url stringlengths 63 66 | repository_url stringclasses 1
value | labels_url stringlengths 77 80 | comments_url stringlengths 72 75 | events_url stringlengths 70 73 | html_url stringlengths 52 56 | id int64 3.39M 3.04B | node_id stringlengths 18 32 | number int64 1 4.39k | title stringlengths 3 367 | user dict | labels listlengths 0 5 | state stringclasses 2
values | locked bool 2
classes | assignee dict | assignees listlengths 0 2 | milestone null | comments listlengths 0 30 | created_at timestamp[s]date 2012-02-26 12:10:46 2025-05-02 18:11:41 | updated_at timestamp[s]date 2012-02-26 14:52:41 2025-05-02 18:16:27 | closed_at stringlengths 0 20 | author_association stringclasses 3
values | type stringclasses 1
value | active_lock_reason stringclasses 2
values | sub_issues_summary dict | body stringlengths 0 119k | closed_by dict | reactions dict | timeline_url stringlengths 72 75 | performed_via_github_app null | state_reason stringclasses 4
values | is_pull_request bool 2
classes | draft bool 2
classes | pull_request dict |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
https://api.github.com/repos/materialsproject/pymatgen/issues/1301 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1301/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1301/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1301/events | https://github.com/materialsproject/pymatgen/issues/1301 | 371,766,457 | MDU6SXNzdWUzNzE3NjY0NTc= | 1,301 | miller_index_from_sites gives wrong miller index | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@richardtran415 Pls investigate.",
"Looking into it",
"I've got a fix for this. Just doing some testing but will submit a PR tomorrow.",
"Fixed in #1302 "
] | 2018-10-19T00:49:39 | 2018-10-24T20:44:53 | 2018-10-24T20:44:53Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | The `pymatgen.core.surface.miller_index_from_sites` method gives incorrect results. It also seems quite temperamental about the choice of coordinates. E.g.
```python
from pymatgen.core.structure import Structure
from pymatgen.core.surface import miller_index_from_sites
structure = Structure(
[10, 0, 0, 0, ... | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1301/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1301/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1302 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1302/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1302/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1302/events | https://github.com/materialsproject/pymatgen/pull/1302 | 372,112,103 | MDExOlB1bGxSZXF1ZXN0MjI0NDA3Mjc0 | 1,302 | miller_index_from_sites now supports more than 3 sites | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"> One thing to note is that previously miller_index_from_sites required the lattice matrix as input, whereas now it requires a Lattice object. \r\n\r\nI know this was discussed in a previous PR, but since this requires a `Lattice` object, perhaps it should be a method on Lattice? I think a convenience method on St... | 2018-10-19T20:52:40 | 2018-10-24T20:06:23 | 2018-10-24T20:06:23Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Fixed bugs in `miller_index_from_sites` detailed in #1301.
I also extended `miller_index_from_sites` to support passing more than 3 sites. In this case, the "best" plane that minimizes the distance from all atoms to the plane will be calculated using singular value decomposition. This behavior is the ... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1302/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1302/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1302",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1302",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1302.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1302.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1303 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1303/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1303/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1303/events | https://github.com/materialsproject/pymatgen/pull/1303 | 372,381,681 | MDExOlB1bGxSZXF1ZXN0MjI0NTgxNDg1 | 1,303 | Fix missing Miller indices in SlabGenerator | {
"login": "CifLord",
"id": 8036054,
"node_id": "MDQ6VXNlcjgwMzYwNTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8036054?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CifLord",
"html_url": "https://github.com/CifLord",
"followers_url": "https://api.github.com/users/CifLord/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-10-22T02:55:09 | 2018-10-30T20:12:06 | 2018-10-22T20:02:00Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | This PR mainly addresses issue #1294 . The get_symmetrically_distinct_miller_indices() function will enumerate through families of planes in the rhombohedral setting instead of the hexagonal setting when dealing with trigonal structures.
| {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1303/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1303/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1303",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1303",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1303.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1303.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1304 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1304/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1304/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1304/events | https://github.com/materialsproject/pymatgen/pull/1304 | 373,220,777 | MDExOlB1bGxSZXF1ZXN0MjI1MjAxMDQ3 | 1,304 | Fix defect_generate_structure issue with velocity site property | {
"login": "dbroberg",
"id": 5498596,
"node_id": "MDQ6VXNlcjU0OTg1OTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/5498596?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dbroberg",
"html_url": "https://github.com/dbroberg",
"followers_url": "https://api.github.com/users/dbrob... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks Danny!\r\n\r\nCould you imagine this issue recurring with other site_properties, not just velocity?",
"Also saw that all tests pass here, but we're just started getting errors on AppVeyor from the defects module. Seems pretty weird, related to matplotlib, so might be completely unrelated to this PR. Do yo... | 2018-10-23T21:58:46 | 2018-10-24T18:35:53 | 2018-10-24T17:13:38Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Previously a Substitutional or Interstitial defect structure could be generated (from generate_defect_structure) with a velocity property which was not consistent with the initial bulk_structure.
This PR fixes this issue for the Substitution and Interstitial objects and adds a unit test to ensure the fix works. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1304/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1304/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1304",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1304",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1304.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1304.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1305 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1305/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1305/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1305/events | https://github.com/materialsproject/pymatgen/pull/1305 | 373,684,162 | MDExOlB1bGxSZXF1ZXN0MjI1NTU2MjMz | 1,305 | Add get_chempot_correction method in interface_reactions module | {
"login": "yihanxiao92",
"id": 25351305,
"node_id": "MDQ6VXNlcjI1MzUxMzA1",
"avatar_url": "https://avatars.githubusercontent.com/u/25351305?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yihanxiao92",
"html_url": "https://github.com/yihanxiao92",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"(Note that the AppVeyor failure `ImportError: cannot import name 'get_backend' from 'matplotlib' (c:\\miniconda36-x64\\lib\\site-packages\\matplotlib\\__init__.py)` is not a result of this Pull Request -- I'm still trying to figure out what's causing this error.)",
"Ok, could you let me know if I should re-open ... | 2018-10-24T21:26:58 | 2018-10-24T23:26:37 | 2018-10-24T23:26:37Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Added get_chempot_correction method in the interface_reactions module with its tests, the purpose is to enable users to obtain correction term for chemical potential of gaseous phase at given temperature and pressure. The reference state is T=298.15 K and p = 1 bar. This method can be used in the interfac... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1305/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1305/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1305",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1305",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1305.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1305.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1306 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1306/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1306/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1306/events | https://github.com/materialsproject/pymatgen/issues/1306 | 373,695,080 | MDU6SXNzdWUzNzM2OTUwODA= | 1,306 | get_distance input (jimage) does not take tuple | {
"login": "hmlli",
"id": 42851962,
"node_id": "MDQ6VXNlcjQyODUxOTYy",
"avatar_url": "https://avatars.githubusercontent.com/u/42851962?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hmlli",
"html_url": "https://github.com/hmlli",
"followers_url": "https://api.github.com/users/hmlli/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks @hello-underworld, this now has been fixed: https://github.com/materialsproject/pymatgen/commit/a1f48c89400405e22ca6fef2befbf8786f07368f\r\n\r\nPlease also feel welcome to submit a pull request if you encounter any further issues."
] | 2018-10-24T22:02:45 | 2018-10-24T22:49:38 | 2018-10-24T22:49:38Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | In core.structure module, there is a get_distance feature that looks like
def get_distance(i, j, jimage)
to get the distance of site index i and j with lattice translation of jimage. However, when inputted a tuple (say, I do get_distance(0,0,(1,0,0)), it gives me an error that says
"can only concatenate tuple ... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1306/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1306/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1307 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1307/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1307/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1307/events | https://github.com/materialsproject/pymatgen/pull/1307 | 373,834,917 | MDExOlB1bGxSZXF1ZXN0MjI1NjcwMTE2 | 1,307 | Boltztrap2 for emmet | {
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fra... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Need unittests...\r\n",
"The test files are not in the right place. The tests are failing because of that."
] | 2018-10-25T08:41:19 | 2018-11-25T23:19:53 | 2018-11-25T23:19:52Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | BandstructureLoader supports single spin component in order to calculate the relative dos.
A merge function to get a complete (up/down) dos has been added too.
This commit allow to run Doses for MP with Boltztrap2DosBuilder in Emmet. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1307/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1307/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1307",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1307",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1307.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1307.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1308 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1308/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1308/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1308/events | https://github.com/materialsproject/pymatgen/issues/1308 | 374,118,494 | MDU6SXNzdWUzNzQxMTg0OTQ= | 1,308 | Issues parsing Hydrogen potcars with non-integer charge | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-10-25T20:27:02 | 2018-11-04T20:39:22 | 2018-11-04T20:39:22Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
e.g. POTCAR.H1.25.gz, pop from empty list error. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1308/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1308/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1309 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1309/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1309/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1309/events | https://github.com/materialsproject/pymatgen/issues/1309 | 374,539,787 | MDU6SXNzdWUzNzQ1Mzk3ODc= | 1,309 | Bug in StructureGraph __mul__ method | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks for opening this, I'm going to add the minimal example you shared with me here for a reference:\r\n\r\n```\r\ndimer = Structure([8, 0, 0, 0, 8, 0, 0, 0, 8], ['I'] * 2, [[-0.2, 0, 0], [0.2, 0, 0]])\r\n\r\ndimer_bonded = cnn.get_bonded_structure(dimer)\r\nn_dimers_in_unit_cell = len(list(nx.weakly_connected_c... | 2018-10-26T20:39:55 | 2023-08-08T21:30:28 | 2023-08-08T21:30:28Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Creating a supercell then calculating the `StructureGraph` gives different result to first calculating the bonding then creating a supercell.
Issue appears to be in the `__mul__` method of `StructureGraph` as the bug occurs for different graph creation algorithms.
