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https://api.github.com/repos/materialsproject/pymatgen/issues/1401 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1401/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1401/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1401/events | https://github.com/materialsproject/pymatgen/issues/1401 | 413,151,373 | MDU6SXNzdWU0MTMxNTEzNzM= | 1,401 | Unhelpful error message in BabelMolAdaptor | {
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"I found the helpful error message later. :)"
] | 2019-02-21T22:22:10 | 2019-02-21T23:18:51 | 2019-02-21T23:17:49Z | NONE | {
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} | **Describe the bug**
When I use BabelMolAdaptor.from_file() from pymatgen.io.babel, if I don't have OpenBabel installed, I get the following error:
```
312 BabelMolAdaptor object
313 """
--> 314 mols = list(pb.readfile(str(file_format), str(filename)))
315 retur... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1402 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1402/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1402/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1402/events | https://github.com/materialsproject/pymatgen/pull/1402 | 413,625,993 | MDExOlB1bGxSZXF1ZXN0MjU1NTY5ODYz | 1,402 | Fix NearNeighbors._get_image to work properly for sites not in unitcell | {
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"Thanks @lan496 !",
"(p.s. this fixed an unrelated issue I hadn't had chance to track down yet, so thanks again! saved me a lot of time)"
] | 2019-02-23T00:06:46 | 2020-08-14T13:16:42 | 2019-02-23T19:13:39Z | CONTRIBUTOR | {
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} | ## Summary
- fix behavior of `NearNeighbors._get_image` to deal with cases such that initial sites are not in unitcell(fix https://github.com/materialsproject/pymatgen/issues/1321)
An image is defined as displacement from original site in structure to a given site.
For example, if structure has a site at (-0.1, 1.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1403 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1403/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1403/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1403/events | https://github.com/materialsproject/pymatgen/pull/1403 | 414,266,618 | MDExOlB1bGxSZXF1ZXN0MjU2MDE1ODI3 | 1,403 | Various bug fixes (graphs, phase diagram, magnetism) | {
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"Note to self: tests can fail due to `muellergroup.jhu.edu:8080` being offline for `pymatgen.ext.tests.test_jhu.JhuTest`, will try to handle this more gracefully.",
"I suggest adding a pymatgen.util.typing module with the useful type hints like Vector.",
"That said, I would suggest no need to go overboard. Let'... | 2019-02-25T19:25:42 | 2019-02-26T18:14:08 | 2019-02-26T18:14:08Z | MEMBER | {
"total": 0,
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} | ## Summary
Fixes MSONable for PhaseDigram when non-PDEntries used. Fixes graph bug (thanks Jack Sundberg). See individual commit messages for more, includes code reformatting. Will merge once CI passes. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1404 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1404/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1404/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1404/events | https://github.com/materialsproject/pymatgen/issues/1404 | 416,165,260 | MDU6SXNzdWU0MTYxNjUyNjA= | 1,404 | Missing some radii & mistakes in commonness of some oxidation states | {
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"Thanks. I agree the ionic radii tabulation is incomplete. In the first place, only one ionic radius is assigned to each oxidation state. Some of the elements have multiple ionic radius depending on coordination environment, oxidation state as well as high/low spin. The source of the ionic radii is https://www.wiki... | 2019-03-01T15:54:39 | 2019-03-03T02:17:49 | 2019-03-03T02:17:49Z | NONE | {
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} | There are some mistakes in the common oxidation state of some elements and some radii are missing.
When I do the following :
from pymatgen.core.periodic_table import Element
for Elem in Element:
print(Elem)
print(Element(Elem).common_oxidation_states)
print(Element(Elem).ionic_radii)
I have the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1405 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1405/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1405/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1405/events | https://github.com/materialsproject/pymatgen/issues/1405 | 416,907,149 | MDU6SXNzdWU0MTY5MDcxNDk= | 1,405 | Abandoning immutability for Site, PeriodicSite, Structure and Molecule | {
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"I'm on board with this change.\r\n\r\nIn general, I like immutable data structures, and think they lend themselves to better code. However, they're only useful if they are used. I think the majority of pymatgen/MP users (and probably devs) have never used or are not aware of IStructure or IMolecule, people assume ... | 2019-03-04T17:19:17 | 2019-05-23T13:49:26 | 2019-05-23T13:49:26Z | MEMBER | {
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} | Historically, Site and PeriodicSite are considered immutable, as are IStructure and IMolecule. This is due to bad coding in the early days, which ports over the coding styles of Java to Python due to inexperience of @shyuep at that time.
These impositions are artificial, and indeed, have been violated in common prac... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1406 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1406/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1406/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1406/events | https://github.com/materialsproject/pymatgen/issues/1406 | 417,131,758 | MDU6SXNzdWU0MTcxMzE3NTg= | 1,406 | TypeError: invalid file pymatgen/core/periodic_table.json | {
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"Hi there, given that Python is now at 3.7 going to 3.8, v3.5 is rather old. Can you upgrade your Python version and see if it persists? ",
"I had the same problem with python 3.5 on one computer and updated to python 3.7. With python 3.7, it worked fine. ",
"Closing this issue. ",
"@shyuep THX! I will think ... | 2019-03-05T06:01:25 | 2019-03-11T07:21:48 | 2019-03-05T14:31:04Z | NONE | {
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} | **Describe the bug**
import pymatgen in python3.5 will raise ``TypeError: invalid file pymatgen/core/periodic_table.json``
**To Reproduce**
Steps to reproduce the behavior:
1. pip install pymatgen=2019.2.28
2. import pymatgen
3. See error
**Logs**
```
tests/datatools/test_boxcox.py:10: in <module>
fro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1407 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1407/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1407/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1407/events | https://github.com/materialsproject/pymatgen/issues/1407 | 417,168,776 | MDU6SXNzdWU0MTcxNjg3NzY= | 1,407 | Potential bug in `CifParser` | {
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"@sphuber in the example CIF the terminating `;` is missing in the line right after\r\n```\r\n 4 x-1/2,-y-1/2,z-1/2\r\n```\r\nas multiline CIF fields are expected to start and end with `;`.",
"@merkys thanks a lot, I have updated the example",
"Thanks. A fix has been pushed to master.",
"@shyuep thanks a lo... | 2019-03-05T08:11:58 | 2019-03-14T17:07:15 | 2019-03-13T19:04:17Z | NONE | {
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} | **Describe the bug**
Due to the logic in the detection of `CifBlocks` in the content of a CIF, the `CifParser` can fail for certain CIFs with valid structure and syntax
**To Reproduce**
Call `CifParser` on a file with the following content:
```
data_1526655
_journal_name_full
_space_group_IT_number 2... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1408 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1408/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1408/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1408/events | https://github.com/materialsproject/pymatgen/issues/1408 | 417,242,246 | MDU6SXNzdWU0MTcyNDIyNDY= | 1,408 | surface.py and symmetrized slabs / vacuumless slab | {
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"@richardtran415 Pls look into Case 1.\r\n\r\nFor case 2, what you want is not to give a 0 vacuum. You should just simply get the `oriented_unit_cell` property for each slab, which gives the oriented bulk structure. The slabs generator assumes you actually want a slab structure, and so imposes some minimum space.\r... | 2019-03-05T11:05:50 | 2019-03-08T16:01:33 | 2019-03-05T19:33:10Z | NONE | {
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} | 1. SlabGenerator.nonstoichiometric_symmetrized_slab will not make a symmetrized surface of a conventional Silicon unit cell in the [1,0,0] direction. It returns a non symmetrized surface.
2. SlabGenerator() with 0 vacuum should return a crystal oriented in the direction of [h,k,l]?
A clear and concise description... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1409 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1409/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1409/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1409/events | https://github.com/materialsproject/pymatgen/issues/1409 | 417,918,252 | MDU6SXNzdWU0MTc5MTgyNTI= | 1,409 | Structure.get_primitive_structure incredibly memory intensive | {
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"No to (a). I would say you can add an option to select the primitive finder for (b). Structure matching is meant to be symmetry independent. The Structure.get_primitive is also non-symmetry dependent. SpacegroupAnalyzer is symmetry dependent. \r\n\r\nIf you are getting structures from a expt database, by all means... | 2019-03-06T17:15:37 | 2019-03-13T07:51:55 | 2019-03-13T07:51:55Z | MEMBER | {
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} | For certain structures, the `Structure.get_primitive_structure` can be incredibly memory intensive.
