please inspect this error and help me understand what's happening? \r\n\r\nBecause of the hash checking, whenever we init a `DictSet` or derived class we now loop through each of the potcars. Doing so causes a call to `self.potcar_symbols`, whic... | 2020-02-08T01:24:37 | 2020-02-18T21:26:32 | 2020-02-18T19:32:43Z | CONTRIBUTOR | {
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* md5 hashes of the POTCAR files and the POTCAR data itself (`potcar.hash`) were recomputed against the complete set of freshly-downloaded files distributed with VASP 5.4.4.
* Th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1761 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1761/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1761/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1761/events | https://github.com/materialsproject/pymatgen/issues/1761 | 561,950,409 | MDU6SXNzdWU1NjE5NTA0MDk= | 1,761 | Improve input set warnings | {
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https://github.com/materialsproject/pymatgen/blob/749ee4dacab0698acf60120ac35b5065a4ad1f0a/pymatgen/io/vasp/sets.py#L573
Edit: Actually, the logic seems fine, however still getting the error on an MPStaticSet (eg of Al). | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1762 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1762/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1762/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1762/events | https://github.com/materialsproject/pymatgen/issues/1762 | 562,202,496 | MDU6SXNzdWU1NjIyMDI0OTY= | 1,762 | visualize multiple molecules | {
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"I think your original post already answers the question. I think (1) can be done with nglview and you can make sure all the molecule plots are the same size. (2) Once you have 100 images from (1), you can easily use the Pillow package to stitch images. See https://stackoverflow.com/questions/10657383/stitching-pho... | 2020-02-09T16:29:22 | 2020-02-10T15:12:15 | 2020-02-10T15:12:15Z | NONE | {
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I am trying to visualize multiple molecules to get the sense of the whole dataset. First, I tried [nglview](https://github.com/arose/nglview/issues/864) it works for single-molecule but not work for multiple ones. From this [post](https://github.com/materialsproject/pymatgen/issues/1310) , pymatgen.vis.struc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1763 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1763/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1763/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1763/events | https://github.com/materialsproject/pymatgen/pull/1763 | 562,280,547 | MDExOlB1bGxSZXF1ZXN0MzcyOTA0NTgy | 1,763 | Minor fixes to structure mactcher and volumetric data | {
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"References #1665 "
] | 2020-02-10T01:42:20 | 2020-02-11T15:09:19 | 2020-02-11T15:09:19Z | CONTRIBUTOR | {
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- Allow the fit function in structure matcher to be symmetric
- Updated the from_hdf5 function so that inherited classes can use it more readily.
- Changed the way Chgcar objects are initialized so work with the above change
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https://api.github.com/repos/materialsproject/pymatgen/issues/1764 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1764/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1764/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1764/events | https://github.com/materialsproject/pymatgen/issues/1764 | 562,302,297 | MDU6SXNzdWU1NjIzMDIyOTc= | 1,764 | MaterialsProjectCompatibility method process_entries fails if symmetry determination of any entry fails | {
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"Hmmm interesting. But it is very rare that symmetry detection fails. Typically the worst case scenario is that the structure returns a P1. Failure usually occurs only when you have colliding atoms, in which case the calculation is completely useless....\r\n\r\nDo you have an example where this failure occured on a... | 2020-02-10T03:26:29 | 2020-02-11T14:47:47 | 2020-02-11T14:47:47Z | NONE | {
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from pymatgen.entries.compatibility import MaterialsProjectCompatibility
processed_entries = compat.process_entries(all_entries)
I got exception
`/home/youjin/.local/lib64/python3.6/site-packages/pyma... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1765 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1765/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1765/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1765/events | https://github.com/materialsproject/pymatgen/issues/1765 | 562,314,763 | MDU6SXNzdWU1NjIzMTQ3NjM= | 1,765 | visualization | {
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"Check out StructureVis: https://pymatgen.org/pymatgen.vis.structure_vtk.html"
] | 2020-02-10T04:18:40 | 2020-02-13T02:39:47 | 2020-02-13T02:39:47Z | NONE | {
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Sorry I have to reopen this issue. https://github.com/materialsproject/pymatgen/issues/1762. It turns out that ngl cannot save visualization of a single molecule in python script. (only support Jupiter notebook) So right now I don't even know how to visualize a single molecule (cif file) in a python script.