```python
import networkx as nx
import numpy as... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1309/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1309/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1310 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1310/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1310/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1310/events | https://github.com/materialsproject/pymatgen/issues/1310 | 374,752,386 | MDU6SXNzdWUzNzQ3NTIzODY= | 1,310 | pymatgen.vis.structure_chemview bug | {
"login": "yjzhang97",
"id": 43169876,
"node_id": "MDQ6VXNlcjQzMTY5ODc2",
"avatar_url": "https://avatars.githubusercontent.com/u/43169876?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yjzhang97",
"html_url": "https://github.com/yjzhang97",
"followers_url": "https://api.github.com/users/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"> I think it is a bug because of the chemview .It is too old.\r\n\r\nI think you're right, we're actively exploring different visualization options for pymatgen, and currently have a new solution in development.\r\n\r\nWe've had problems getting chemview working in other contexts too, and chemview itself is now o... | 2018-10-28T13:11:04 | 2023-08-08T21:30:15 | 2023-08-08T21:30:15Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
When I run this code in the jupyter notebook, it has a mistake.The prompt message is **A Jupyter widget could not be displayed because the widget state could not be found. This could happen if the kernel storing the widget is no longer available, or if the widget state was not saved in the noteboo... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1310/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1310/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1311 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1311/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1311/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1311/events | https://github.com/materialsproject/pymatgen/issues/1311 | 376,957,754 | MDU6SXNzdWUzNzY5NTc3NTQ= | 1,311 | no "cut off" values in "def get_connections(self)" | {
"login": "SeoinBack",
"id": 38265800,
"node_id": "MDQ6VXNlcjM4MjY1ODAw",
"avatar_url": "https://avatars.githubusercontent.com/u/38265800?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/SeoinBack",
"html_url": "https://github.com/SeoinBack",
"followers_url": "https://api.github.com/users/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-11-02T20:30:58 | 2023-08-08T21:30:02 | 2023-08-08T21:30:01Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
In "pymatgen/analysis/structure_analyzer.py", "get_connections" has no cutoff setup while "class VoronoiConnectivity" has.
def get_connections(self):
"""
Returns a list of site pairs that are Voronoi Neighbors, along
with their real-space distances.
"""... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1311/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1311/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1312 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1312/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1312/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1312/events | https://github.com/materialsproject/pymatgen/pull/1312 | 377,001,107 | MDExOlB1bGxSZXF1ZXN0MjI4MDg0NjE0 | 1,312 | small changes to insertion battery | {
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Could you add a very quick test for this? Just something sensible that would've caught the `pair.pair.muO2_discharge` error.",
"So none of the testsets actually have muO2 data, and adding muO2 data will require me to update way entries are stored. I will have to look into this a little more.",
"Right, this is... | 2018-11-02T23:53:02 | 2018-11-03T22:10:13 | 2018-11-03T22:10:12Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | * fixed typo in get_max_muO2 and get_min_muO2.
* added the entry_ids of the charged and discharged materials to the summary. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1312/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1312/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1312",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1312",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1312.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1312.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1313 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1313/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1313/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1313/events | https://github.com/materialsproject/pymatgen/pull/1313 | 377,101,831 | MDExOlB1bGxSZXF1ZXN0MjI4MTQ2NDE0 | 1,313 | fixed the accidental overide of get_min_instability | {
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Ok, thank you.",
"The tests have been added."
] | 2018-11-03T23:02:50 | 2018-11-04T23:57:21 | 2018-11-04T23:57:21Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | fixed the accidental override of get_min_instability
I also realized that there is no test for the get_min_instability and get_max_instability functions, and I will write them as part of this pull request, I just want to let you know that a typo was made on the last one that was not caught by the tests. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1313/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1313/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1313",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1313",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1313.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1313.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1314 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1314/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1314/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1314/events | https://github.com/materialsproject/pymatgen/issues/1314 | 377,110,173 | MDU6SXNzdWUzNzcxMTAxNzM= | 1,314 | Missing test data for EOS analysis | {
"login": "tlsong",
"id": 35188774,
"node_id": "MDQ6VXNlcjM1MTg4Nzc0",
"avatar_url": "https://avatars.githubusercontent.com/u/35188774?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tlsong",
"html_url": "https://github.com/tlsong",
"followers_url": "https://api.github.com/users/tlsong/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks @tlsong \r\n\r\n@katherinelatimer2013 is this correct?",
"Yes, I used eta = (v0 / volume) ** (1. / 3.) (the same as what @tlsong has suggested) in the EOS analysis. Not sure at what point this bug arose but it should be changed. Thanks for pointing it out!",
"Ok, that's good to know, thank you! I can se... | 2018-11-04T01:19:35 | 2018-11-25T23:04:25 | 2018-11-25T23:04:25Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Maybe eta = (volume / v0) ** (1. / 3.) should be change to eta = (v0 / volume) ** (1. / 3.)??
In the code below:
`class BirchMurnaghan(EOSBase):
def _func(self, volume, params):
"""
BirchMurnaghan equation from PRB 70, 224107
"""
e0, b0, b1, v0 = tuple(params)
eta... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1314/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1314/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1315 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1315/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1315/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1315/events | https://github.com/materialsproject/pymatgen/pull/1315 | 377,192,146 | MDExOlB1bGxSZXF1ZXN0MjI4MjAxMjE1 | 1,315 | Fix for POTCARs with non-integer charge #1308 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-04T20:39:08 | 2018-11-04T20:39:22 | 2018-11-04T20:39:22Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Fixes #1308, no test for this since cannot distribute VASP-owned POTCAR. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1315/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1315/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1315",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1315",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1315.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1315.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1316 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1316/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1316/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1316/events | https://github.com/materialsproject/pymatgen/pull/1316 | 377,200,460 | MDExOlB1bGxSZXF1ZXN0MjI4MjA2NTk2 | 1,316 | Fix for BirchMurnaghan EOS | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-04T22:10:30 | 2018-11-05T01:39:29 | 2018-11-05T01:39:29Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
See #1314 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1316/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1316/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1316",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1316",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1316.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1316.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1317 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1317/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1317/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1317/events | https://github.com/materialsproject/pymatgen/pull/1317 | 377,608,242 | MDExOlB1bGxSZXF1ZXN0MjI4NTExNDI3 | 1,317 | CrystalNN takes into account ionic radii | {
"login": "computron",
"id": 986759,
"node_id": "MDQ6VXNlcjk4Njc1OQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/986759?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/computron",
"html_url": "https://github.com/computron",
"followers_url": "https://api.github.com/users/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Note: the failing test on CircleCI looks to be due to gulp_caller and unrelated to this PR:\r\n```\r\n======================================================================\r\nERROR: test_get_energy_relax_structure_buckingham (pymatgen.command_line.tests.test_gulp_caller.GlobalFunctionsTest)\r\n-------------------... | 2018-11-05T22:22:24 | 2018-11-05T22:31:28 | 2018-11-05T22:31:28Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
If a structure has oxidation states set, CrystalNN will try to use ionic radii instead of covalent/atomic radii.
* PeriodicTable has two new attributes per element: ``average_cationic_radius`` and ``average_anionic_radius``. These are used in the new CrystalNN, and for elements like N, P, S etc that ca... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1317/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1317/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1317",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1317",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1317.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1317.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1318 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1318/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1318/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1318/events | https://github.com/materialsproject/pymatgen/pull/1318 | 378,126,894 | MDExOlB1bGxSZXF1ZXN0MjI4OTA2Mjcx | 1,318 | Add substitutional dopant predictor and tests | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Very nice! Thanks @utf "
] | 2018-11-07T03:21:53 | 2018-11-08T17:19:15 | 2018-11-08T17:19:12Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Adds two functions to predict n- and p-type substitutional dopants using two methods:
- The difference in Shannon radii between the dopant and original site.
- The substitution probabilities defined in `SubstitutionPredictor`.
Related to materialsvirtuallab/matgenb#17.
An example usage of the code... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1318/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1318/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1318",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1318",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1318.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1318.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1319 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1319/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1319/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1319/events | https://github.com/materialsproject/pymatgen/pull/1319 | 378,516,634 | MDExOlB1bGxSZXF1ZXN0MjI5MjA0OTY0 | 1,319 | allow choosing element to add | {
"login": "hmlli",
"id": 42851962,
"node_id": "MDQ6VXNlcjQyODUxOTYy",
"avatar_url": "https://avatars.githubusercontent.com/u/42851962?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hmlli",
"html_url": "https://github.com/hmlli",
"followers_url": "https://api.github.com/users/hmlli/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I need a unit test for this functionality. Thanks."
] | 2018-11-07T23:40:16 | 2018-11-09T22:12:01 | 2018-11-09T22:12:01Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | For the ChargeDensityAnalyzer function, I was trying to insert a certain specie to the structure but original version only allows a dummy specie 'X'. Changed the default to 'X' but allowed choosing an element to add as well. Thanks. | {
"login": "hmlli",
"id": 42851962,
"node_id": "MDQ6VXNlcjQyODUxOTYy",
"avatar_url": "https://avatars.githubusercontent.com/u/42851962?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hmlli",
"html_url": "https://github.com/hmlli",
"followers_url": "https://api.github.com/users/hmlli/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1319/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1319/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1319",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1319",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1319.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1319.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1320 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1320/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1320/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1320/events | https://github.com/materialsproject/pymatgen/pull/1320 | 378,549,550 | MDExOlB1bGxSZXF1ZXN0MjI5MjI5MTQ4 | 1,320 | Final energy contributions Outcar attribute | {
"login": "CifLord",
"id": 8036054,
"node_id": "MDQ6VXNlcjgwMzYwNTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8036054?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CifLord",
"html_url": "https://github.com/CifLord",
"followers_url": "https://api.github.com/users/CifLord/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-08T02:15:40 | 2018-11-14T23:02:49 | 2018-11-08T03:23:44Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | The total energy stored in an OUTCAR file is the sum of individual contributions (e.g. contributions from alpha Z, Ewald energy, Hartree energy, exchange, V(xc)+E(xc), PAW double counting entropy T*S, eigenvalues, atomic energy and Solvation).