For example, for this structure (https://gist.github.com/utf/3982741b90a4fcb500998433e582d031), calling the function uses 20 GB of memory and takes ~2 min. Admittedly this structure has a very large unit cell (~800 a... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1410 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1410/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1410/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1410/events | https://github.com/materialsproject/pymatgen/issues/1410 | 419,567,962 | MDU6SXNzdWU0MTk1Njc5NjI= | 1,410 | Wulffshape for hexagonal lattice | {
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"You do not have enough surface energies to generate a closed Wulff shape. Specifically, none of your surfaces contain the (001) direction. "
] | 2019-03-11T16:35:42 | 2019-03-13T07:54:03 | 2019-03-13T07:54:03Z | NONE | {
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} | **Describe the bug**
When I try to construct a Wulff shape for a hexagonal lattice Qhull generates the error
QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point
**To Reproduce**
Steps to reproduce the behavior:
Execute the following commands with python 3.6.7
fro... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1411 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1411/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1411/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1411/events | https://github.com/materialsproject/pymatgen/issues/1411 | 420,169,429 | MDU6SXNzdWU0MjAxNjk0Mjk= | 1,411 | Outcar class reads in elements for ZVAL dictionary non-robustly | {
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"This is not a bad idea, would be interested in implementing the change?",
"Not at this time. I expect to be very busy for the next while. Someone else\ncould almost certainly have it implemented before I would get around to it.\n\nOn Tue, Mar 12, 2019, 4:09 PM Matthew Horton <notifications@github.com>\nwrote:\n\... | 2019-03-12T19:36:16 | 2021-05-13T18:10:07 | 2021-05-13T18:10:07Z | NONE | {
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} | Hello,
The Outcar class in pymatgen.io.vasp reads in the atomic species by searching for the name of the POSCAR file in the OUTCAR. This is not required to have anything to do with the atomic species for VASP calculations and can cause errors importing OUTCARs made from POSCARS that were not produced with pymatgen. ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1412 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1412/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1412/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1412/events | https://github.com/materialsproject/pymatgen/pull/1412 | 420,171,115 | MDExOlB1bGxSZXF1ZXN0MjYwNTA5NDA4 | 1,412 | Fix Python 3.5 compatibility | {
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"Thanks. Though people should start moving to py36/37....",
"Btw: You are at TMS right? ",
"I was. Had to leave on Monday as I have to teach. "
] | 2019-03-12T19:40:42 | 2019-03-12T20:04:23 | 2019-03-12T19:41:15Z | CONTRIBUTOR | {
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"In terms of backwards incompatibility, the most important thing is that v2019.x onwards is Python 3 only, which was announced both in the docs and in the mailing list.\r\n\r\nGenerally, I think pymatgen has been fairly good about backwards compatibility and deprecations. Have you noticed specific breaking changes ... | 2019-03-12T21:30:17 | 2023-06-23T23:55:26 | 2023-06-23T22:38:27Z | MEMBER | {
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} | #213 clarified that backwards-incompatible changes used to be signaled with the bumping of the so-called minor version, e.g. someone upgrading pymatgen 3.3.x to 3.4.y should expect the possibility of breaking changes and should consult the [change log](http://pymatgen.org/change_log.html). However, since `v2017.6.8`, p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1414 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1414/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1414/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1414/events | https://github.com/materialsproject/pymatgen/pull/1414 | 420,233,323 | MDExOlB1bGxSZXF1ZXN0MjYwNTU5MzQ3 | 1,414 | [WIP] Add user-agent header to MPRester session requests | {
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"Excellent idea!",
"Do you think it might be useful to add Python version also? It might also be a good idea to mention this in the docstring to ensure that users are appropriately informed that this information is being shared.",
"I'm on the fence for this from a user privacy perspective. In favor, I think thi... | 2019-03-12T22:26:15 | 2021-02-13T17:25:20 | 2019-03-27T23:43:30Z | MEMBER | {
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} | Add a user-agent header of [conventional syntax](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/User-Agent) to identify pymatgen and its version to the MP server.
* Allows server, if it is running a later version of pymatgen than the user, to suggest upgrading (e.g. through adding a note in the response "... | {
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"I can certainly fix this problem, but as far as I know, this is bad CIF syntax. The ; is used as an indicator of a multiline string. Here, you have ; with `_iucr_refine_fcf_details`, which is not closed until after the data_symmetries loop.",
"@shyuep you are absolutely right, my mistake. I updated the example t... | 2019-03-14T17:12:33 | 2019-03-15T15:53:11 | 2019-03-15T15:32:59Z | NONE | {
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} | **Describe the bug**
A bug in the `CifParser.from_string` method was reported in #1407 which was addressed in [this commit](https://github.com/materialsproject/pymatgen/commit/c34a6c0b69a6654bc6b8e9164341d5b8d6769e18). However, the solution does not actually solve the problem because now the `get_structures` method wi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1416 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1416/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1416/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1416/events | https://github.com/materialsproject/pymatgen/issues/1416 | 421,432,947 | MDU6SXNzdWU0MjE0MzI5NDc= | 1,416 | bug in work function plot | {
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"@richardtran415 Pls check and follow-up",
"What's more, the model I used is a surface slab model.",
"Looking into it"
] | 2019-03-15T09:45:27 | 2019-05-23T13:48:20 | 2019-05-23T13:48:20Z | NONE | {
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} | **Describe the bug**
if the slab contain any atom with very big frac_z (e.g. z = 0.99 which is supposed to be -0.01 due to the perodicity), the ave_bulk_p will be wrongly calculated because the the frac_z is not a right limitation of the bulk region.
**Expected behavior**
I think during the initiation, any site wi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1417 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1417/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1417/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1417/events | https://github.com/materialsproject/pymatgen/pull/1417 | 421,732,641 | MDExOlB1bGxSZXF1ZXN0MjYxNzIxMzU3 | 1,417 | [WIP] Piezo Sensitivity and Site symmetries packages added | {
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"Thanks for the contributions. Yes, you can add this to pymatgen.analysis. However, I would ask that you document the methods. Site symmetries should be put in the pymatgen.symmetry.analyzer module.",
"Are the site symmetry routines not uses in the PIezo sensitivity analysis?\r\n\r\nThings to do:\r\n- Write a Bor... | 2019-03-15T22:56:08 | 2019-05-09T16:04:30 | 2019-05-09T02:34:48Z | CONTRIBUTOR | {
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## Summary
Added piezo_sensitivity and site_symmetry packages under analysis. Site_symmetries allow for users to get the point symmetries of atomic sites and symmetry operations relating sites. Piezo sensitivity allows for random generation of piezoelectric components and the calculation of the piezoelectric ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1418 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1418/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1418/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1418/events | https://github.com/materialsproject/pymatgen/issues/1418 | 421,914,148 | MDU6SXNzdWU0MjE5MTQxNDg= | 1,418 | I cant use the rotation function in the structure lib | {
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"`rotate_sites` is a function that is part of the Structure class, not the structure module.\r\nIn your code, use `structure1.rotate_sites`. The indices should be numbers.\r\nPls post such question at https://pymatgen.discourse.group in future. Github Issues is meant for bug reports and feature requests. "
] | 2019-03-17T12:03:36 | 2019-03-17T14:52:09 | 2019-03-17T14:52:09Z | CONTRIBUTOR | {
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Is there something wrong with my codes? | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1419 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1419/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1419/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1419/events | https://github.com/materialsproject/pymatgen/pull/1419 | 422,423,703 | MDExOlB1bGxSZXF1ZXN0MjYyMjE3OTI0 | 1,419 | Update to make new builder work | {
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"Thanks @jmmshn will merge once tests pass",
"There are some test errors related to the PR, `ERROR: test_as_dict_summary (pymatgen.apps.battery.tests.test_insertion_battery.InsertionElectrodeTest)`",
"oops, I forgot to check that before submitting",
"The checks all passed this time, I didn't account for the ... | 2019-03-18T20:39:04 | 2019-03-20T21:08:47 | 2019-03-20T21:08:47Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1420 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1420/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1420/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1420/events | https://github.com/materialsproject/pymatgen/pull/1420 | 422,645,496 | MDExOlB1bGxSZXF1ZXN0MjYyMzg4ODg2 | 1,420 | Some bug fixes and binary van Arkel-Ketelaar triangle | {
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} | ## Summary
Some fixes to the periodic boundary condition for plotting work function, new method for getting a primitive oriented unit cell, added binary van Arkel-Ketelaar triangle, temporary fix to ReconstructionGenerator tests, also new function to determine slab layer regions in a slab cell when the slab layer is... | {
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Updated the development script of ChemEnv to be compatible with Python 3.x | {
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"Thanks for the contribution. However, please provide a unittest with an example input file of how this will be used. Thanks.",
"Hi @shyuep ,\r\n\r\nI guess I added a simple unittest in the test_outputs.py.\r\nCould you please check if its good enough?\r\n\r\nThanks\r\n",
"Thanks!"
] | 2019-03-20T15:04:58 | 2019-03-21T14:39:15 | 2019-03-21T14:39:10Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1423 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1423/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1423/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1423/events | https://github.com/materialsproject/pymatgen/pull/1423 | 423,737,747 | MDExOlB1bGxSZXF1ZXN0MjYzMjQxODg3 | 1,423 | New methods for COHP classes | {
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} | ## Summary
Included a method which allows to get a summed orbital-resolved cohp and a method to assess whether there are antibonding contributions in a cohp below or at the Fermi level. I also included tests.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1424 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1424/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1424/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1424/events | https://github.com/materialsproject/pymatgen/issues/1424 | 424,168,623 | MDU6SXNzdWU0MjQxNjg2MjM= | 1,424 | Harmful standardize=True in MPNonSCF/MPStatic.from_prev_calc() | {
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"There are reasons why standardization is sometimes necessary.\r\nWhat I would suggest instead is that if standardize is True, the CHGCAR copy is not allowed and a warning is raised.",
"Yes, I think a warning is mandatory there.\r\nI am curious to know at least one case where is necessary to standardize at that p... | 2019-03-22T11:40:32 | 2019-04-01T14:27:35 | 2019-04-01T14:27:07Z | CONTRIBUTOR | {
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} | MPNonSCF/MPStatic.from_prev_calc(standardize=True) leads to have a CHGCAR from previous calculation and POSCAR with a NEW structure that does not match anymore with
the charge. This brings for example to a band structure completely wrong.