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1766 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1766/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1766/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1766/events | https://github.com/materialsproject/pymatgen/pull/1766 | 562,767,264 | MDExOlB1bGxSZXF1ZXN0MzczMzAyODI4 | 1,766 | Minor fixes to Zeo++ interface | {
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} | ## Summary
Fixes minor bugs on Zeo++ interface.
* `from_parameters(structure.lattice.parameters)` -> `from_parameters(*structure.lattice.parameters)` (starred)
* `self._mol` does not exist in `pymatgen.io.xyz.XYZ` anymore. Replaced by `self._mols[0]`.
* Test for getting free sphere parameters skipped, as file `... | {
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"I will work on a test.",
"Travis CI is complaining about missing docstrings. Do I need to change this?\r\nThanks.",
"Should I add the docstrings? If so, let me know.",
"Yes pls. Thanks.",
"I think it is ready to be merged.",
"Thanks!"
] | 2020-02-12T10:26:45 | 2020-02-18T19:32:33 | 2020-02-18T19:32:28Z | MEMBER | {
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} | ## Summary
I am commiting two very small bug fixes. One allows to open gzipped ICOHPLIST.lobster files. The other one closes the plt after saving a plot with a phonon dos with the PhononDosPlotter. This is done similar to "save_plot" in PhononBSPlotter.
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"Thanks!\r\n\r\nYes, I think they're unrelated -- I was trying to track those down too but the noisy tests were making it difficult, so thanks for fixing :-)"
] | 2020-02-18T03:55:52 | 2020-02-18T04:46:41 | 2020-02-18T04:46:41Z | CONTRIBUTOR | {
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@mkhorton I think this should fix the noisy py3test issue on CircleCi, as I didn't see the previous messages from my tests flooding CircleCi anymore, but I did see some errors in things like test_molecule_matcher.py, though I don't think ... | {
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Adaptor for critic2 analysis code, deprecating the old parsing method (from stdout) and adding a new method to parse from JSON.
Have a few changes before merging. | {
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"Thanks @ayushsgupta, this looks like a good start but there's a lot of items that will need to be addressed:\r\n\r\n* you should move the unit registry out of the root pymatgen init, this should live in pymatgen.core.units\r\n\r\n* this will be *much* easier to merge if it's two separate pull requests: the first p... | 2020-02-20T19:01:18 | 2020-12-01T16:34:42 | 2020-12-01T16:34:42Z | CONTRIBUTOR | {
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} | The goal of this project is to replace the current pymatgen unit system with that of pint, which will allow for more comprehensive and robust unit handling
* Replace all instances of FloatWithUnit with the Quantity class from pint
* Calculations in pymatgen use Quantity.magnitude
* TODO: Lots of tests still fail, ... | {
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"Forget about it. The default eigenvalue tolerance is just too low for something like this. I have:\r\n\r\n```\r\nDEBUG:pymatgen.symmetry.analyzer:Spherical top molecule detected\r\nDEBUG:pymatgen.symmetry.analyzer:Accidental speherical top!\r\nDEBUG:pymatgen.symmetry.analyzer:Eigenvalues = [0.66670374 0.66659252 0... | 2020-02-21T15:27:05 | 2023-08-13T16:32:57 | 2023-08-13T16:32:57Z | NONE | {
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} | **Describe the bug**
pymatgen 2020.1.28 fails to identify proper point group with pymatgen.symmetry.analyzer.PointGroupAnalyzer
**To Reproduce**
1. Create a file called `Cluster_H.xyz` with this content: https://gist.github.com/fxcoudert/def477b148e95b8cad61804e26e89271
2. Run the following code:
```
import... | {
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* Added wrappers to the c memory allocation functions malloc and realloc. In the case memory allocation failure, the cython code will raise MemoryError instead of relying on c behavior.