Having this information stored as an attribute of the Outcar class (as a... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1320/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1320/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1320",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1320",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1320.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1320.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1321 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1321/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1321/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1321/events | https://github.com/materialsproject/pymatgen/issues/1321 | 378,873,865 | MDU6SXNzdWUzNzg4NzM4NjU= | 1,321 | Bug in NearNeighbors.get_all_nn_info | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Agree with @WardLT's comment here that this should probably just me moved to be a `image` property on PeriodicSite (as well as fixing the underlying bug).",
"Yea, the `_get_image` operation has worried me for a while. While `_get_image` should account for wrapping of coordinates (if I understand the issue correc... | 2018-11-08T19:04:53 | 2019-02-23T19:13:02 | 2019-02-23T19:13:02Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | When the fractional coordinates of a site contain `1.`, the bonding to the site is duplicated.
**To Reproduce**
```python
from pymatgen.core.structure import Structure
from pymatgen.analysis.local_env import CrystalNN
cnn = CrystalNN()
sites = [[0., 0.2, 0.2], [0, 0, 0]]
structure = Structure([7, 0,... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1321/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1321/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1322 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1322/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1322/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1322/events | https://github.com/materialsproject/pymatgen/issues/1322 | 378,955,728 | MDU6SXNzdWUzNzg5NTU3Mjg= | 1,322 | Refactoring dimensionality functionalities | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Definitely should be combined into a common place. Perhaps all three in `pymatgen.analysis.dimensionality`? I could see a `Structure.get_dimension(algorithm='...')` convenience method maybe.\r\n\r\nI believe the author of `pymatgen.analysis.find_dimension` is currently re-factoring their implementation for speed a... | 2018-11-08T23:09:26 | 2018-11-14T18:33:05 | 2018-11-14T18:33:04Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Currently there are two dimensionality finders in pymatgen, one in `pymatgen.analysis.find_dimension`, the other in `pymatgen.analysis.structure_analyzer`. I am about to submit a PR for a third dimensionality finding routine which is faster and more reliable than both the existing methods.
It seems like we should c... | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1322/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1322/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1323 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1323/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1323/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1323/events | https://github.com/materialsproject/pymatgen/pull/1323 | 378,992,237 | MDExOlB1bGxSZXF1ZXN0MjI5NTY1ODY5 | 1,323 | Add dimensionality finder for bonded structures and refactor existing methods | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This looks good, thanks for the clean up/consolidation also! 👍 "
] | 2018-11-09T01:58:34 | 2018-11-14T18:28:46 | 2018-11-14T18:28:46Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
This pull request implements a new dimensionality finder based on the modified breadth-first-search algorithm described in: https://arxiv.org/abs/1808.02114
Unlike the previous algorithms in pymatgen, this implementation:
- Is based on `StructureGraph` objects.
- Is robust and does not suffer from th... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1323/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1323/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1323",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1323",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1323.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1323.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1324 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1324/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1324/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1324/events | https://github.com/materialsproject/pymatgen/pull/1324 | 379,365,293 | MDExOlB1bGxSZXF1ZXN0MjI5ODUzNjQx | 1,324 | Add query-chunking capability to MPRester.query | {
"login": "dwinston",
"id": 1497854,
"node_id": "MDQ6VXNlcjE0OTc4NTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1497854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dwinston",
"html_url": "https://github.com/dwinston",
"followers_url": "https://api.github.com/users/dwins... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"FYI two of the three Codacy checks seem misleading. They complain about unused imports, but I think they are only unused by the Codacy environment. If a user has `tqdm` installed, one of the imports will be used, and if a user is in a Jupyter notebook with `tqdm` installed, the other import will be used.\r\n\r\nAs... | 2018-11-10T00:16:22 | 2018-11-16T03:36:12 | 2018-11-16T03:36:12Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Add a `bulk_query` method to `MPRester`, which wraps `query` to provide a better user experience for fetching a large sum of data across many materials. Fixes issue where user requests not too much data per material, but too much data overall in one query because the number of materials matching criteria ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1324/reactions",
"total_count": 3,
"+1": 3,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1324/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1324",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1324",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1324.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1324.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1325 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1325/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1325/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1325/events | https://github.com/materialsproject/pymatgen/issues/1325 | 379,522,373 | MDU6SXNzdWUzNzk1MjIzNzM= | 1,325 | Error when downloading the data from Material project | {
"login": "AustinApple",
"id": 42490261,
"node_id": "MDQ6VXNlcjQyNDkwMjYx",
"avatar_url": "https://avatars.githubusercontent.com/u/42490261?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/AustinApple",
"html_url": "https://github.com/AustinApple",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Please do not post your API key in public space.\r\n\r\nThis is not a pymatgen issue. Occasionally the MP website has too many users for our current web servers and this causes this error. "
] | 2018-11-11T13:23:27 | 2018-11-28T20:57:56 | 2018-11-28T20:57:56Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
I try to access the unit_cell_formula from Material project. In the beginning, it performance normally. However, sometimes, the error pops out
"('REST query returned with error status code 500. Content: b\'<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">\\n<html><head>\\n<title>500 Internal Ser... | {
"login": "shyamd",
"id": 16827130,
"node_id": "MDQ6VXNlcjE2ODI3MTMw",
"avatar_url": "https://avatars.githubusercontent.com/u/16827130?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyamd",
"html_url": "https://github.com/shyamd",
"followers_url": "https://api.github.com/users/shyamd/fo... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1325/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1325/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1326 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1326/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1326/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1326/events | https://github.com/materialsproject/pymatgen/issues/1326 | 379,599,431 | MDU6SXNzdWUzNzk1OTk0MzE= | 1,326 | Is there a Enum of materials properties of MP database? | {
"login": "tamuhey",
"id": 24998666,
"node_id": "MDQ6VXNlcjI0OTk4NjY2",
"avatar_url": "https://avatars.githubusercontent.com/u/24998666?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tamuhey",
"html_url": "https://github.com/tamuhey",
"followers_url": "https://api.github.com/users/tamuhe... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi @tamuhey, I think I misread your comment initially. We already have something similar to this Enum in `MPRester.supported_properties` in `pymatgen.ext.matproj`. In general, the list of properties available on Materials Project does change, so I'm not sure that an Enum like this would be useful for us, but than... | 2018-11-12T02:42:24 | 2018-11-12T03:49:28 | 2018-11-12T03:49:28Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Hi,
I want a python Enum of materials properties of MP database, like below
```python
class MaterialProperties(Enum):
anonymous_formula = "anonymous_formula"
band_gap = "band_gap"
...
```
I tried to write a script ([gist](https://gist.github.com/tamuhey/c3... | {
"login": "tamuhey",
"id": 24998666,
"node_id": "MDQ6VXNlcjI0OTk4NjY2",
"avatar_url": "https://avatars.githubusercontent.com/u/24998666?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tamuhey",
"html_url": "https://github.com/tamuhey",
"followers_url": "https://api.github.com/users/tamuhe... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1326/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1326/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1327 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1327/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1327/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1327/events | https://github.com/materialsproject/pymatgen/pull/1327 | 380,303,473 | MDExOlB1bGxSZXF1ZXN0MjMwNTM0ODY0 | 1,327 | Class to handle IR spectra | {
"login": "henriquemiranda",
"id": 5531862,
"node_id": "MDQ6VXNlcjU1MzE4NjI=",
"avatar_url": "https://avatars.githubusercontent.com/u/5531862?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/henriquemiranda",
"html_url": "https://github.com/henriquemiranda",
"followers_url": "https://api.g... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi Henrique,\r\n\r\nA few things that would make this easier for everyone else to use:\r\n1.) Could you change the variable names to be more explicit? It took me a while to figure out what epsinf was until I realized it was the high-frequency dielectric limit. Still, this would have been easier if it was just name... | 2018-11-13T16:10:58 | 2019-09-24T22:01:28 | 2019-09-24T22:01:28Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | The new class contains the IR oscillator matrix elements.
Allows plotting the IR spectra with user-defined broadenings.
The oscillator matrix elements are computed with DFPT as implemented in Abinit.
It will be possible to start this class from the MPRester once the endpoints are created. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1327/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1327/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1327",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1327",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1327.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1327.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1328 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1328/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1328/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1328/events | https://github.com/materialsproject/pymatgen/pull/1328 | 380,374,716 | MDExOlB1bGxSZXF1ZXN0MjMwNTg4NDI4 | 1,328 | [Test failures] Add more patterns to PWOutput | {
"login": "zooks97",
"id": 8887252,
"node_id": "MDQ6VXNlcjg4ODcyNTI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8887252?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/zooks97",
"html_url": "https://github.com/zooks97",
"followers_url": "https://api.github.com/users/zooks97/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"There seem to be errors in these changes?\r\n\r\n```\r\n======================================================================\r\nERROR: test_get_celldm (pymatgen.io.tests.test_pwscf.PWOuputTest)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n Fi... | 2018-11-13T18:58:06 | 2019-02-12T00:46:18 | 2019-02-12T00:46:18Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | These cover most of the input summary block and some new outputs like total stress, total force, and total scf correction on the force. A few entries in the input summary block can be added (convergence threshold, number of iterations used, Exchange-correlation), but they require more complicated expressions (convergen... | {
"login": "zooks97",
"id": 8887252,
"node_id": "MDQ6VXNlcjg4ODcyNTI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8887252?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/zooks97",
"html_url": "https://github.com/zooks97",
"followers_url": "https://api.github.com/users/zooks97/... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1328/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1328/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1328",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1328",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1328.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1328.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1329 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1329/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1329/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1329/events | https://github.com/materialsproject/pymatgen/pull/1329 | 380,424,956 | MDExOlB1bGxSZXF1ZXN0MjMwNjI1ODUx | 1,329 | Tools for EPH calculations | {
"login": "gmatteo",
"id": 3811747,
"node_id": "MDQ6VXNlcjM4MTE3NDc=",
"avatar_url": "https://avatars.githubusercontent.com/u/3811747?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gmatteo",
"html_url": "https://github.com/gmatteo",
"followers_url": "https://api.github.com/users/gmatteo/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I accidentally clicked merge. I have reverted this PR. Pls implement proper unittests to show that all new functionality work as intended. Then resubmit a new PR. Thanks.",
"Hi Shyue,\r\n\r\nThese new tools are used to automate electron-phonon calculations.\r\nWriting proper *integration* tests would require the... | 2018-11-13T21:10:59 | 2018-11-14T23:35:49 | 2018-11-13T21:43:17Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
* Add workflows for EPH calculations (require dev-version of Abinit)
| {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1329/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1329/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1329",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1329",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1329.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1329.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1330 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1330/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1330/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1330/events | https://github.com/materialsproject/pymatgen/pull/1330 | 380,437,421 | MDExOlB1bGxSZXF1ZXN0MjMwNjM1MzI1 | 1,330 | Revert "Tools for EPH calculations" | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-13T21:43:44 | 2019-02-25T20:08:41 | 2018-11-13T21:43:53Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Reverts materialsproject/pymatgen#1329 | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1330/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1330/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1330",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1330",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1330.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1330.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1331 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1331/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1331/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1331/events | https://github.com/materialsproject/pymatgen/issues/1331 | 380,782,017 | MDU6SXNzdWUzODA3ODIwMTc= | 1,331 | MPRester fails to retrieve entries | {
"login": "fxcoudert",
"id": 1980544,
"node_id": "MDQ6VXNlcjE5ODA1NDQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1980544?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fxcoudert",
"html_url": "https://github.com/fxcoudert",
"followers_url": "https://api.github.com/users/fx... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"The reason why this fails is because too much data is requested in one query. If you just need the elasticity data, it is not good to do it via this route. It asks for a lot of unnecessary data. Use the query method to do a more fine-grained query. REfer to the http://bit.ly/materialsapi and http://matgenb.materia... | 2018-11-14T16:32:11 | 2023-07-24T15:22:07 | 2018-11-14T16:44:22Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
Results from a particular MPRester query are wrong (no entries are retrieved, even though they exist).