I think that the standardization of a structure should not be allowed in this... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1425 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1425/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1425/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1425/events | https://github.com/materialsproject/pymatgen/issues/1425 | 424,314,854 | MDU6SXNzdWU0MjQzMTQ4NTQ= | 1,425 | Pymatgen Slabs Not Json Serializable from .as_dict() | {
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"Generally, serialization is done using the MontyEncoder and MOntyDecoder. If you use that, the numpy array is automatically converted to a serializable form. The easiest way is to simply use the loadfn or dumpfn functions in monty.serialization.\r\n\r\n```python\r\nfrom monty.serialization import loadfn, dumpfn\r\... | 2019-03-22T17:14:01 | 2019-03-27T16:36:11 | 2019-03-22T17:15:53Z | NONE | {
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} | Currently pymatgen Structure objects are Json serializable from the `.as_dict()` but Slab objects are not Json serializable because the `scale_factor` variable is a numpy array.
This can be easily fixed by modifying the `as_dict` function to return it as a list like this:
d["scale_factor"] = self.scale_fa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1426 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1426/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1426/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1426/events | https://github.com/materialsproject/pymatgen/pull/1426 | 424,381,429 | MDExOlB1bGxSZXF1ZXN0MjYzNzQ3NzU0 | 1,426 | Propagate site properties to orthogonal slab | {
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"CAn we have unittests pls? Thanks.",
"Unit tests added! :D"
] | 2019-03-22T20:11:30 | 2019-04-06T13:04:33 | 2019-04-06T13:04:33Z | CONTRIBUTOR | {
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} | ## Summary
Previously site properties in slabs were not passed to the new slab when getting an orthogonal c slab.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1427 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1427/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1427/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1427/events | https://github.com/materialsproject/pymatgen/pull/1427 | 425,613,613 | MDExOlB1bGxSZXF1ZXN0MjY0NjY3NTU0 | 1,427 | Allow user kpoints in NSCF calculations | {
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"Need unittests.",
"The tests failed.",
"THanks."
] | 2019-03-26T19:41:50 | 2019-03-26T22:09:03 | 2019-03-26T22:08:56Z | CONTRIBUTOR | {
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} | ## Summary
Users were not able to supply their own kpoints settings in NSCF calculations. This pull request allows for a Kpoints object to override the Kpoints object generated by default by pymatgen.
This was an issue raised in atomate (https://github.com/hackingmaterials/atomate/issues/278) | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1428 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1428/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1428/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1428/events | https://github.com/materialsproject/pymatgen/pull/1428 | 426,162,634 | MDExOlB1bGxSZXF1ZXN0MjY1MDg0NDQ0 | 1,428 | Add MagneticStructureEnumerator (moved from atomate) | {
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} | Used to generate list of magnetic orderings from an input structure and MagOrderingTransformation by trying different enumeration strategies (eg antiferromagnetic, ferrimagnetic, afm/ferrimagnetic on different sub lattices, etc.)
Old code, moved from atomate. Works + tested, but subject to future improvements. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1429 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1429/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1429/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1429/events | https://github.com/materialsproject/pymatgen/pull/1429 | 426,227,230 | MDExOlB1bGxSZXF1ZXN0MjY1MTM2NTc3 | 1,429 | Implement new OrderDisorderElementComparator | {
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"Thanks @utf! Will review and merge once tests pass",
"Can you think of any reason where the old behavior would be desirable? (I can't, just curious if this is an explicit bug or if there was a use case I wasn't considering)",
"I couldn't think of any scenarios where you'd want the old behavior. I think it is j... | 2019-03-27T23:30:09 | 2019-03-29T18:46:54 | 2019-03-28T00:06:55Z | MEMBER | {
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} | ## Summary
The current OrderDisorderElementComparator will match in unexpected cases. E.g.,
1. A structure with the fractional composition Sn0.2 O0.8 will match a structure with the composition Sn0.5 O0.5.
2. A structure with a 50:50 Sn:Pb site would match with a structure with a 50:50 Sn:O site.
This PR fixe... | {
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"Do you have a suggested fix, would considering lattice points up to 2 unit cells away fix the edge cases?",
"I don't think it would cover _every_ case. In this example, the highlighted atom pair is three unit cells apart.\r\n\r\n![stupid-cell](https://user-images.githubusercontent.com/2511383/56023684-56441480-5... | 2019-03-28T13:11:26 | 2023-08-10T14:59:05 | 2023-08-10T14:59:04Z | CONTRIBUTOR | {
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} | **Describe the bug**
The implementation of the Wigner-Seitz cell builder only considers lattice points up to one unit cell away
```python
for i, j, k in itertools.product([-1, 0, 1], [-1, 0, 1], [-1, 0, 1]):
list_k_points.append(i * vec1 + j * vec2 + k * vec3)
```
but this does not cover all p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1431 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1431/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1431/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1431/events | https://github.com/materialsproject/pymatgen/issues/1431 | 427,570,904 | MDU6SXNzdWU0Mjc1NzA5MDQ= | 1,431 | io.phonopy.get_displaced_structures() calls for non-existent method | {
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"@mkhorton Can you look into this one",
"I’ll take a look. Phonopy changed a lot of their API recently, broke some workflows in atomate too.",
"Yeah, we're pinned to a pre-v2 version of phonopy, I'll update + see what else is broken. Looks like there also isn't a unit test with `yaml_fname` set in `get_displace... | 2019-04-01T08:19:03 | 2019-04-12T04:34:03 | 2019-04-12T04:34:02Z | NONE | {
"total": 0,
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} | **Describe the bug**
In the method _pymatgen.io.phonopy.get_displaced_structures()_,
the call to _phonon.get_displacement_directions()_ raises an error.
**To Reproduce**
Steps to reproduce the behavior:
**1**. import pymatgen.io.phonopy as pmg_phonopy
from pymatgen.core import Structure
**2** . s=Structure... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1432 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1432/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1432/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1432/events | https://github.com/materialsproject/pymatgen/issues/1432 | 427,712,672 | MDU6SXNzdWU0Mjc3MTI2NzI= | 1,432 | pymatgen.io.aiida broken with aiida_core >= 1.0 | {
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"I would say this depends entirely on the aiida developers. I would be fine with just deprecating this function and raising an error and pointing to the aiida package. Because there are no unittests written for pymatgen.io.aiida, we have no way of testing the functionality at all.\r\n\r\nI will just completely depr... | 2019-04-01T13:42:09 | 2019-04-02T07:47:53 | 2019-04-01T14:08:49Z | NONE | {
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} | The [pymatgen.io.aiida](http://pymatgen.org/_modules/pymatgen/io/aiida.html) module is broken in AiiDA core v1.0 and onwards.