* Reduced the theoretical amortized time by doubling the neighbor size everytime maximum number is hit. Previously a co... | {
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"Hi @misterblonde, can you be more specific about what you mean by \"extract the single molecule in the asymmetric unit of a .cif file\"?\r\n\r\n> the entire function is not documented anywhere.\r\n\r\nFunctions with leading underscores in Python are considered \"private\" so may not contain docstrings. They're th... | 2020-02-24T20:43:00 | 2023-08-13T16:32:57 | 2023-08-13T16:32:57Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
I'm always frustrated when I try to use Pymatgen to extract the single molecule in the asymmetric unit of a .cif file. I hope that _unique_coords() inside cif.py would offer this functionality, but I don't seem to get this to work? I only have sites b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1775 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1775/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1775/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1775/events | https://github.com/materialsproject/pymatgen/pull/1775 | 571,025,360 | MDExOlB1bGxSZXF1ZXN0Mzc5OTcyNDUz | 1,775 | Add functions to generate phonon DOS & BS from force constants | {
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"Failing tests are unrelated to this PR.",
"This should be ready to merge now.",
"Thanks @utf, planning to push a release later today"
] | 2020-02-26T02:26:37 | 2020-02-28T20:47:08 | 2020-02-28T20:47:08Z | MEMBER | {
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} | ## Summary
Added methods for generating `CompletePhononDos`, `PhononBandStructure`, and `PhononBandStructureSymmLine` directly from phonopy force constants.
This complements existing methods for generating these objects from text files.
Tests have been added.
## Checklist
Before a pull request can be mer... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1776 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1776/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1776/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1776/events | https://github.com/materialsproject/pymatgen/pull/1776 | 571,032,648 | MDExOlB1bGxSZXF1ZXN0Mzc5OTc4Mjg5 | 1,776 | Add MonteCarloRattleTransformation and general refactoring | {
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"The remaining mypy errors don't seem particularly reasonable.\r\n\r\n~~EDIT: WIP while I fix a potential bug.~~",
"This should also be ready to merge now.",
"Thanks!\r\n"
] | 2020-02-26T02:51:19 | 2020-02-28T21:25:38 | 2020-02-28T21:25:33Z | MEMBER | {
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} | ## Summary
This pull request introduces a number of miscellaneous features as part of an atomate workflow to calculate lattice thermal conductivity.
- Added MonteCarloRattleTransformation. Uses the hiPhive package to displace atomic sites according to a Monte Carlo routine which punishes small bond distances. I'v... | {
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"Thanks!"
] | 2020-02-26T08:31:50 | 2020-02-26T15:19:18 | 2020-02-26T15:09:20Z | CONTRIBUTOR | {
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* Bugfix for StructureVis.add_structure: New `get_neighbors` returns PeriodicNeighbor object. | {
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"Same issue currently."
] | 2020-02-26T17:01:25 | 2024-09-13T02:30:50 | 2023-08-13T16:33:40Z | NONE | {
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} | I got following error in reading PROCAR file. Could you please suggest me, how should I deal with this problem?
C:\ProgramData\Anaconda3\envs\Pymatgen\lib\site-packages\pymatgen\io\vasp\outputs.py in __init__(self, filename)
3477 for orb in range(len(headers)):
3478 ... | {
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"Thanks!"
] | 2020-02-28T00:38:54 | 2020-03-09T19:20:43 | 2020-03-09T19:20:43Z | CONTRIBUTOR | {
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} | run mcsqs in scratch dir to deal with multiple files better
## Summary
Include a summary of major changes in bullet points:
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
s... | {
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"Thanks @ayushsgupta ! I'll just add some additional context, as I think this has value to pymatgen users regardless of what we decide about the units.\r\n\r\nIn addition to facilitating the units implementation, this PR was also partly motivated by my experience learning pymatgen as a new user over the last year.... | 2020-03-01T19:41:57 | 2020-06-22T22:01:02 | 2020-03-03T23:18:29Z | CONTRIBUTOR | {
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} | * Creates a new Entry class from which ComputedEntry and PDEntry now inherit
* If some form of pull request #1771 (units with pint) is implemented, this will simplify the integration of units into pymatgen
* In general, will make pymatgen easier to maintain by reducing redundancy in the various entry classes
![exis... | {
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"Thanks!",
"That was quick. Glad you approve.\n\n\t\t\t\t\t\tNoam\n",
"Hi @bernstei, thanks for this PR. Could you fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can properly acknowledge you in the [pymatgen documentation](https://pymatgen.org/team.html)? I have been checking our acknowledgment... | 2020-03-02T19:59:31 | 2020-08-05T06:47:52 | 2020-03-03T14:08:01Z | CONTRIBUTOR | {
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} | ## Summary
Extend `pymatgen.io.vasp.outputs.Wavecar` to read from gamma-point only executable.