**To Reproduce**
Running this script:
```
from pymatgen import MPRester
api = MPRester('XXXXXXXXXXX')
n = 0
for i in range(1, 8):
entries = api.get_entries({'nelements': i}, pro... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1331/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1331/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1332 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1332/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1332/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1332/events | https://github.com/materialsproject/pymatgen/pull/1332 | 380,937,523 | MDExOlB1bGxSZXF1ZXN0MjMxMDIxNTk0 | 1,332 | Revert "Revert "Tools for EPH calculations"" | {
"login": "gmatteo",
"id": 3811747,
"node_id": "MDQ6VXNlcjM4MTE3NDc=",
"avatar_url": "https://avatars.githubusercontent.com/u/3811747?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gmatteo",
"html_url": "https://github.com/gmatteo",
"followers_url": "https://api.github.com/users/gmatteo/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-14T23:47:32 | 2018-11-15T00:25:47 | 2018-11-15T00:25:46Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Reverts materialsproject/pymatgen#1330 | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1332/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1332/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1332",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1332",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1332.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1332.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1333 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1333/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1333/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1333/events | https://github.com/materialsproject/pymatgen/issues/1333 | 381,840,457 | MDU6SXNzdWUzODE4NDA0NTc= | 1,333 | pymatgen.io.vasp.outputs.Procar() doesn't read phase factors for VASP 5.4.4 | {
"login": "dkorotin",
"id": 2283363,
"node_id": "MDQ6VXNlcjIyODMzNjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2283363?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dkorotin",
"html_url": "https://github.com/dkorotin",
"followers_url": "https://api.github.com/users/dkoro... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-17T08:07:22 | 2023-08-08T21:28:29 | 2023-08-08T21:28:29Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | It seems that PROCAR file format was changed somewhere between VASP versions 5.4.1 and 5.4.4. Consequently, Procar() class constructor is unable to read phase factors properly.
**`head -20 PROCAR` for VASP 5.4.4:**
```
PROCAR lm decomposed + phase
# of k-points: 13 # of bands: 20 # of ions: ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1333/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1333/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1334 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1334/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1334/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1334/events | https://github.com/materialsproject/pymatgen/pull/1334 | 381,859,280 | MDExOlB1bGxSZXF1ZXN0MjMxNzI1NjEy | 1,334 | Fix for the issue #1333 | {
"login": "dkorotin",
"id": 2283363,
"node_id": "MDQ6VXNlcjIyODMzNjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2283363?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dkorotin",
"html_url": "https://github.com/dkorotin",
"followers_url": "https://api.github.com/users/dkoro... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Can you please implement a unittest? Thanks.",
"> Can you please implement a unittest? Thanks.\r\n\r\nTo my shame, I do not know what it is and how to implement it. Probably you can show me an example...",
"An appropriate place to add a test would be here: \r\n\r\nhttps://github.com/materialsproject/pymatgen/b... | 2018-11-17T12:35:33 | 2018-12-04T01:08:05 | 2018-12-04T01:08:05Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | It fixes new format for phase_factors in PROCAR of VASP 5.4.4.
The VASP version check is a bit rude, if one knows how to make it better – please, do it. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1334/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1334/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1334",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1334",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1334.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1334.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1335 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1335/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1335/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1335/events | https://github.com/materialsproject/pymatgen/pull/1335 | 382,030,482 | MDExOlB1bGxSZXF1ZXN0MjMxODM0MzY1 | 1,335 | Ferroelectric np.matrix deprecation fix | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-19T02:04:27 | 2018-11-19T02:54:48 | 2018-11-19T02:54:48Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Resolves #1280 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1335/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1335/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1335",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1335",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1335.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1335.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1336 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1336/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1336/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1336/events | https://github.com/materialsproject/pymatgen/pull/1336 | 382,751,889 | MDExOlB1bGxSZXF1ZXN0MjMyMzg2MjUw | 1,336 | Add additional EOS test data | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-20T16:42:44 | 2018-11-25T23:04:25 | 2018-11-25T23:04:25Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Resolves #1314 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1336/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1336/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1336",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1336",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1336.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1336.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1337 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1337/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1337/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1337/events | https://github.com/materialsproject/pymatgen/pull/1337 | 382,759,744 | MDExOlB1bGxSZXF1ZXN0MjMyMzkyMTcx | 1,337 | Fix bug in analysis.graphs | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks to @utf for reporting"
] | 2018-11-20T16:59:48 | 2018-12-03T01:08:31 | 2018-11-20T18:59:58Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Ensure `jimage` kwarg is respected in `get_connected_sites` | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1337/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1337/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1337",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1337",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1337.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1337.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1338 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1338/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1338/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1338/events | https://github.com/materialsproject/pymatgen/pull/1338 | 383,117,358 | MDExOlB1bGxSZXF1ZXN0MjMyNjYyODMy | 1,338 | Implementation of VASP's PAW PSP recommendations | {
"login": "HanmeiTang",
"id": 12416538,
"node_id": "MDQ6VXNlcjEyNDE2NTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/12416538?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/HanmeiTang",
"html_url": "https://github.com/HanmeiTang",
"followers_url": "https://api.github.com/use... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Can this already be done by supplying a PSP argument to MPRelax? Other than the PSP choice, what other parameters are changed?",
"The PSP choice is the only change made, which results in 21 elements different from`MPRelaxSet`. This class uses either `PBE_52` or `PBE_54` according to the VASP manual and it is equ... | 2018-11-21T13:26:24 | 2018-11-26T16:55:32 | 2018-11-26T16:55:32Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
VASP recently added the recommended PAW potentials for DFT calculations using vasp.5.2 to the manual on Oct 28, 2018. This PR adds a new input set class `MVLRelaxSet` to utilize the recommended potentials.
* Added config file "MVLRelaxSet_52.yaml" to implement VASP's PAW PSP recommendations, while INCA... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1338/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1338/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1338",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1338",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1338.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1338.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1339 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1339/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1339/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1339/events | https://github.com/materialsproject/pymatgen/issues/1339 | 383,287,669 | MDU6SXNzdWUzODMyODc2Njk= | 1,339 | More transparency with elemental reference energies | {
"login": "CJBartel",
"id": 26173737,
"node_id": "MDQ6VXNlcjI2MTczNzM3",
"avatar_url": "https://avatars.githubusercontent.com/u/26173737?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CJBartel",
"html_url": "https://github.com/CJBartel",
"followers_url": "https://api.github.com/users/CJB... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2018-11-21T20:50:24 | 2023-08-08T21:29:43 | 2023-08-08T21:29:42Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | I've sometimes found it difficult to figure out what elemental reference energies are used to map total energy to formation energy. This seems like a relatively straightforward feature to add - e.g., when querying the database allow a user to download a dictionary {el1 : mu_el1, el2 : mu_el2} for each chemical formula ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1339/reactions",
"total_count": 4,
"+1": 4,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1339/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1340 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1340/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1340/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1340/events | https://github.com/materialsproject/pymatgen/issues/1340 | 383,382,837 | MDU6SXNzdWUzODMzODI4Mzc= | 1,340 | Reorganization of SlabGenerator (or make a subclass of SlabTransformations for terminations) | {
"login": "CifLord",
"id": 8036054,
"node_id": "MDQ6VXNlcjgwMzYwNTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8036054?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CifLord",
"html_url": "https://github.com/CifLord",
"followers_url": "https://api.github.com/users/CifLord/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I agree @richardtran415 .\r\n\r\nI think Slab should be part of the core and the methods of generating slabs should be in analysis. SlabGenerator should be a module with one generator for each type of method. ",
"Should note this other set of algorithms for slab generation from Hinuma: https://arxiv.org/pdf/1508... | 2018-11-22T05:09:58 | 2024-03-20T03:41:10 | 2023-08-08T21:28:59Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | There are several methods of generating specific termination in surface.py:
- Simple cleavage: The original algorithm whereby we simply insert a vacuum at a termination to create a slab. This preserves the stoichiometry relative to bulk.