This is due to the refactoring of AiiDA which breaks the import line:
https://github.com/materialsproject/pymatgen/blob/5f652417aa3a03214e8dfe726fc9747ed71f13e2/pymatgen/io/aiida.py#L21
Th... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1433 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1433/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1433/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1433/events | https://github.com/materialsproject/pymatgen/pull/1433 | 428,424,921 | MDExOlB1bGxSZXF1ZXN0MjY2Nzk0ODkx | 1,433 | Update LICENSE.rst | {
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} | ## Summary
Change institution for license from LBNL to UC Regents via LBNL | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1434 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1434/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1434/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1434/events | https://github.com/materialsproject/pymatgen/pull/1434 | 428,438,908 | MDExOlB1bGxSZXF1ZXN0MjY2ODA1MTYw | 1,434 | Allow averaging of site_properties when merging sites | {
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} | ## Summary
Added new mode for merge_sites and updated test_merge_sites
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https://api.github.com/repos/materialsproject/pymatgen/issues/1435 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1435/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1435/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1435/events | https://github.com/materialsproject/pymatgen/pull/1435 | 429,880,012 | MDExOlB1bGxSZXF1ZXN0MjY3OTIwNzkx | 1,435 | Hops dev | {
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"Pls check the pymatgen-diffusion package and make sure it is not already implemented there.",
"Even if some parts of it is not implemented there, I would prefer if those portions be integrated there rather than having duplicate code. E.g., I think charge density is not implemented (though our experience is that ... | 2019-04-05T18:22:18 | 2019-04-05T19:53:53 | 2019-04-05T19:53:53Z | CONTRIBUTOR | {
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} | ## Summary
New methods for analyzing the migration path of a material using the following scheme:
1. start with an empty structure and multiple structures with a single cation
2. Map the positions of the relaxed structures back onto the empty host lattice
3. Apply symmetry operations of the empty lattice to o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1436 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1436/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1436/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1436/events | https://github.com/materialsproject/pymatgen/issues/1436 | 430,128,675 | MDU6SXNzdWU0MzAxMjg2NzU= | 1,436 | GulpCaller crashes because cell input string too long | {
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"This workaround makes code above run without problem\r\n```\r\ndef prepare_input(bad_input):\r\n input = ''\r\n for n, line in enumerate(bad_input.split('\\n')):\r\n if n == 2:\r\n input += '{:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f}'.format(*map(float, line.split())) + '\\n'\r\n else... | 2019-04-07T10:31:28 | 2019-05-01T13:05:12 | 2019-05-01T13:05:12Z | NONE | {
"total": 0,
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} | **Describe the bug**
Gulp cannot parse cell if it is too long
**To Reproduce**
Steps to reproduce the behavior:
`from pymatgen.command_line.gulp_caller import GulpCaller, BuckinghamPotential, GulpIO
from pymatgen import Structure
struct = Structure.from_str("""Mg2 Al4 O8
1.0
5.003532 0.000000 2.888790
1.66... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1437 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1437/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1437/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1437/events | https://github.com/materialsproject/pymatgen/issues/1437 | 430,130,654 | MDU6SXNzdWU0MzAxMzA2NTQ= | 1,437 | GulpIO.get_energy cannot get enthalpy (under pressure) | {
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"```\r\ndef get_energy(self, gout):\r\n energy = None\r\n enthalpy = None\r\n for line in gout.split(\"\\n\"):\r\n if \"Total lattice energy\" in line and \"eV\" in line:\r\n energy = line.split()\r\n elif \"Non-primitive unit cell\" in line and \"eV\" in line:\r\n energ... | 2019-04-07T10:56:10 | 2023-08-13T16:32:53 | 2023-08-13T16:32:53Z | NONE | {
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} | **Describe the bug**
If pressure is not zero, gulp prints "Total lattice enthalpy" instead of "Total lattice energy"
and output cannot be parsed by GulpIO().get_energy()
**To Reproduce**
Steps to reproduce the behavior:
Try to read any gulp calculation with pressure
**Expected behavior**
A clear and concise ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1438 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1438/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1438/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1438/events | https://github.com/materialsproject/pymatgen/issues/1438 | 430,794,211 | MDU6SXNzdWU0MzA3OTQyMTE= | 1,438 | New constructor _BaderAnalysis.from_ACF()_ | {
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"Sure. Pls go ahead and implement and submit a pull request. Thanks,",
"Ok :-) ",
"This issue has been outstanding for a number of years. So I am closing it. Feel free to reopen if still valid."
] | 2019-04-09T06:45:29 | 2023-08-10T14:58:05 | 2023-08-10T14:58:05Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
In the module _pymatgen.command_line.bader_caller_
I would like to build an instance of _BaderAnalysis_ from an already calculated Bader data so as to avoid repeating the summation each time I study the run without the need to dump a json.
Consequent... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1439 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1439/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1439/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1439/events | https://github.com/materialsproject/pymatgen/pull/1439 | 430,948,741 | MDExOlB1bGxSZXF1ZXN0MjY4NzIzNjMx | 1,439 | New lobsterout class plus tests | {
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"total": 0,
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} | ## Summary
I included a class to read lobsterout files from Lobster (www.cohp.de). Regarding the design of the class, I am happy to do some adaptions. I have also included several tests to make sure that the files are read in correctly. This class might be extended in the future to cover newer features of Lobster.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1440 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1440/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1440/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1440/events | https://github.com/materialsproject/pymatgen/pull/1440 | 431,636,976 | MDExOlB1bGxSZXF1ZXN0MjY5MjY4Mjkw | 1,440 | allow the MimimumDistanceNN class to only use the cutoff distance as … | {
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"Thanks @jmmshn, will merge once a test has been added"
] | 2019-04-10T18:00:46 | 2019-04-11T04:17:21 | 2019-04-11T04:17:21Z | CONTRIBUTOR | {
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} | ## New option in MimimumDistanceNN
Allow the MimimumDistanceNN class to only use the cutoff distance as the filter.
So you can ignore the tolerance value.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1441 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1441/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1441/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1441/events | https://github.com/materialsproject/pymatgen/issues/1441 | 432,939,246 | MDU6SXNzdWU0MzI5MzkyNDY= | 1,441 | dielectric function parsing in OUTCAR lists "frequencies" but it should be energies | {
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} | **Describe the bug**
The OUTCAR parsing in pymatgen can parse the dielectric function. The first column is the energies (in eV). Pymatgen lists this column as "frequencies". It should be called "energies".
This is what an OUTCAR looks like for dielectric function - note the first column is E in eV
```
frequen... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1442 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1442/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1442/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1442/events | https://github.com/materialsproject/pymatgen/issues/1442 | 434,819,906 | MDU6SXNzdWU0MzQ4MTk5MDY= | 1,442 | waveder AttributeError: can't set attribute | {
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"This is also the case for the `nbands` and `nelect` attributes.",
"I am also a little confused about cder_data. Should it be a complex vector with x,y,z components for each spin? Then it should have 6 float numbers for each (band1, band2, kpoint, spin)? But from the code, we only get 3 float numbers. It should b... | 2019-04-18T15:08:43 | 2019-06-18T20:05:10 | 2019-06-18T20:05:10Z | NONE | {
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} | Unable to use the Waveder class in pymatgen.io.vasp.outputs
Error message below:
```
4400 cder_data = cder.reshape((nbands, nelect, nk, ispin, 3))
4401 self.cder_data = cder_data
-> 4402 self.nkpoints = nk
4403 self.ispin = ispin
4404 se... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1443 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1443/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1443/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1443/events | https://github.com/materialsproject/pymatgen/pull/1443 | 434,933,493 | MDExOlB1bGxSZXF1ZXN0MjcxODE1NDY4 | 1,443 | Speed up get_ir_reciprocal_mesh function | {
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"Fantastic, thank you!"
] | 2019-04-18T19:53:01 | 2019-04-18T20:42:20 | 2019-04-18T20:42:20Z | MEMBER | {
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} | ## Summary
Currently the implementation of `SpacegroupAnalyzer. get_ir_reciprocal_mesh` is woefully slow for very large meshes (due to unnecessary repeated calls to `list.count`). This pull request massively speeds up the implementation.
GaAs using a 80x80x80 k-point mesh, the time to calculate the ir mesh went f... | {
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} | ## Summary
The fast pourbaix construction algorithm is applied to the get_decomposition_energy method within the pourbaix_diagram.py script.
Within the get_decomposition_energy method:
* Checks for a consistent composition between forced entry and pourbaix diagram
* If composition is consistent, calls the fast ... | {
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"Hi @darnoceloc, thanks for your PR. Can you review the failing tests, and also check the diff, it looks like this PR is accidentally removing the `Waveder` class? You might be working from an old branch.",
"Some of the errors are coming from test files according to the **python3 setup.py nosetests** routine.\r\n... | 2019-04-21T00:11:27 | 2019-05-09T02:28:26 | 2019-05-09T02:28:26Z | CONTRIBUTOR | {
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} | AFLOW released ~300 more prototypes as part 2 of their library of crystallographic prototypes. These should be added to the `AflowPrototypeMatcher`.
https://www.sciencedirect.com/science/article/pii/S0927025618307146
Assigning this to myself. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1447 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1447/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1447/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1447/events | https://github.com/materialsproject/pymatgen/pull/1447 | 436,708,747 | MDExOlB1bGxSZXF1ZXN0MjczMTQwMzE3 | 1,447 | Plot fatbands from Lobster and option to force the reading of hybrid-like bandstructure for other functionals | {
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"I had to fix another test (a borg test). Not sure it was the correct thing to do.",
"Thanks for this PR, the new functionality looks very useful.\r\n\r\nIt's not clear to me why the Borg test needed to be changed because of the new functionality you've added? How does the ComputedEntry differ from previously?",
... | 2019-04-24T13:49:09 | 2019-05-02T14:30:52 | 2019-04-28T20:54:59Z | MEMBER | {
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I included classes and tests to plot FATBAND files from Lobster. I had to add several classes to do so. I also added tests.
Furthermore, I added an option to the Vasprun class to make it possible to read in self-consistent band structure calculations for every type of functional. I have already needed this severa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1448 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1448/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1448/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1448/events | https://github.com/materialsproject/pymatgen/issues/1448 | 436,789,882 | MDU6SXNzdWU0MzY3ODk4ODI= | 1,448 | ”UserWarning:The input structure does not match the expected standard primitive!“ | {
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"I really want to know the answer. If my description is not clear, please let me know. Thank you very much",
"@hautierg Can you help with this?",
"The issue with CifWriter, which doesn't write the lattice matrix, but rather the a,b,c lengths and angles: https://github.com/materialsproject/pymatgen/blob/9d8c75e8... | 2019-04-24T16:20:15 | 2019-05-09T02:14:25 | 2019-05-09T02:14:23Z | NONE | {
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When I do the band calculation，it always gives this：
“UserWarning:
The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.”