* New bool gamma argument for `Wavecar.__init__()`, otherwise tries to guess from file contents.
* Test comparing H2 WAVECARs from regular and gamma-point only executables
## Additional dependencies introduced (if a... | {
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"Am I supposed to fix those docstring??? ",
"The shengbte, structure_vtk and advanced_transformations are the responsibility of other contributors. Any other errors you would have to correct, this is the result of stricter checking for docstrings on commit (if you touch a file that has bad docstrings, it will fla... | 2020-03-03T00:21:10 | 2020-03-03T14:07:04 | 2020-03-03T14:06:54Z | CONTRIBUTOR | {
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} | ## Summary
*The box size values in the CombinedData object is now automatically updated by the min/max values of the coordinates.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1783 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1783/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1783/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1783/events | https://github.com/materialsproject/pymatgen/issues/1783 | 574,694,855 | MDU6SXNzdWU1NzQ2OTQ4NTU= | 1,783 | Error in calculating Pourbaix diagram | {
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"As people who have touched Pourbaix and reaction calculator, I'm tagging @montoyjh and @mattmcdermott for ideas.",
"Wow that's a big problem! When this is solved, I suggest adding a unittest\nfor the Pourbaix diagram for the Bi/V system, so that if something breaks\nelsewhere in Pymatgen, this is caught at the u... | 2020-03-03T14:10:06 | 2020-04-10T00:01:45 | 2020-04-10T00:01:44Z | NONE | {
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} | **Describe the bug**
The calculated Pourbaix diagram is wrong with pymatgen of version later than 2019.12.3.
**To Reproduce**
Steps to reproduce the behavior:
from pymatgen import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
%matplotlib inline
mpr = MPRester()
entr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1784 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1784/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1784/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1784/events | https://github.com/materialsproject/pymatgen/issues/1784 | 574,749,109 | MDU6SXNzdWU1NzQ3NDkxMDk= | 1,784 | Structure.to(fmt='cif') Precision Issues | {
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"Can you clarify what you mean by \"CIF writer has no precision\"?\r\n\r\nIf you want to increase the number of decimal places we print in the CIF we can do that.",
"Perhaps he refers to the default format used to write floats when structure.to() is invoked.\r\n\r\nIndeed, there's no option to specify the number ... | 2020-03-03T15:29:38 | 2020-03-04T13:57:16 | 2020-03-04T12:35:21Z | NONE | {
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} | **It makes it difficult to reproduce bugs or get a good nearest neighbour precision when the CIF writer has no precision**
CIF writer seems to have no precision for output, can give some errors in calculations if a certain precision is needed.
**Add the number of decimals or precision to output when saving a file a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1785 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1785/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1785/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1785/events | https://github.com/materialsproject/pymatgen/pull/1785 | 575,638,929 | MDExOlB1bGxSZXF1ZXN0MzgzNzU5MDAz | 1,785 | Pourbaix fix | {
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"Thanks!\r\n"
] | 2020-03-04T18:13:49 | 2020-03-04T19:59:24 | 2020-03-04T19:59:19Z | CONTRIBUTOR | {
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} | ## Fix to two bugs in Pourbaix Diagram code
* Fixes issue where Pourbaix diagram was considering MultiEntries where reaction calculator finds a balanced reaction with no product.
* Fixes issue with MPRester PourbaixEntry processing due to Entry refactor. Specifically, `_energy`/`uncorrected_energy` mix-up.
## T... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1786 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1786/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1786/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1786/events | https://github.com/materialsproject/pymatgen/pull/1786 | 575,780,239 | MDExOlB1bGxSZXF1ZXN0MzgzODg0MzI1 | 1,786 | [WIP] Heisenberg | {
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"Thanks. But can you resolve the branch conflicts first? Pls merge the latest pymatgen master to your fork.",
"Thanks @ncfrey !"