- get_tasker2_slabs(): This is a method built into the Slab object. It enume... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1340/reactions",
"total_count": 2,
"+1": 2,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1340/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1341 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1341/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1341/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1341/events | https://github.com/materialsproject/pymatgen/pull/1341 | 383,857,401 | MDExOlB1bGxSZXF1ZXN0MjMzMjI2NzI4 | 1,341 | fix a bug of Element.valence of noble gases, and add tests | {
"login": "tamuhey",
"id": 24998666,
"node_id": "MDQ6VXNlcjI0OTk4NjY2",
"avatar_url": "https://avatars.githubusercontent.com/u/24998666?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tamuhey",
"html_url": "https://github.com/tamuhey",
"followers_url": "https://api.github.com/users/tamuhe... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This PR has an error:\r\n\r\n```\r\n======================================================================\r\nERROR: test_valence (pymatgen.core.tests.test_periodic_table.ElementTestCase)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n File \"/ho... | 2018-11-23T15:12:17 | 2018-11-27T00:11:57 | 2018-11-23T15:24:26Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | # Summary
Fix a bug of [Element valence](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/core/periodic_table.py#L609) with noble gases.
# bug
```Python
import pymatgen as mg
he=mg.Element("He")
he.valence
```
causes an error:
```
--> 585 valence.append((l, ne))
IndexErro... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1341/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1341/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1341",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1341",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1341.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1341.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1342 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1342/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1342/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1342/events | https://github.com/materialsproject/pymatgen/pull/1342 | 384,564,717 | MDExOlB1bGxSZXF1ZXN0MjMzNzM4NDQ4 | 1,342 | fix: missing "import numpy" | {
"login": "tamuhey",
"id": 24998666,
"node_id": "MDQ6VXNlcjI0OTk4NjY2",
"avatar_url": "https://avatars.githubusercontent.com/u/24998666?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tamuhey",
"html_url": "https://github.com/tamuhey",
"followers_url": "https://api.github.com/users/tamuhe... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thank you !"
] | 2018-11-27T00:11:32 | 2018-11-27T01:29:33 | 2018-11-27T01:29:32Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | #1341 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1342/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1342/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1342",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1342",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1342.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1342.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1343 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1343/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1343/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1343/events | https://github.com/materialsproject/pymatgen/pull/1343 | 385,461,366 | MDExOlB1bGxSZXF1ZXN0MjM0NDI3NTg0 | 1,343 | ScaleToRelaxedTransformation | {
"login": "CifLord",
"id": 8036054,
"node_id": "MDQ6VXNlcjgwMzYwNTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8036054?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CifLord",
"html_url": "https://github.com/CifLord",
"followers_url": "https://api.github.com/users/CifLord/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi @richardtran415, this looks useful! My only concern is that the `apply_transformation()` method signature is different from the other transformations. This should either just be `apply_transformation(structure)` or `apply_transformation(structure, return_ranked_list=...)` (in the case of one-to-many transformat... | 2018-11-28T21:19:42 | 2019-01-08T21:17:32 | 2018-11-29T19:26:49Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | New Transformation class. This transformation takes an initial unrelaxed structure and a corresponding relaxed structure. It determines a matrix containing the percent change in each scalar in going from the initial lattice matrix to the relax lattice matrix.
When using apply_transformation(), a similar structure (... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1343/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1343/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1343",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1343",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1343.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1343.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1344 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1344/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1344/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1344/events | https://github.com/materialsproject/pymatgen/pull/1344 | 385,488,114 | MDExOlB1bGxSZXF1ZXN0MjM0NDQ4Nzk1 | 1,344 | Structure component enhancements | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks!"
] | 2018-11-28T22:41:12 | 2018-11-29T00:01:36 | 2018-11-28T23:59:05Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Added a number of features relating to structure components.
* `get_structure_component_info` renamed to `get_structure_components`
* `get_structure_components` can now return the indices of the corresponding sites in the original structure.
* Can also return `MoleculeGraph` objects for any zero dime... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1344/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1344/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1344",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1344",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1344.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1344.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1345 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1345/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1345/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1345/events | https://github.com/materialsproject/pymatgen/pull/1345 | 385,515,222 | MDExOlB1bGxSZXF1ZXN0MjM0NDY5ODIz | 1,345 | Properly catch non 0D graphs in zero_d_graph_to_molecule_graph | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Please don't merge this as I have some further commits.",
"If the tests pass then this should be ok to merge.",
"Cool, thanks! It'd be useful to add [WIP] to the title of future PRs if they're not ready to merge, just to communicate explicitly that you're still working on them."
] | 2018-11-29T00:27:38 | 2018-11-29T18:19:05 | 2018-11-29T18:19:05Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
An exception is now thrown when trying to convert non-zero dimensional graphs to `MoleculeGraph`s.
A test to ensure this behavior has been added. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1345/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1345/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1345",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1345",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1345.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1345.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1346 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1346/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1346/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1346/events | https://github.com/materialsproject/pymatgen/pull/1346 | 385,531,881 | MDExOlB1bGxSZXF1ZXN0MjM0NDgyMTMy | 1,346 | Bug fix for `calculate_vol` | {
"login": "HanmeiTang",
"id": 12416538,
"node_id": "MDQ6VXNlcjEyNDE2NTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/12416538?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/HanmeiTang",
"html_url": "https://github.com/HanmeiTang",
"followers_url": "https://api.github.com/use... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi @HanmeiTang, the diff for this PR seems very large for a small bug fix, is this correct?",
"Hi @mkhorton, sorry for the confusion. What I actually changed is line#1203 in the original \"utils.py\". Other changes are simply formatting to meet the PEP8 80-char-per-line requirement. I can undo the formatting if ... | 2018-11-29T01:46:12 | 2018-11-29T18:18:18 | 2018-11-29T18:18:06Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Minor buf fix for `calculate_vol`.
This bug can be reproduced as:
```python
>>> from pymatgen.analysis.defects.utils import TopographyAnalyzer, calculate_vol
>>> from pymatgen.core import Structure
>>> s = Structure.from_file("pymatgen/test_files/chgden/LiFePO4.cif")
>>> a = TopographyAnalyzer(s... | {
"login": "HanmeiTang",
"id": 12416538,
"node_id": "MDQ6VXNlcjEyNDE2NTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/12416538?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/HanmeiTang",
"html_url": "https://github.com/HanmeiTang",
"followers_url": "https://api.github.com/use... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1346/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1346/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1346",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1346",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1346.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1346.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1347 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1347/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1347/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1347/events | https://github.com/materialsproject/pymatgen/pull/1347 | 385,691,619 | MDExOlB1bGxSZXF1ZXN0MjM0NjAyNzI4 | 1,347 | fixed symmetrically_remove_atoms() for multiple indices removal | {
"login": "yiming-xu",
"id": 33731382,
"node_id": "MDQ6VXNlcjMzNzMxMzgy",
"avatar_url": "https://avatars.githubusercontent.com/u/33731382?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yiming-xu",
"html_url": "https://github.com/yiming-xu",
"followers_url": "https://api.github.com/users/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-11-29T11:31:01 | 2018-11-29T18:08:01 | 2018-11-29T18:07:11Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Added removal_list to store all indices to be removed, and call remove_sites only if all indices have equivalent sites for removal.
* Previous implementation removes site (and its equivalent) for each point during the loop, while not updating the symmetric structure used for reference. This could poten... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1347/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1347/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1347",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1347",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1347.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1347.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1348 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1348/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1348/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1348/events | https://github.com/materialsproject/pymatgen/issues/1348 | 385,869,406 | MDU6SXNzdWUzODU4Njk0MDY= | 1,348 | Clean up of warnings in test outputs | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I should note I'm responsible for the CIF warnings -- I wanted to be clear if we were making changes to the CIF file during parsing to fix errors, will have a think about what best to do to suppress these however since we use a lot of CIF files in the tests.",
"Generally, people should not be using CIF files to ... | 2018-11-29T18:32:46 | 2023-08-08T21:29:18 | 2023-08-08T21:29:18Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Need to clean up warnings in test outputs to make test results easier to read.
Three main culprits: CrystalNN ("locate an appropriate radius", "distance cutoffs"), site merging in grain boundary (due to warning in Structure, "Sites with different site property grain_label are merged.so property is set to none"), and... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1348/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1348/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1349 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1349/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1349/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1349/events | https://github.com/materialsproject/pymatgen/pull/1349 | 385,872,445 | MDExOlB1bGxSZXF1ZXN0MjM0NzQ0MzQx | 1,349 | Update MPRester to load endpoint from PMG_MAPI_ENDPOINT | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Given that we are going to expose the endpoint, we might as well just hard code the endpoint in the tests themselves? i.e., initialize MPRester with endpoint=zola?",
"I set it as an environment variable because there are some tests that use the MPRester that aren't in ext.matproj (e.g. the Pourbaix pipeline test... | 2018-11-29T18:40:58 | 2018-12-03T01:08:29 | 2018-12-02T20:16:06Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
To support setting the MPRester endpoint via an env variable (for testing purposes). | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1349/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1349/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1349",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1349",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1349.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1349.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1350 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1350/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1350/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1350/events | https://github.com/materialsproject/pymatgen/pull/1350 | 385,872,523 | MDExOlB1bGxSZXF1ZXN0MjM0NzQ0NDAw | 1,350 | Bug fix for `calculate_vol` | {
"login": "HanmeiTang",
"id": 12416538,
"node_id": "MDQ6VXNlcjEyNDE2NTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/12416538?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/HanmeiTang",
"html_url": "https://github.com/HanmeiTang",
"followers_url": "https://api.github.com/use... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Ah, this looks much better! Thanks @HanmeiTang !"
] | 2018-11-29T18:41:09 | 2018-11-29T20:27:44 | 2018-11-29T20:27:44Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Hi @mkhorton, I have fixed the unittest, where I commited the wrong file. This PR fixes bug in `calculate_vol` and corresponding test has been added.