So，I check it carefully，use these code：
**1. first step:**
`
from pymatgen import Structure
from pym... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1449 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1449/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1449/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1449/events | https://github.com/materialsproject/pymatgen/pull/1449 | 437,437,266 | MDExOlB1bGxSZXF1ZXN0MjczNzE0ODcx | 1,449 | NMR symmetrize tensor update | {
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"I'm was having trouble managing my local branches, hopefully this only changes the one nmr file? ",
"Yes, that’s correct, this only changes the one file",
"Hi @dongsenfo, tests need to be updated to reflect this change since they're currently failing.",
"I've updated the test, hopefully things should work n... | 2019-04-25T23:25:35 | 2019-05-09T02:35:22 | 2019-05-09T02:34:47Z | CONTRIBUTOR | {
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} | ## Summary
Symmetrize the tensor before returning the principal axis system
Uses the symmetrize method from the tensor class
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https://api.github.com/repos/materialsproject/pymatgen/issues/1450 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1450/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1450/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1450/events | https://github.com/materialsproject/pymatgen/issues/1450 | 437,830,919 | MDU6SXNzdWU0Mzc4MzA5MTk= | 1,450 | Is it possible to apply biaxial deformation? | {
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"@mkhorton I think so?",
"For future reference, pls post queries on https://pymatgen.discourse.group and use Github Issues for only bug reports.",
"Hi @afonari, it's possible to apply any arbitrary deformation. You can initialize directly from a `Strain` object:\r\n\r\n```\r\nfrom pymatgen.analysis.elasticity.s... | 2019-04-26T20:19:55 | 2019-05-23T13:46:15 | 2019-05-23T13:46:15Z | CONTRIBUTOR | {
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} | Is it possible to apply biaxial deformation besides shear and non-shear modes defined in the DeformedStructureSet:
```# Generate deformations
for ind in [(0, 0), (1, 1), (2, 2)]:
for amount in norm_strains:
strain = Strain.from_index_amount(ind, amount)
self.defo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1451 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1451/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1451/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1451/events | https://github.com/materialsproject/pymatgen/pull/1451 | 438,736,333 | MDExOlB1bGxSZXF1ZXN0Mjc0Njk3OTg2 | 1,451 | Updated publication info for dimensionality module | {
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"@utf Nice implementation!\r\n\r\nThe rank calculation is the bottleneck here. The contents of `seen_comp_vertices` is always full-rank, so we can skip recalculating its rank.\r\n\r\nPost-publication it occurred to me that we do not need to add nodes to the queue which are not added to a component. This change (... | 2019-04-30T11:46:02 | 2019-05-01T18:38:19 | 2019-04-30T13:15:07Z | NONE | {
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} | ## Summary
The paper cited in the "get_dimensionality_larsen" function has been published. I have replaced the arXiv reference with the published one.
I have also made a two small changes to the function, which improves the speed by 2-3x. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1452 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1452/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1452/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1452/events | https://github.com/materialsproject/pymatgen/pull/1452 | 438,970,085 | MDExOlB1bGxSZXF1ZXN0Mjc0ODgxNzA3 | 1,452 | A small bug fix for gulp_caller | {
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"Thanks @kmu!",
"Many thanks."
] | 2019-04-30T20:46:44 | 2019-04-30T21:28:17 | 2019-04-30T21:28:17Z | CONTRIBUTOR | {
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} | ## Summary
A bug addressed in #1436 was fixed.
Old code can generate a too long line for cell parameters, which cannot be handled by GULP.
This patch fixes this issue.
A unit test was added to reproduce the bug.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1453 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1453/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1453/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1453/events | https://github.com/materialsproject/pymatgen/issues/1453 | 439,264,705 | MDU6SXNzdWU0MzkyNjQ3MDU= | 1,453 | MPNonSCFSet k-point generation incompatible with tetrahedron smearing | {
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"This was a while ago but I remember that the reason we went for explicit generation of k-points is symmetry. VASP uses a certain way of setting symmetries that is sometimes incompatible with other assignment for instance in spglib and from what I remember not super clear from the source code. That means spglib wil... | 2019-05-01T18:20:06 | 2019-12-10T09:57:38 | 2019-05-09T20:50:47Z | MEMBER | {
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} | Currently, `MPNonSCFSet` with `mode=uniform` creates an explicit list of k-points using `SpacegroupAnalyzer.get_ir_reciprocal_mesh`. As this list of k-points does not include tetrahedron information, the generated k-points file is incompatible with setting `ISMEAR = -5`. A recent update to the MPNonSCFSet set the defau... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1454 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1454/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1454/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1454/events | https://github.com/materialsproject/pymatgen/pull/1454 | 439,389,338 | MDExOlB1bGxSZXF1ZXN0Mjc1MjA1MjUz | 1,454 | Updates to defect modules and FermiDos scissor operator fix | {
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"Thanks @dbroberg \r\n\r\nRegarding the velocities issue, I remember there was some discussion of this previously...can you remember where that was, or who wanted it?",
"It was me reporting the issue and the previous fix I made was overly complicated. This fixes the same issue but in a more simple manner.",
"Ah... | 2019-05-02T00:48:39 | 2019-05-03T11:53:46 | 2019-05-03T11:53:46Z | CONTRIBUTOR | {
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A number of major changes and fixes for point defect modules.
* Update multiplicity approach for Defect class such that Vacancy and Substitution defect types raise early ValueErrors if a defect_site is fed to it which isn't in the bulk structure
* Remove overly complicated approach for accommodating s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1455 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1455/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1455/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1455/events | https://github.com/materialsproject/pymatgen/pull/1455 | 439,514,379 | MDExOlB1bGxSZXF1ZXN0Mjc1MzAyMjUz | 1,455 | Repair failing tests | {
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"Note that it is still segfaulting on CircleCI. Is something particularly memory intensive in these tests?",
"I will look into this again. "
] | 2019-05-02T10:07:06 | 2019-05-02T14:56:34 | 2019-05-02T14:15:00Z | MEMBER | {
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I also had some problems when running "test_cohp.py" and other files locally because there was no "@version" key in my dicts.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1456 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1456/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1456/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1456/events | https://github.com/materialsproject/pymatgen/pull/1456 | 439,717,751 | MDExOlB1bGxSZXF1ZXN0Mjc1NDYzMzgz | 1,456 | Smaller test file + different testing of bandgap | {
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"It failed again. Any other idea where this could come from? I don't think it is a memory problem.",
"Yeah, honestly I don't know. It passed when you were running it. But failed when I merged it. I think I have an idea... Let me push a fix.",
"What makes you think this isn’t a memory problem?\n\nOn Thu, May 2, ... | 2019-05-02T18:05:36 | 2019-05-02T23:12:24 | 2019-05-02T21:49:33Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1457 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1457/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1457/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1457/events | https://github.com/materialsproject/pymatgen/pull/1457 | 439,951,858 | MDExOlB1bGxSZXF1ZXN0Mjc1NjM4MTg4 | 1,457 | Fix for fatband tests | {
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"It is finally working. Thanks for your help. And, I will avoid assertDictEqual tests in the future... "
] | 2019-05-03T09:00:32 | 2019-05-03T12:26:37 | 2019-05-03T11:53:13Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1458 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1458/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1458/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1458/events | https://github.com/materialsproject/pymatgen/pull/1458 | 440,251,142 | MDExOlB1bGxSZXF1ZXN0Mjc1ODcxOTIy | 1,458 | Add boltztrap mode to MPNonSCFSet | {
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"Fyi, the `test_optics` tests are failing with this change.",
"Thanks @utf "
] | 2019-05-03T22:55:14 | 2019-05-04T04:08:51 | 2019-05-04T04:08:51Z | MEMBER | {
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} | ## Summary
As discussed in #1453, currently the MPNonSCFSet k-point generation routines are incompatible with tetrahedron smearing for uniform calculations. Historically, this decision was made to enable compatibility with Boltztrap calculations.
As we are transitioning to using tetrahedron smearing for higher qu... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1459 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1459/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1459/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1459/events | https://github.com/materialsproject/pymatgen/pull/1459 | 440,932,519 | MDExOlB1bGxSZXF1ZXN0Mjc2MzcyNjky | 1,459 | Updated run_type method clean version. | {
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"Hi @darnoceloc , thanks for persevering with this. This still needs tests to be updated before it can be merged.\r\n\r\nAlso, I have a request/comment, I saw:\r\n\r\n```\r\n param[\"run_type\"] = \"GGA+U\" if param[\"is_hubbard\"] else Vasprun.run_type\r\n```\r\n\r\nIs this correct? e.g. `is_hubbard... | 2019-05-06T22:39:03 | 2019-06-20T00:21:26 | 2019-06-19T23:44:28Z | CONTRIBUTOR | {
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} | ## Summary
Short few sentences, and summary of the major changes in bullet
points
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1460 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1460/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1460/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1460/events | https://github.com/materialsproject/pymatgen/issues/1460 | 441,395,317 | MDU6SXNzdWU0NDEzOTUzMTc= | 1,460 | Use 0 based index for CifWriter | {
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"If this isn't mandated by the core CIF spec, I'd be on board with changing it.",
"I tested 0 based CIF file and 1 based CIF file by [checkCIF](http://journals.iucr.org/services/cif/checkcif.html) and got essentially identical results.\r\nBoth files can be opened by CrystalMaker and VESTA without problems.\r\n\r\... | 2019-05-07T18:53:55 | 2019-05-07T21:44:28 | 2019-05-07T21:44:28Z | CONTRIBUTOR | {
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https://github.com/materialsproject/pymatgen/blob/19f56d4d918c3b7fdc445aaca7d56d0d9bc3ddb6/pymatgen/io/cif.py#L1283-L1292
I'm always frustrated when I export a structure to a CIF file, open by VESTA, and try to inspe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1461 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1461/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1461/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1461/events | https://github.com/materialsproject/pymatgen/pull/1461 | 441,441,318 | MDExOlB1bGxSZXF1ZXN0Mjc2NzY3ODk5 | 1,461 | Use 0 based index for CifWriter | {
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"thanks."