] | 2020-03-04T21:15:48 | 2020-03-10T23:27:25 | 2020-03-10T23:27:19Z | CONTRIBUTOR | {
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} | ## Summary
@mkhorton
* Added option to use an effective <J> exchange parameter from lowest energy FM and AFM configurations.
* Fixes to MSONable object handling.
## TODO
* Additional methods for obtaining exchange parameters.
* Options to fix magnetic moment magnitudes.
* Add type hints | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1787 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1787/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1787/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1787/events | https://github.com/materialsproject/pymatgen/issues/1787 | 577,275,146 | MDU6SXNzdWU1NzcyNzUxNDY= | 1,787 | POTCAR with symbol Si has metadata that does not match any VASP POTCAR known to pymatgen. | {
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"Hi @hongyi-zhao, it’s just a warning. If you’re comfortable you’re using the correct POTCAR you can ignore it.\r\n\r\nIt’s basically saying that the functional is compatible with those distributed as PBE_52/54 by VASP, but a specific variation we haven’t encountered before. This doesn’t mean it’s wrong.\r\n\r\n(Fl... | 2020-03-07T04:20:59 | 2023-06-20T16:30:28 | 2023-06-20T16:30:28Z | CONTRIBUTOR | {
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} | Hi,
I try to run the examples here:
https://ma.issp.u-tokyo.ac.jp/en/app-post/1146
With the following code to generate the band-structure plot:
```
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
vaspout = Vasprun("./vasprun.xml")
bandstr = vasp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1788 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1788/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1788/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1788/events | https://github.com/materialsproject/pymatgen/issues/1788 | 577,336,633 | MDU6SXNzdWU1NzczMzY2MzM= | 1,788 | Need fix for the enumlib's repo url. | {
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"Done. Thanks.",
"But when I opened the website https://pymatgen.org/installation.html, it still shows the wrong url I reported here.\r\n\r\nRegards",
"Sometimes it takes a while to update on the website after a change has been made due to the content delivery networks that GitHub Pages uses (which is where pym... | 2020-03-07T13:43:02 | 2020-03-09T13:49:11 | 2020-03-07T16:08:37Z | CONTRIBUTOR | {
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The following webpage: https://pymatgen.org/installation.html, says that:
```
2. enum:
Get it at http://enum.sourceforge.net and follow the instructions to compile multienum.x and makestr.x.
```
But this project has moved to github in 2015 as noted on the above website:
`(We have migrated this proj... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1789 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1789/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1789/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1789/events | https://github.com/materialsproject/pymatgen/issues/1789 | 577,372,471 | MDU6SXNzdWU1NzczNzI0NzE= | 1,789 | Space group symmetry operator issues | {
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"Hi @pietakio,\r\n\r\nWhen building structure from space groups you have to be very careful with the precision of your inputs. Have you tried:\r\n\r\n`siha_atom_coords = [[1/3, 2/3, 0.00195], ...`\r\n\r\ninstead?\r\n\r\nWhen this happens, it's usually because 0.33333 != 1/3 from the point of view of applying a symm... | 2020-03-07T17:23:54 | 2020-03-08T22:10:58 | 2020-03-08T16:03:59Z | NONE | {
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Thank you for making Pymatgen -- it's a fabulously helpful and awesome program.
I've encountered two major issues when working with generation of Structures using Structure.from_spacegroup().
**First case**
In the first case (for space group 'P6_3/m', with equivalent results using the space group numb... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1790 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1790/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1790/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1790/events | https://github.com/materialsproject/pymatgen/issues/1790 | 577,419,153 | MDU6SXNzdWU1Nzc0MTkxNTM= | 1,790 | site_matching_indices in KumagaiCorrection | {
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} | I am trying to use KumagaiCorrection from pymatgen.analysis.defects.corrections.