This bug can be reproduced as:
```python
>>> from pymatgen.analysis.defects.utils import TopographyAnalyzer, calculate_vol
>>> from pymatgen.core impo... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1350/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1350/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1350",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1350",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1350.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1350.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1351 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1351/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1351/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1351/events | https://github.com/materialsproject/pymatgen/pull/1351 | 387,058,730 | MDExOlB1bGxSZXF1ZXN0MjM1NjMzNzcw | 1,351 | Small bug fix | {
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-12-03T23:58:02 | 2018-12-04T01:07:43 | 2018-12-04T01:07:43Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | The new merged coordinate sometimes likes outside the [0,1) range | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1351/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1351/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1351",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1351",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1351.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1351.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1352 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1352/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1352/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1352/events | https://github.com/materialsproject/pymatgen/pull/1352 | 388,343,414 | MDExOlB1bGxSZXF1ZXN0MjM2NjMwMjMy | 1,352 | Add IUPAC ordering for Composition formulae | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Isn't this almost like ordering by Mendeleev number? The Pettifor Mendeleev number effectively goes in the same manner (specific orderings may differ a little).",
"It is very similar but the main difference is the position of Hydrogen which is exactly what this ordering aims to fix."
] | 2018-12-06T18:36:44 | 2018-12-06T19:31:04 | 2018-12-06T19:21:12Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
The IUPAC red book details a system for ordering elements in chemical formulae. The ordering is detailed in Table IV shown below. The ordering produces formula slightly different to ordering by electronegativity. For example, `H6CN` goes to `CNH6`.
![screen shot 2018-11-29 at 3 21 58 pm](https://user-im... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1352/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1352/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1352",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1352",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1352.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1352.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1353 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1353/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1353/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1353/events | https://github.com/materialsproject/pymatgen/pull/1353 | 388,363,076 | MDExOlB1bGxSZXF1ZXN0MjM2NjQ1MDc2 | 1,353 | Add error throwing for negative max_sites in Composition.oxi_state_guesses | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-12-06T19:29:42 | 2018-12-07T23:13:01 | 2018-12-07T23:13:01Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Composition.oxi_state_guesses currently has a `max_sites` option where, if possible, the composition will be reduced to at most this many sites to speed up oxidation state guesses. If the structure cannot be reduced to this many sites an error will be thrown. If `-1` is passed to `max_sites` the compositi... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1353/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1353/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1353",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1353",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1353.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1353.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1354 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1354/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1354/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1354/events | https://github.com/materialsproject/pymatgen/issues/1354 | 388,403,615 | MDU6SXNzdWUzODg0MDM2MTU= | 1,354 | How do I customize my INCAR ? | {
"login": "Shuyangzero",
"id": 35701741,
"node_id": "MDQ6VXNlcjM1NzAxNzQx",
"avatar_url": "https://avatars.githubusercontent.com/u/35701741?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Shuyangzero",
"html_url": "https://github.com/Shuyangzero",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"See http://matgenb.materialsvirtuallab.org/2017/04/14/Inputs-and-Analysis-of-VASP-runs.html"
] | 2018-12-06T21:23:26 | 2018-12-06T21:54:02 | 2018-12-06T21:54:02Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Hi,
I am wondering if I can customize my INCAR by pymatgen ? For instance, is there a way to automatically write GGA+U 's parameters U and J in INCAR by the elements' order in POSCAR ? Other tags like MAGMOM and different values for EDIFF ? Thanks ! | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1354/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1354/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1355 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1355/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1355/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1355/events | https://github.com/materialsproject/pymatgen/pull/1355 | 388,467,608 | MDExOlB1bGxSZXF1ZXN0MjM2NzI3MDc0 | 1,355 | Insert site group | {
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-12-07T01:26:21 | 2018-12-07T14:50:22 | 2018-12-07T14:50:22Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Update/Bug fixes for in analysis.defects.utils
* fixed the floating point problem that causes the sites to fall outside the first BZ
* Store the average charge density instead of the total charge density around each local minima | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1355/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1355/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1355",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1355",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1355.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1355.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1356 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1356/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1356/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1356/events | https://github.com/materialsproject/pymatgen/issues/1356 | 388,668,612 | MDU6SXNzdWUzODg2Njg2MTI= | 1,356 | A Bug in MPSOCSet with DFT+U | {
"login": "Shuyangzero",
"id": 35701741,
"node_id": "MDQ6VXNlcjM1NzAxNzQx",
"avatar_url": "https://avatars.githubusercontent.com/u/35701741?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Shuyangzero",
"html_url": "https://github.com/Shuyangzero",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Please provide some test code that shows this behavior. "
] | 2018-12-07T14:06:41 | 2023-08-08T21:30:41 | 2023-08-08T21:30:41Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Hi,
The MpSOCSet doesn't have the correct format for LDAUU, LDAUJ, LDAUL.
I specify 'LDAUJ':{'Eu':1}, 'LDAUU':{'Eu':8},'LDAUL':{'Eu':3} in my user_setting for MPSOCSet
But in INCAR, it displays as
LDAUJ = {'Eu': 1}
LDAUL = {'Eu': 3}
LDAUPRINT = 1
LDAUTYPE = 2
LDAUU = {'Eu': 8}
which doesn't extract t... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1356/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1356/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1357 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1357/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1357/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1357/events | https://github.com/materialsproject/pymatgen/issues/1357 | 388,709,671 | MDU6SXNzdWUzODg3MDk2NzE= | 1,357 | Search Pt, seemed got wrong result | {
"login": "fallleave001",
"id": 29368603,
"node_id": "MDQ6VXNlcjI5MzY4NjAz",
"avatar_url": "https://avatars.githubusercontent.com/u/29368603?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fallleave001",
"html_url": "https://github.com/fallleave001",
"followers_url": "https://api.github.c... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi @fallleave001, in what way does it seem wrong to you? They look correct. Note that the structure retrieved by the API is in a primitive setting and since Pt is a face-centered cubic crystal the lattice parameters in the primitive and conventional setting are not the same but are related by sqrt(2), so that the ... | 2018-12-07T15:51:47 | 2018-12-10T05:54:37 | 2018-12-10T05:54:37Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
When using api to search Pt crystalline, got the following:
[Structure Summary
Lattice
abc : 2.8120017156650783 2.8120017104377606 2.81200171
angles : 59.99999988751204 59.999999949004994 59.99999997242852
volume : 15.722867111767158
A : 2.43526492 0.0 1.40600086
B : 0... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1357/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1357/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1358 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1358/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1358/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1358/events | https://github.com/materialsproject/pymatgen/pull/1358 | 388,817,116 | MDExOlB1bGxSZXF1ZXN0MjM2OTk2MTM0 | 1,358 | Bug fix in core.composition | {
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Can you add a unitest. THanks."
] | 2018-12-07T21:17:34 | 2018-12-07T23:12:02 | 2018-12-07T23:12:02Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | to_data_dict['element'] returned <dict_keys> which is a generator and cannot be pickled | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1358/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1358/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1358",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1358",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1358.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1358.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1359 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1359/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1359/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1359/events | https://github.com/materialsproject/pymatgen/pull/1359 | 388,847,531 | MDExOlB1bGxSZXF1ZXN0MjM3MDE5Njg5 | 1,359 | Remove logging.basicConfig call in graphs.py | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks!"
] | 2018-12-07T23:17:02 | 2018-12-08T20:47:29 | 2018-12-08T20:47:29Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
`graphs.py` currently has a call to `logging.basicConfig` to set the logging level. This will affect the top level logger rather than the module level logger. The code now sets the logging level of the module level logger. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1359/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1359/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1359",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1359",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1359.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1359.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1360 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1360/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1360/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1360/events | https://github.com/materialsproject/pymatgen/pull/1360 | 388,969,690 | MDExOlB1bGxSZXF1ZXN0MjM3MDk3NzQ1 | 1,360 | Fix integer miller indices | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks!"
] | 2018-12-08T23:30:44 | 2018-12-09T19:12:39 | 2018-12-09T19:12:36Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
The `get_integer_index` function for miller indices now correctly returns integer indices when possible (if an integer index cannot be determined a floating point index is given).
E.g. `get_integer_index((2, 2, 0))` now gives `(1, 1, 0)` rather than `(1.0, 1.0, 0)`. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1360/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1360/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1360",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1360",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1360.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1360.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1361 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1361/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1361/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1361/events | https://github.com/materialsproject/pymatgen/issues/1361 | 388,987,448 | MDU6SXNzdWUzODg5ODc0NDg= | 1,361 | Suppression of warnings in CrystalNN | {
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.gith... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Agreed these should be reduced (this is also mentioned in #1348, since the warnings are crowding the test logs)",
"Ah, I didn't catch the recent issue you opened. Well, glad we're on the same page! For context, I brought this up because I have a few codes I plan to release that use Pymatgen's `CrystalNN`, but ha... | 2018-12-09T04:54:51 | 2019-02-25T20:55:05 | 2019-02-25T20:55:05Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Is your feature request related to a problem? Please describe.**
The warnings are a bit overkill with `CrystalNN` when there are no oxidation states added for the structure. Oxidation states are often not feasible to add for complex materials, but `CrystalNN` is still one of the best NN algorithms implemented in Pym... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1361/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1361/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1362 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1362/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1362/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1362/events | https://github.com/materialsproject/pymatgen/pull/1362 | 389,095,720 | MDExOlB1bGxSZXF1ZXN0MjM3MTc0NjUy | 1,362 | Add option to return graph for structure components | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Doesn't the MoleculeGraph itself contain the networkx graph as an attribute?",
"The molecule graph is only returned when the component is zero-dimensional. I agree that this method is getting a little messy. I’m tempted to rewrite it so that instead of a structure it always returns a `StructureGraph`, with a `Mo... | 2018-12-10T01:28:56 | 2018-12-11T19:35:56 | 2018-12-11T19:35:56Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Added the `inc_graph` option to `get_structure_components()` to allow returning of networkx graphs for structure components.