] | 2019-05-07T20:52:51 | 2019-05-07T21:43:22 | 2019-05-07T21:43:15Z | CONTRIBUTOR | {
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} | ## Summary
`CifWriter` now uses 0 based index for the consistency with `Structure`.
You can compare the site index in VESTA and that for pymatgen without confusion.
See #1460.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1462 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1462/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1462/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1462/events | https://github.com/materialsproject/pymatgen/issues/1462 | 441,634,788 | MDU6SXNzdWU0NDE2MzQ3ODg= | 1,462 | How to create input files for abinit by using pymatgen? | {
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"Please post questions on https://pymatgen.discourse.group . @gmatteo Can you answer this pls? It would be helpful if you write a simple example notebook at https://matgenb.materialsvirtuallab.org for ABINIT io."
] | 2019-05-08T09:19:58 | 2019-05-10T14:10:22 | 2019-05-10T14:10:22Z | NONE | {
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I found pymatgen supports the input/output operations for abinit, and tried to use pymatgen to generate the input files. However, little documents or descriptions for abinit can be found in http://pymatgen.org/. I found it easy to create POSCAR from cif file for vasp:
```
>>> structure = mg.Str... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1463 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1463/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1463/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1463/events | https://github.com/materialsproject/pymatgen/issues/1463 | 441,998,834 | MDU6SXNzdWU0NDE5OTg4MzQ= | 1,463 | Inconsistency btw SpacegroupAnalyzer & SpaceGroup | {
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"Welcome @mt-huebsch !\r\n\r\nRegarding your bug, I'm not sure I can re-produce. If you look at the 0.1.mcif file, in the file itself we see the symmetry operations:\r\n\r\n```\r\n1 x,y,z,+1 \r\n2 -x,y+1/2,-z,+1 \r\n3 -x,-y,-z,+1 \r\n4 x,-y+1/2,z,+1 \r\n5 x+1/2,-y+1/2,-z+1/2,-1 \r\n6 -x+1/2,-y,z+1/2,-1 \r\n7 -x+1/2... | 2019-05-09T00:30:02 | 2023-08-10T15:07:09 | 2023-08-10T15:07:09Z | NONE | {
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} | Hello everyone,
I am a first-timer. Thank you for taking the time.
Best, Marie-Therese
**Describe the bug**
The symmetry operations returned by pymatgen.symmetry.analyzer SpacegroupAnalyzer.get_symmetry_operations() and pymatgen.symmetry.groups SpaceGroup.symmetry_ops do not agree.
**To Reproduce**
See here... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1464 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1464/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1464/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1464/events | https://github.com/materialsproject/pymatgen/issues/1464 | 442,352,762 | MDU6SXNzdWU0NDIzNTI3NjI= | 1,464 | Changing the signature of vaspinputset.from_prev() | {
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"My view is that there are both use cases. The problem with the suggested Option 2 is that the logic flow is strange. Initialization VaspInputSet requires a Structure, which presumably is being read from a previous calculation in these cases. I would also prefer not to wreak havoc on a lot of people's scripts (incl... | 2019-05-09T17:40:43 | 2019-05-16T00:13:00 | 2019-05-16T00:13:00Z | MEMBER | {
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} | Currently, the from_prev() method in the VaspInputSets is a wild west of parameters - i.e., there is no consistency in the signature of from_prev() between different VaspInputSets.
This ends up causing a lot of downstream complexity in atomate. Although the atomate FireTasks can take in a VaspInputSet object to help... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1465 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1465/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1465/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1465/events | https://github.com/materialsproject/pymatgen/pull/1465 | 442,373,593 | MDExOlB1bGxSZXF1ZXN0Mjc3NTAwODg0 | 1,465 | Fix piezo and piezo sensitivity | {
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"Is this ready to merge?",
"I believe @shyamd was going to merge when ready? ",
"Asking because I saw the WIP label disappeared\n\nOn Fri, Aug 23, 2019 at 11:44, dongsenfo <notifications@github.com> wrote:\n\n> I believe @shyamd <https://github.com/shyamd> was going to merge when\n> ready?\n>\n> —\n> You are re... | 2019-05-09T18:33:05 | 2019-08-26T18:14:48 | 2019-08-26T18:14:48Z | CONTRIBUTOR | {
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} | Write tests and update style for piezo and piezo sensitivity
## Summary
Past branch accidently merged so this is an update
Added piezo_sensitivity and site_symmetry packages under analysis. Site_symmetries allow for users to get the point symmetries of atomic sites and symmetry operations relating sites. Piezo s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1466 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1466/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1466/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1466/events | https://github.com/materialsproject/pymatgen/pull/1466 | 443,594,855 | MDExOlB1bGxSZXF1ZXN0Mjc4NDI5Njgz | 1,466 | Add override_from_prev_calc to VASP input sets | {
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"With regards to the ‘standardize’ option, is there a good reason to prefer the standard primitive over a reduced cell?",
"The main reason would be for defining the k-point lines along which to compute and plot band structure.",
"That’s fair, but the primitive standard cells aren’t always great, eg I saw a case... | 2019-05-13T20:49:12 | 2019-05-15T22:49:20 | 2019-05-15T22:49:20Z | MEMBER | {
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} | ## Summary
Based on the discussion in #1464, I have added `override_from_prev_calc` methods to the VASP input sets that already define `from_prev_calc`. In each case, the old `from_prev_calc` method has been rewritten to use `override_from_prev_calc`. This new approach has several advantages, including:
- The `fr... | {
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"Thanks. Instead of this approach, I would suggest that you simply allow nimages to take either an int (in which it will be linearly spaced like the default) or if a sequence of values is provided, it will use those to construct the images. ",
"Okay, I can easily make that change. In that case, \"images\" is prob... | 2019-05-14T03:29:06 | 2019-05-16T04:10:55 | 2019-05-16T00:12:40Z | CONTRIBUTOR | {
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} | ## Summary
Added the argument "ximages" to IStructure.interpolate. This allows you to define an arbitrary grid of interpolation points between the two lattices. This is useful for making configuration coordinate diagrams.
"nimages" was left intact to maintain backwards compatibility. "ximages" may not be the best... | {
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} | ## Summary
* Fix the rgb_label of 2 elements band structure
After fix:
<img src="https://user-images.githubusercontent.com/18021558/58139835-969e8880-7c0a-11e9-8164-ef6039859383.png" width=150/>
Before fix:
<img src="https://user-images.githubusercontent.com/18021558/58139864-b9c93800-7c0a-11e9-9b08-27f8063... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1470 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1470/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1470/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1470/events | https://github.com/materialsproject/pymatgen/pull/1470 | 446,925,318 | MDExOlB1bGxSZXF1ZXN0MjgxMDI3Mzcz | 1,470 | Segmented drawing different branches of band structure | {
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"Thanks."
] | 2019-05-22T04:17:42 | 2019-05-23T13:44:52 | 2019-05-23T13:44:44Z | CONTRIBUTOR | {
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## Summary
Segmented drawing different branches of band structure in BSDOSPlotter. Look nicer between two discontinuous k-path branches
* After fix
<img src="https://user-images.githubusercontent.com/18021558/58146970-64028900-7c26-11e9-899c-2188ed9e5de2.png" width=100/>
* Before fix
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"Thanks @utf! I share your concern about breaking backwards compat, but\ncases like this seem pretty clear it should be tidied up. Will merge this\nfix regardless\n\nOn Wed, May 22, 2019 at 18:21, Alex Ganose <notifications@github.com> wrote:\n\n> Summary\n>\n> Currently, FermiDos objects are not MSONable for two r... | 2019-05-23T01:20:54 | 2019-05-24T03:56:38 | 2019-05-24T03:56:38Z | MEMBER | {
"total": 0,
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} | ## Summary
Currently, FermiDos objects are not MSONable for two reasons:
1. They have a strange constructor that requires a Dos object rather than energies, densities and a Fermi level like other Dos subclasses.