As I did not find any tutorial or examples available, I am trying to reproduce a KumagaiCorrection using the test cases in the unittest. Basically it is the function test_kumagai [here](https://github.com/materialsproject/pymatgen/blob/8... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1791 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1791/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1791/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1791/events | https://github.com/materialsproject/pymatgen/issues/1791 | 577,422,522 | MDU6SXNzdWU1Nzc0MjI1MjI= | 1,791 | The list of vasp's INCAR tags supported by pymatgen currently. | {
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"You can use any VASP INCAR tag via pymatgen using `user_incar_settings`. ",
"I mean whether the pymatgen has already built-in usage instructions for all of these tags. The tag list is huge to some extent, so have the build-in usage instructions for them may be more useful for writing the job scripts with the he... | 2020-03-08T00:30:43 | 2020-03-10T00:12:23 | 2020-03-09T14:43:45Z | CONTRIBUTOR | {
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} | Hi,
The complete list of vasp INCAR tags is here:
https://www.vasp.at/wiki/index.php/Category:INCAR
I want to know which of them supported by pymatgen currently?
Regards | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1792 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1792/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1792/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1792/events | https://github.com/materialsproject/pymatgen/issues/1792 | 577,499,891 | MDU6SXNzdWU1Nzc0OTk4OTE= | 1,792 | Abouth the kpath determining method used in pymatgen. | {
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"You're welcome to use SeeK if you want, they distribute their algorithm as a Python code too. We will not be changing the default algorithm at this time, but stay tuned for an update from MP on this later in the year.",
"Matthew Horton <notifications@github.com> 于2020年3月9日周一 上午9:34写道：\r\n\r\n> You're welcome to... | 2020-03-08T13:20:21 | 2020-03-09T02:58:01 | 2020-03-09T01:32:05Z | CONTRIBUTOR | {
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} | Hi,
I noted that the HighSymmKpath class is implemented based on the paper:
http://dx.doi.org/10.1016/j.commatsci.2010.05.010
While there is another well know paper for dealing with this type of job, it's:
http://dx.doi.org/10.1016/j.commatsci.2016.10.015
The latter paper is more recent and exhaustive ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1793 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1793/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1793/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1793/events | https://github.com/materialsproject/pymatgen/pull/1793 | 577,915,280 | MDExOlB1bGxSZXF1ZXN0Mzg1NTkzMDk4 | 1,793 | fix sites's doc (delete duplication) | {
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"Thanks."
] | 2020-03-09T13:37:44 | 2020-03-09T13:40:48 | 2020-03-09T13:40:42Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding one... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1794 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1794/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1794/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1794/events | https://github.com/materialsproject/pymatgen/issues/1794 | 578,262,660 | MDU6SXNzdWU1NzgyNjI2NjA= | 1,794 | Some properties of the Element class not defined with decorate @property. | {
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"The @property is only used if we are using a hidden variable or it is a property that is computed on the fly. In this case, the atomic mass is important enough that we write a special decorator for it. The melting point and boiling point are much less frequently used and so we just leave it to the get_attr functio... | 2020-03-10T00:22:59 | 2020-03-11T13:14:33 | 2020-03-11T13:14:32Z | CONTRIBUTOR | {
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Say for the following code snippets:
```
import pymatgen as mg
fe = mg.Element("Fe")
print(fe.atomic_mass)
print(fe.melting_point)
print(fe.boiling_point)
```
The atomic_mass is defined as a property with decorate @property, but the other two are not. This will cause the property's name cannot be au... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1795 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1795/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1795/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1795/events | https://github.com/materialsproject/pymatgen/issues/1795 | 578,617,834 | MDU6SXNzdWU1Nzg2MTc4MzQ= | 1,795 | Want to make a PR for fixing the installation.rst | {
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"Yes, submitting a PR would be fine. In fact, we prefer small PRs, even when the functionality is big, it is preferable they are broken up into simple chunks.",
"Thanks. Another issue also said on the installation page, see following:\r\n\r\n```\r\n$ pip install pymatgen[extra] \r\nLooking in indexes: https://py... | 2020-03-10T14:24:22 | 2020-03-10T16:01:52 | 2020-03-10T14:29:12Z | CONTRIBUTOR | {
"total": 0,
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} | Hi,
I noted that the following description is outdated here:
https://github.com/materialsproject/pymatgen/blob/master/docs_rst/installation.rst
`3. Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the adapters in pymatgen.io.aseio between pymatgen's core Structure object and the Atoms obje... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1796 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1796/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1796/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1796/events | https://github.com/materialsproject/pymatgen/issues/1796 | 578,677,340 | MDU6SXNzdWU1Nzg2NzczNDA= | 1,796 | Report a bug or issue | {
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"Sorry, but there is a lot happening in your script. Pls report the issue/bug properly with a *short* script that reproduces the problem with a minimum number of lines and inputs. We cannot debug a long script where we do not even know where the bug occurred and whether it is even in a Pymatgen related method or on... | 2020-03-10T15:44:40 | 2020-03-10T15:59:27 | 2020-03-10T15:59:27Z | NONE | {
"total": 0,
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} | **Describe the bug**
I prefer using issue report instead of bug report. I am not fully sure it is a bug. But it shows that the inconsistent results with same input, setting, and environments.