The graphs have their nodes indexed to match the returned component `Structure` objects rather than initial structure passed to `get_structure_components`. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1362/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1362/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1362",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1362",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1362.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1362.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1363 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1363/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1363/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1363/events | https://github.com/materialsproject/pymatgen/pull/1363 | 389,560,079 | MDExOlB1bGxSZXF1ZXN0MjM3NTIzNDMx | 1,363 | Added all_in_polar option for Polarization class | {
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks! Is there a test for the new functionality? (i.e. with `all_in_polar=True`)",
"Additional tests added!",
"Looks like continuous integration is failing, but at least from my read of the error it is not related to my code.",
"Thanks @blondegeek , it's not clear to me why the AppVeyor tests are suddenly ... | 2018-12-11T01:38:46 | 2018-12-13T20:46:42 | 2018-12-13T20:46:42Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | I added an all_in_polar option for the Polarization class and updated the tests to be for the option where all_in_polar= False. all_in_polar uses the polar lattice to calculate "proper" polarization differences.
There is usually little or no difference between the output of the Polarization class methods using all_... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1363/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1363/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1363",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1363",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1363.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1363.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1364 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1364/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1364/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1364/events | https://github.com/materialsproject/pymatgen/issues/1364 | 390,743,833 | MDU6SXNzdWUzOTA3NDM4MzM= | 1,364 | Extracting new basis vector from core.surface.Slab | {
"login": "cpashartis",
"id": 7492783,
"node_id": "MDQ6VXNlcjc0OTI3ODM=",
"avatar_url": "https://avatars.githubusercontent.com/u/7492783?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/cpashartis",
"html_url": "https://github.com/cpashartis",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Each slab is simply a structure. It also contains the oriented unit cell. So just looking at the lattice vectors of those will give you the basis vectors. \r\n\r\nFor general help that is unrelated to bugs and issues, please post on pymatgen google groups https://groups.google.com/forum/?fromgroups&nomobile=true#!... | 2018-12-13T15:58:09 | 2018-12-13T17:26:59 | 2018-12-13T16:41:01Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Hello,
I hope I am in the right place.
I'm looking at trying to rotate the elastic tensor of a crystal structure to the direction of the slab surface I am looking at (h,k,l). However, there does not seem to be an easy way (the code is a bit unclear to me) of extracting **_which_** vectors the slab generator funct... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1364/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1364/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1365 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1365/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1365/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1365/events | https://github.com/materialsproject/pymatgen/pull/1365 | 391,298,771 | MDExOlB1bGxSZXF1ZXN0MjM4ODU4MjIw | 1,365 | Change default MPRester endpoint at request of @dwinston | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-12-14T22:20:14 | 2019-05-31T16:21:20 | 2018-12-20T07:20:29Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | materialsproject.org without the www will be the preferred endpoint going forwards | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1365/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1365/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1365",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1365",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1365.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1365.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1366 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1366/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1366/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1366/events | https://github.com/materialsproject/pymatgen/pull/1366 | 391,739,160 | MDExOlB1bGxSZXF1ZXN0MjM5MTY1Mzc0 | 1,366 | Added Trajectory class for MD trajectory analysis | {
"login": "sivonxay",
"id": 25111118,
"node_id": "MDQ6VXNlcjI1MTExMTE4",
"avatar_url": "https://avatars.githubusercontent.com/u/25111118?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sivonxay",
"html_url": "https://github.com/sivonxay",
"followers_url": "https://api.github.com/users/siv... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"It is unclear to me what this is supposed to do, given that diffusion_analyzer pretty much handles a lot of this. And the construct of this Trajectories class violates a lot of python internal constructs for lists/sequences. In particular, having functions like `change_index` to change indices is definitely not no... | 2018-12-17T14:34:09 | 2019-01-24T23:56:20 | 2019-01-24T23:56:20Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Added a Trajectory class which decreases memory overhead for working with MD trajectories in pymatgen. Here, the trajectory is stored as a singular structure and a set of displacements, which allow the positions at any timestep to be reconstructed.
* Added Trajectory Class
* Added MPMDSet
## Addit... | {
"login": "sivonxay",
"id": 25111118,
"node_id": "MDQ6VXNlcjI1MTExMTE4",
"avatar_url": "https://avatars.githubusercontent.com/u/25111118?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sivonxay",
"html_url": "https://github.com/sivonxay",
"followers_url": "https://api.github.com/users/siv... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1366/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1366/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1366",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1366",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1366.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1366.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1367 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1367/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1367/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1367/events | https://github.com/materialsproject/pymatgen/pull/1367 | 391,809,277 | MDExOlB1bGxSZXF1ZXN0MjM5MjIwNTgx | 1,367 | Update Team List | {
"login": "shyamd",
"id": 16827130,
"node_id": "MDQ6VXNlcjE2ODI3MTMw",
"avatar_url": "https://avatars.githubusercontent.com/u/16827130?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyamd",
"html_url": "https://github.com/shyamd",
"followers_url": "https://api.github.com/users/shyamd/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2018-12-17T17:12:25 | 2020-05-12T15:47:23 | 2018-12-17T19:03:19Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Updating the team list. Please suggest any additional changes. | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1367/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1367/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1367",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1367",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1367.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1367.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1368 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1368/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1368/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1368/events | https://github.com/materialsproject/pymatgen/issues/1368 | 392,047,050 | MDU6SXNzdWUzOTIwNDcwNTA= | 1,368 | `AdsorbateSiteFinder.find_adsorption_sites()` assumes `mvec` is array | {
"login": "fallleave001",
"id": 29368603,
"node_id": "MDQ6VXNlcjI5MzY4NjAz",
"avatar_url": "https://avatars.githubusercontent.com/u/29368603?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fallleave001",
"html_url": "https://github.com/fallleave001",
"followers_url": "https://api.github.c... | [
{
"id": 4708633439,
"node_id": "LA_kwDOACgets8AAAABGKgLXw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20repro",
"name": "needs repro",
"color": "d93f0b",
"default": false,
"description": "Bug report that needs a reproduction"
},
{
"id": 552560888... | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Is there a way of instantiating `AdsorbateSiteFinder` where `mvec` isn't already an `np.array`? Didn't find one. If you have one, would be good to add as test case.\r\n\r\nEither way doesn't cost much to wrap `self.mvec` in `np.asarray(self.mvec)` and gives peace of mind. 😄 Thanks for the pointer."
] | 2018-12-18T08:35:16 | 2023-06-18T17:48:49 | 2023-06-18T17:48:49Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | in adsorption.py module, the function find_adsorption_sites(...), last line
```
sites = [site + distance * self.mvec for site in sites]
```
seems should change to:
```
sites = [site + distance * np.array(self.mvec) for site in sites]
```
| {
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/fo... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1368/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1368/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1369 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1369/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1369/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1369/events | https://github.com/materialsproject/pymatgen/pull/1369 | 396,687,233 | MDExOlB1bGxSZXF1ZXN0MjQyODEwODEz | 1,369 | Add defect sublattice generator and point defect matcher | {
"login": "dbroberg",
"id": 5498596,
"node_id": "MDQ6VXNlcjU0OTg1OTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/5498596?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dbroberg",
"html_url": "https://github.com/dbroberg",
"followers_url": "https://api.github.com/users/dbrob... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Sorry - having git issues. I will reopen this when I fix it."
] | 2019-01-07T23:13:45 | 2019-01-08T00:16:10 | 2019-01-08T00:15:46Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | This PR adds a few essential features for defect analysis which relate to the use of a new sub-lattice generator. The newly added create_saturated_interstitial_structure function generates the sub-lattice of an interstitial defect object via a "saturated interstitial structure". This is done by generating a new struct... | {
"login": "dbroberg",
"id": 5498596,
"node_id": "MDQ6VXNlcjU0OTg1OTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/5498596?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dbroberg",
"html_url": "https://github.com/dbroberg",
"followers_url": "https://api.github.com/users/dbrob... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1369/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1369/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1369",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1369",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1369.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1369.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1370 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1370/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1370/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1370/events | https://github.com/materialsproject/pymatgen/pull/1370 | 396,721,521 | MDExOlB1bGxSZXF1ZXN0MjQyODM2NDg3 | 1,370 | Add defect sublattice generator and point defect matcher | {
"login": "dbroberg",
"id": 5498596,
"node_id": "MDQ6VXNlcjU0OTg1OTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/5498596?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dbroberg",
"html_url": "https://github.com/dbroberg",
"followers_url": "https://api.github.com/users/dbrob... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This PR is one of a larger set of defect analysis functionalities which I have already written. These are all needed for full functionality of the point defect atomate workflow. Right now I am opting to submit several smaller PR's but if you would prefer that I submit a large PR so that everything can be digested ... | 2019-01-08T02:05:37 | 2019-01-13T16:17:33 | 2019-01-13T16:17:33Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | This PR adds a few essential features for defect analysis:
- A "create_saturated_interstitial_structure" function which generates the sub-lattice of an interstitial defect object via a "saturated interstitial structure" function which generates a new structure with a fully occupied sub-lattice for the defect (under... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1370/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1370/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1370",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1370",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1370.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1370.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1371 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1371/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1371/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1371/events | https://github.com/materialsproject/pymatgen/pull/1371 | 398,066,486 | MDExOlB1bGxSZXF1ZXN0MjQzODY3ODU2 | 1,371 | Simplification of COHP Plotting | {
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-01-10T23:45:56 | 2019-01-13T16:16:33 | 2019-01-13T16:16:32Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
I have removed the methods get_cohp and get_icohp in CompleteCohp. They are now inherited from Cohp and give an array with the average cohp. Instead, I included get_cohp_by_label which gives a Cohp object that can now be easily plotted with CohpPlotter. Furthermore, I included tests. I am also planning to... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1371/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1371/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1371",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1371",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1371.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1371.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1372 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1372/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1372/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1372/events | https://github.com/materialsproject/pymatgen/pull/1372 | 398,602,696 | MDExOlB1bGxSZXF1ZXN0MjQ0MjQ5MTM3 | 1,372 | PARCHG from WAVECAR | {
"login": "mturiansky",
"id": 8866816,
"node_id": "MDQ6VXNlcjg4NjY4MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8866816?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mturiansky",
"html_url": "https://github.com/mturiansky",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is really nice, thank you 👍 "
] | 2019-01-12T23:33:11 | 2019-01-13T23:50:01 | 2019-01-13T16:17:16Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Adds the function "get_parchg" to the Wavecar class. This function outputs a Chgcar object that corresponds to the charge density of the specified wavefunction. This emulates the PARCHG output from VASP, but it does not include augmentation from the PAWs.