2. The nelecs variable is not stored, even as a private variable.
Ideally I'd correct the constructo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1472 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1472/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1472/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1472/events | https://github.com/materialsproject/pymatgen/pull/1472 | 448,406,418 | MDExOlB1bGxSZXF1ZXN0MjgyMTk5Mjk1 | 1,472 | Fix the color issue of segmented drawing different branches of band s… | {
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} | ## Summary
Fix the color issue of segmented drawing different branches of the band structure in BSDOSPlotter.
* After fix
* Before fix
![image](https://user-images.githubusercontent.com/18021558/58363... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1473 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1473/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1473/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1473/events | https://github.com/materialsproject/pymatgen/pull/1473 | 450,045,034 | MDExOlB1bGxSZXF1ZXN0MjgzNDUxMjE0 | 1,473 | Add Interface class and InterfaceBuilder | {
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"Thanks @kylebystrom, are you happy for this to merged now while it’s still in “prototype” stage? It already looks quite substantial, though I can’t tell what the test coverage is like from a quick read.",
"Looking back at it, I think the test coverage is still a bit low, so Shyam and I are going to add a couple ... | 2019-05-29T22:17:55 | 2019-06-17T23:12:00 | 2019-06-17T23:12:00Z | CONTRIBUTOR | {
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} | ## Summary
Adding Interface and InterfaceBuilder classes (prototype stage) along with a few basic unit tests. Initial code written by @shyamd and @sivonxay and debugged/documented by myself.
* Store and edit interfaces in the Interface class
* Create new interfaces with the InterfaceBuilder | {
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"For future reference, pls post such questions at http://pymatgen.discourse.group .\r\nYou can ignore the deprecation message. \r\n\r\nThe issue is related to the fact that you are running in a Jupyter notebook. The figure is indeed generated, as can be seen from the `<Figure size ...>` in your output. For matplotl... | 2019-05-30T15:45:35 | 2019-05-30T16:42:17 | 2019-05-30T16:42:16Z | NONE | {
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} | **Describe the bug**
Dear pymatgen communities,
I am running a Si Wulff Shape Construction based on the excellent tutorial from https://matgenb.materialsvirtuallab.org/2017/04/03/Slab-generation-and-Wulff-shape.html
However, when running the code, no Wulff shape plot was displayed at the end, and a warning messa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1475 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1475/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1475/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1475/events | https://github.com/materialsproject/pymatgen/pull/1475 | 450,442,668 | MDExOlB1bGxSZXF1ZXN0MjgzNzYwNzYz | 1,475 | [WIP] Change NearNeighbors API | {
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} | ## Summary
This will be a breaking change. This Is for #1273. If you rely on NearNeighbors please make note of the changes. This is to improve efficiency of the class.
WIP since lots of tedious test changes still to be done. | {
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"@utf do you want this merged?",
"Noting here for future ref, some mineral names have LaTeX in them so need to be proofed, and some mineral names are archaic (see example \"Lavarevi\\'{c}ite\" which apparently is now known as \"Colusite\").",
"another part of the prototype library has been prepared: https://arx... | 2019-05-30T23:15:21 | 2021-10-06T09:29:11 | 2021-10-06T09:29:11Z | MEMBER | {
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} | ## Summary
Add part 2 of the AFLOW prototype library to the set of prototypes used by `AFLOWPrototypeMatcher`. See #1446. | {
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"This might be surprising, but yes, these are valid. Basically, pymatgen treats any non-element symbol starting with an upper-case as a DummySpecie, unless it violates the rule that the upper case letter itself is an element. For example, Composition(\"Stuff\") would not work because S is an element. \r\n\r\nYou ca... | 2019-05-31T04:23:21 | 2019-05-31T16:15:09 | 2019-05-31T14:05:02Z | MEMBER | {
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} | Composition objects allow initializing with an input that is clearly not a valid formula.
For example:
```python
from pymatgen import Composition
Composition("Madeupstuff")
Composition("Lonsdalite")
Composition("MyGranddadGoesToMarketEveryTuesday")
```
None of which raise an exception.
Is this beha... | {
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"Oops realized I created this branch from my NearNeighbors branch instead of from master as intended, will merge later"
] | 2019-05-31T10:39:34 | 2019-05-31T16:21:22 | 2019-05-31T12:53:09Z | MEMBER | {
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"Hi @chc273 , this looks great!\r\n\r\nIf the output is identical to `get_all_neighbors` why not combine them? You could rename `get_all_neighbors_cell_list` to `_get_all_neighbors_cell_list` and then add a new `method=\"cell_list\"` keyword argument to `get_all_neighbors`. If someone wants the old algorithm, they ... | 2019-05-31T20:51:46 | 2019-06-04T22:52:59 | 2019-06-02T20:03:21Z | CONTRIBUTOR | {
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} | ## Summary
Implemented a linear scaling `get_all_neighbors_cell_list` method for `Structure`. This method gives identical results to `get_all_neighbors` but uses a cell list method that scales linearly with the number of atoms, i.e., O(N). The original `get_all_neighbors` has a O(N^2) scaling.
Reference: https://e... | {
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"If more problems occur, I will fix them in one of the next days.",
"Is there anything else I should do before it can be merged. Thanks. ",
"Thanks."
] | 2019-05-31T22:27:19 | 2019-06-03T13:49:51 | 2019-06-03T13:49:48Z | MEMBER | {
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} | ## Summary
I have implemented a new Lobsterin class in pymatgen.io.lobster to handle input for Lobster. This class works very similar to the INCAR class (subclass from dict and MSONable). Furthermore, it can write several input files (e.g. lobsterin, INCAR with lobster specific settings, KPOINTS for fatband calculat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1482 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1482/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1482/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1482/events | https://github.com/materialsproject/pymatgen/pull/1482 | 451,195,829 | MDExOlB1bGxSZXF1ZXN0Mjg0MzQ1MDEz | 1,482 | fix CovalentBondNN.get_bonded_structure | {
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"Thanks.",
"Thanks @Ian496! Fyi we are updating this class for better molecule support throughout, the NearNeighbor classes were originally designed with only ordered crystal structures in mind. This may have some minor API changes when this happens."
] | 2019-06-02T14:08:11 | 2019-06-03T16:27:27 | 2019-06-03T13:48:41Z | CONTRIBUTOR | {
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} | ## Summary
In the current master branch, `pymatgen.analysis.local_env.CovalentBondNN` returns AttributeError with the following code:
```
from pymatgen.core import Molecule
from pymatgen.analysis.local_env import CovalentBondNN
H2 = Molecule(['H', 'H'], [[0, 0, 0], [0, 0, 1.0]])
bonds = H2.get_covalent_bonds()
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1483 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1483/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1483/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1483/events | https://github.com/materialsproject/pymatgen/pull/1483 | 451,527,829 | MDExOlB1bGxSZXF1ZXN0Mjg0NjAwMjU3 | 1,483 | Fix small bug in Lobsterin | {
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} | While writing a sample script for the use of the Lobsterin class, I have found a small bug in the automatic determination of the basis functions for Lobster. I have fixed the bug and included test code to avoid the bug in the future.
Furthermore, I have modified the method to generate KPOINTS a bit and included a tes... | {
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"Actually this is still not correct. The legnth of the list of lists should be equal to number of sites.",
"Pls resubmit a PR and include a test for this case."
] | 2019-06-04T21:04:37 | 2019-06-04T21:13:23 | 2019-06-04T21:07:46Z | CONTRIBUTOR | {
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} | ## Bug fix for Structure.get_all_neighbors
Previously if the cutoff radius is too small and no neighbors are found, the `get_all_neighbors` method will return an empty list `[]`, while it should be a list of empty list `[[]]`.
This PR corrects return types. | {
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"I added one more test for the small distance as well as @mkhorton's Mag structure coincident site test. I also removed the unnecessary checks for empty lists. Those checks are more trouble than it is worth. Without those, the code automatically returns the correct list of empty lists when cutoff is too small."
] | 2019-06-05T05:04:06 | 2019-06-05T13:34:44 | 2019-06-05T13:24:52Z | CONTRIBUTOR | {
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} | ## Summary
1. Fixed the return type of `get_all_neighbors` when no neighbors are found. It should return a list of length n, where each item is `[]` and n is the number of atoms
2. Fixed the `magnetism` test problem. It is an issue with coincide sites. The site with DummySpecie coincides with a normal site and now ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1486 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1486/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1486/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1486/events | https://github.com/materialsproject/pymatgen/issues/1486 | 452,533,594 | MDU6SXNzdWU0NTI1MzM1OTQ= | 1,486 | MagOrderingTransformation Bug with New Enumlib | {
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"@mkhorton I suspect this has to do with the fact that MagOrdering now creates Dummy sites that collide with existing sites. But I can't be sure. In any case, I am unclear why the collision needs to occur. Shouldn't the transformation just replace existing sites with dummy sites rather than adding?",
"It’s becaus... | 2019-06-05T14:27:58 | 2023-08-10T14:59:52 | 2023-08-10T14:59:52Z | MEMBER | {
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} | **Describe the bug**
MagOrderingTransformation seems to work with old enumlib, but fails with new enumlib. CircleCI tests are passing because those are based on the old enumlib.