Note: My structure has partial occupation sites.
Pymatgen was updated in February.
I built a small model using PDFgui. A... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1797 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1797/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1797/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1797/events | https://github.com/materialsproject/pymatgen/issues/1797 | 578,745,125 | MDU6SXNzdWU1Nzg3NDUxMjU= | 1,797 | Add angle_tolerance argument to CifWriter constructor | {
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"Please feel welcome to open a pull request if this would be useful!"
] | 2020-03-10T17:28:43 | 2020-03-11T13:05:32 | 2020-03-11T13:05:32Z | CONTRIBUTOR | {
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} | Pymatgen is very useful for quickly converting between file types, e.g., POSCAR <--> cif, but the `CifWriter` constructor is lacking the `angle_tolerance` parameter which means the default `SpaceGroupAnalyzer` value of 5 degrees is used. This value is too large for many applications and should in principle be configura... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1798 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1798/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1798/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1798/events | https://github.com/materialsproject/pymatgen/pull/1798 | 579,002,376 | MDExOlB1bGxSZXF1ZXN0Mzg2NDc3OTA2 | 1,798 | Fix the notes for python version dependent of the ASE package. | {
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] | 2020-03-11T04:29:57 | 2020-03-11T12:14:20 | 2020-03-11T12:14:12Z | CONTRIBUTOR | {
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} | ## Summary
See here for more info:
https://wiki.fysik.dtu.dk/ase/install.html
Which told the following:
Note that the ASE package is compatible with Python 3.5+ at the moment. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1799 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1799/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1799/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1799/events | https://github.com/materialsproject/pymatgen/pull/1799 | 580,132,055 | MDExOlB1bGxSZXF1ZXN0Mzg3NDAxMTUw | 1,799 | Fix QChem API | {
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"Actually, I take back part of my accusation. Privatizing `check_for_structure_changes` was done by @shyuep in efd386bcdbcc5541aa01c3bb4116999ae8924f68",
"The changes made in #1753 at least were at my request -- it fixed a long-standing bug and cleaned up some of our neighbor detection, but it did also therefor... | 2020-03-12T18:19:04 | 2020-03-12T20:18:13 | 2020-03-12T20:13:27Z | MEMBER | {
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} | ## Summary
A recent pull request ~~(#1753)~~ (efd386b) made the `check_for_structure_changes` method private. Unfortunately, custodian relies on this method so this PR broke both custodian and atomate.
Furthermore, #1753 changed the arguments for `MoleculeGraph.with_local_env_strategy` which also broke atomate.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1800 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1800/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1800/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1800/events | https://github.com/materialsproject/pymatgen/pull/1800 | 580,220,450 | MDExOlB1bGxSZXF1ZXN0Mzg3NDcyNzQx | 1,800 | [WIP] New KPath and HighSymmKpath classes | {
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"Just to double-check, have you verified the original class still works as before when SeeK optional dependency is not installed?\r\n\r\nOtherwise this pull request looks essentially good. Since it's a large one, I'll take some more time to read over it, and can merge once all linting/tests pass. Happy to see it fi... | 2020-03-12T21:07:05 | 2020-03-18T01:11:21 | 2020-03-18T01:11:20Z | MEMBER | {
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} | ## Summary
This pull request introduces support for generating high-symmetry k-paths using two additional conventions. Namely, the SeeK-path convention by Hinuma and coworkers [Y. Hinuma, et al. Band structure diagram paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017)], and a new "on-the-fly" convention... | {
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