**To Reproduce**
Steps to reproduce the behavior:
1. Compile enumlib from https://github.com/msg-byu/enumlib.git
2. Make the new enumli... | {
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"This is because the two functions use different methodologies. `get_band_gap` uses the CBM and VBM points, so it doesn't care about the spin. `get_direct_band_gap` is spin-aware and it turns out in this material the CBM and VBM are from different spins, so `get_direct_band_gap` finds \"another\" direct band_gap wh... | 2019-06-06T22:23:42 | 2019-06-07T15:51:13 | 2019-06-07T15:51:13Z | CONTRIBUTOR | {
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} | **`Bandstructure.get_direct_band_gap` reports different value from `get_band_gap` for material with direct band gap**
I queried the band structure of `mp-782693` using `MPRester.get_bandstructure_by_material_id`. This material has a band gap (direct) of 0.685 eV as shown on the site and as computed by `get_band_gap`... | {
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} | Quick fix, just a docstring typo. Previously the docstring for Site.coords said that the coordinates were fractional, but actually they are cartesian. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1489 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1489/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1489/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1489/events | https://github.com/materialsproject/pymatgen/issues/1489 | 454,301,008 | MDU6SXNzdWU0NTQzMDEwMDg= | 1,489 | Inconsistent number of layers in surface slabs | {
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"@richardtran415 Can you look into this?",
"Looking into it\n\nOn Tue, Jun 11, 2019 at 12:44 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> @richardtran415 <https://github.com/richardtran415> Can you look into\n> this?\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email... | 2019-06-10T18:18:38 | 2019-06-22T01:38:03 | 2019-06-22T01:38:03Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
I want to generate some (111) surfaces of simple FCC metals (e.g., Ag, Au, Cu, Pd, Pt, Rh, and so on), and I need them to have the same number of layers of atoms. My strategy so far has been this:
```python
from pymatgen import Structure, Lattice... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1490 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1490/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1490/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1490/events | https://github.com/materialsproject/pymatgen/pull/1490 | 454,372,881 | MDExOlB1bGxSZXF1ZXN0Mjg2ODM3NDE5 | 1,490 | Added from_vasp_voigt method to piezo. | {
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} | ## Summary
Added from_vasp_voigt method to piezo and tests
Vasp reports the piezoelectric tensor not in the proper voigt notation, this method converts the vasp generated tensor into the full 3x3x3 tensor. | {
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} | The interface classes need some clean up.
- `Interface` needs to be moved to core
- `analysis` needs an interfaces sub_module with `ZSLGenerator`, `StradiGenerator` ,`SubstrateAnalyzer`, and `InterfaceBuilder`
- Convert `GrainBoundary` to inherit from `Interface`
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https://api.github.com/repos/materialsproject/pymatgen/issues/1492 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1492/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1492/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1492/events | https://github.com/materialsproject/pymatgen/pull/1492 | 455,259,413 | MDExOlB1bGxSZXF1ZXN0Mjg3NTQ0ODY1 | 1,492 | Fix for issue #1442 | {
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"Thanks. Can you add unittests to ensure those bugs don't recur in future? ",
"Great catch for the shape of the cder_data!\r\n\r\nBased on the discussion in #1442, it seems like the datatype of the records can be float64 instead of complex64 if the wave function is generated using the gamma point version of VASP.... | 2019-06-12T14:50:06 | 2019-06-13T14:18:54 | 2019-06-13T14:18:54Z | CONTRIBUTOR | {
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} | ## Summary
This commit tries to fix issue #1442 in the pymatgen.io.vasp.outputs.Waveder class.
* Fix 1
The original issue is raised by the fact that the variables and member functions have the same name.
This has been fixed by prepending a underscore to the variable names.
* Fix 2
Additionally, the datatype o... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1493 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1493/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1493/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1493/events | https://github.com/materialsproject/pymatgen/issues/1493 | 455,477,121 | MDU6SXNzdWU0NTU0NzcxMjE= | 1,493 | FEFF IO mistakenly parses feff.inp files | {
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} | **Describe the bug**
.io.feff tests to see if a feff.inp file was created by Pymatgen by checking to see if the word 'pymatgen' shows up in the first line. It does this via the find method for a string, which returns the index of the string at which the desired substring first appears.
```
try:
fe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1494 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1494/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1494/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1494/events | https://github.com/materialsproject/pymatgen/pull/1494 | 455,482,914 | MDExOlB1bGxSZXF1ZXN0Mjg3NzIxNjE0 | 1,494 | Fixed Issue 1493: bug in feff IO when parsing non-pymatgen generated file | {
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"Thanks @stevetorr !"
] | 2019-06-13T00:33:22 | 2019-06-13T04:19:02 | 2019-06-13T04:19:02Z | CONTRIBUTOR | {
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} | ## Summary
This pull request fixes a minor bug in the FEFF IO script which is summarized in Issue 1493:
https://github.com/materialsproject/pymatgen/issues/1493
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"Thanks @clegaspi for help with the regex on this one, @mhsiron this should be ready for your workflow now if you pull from master",
"Did you mean to change the row pattern for spin down? Shouldn't it be the same as spin up? ",
"Hmm, good catch. Yes, I’ll change that. Thanks!"
] | 2019-06-14T00:38:56 | 2021-02-13T17:29:06 | 2019-06-14T01:38:37Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1496 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1496/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1496/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1496/events | https://github.com/materialsproject/pymatgen/issues/1496 | 456,169,154 | MDU6SXNzdWU0NTYxNjkxNTQ= | 1,496 | Incorrect results from MagneticSpaceGroup | {
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"Thanks Simon! I’ll take a look at this.\n\nOn Fri, Jun 14, 2019 at 03:10, Simon Ward <notifications@github.com> wrote:\n\n> *Describe the bug*\n> Some magnetic structures are not being described properly by\n> MagneticSpaceGroup. There has probably been a small error when originally\n> parsing https://stokes.byu.e... | 2019-06-14T10:10:54 | 2019-06-20T18:05:15 | 2019-06-20T18:05:15Z | NONE | {
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} | **Describe the bug**
Some magnetic structures are not being described properly by MagneticSpaceGroup. There has probably been a small error when originally parsing https://stokes.byu.edu/iso/magnetic_data.txt
**To Reproduce**
Steps to reproduce the behavior. E.g the R-3c' spacegroup:
```python
from pymatgen.sym... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1497 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1497/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1497/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1497/events | https://github.com/materialsproject/pymatgen/pull/1497 | 456,470,398 | MDExOlB1bGxSZXF1ZXN0Mjg4NTA5ODUw | 1,497 | Minor updates to surface.py and get_cohesive_energy | {
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"Thanks @richardtran415, labelling bulk Wyckoff sites seems especially useful.\r\n\r\nDo you have any idea why CircleCI is segfaulting with this PR? As far as I can tell nothing in this PR should cause this.",
"I honestly don't know why that would happen, I'll do some additional nosetests on my laptop and CircleC... | 2019-06-14T23:16:34 | 2019-06-18T05:50:56 | 2019-06-18T05:50:56Z | CONTRIBUTOR | {
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} | ## Summary
- Bug fix when using the in_unit_planes parameter in SlabGenerator for getting slabs of a consistent number of atoms. Number of unit planes (p) is always rounded to nearest int to avoid floats such as 2.999999999 or 2.000000001. This should address issue #1489
- Distinguish tol from ftol. These parame... | {
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"I have also corrected for another bug in the calculation of nbands... and adapted one test to avoid this in the future."
] | 2019-06-15T11:20:48 | 2019-06-15T17:04:49 | 2019-06-15T17:04:49Z | MEMBER | {
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After using pip install, "BASIS_PBE_54.yaml" was not found. I have changed the "setup.py" to correct this. | {
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"Better bug fixes than bugs!\r\n\r\nQuestion regarding the io, why the write_INCAR function instead of a `LobsterSet` in io.vasp.sets? The latter may be easier for other people to discover",
"I will probably write a LobsterSet in the future. I have to think a bit more about the design at first. I am not sure abou... | 2019-06-19T09:45:21 | 2019-06-19T15:59:10 | 2019-06-19T15:39:55Z | MEMBER | {
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} | ## Summary
Small BugFix in the lobsterin class to also change LWAVE from False to True when writing a new INCAR. I also adapted the tests.
I am sorry for the very frequent bug fixes at the moment. I hope this will be one of the last ones for now. | {
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"Usually it's better not to have to write custom as_dict/from_dict methods -- what specifically about Interface means they're necessary? (Not a problem if it is necessary)",
"Ok, verdict is that it’s because of Structure’s from_dict. Also making a note that get_sorted_structure and from_sites won’t work on subcla... | 2019-06-19T23:41:47 | 2019-06-21T02:11:23 | 2019-06-21T02:11:23Z | CONTRIBUTOR | {
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} | ## Summary
-Override the as_dict() and from_dict() functions from pymatgen.core.structure.Structure for proper serialization
- Cleaned up extraneous imports
- Fixed option to create copy with site properties (Previously documented as such, with no functionality)
- Override get_sorted_structure() from Structure. Not... | {
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