* PARCHG from a Wavecar object
* For real wave... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1372/reactions",
"total_count": 2,
"+1": 2,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1372/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1372",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1372",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1372.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1372.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1373 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1373/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1373/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1373/events | https://github.com/materialsproject/pymatgen/pull/1373 | 399,268,904 | MDExOlB1bGxSZXF1ZXN0MjQ0NzM0ODg5 | 1,373 | Boltztrap2 bugs fix | {
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fra... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks @fraricci "
] | 2019-01-15T10:00:39 | 2019-01-17T22:14:18 | 2019-01-17T22:14:14Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Some bug fixing for Boltztrap2 interface | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1373/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1373/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1373",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1373",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1373.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1373.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1374 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1374/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1374/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1374/events | https://github.com/materialsproject/pymatgen/pull/1374 | 400,471,457 | MDExOlB1bGxSZXF1ZXN0MjQ1NjUyMDA3 | 1,374 | set point_group attribute from sgencodings and test point_group attri… | {
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks! Will merge once tests pass"
] | 2019-01-17T21:30:34 | 2019-01-19T01:04:49 | 2019-01-17T22:12:49Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | The SpaceGroup.point_group attribute was not being set if int_symbol was not in SYMM_OPs. This would cause an error when calling for the point_group attribute for space groups with underscores in their name, for example, space group 14 with symbol 'P12_1/c1'. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1374/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1374/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1374",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1374",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1374.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1374.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1375 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1375/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1375/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1375/events | https://github.com/materialsproject/pymatgen/pull/1375 | 400,535,076 | MDExOlB1bGxSZXF1ZXN0MjQ1NzAxNTUw | 1,375 | Polarization cartesian fix | {
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"The `convert_cart_to_latt` looks like a really useful function. I know I've wanted something like this in the past (for something unrelated to polarization).\r\n\r\nIt seems to me like it could be a function in the Lattice class instead?\r\n\r\n@blondegeek @mkhorton Thoughts?",
"That method is already in Lattice... | 2019-01-18T01:34:07 | 2019-01-23T20:52:20 | 2019-01-18T14:40:29Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | VASP reports dipole moments in along Cartesian directions. This pull requests adds the ability to specify when creating a Polarization object whether ionic and electronic contributions to the polarization are given in Cartesian or lattice directions. The default for ionic contributions is lattice directions (since it i... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1375/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1375/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1375",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1375",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1375.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1375.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1376 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1376/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1376/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1376/events | https://github.com/materialsproject/pymatgen/issues/1376 | 401,882,033 | MDU6SXNzdWU0MDE4ODIwMzM= | 1,376 | Poscar inputs.py 'selective_dynamics' attribute doesn't assign appropriately passed sdynamics tags when printing or writing to file. Error is in line 487 for the inputs.py script. Currently forces selective dynamics tags to all be T. Proposed change: sd = ["T" if j else "F" for j in self.selective_dynamics[i]] ... | {
"login": "tboland1",
"id": 23020097,
"node_id": "MDQ6VXNlcjIzMDIwMDk3",
"avatar_url": "https://avatars.githubusercontent.com/u/23020097?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/tboland1",
"html_url": "https://github.com/tboland1",
"followers_url": "https://api.github.com/users/tbo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi Tara,\r\n\r\nFrom what I understand, you're providing the selective dynamics as a list of 'T' or 'F' strings (e.g. {['T', 'T', 'T'], ['T', 'F', 'F'],['F', 'F', 'F']]} )\r\n\r\nI don't think this is a bug in the code. The selective dynamics that Structure requires is a list of bool (e.g. {'selective_dynamics': [... | 2019-01-22T17:51:52 | 2019-02-27T00:49:39 | 2019-02-25T20:52:35Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If app... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1376/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1376/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1377 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1377/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1377/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1377/events | https://github.com/materialsproject/pymatgen/pull/1377 | 401,922,257 | MDExOlB1bGxSZXF1ZXN0MjQ2NzI4MjUy | 1,377 | Add VESTA bonding preset to CutOffNN | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-01-22T19:40:37 | 2019-01-22T20:30:44 | 2019-01-22T20:30:44Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Adds the VESTA bonding cut-offs as a preset to the CutOffNN class.
The cut-offs were taken from the style.ini file distributed with VESTA. These cut-offs seem to have been generated based on bond valence parameters but I'm not sure how exactly. | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1377/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1377/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1377",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1377",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1377.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1377.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1378 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1378/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1378/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1378/events | https://github.com/materialsproject/pymatgen/pull/1378 | 402,535,445 | MDExOlB1bGxSZXF1ZXN0MjQ3MTk2NzMz | 1,378 | move convert_cart_to_latt to method get_lattice_coords of Lattice class | {
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks @blondegeek ! Haven't merged yet because I'm just mulling over that `get_lattice_coords` method name, I'm not sure if that might cause confusion for people? I'm not sure what a better name for it might be though. The inverse method might also be helpful (get cart coords from lattice coords).",
"Actually, ... | 2019-01-24T04:15:55 | 2019-01-28T23:35:14 | 2019-01-28T20:24:49Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | See discussion on #1375. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1378/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1378/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1378",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1378",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1378.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1378.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1379 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1379/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1379/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1379/events | https://github.com/materialsproject/pymatgen/pull/1379 | 402,948,029 | MDExOlB1bGxSZXF1ZXN0MjQ3NTE3MTAz | 1,379 | Added Trajectory class for MD trajectory | {
"login": "sivonxay",
"id": 25111118,
"node_id": "MDQ6VXNlcjI1MTExMTE4",
"avatar_url": "https://avatars.githubusercontent.com/u/25111118?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sivonxay",
"html_url": "https://github.com/sivonxay",
"followers_url": "https://api.github.com/users/siv... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Is this ready to merge? Will have a read over if so.",
"Yes, should satisfy the criteria @shyamd listed on the last PR.",
"Ok, this looks like it'd be really useful to have in pymatgen! It seems like the comments from the last thread were addressed, thanks.\r\n\r\nThere are a few last items that need to be add... | 2019-01-24T23:58:29 | 2019-01-28T19:10:14 | 2019-01-28T19:09:38Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Reopened #1366 due to branch contamination.
@shyamd @mkhorton | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1379/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1379/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1379",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1379",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1379.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1379.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1380 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1380/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1380/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1380/events | https://github.com/materialsproject/pymatgen/issues/1380 | 403,989,202 | MDU6SXNzdWU0MDM5ODkyMDI= | 1,380 | XRD diffraction patterns not properly MSONable due to tuple keys ('hkl') | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Tagging @mattmcdermott here also who encountered this bug.",
"The bug does not lie in Spectrum, but specifically in XRD. Spectrum does not impose any restrictions on args or kwargs. ",
"Yes, that's correct; apologies. We should probably also rename `DiffractionPatternCalculator` to `AbstractDiffractionPatternC... | 2019-01-28T20:17:27 | 2019-01-28T21:01:54 | 2019-01-28T21:01:54Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | @czhengsci I saw you created the Spectrum class, would you be willing to investigate this and submit a fix?
XRD patterns `.to_json()` is failing because the (h, k, l) values are stored in a dictionary key as a tuple:
```
'hkls': [{(1, 0, 0): 6, (1, 0, -1): 6},
{(1, 1, -1): 6},
{(2, 0, -1): 12, (1, 1, 0): ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1380/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1380/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1381 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1381/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1381/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1381/events | https://github.com/materialsproject/pymatgen/pull/1381 | 404,493,426 | MDExOlB1bGxSZXF1ZXN0MjQ4NjYzMTMx | 1,381 | Code speedup for get_dimensionality_cheon in analysis.dimension; also includes a fix for tricky_structure in test_dimensionality | {
"login": "gcheon",
"id": 16144609,
"node_id": "MDQ6VXNlcjE2MTQ0NjA5",
"avatar_url": "https://avatars.githubusercontent.com/u/16144609?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gcheon",
"html_url": "https://github.com/gcheon",
"followers_url": "https://api.github.com/users/gcheon/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-01-29T21:25:32 | 2019-01-30T00:33:32 | 2019-01-30T00:33:32Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1381/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1381/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1381",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1381",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1381.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1381.patch",
"merged_at... | ||||
https://api.github.com/repos/materialsproject/pymatgen/issues/1382 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1382/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1382/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1382/events | https://github.com/materialsproject/pymatgen/pull/1382 | 404,958,489 | MDExOlB1bGxSZXF1ZXN0MjQ5MDI0MzMz | 1,382 | Update MPNonSCFSet smearing parameters | {
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"f... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-01-30T20:49:52 | 2019-01-30T20:52:18 | 2019-01-30T20:52:17Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Based on discussions with @shyamd, @mkhorton and @tschaume, I've updated the default smearing parameters for NonSCF uniform calculations.
The parameters I've modified are:
- NEDOS now 2001 for uniform calculations.
- ISMEAR now -5 (tetrahedron method with Blöchl corrections) for uniform calculations.... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1382/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1382/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1382",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1382",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1382.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1382.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1383 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1383/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1383/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1383/events | https://github.com/materialsproject/pymatgen/pull/1383 | 405,037,723 | MDExOlB1bGxSZXF1ZXN0MjQ5MDg2MTA2 | 1,383 | Some odds and end fixes | {
"login": "shyamd",
"id": 16827130,
"node_id": "MDQ6VXNlcjE2ODI3MTMw",
"avatar_url": "https://avatars.githubusercontent.com/u/16827130?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyamd",
"html_url": "https://github.com/shyamd",
"followers_url": "https://api.github.com/users/shyamd/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Is this WIP ? Indentation error in some tests. (Also due credit stub was included; I think this is a good idea, I just wasn't sure whether it was intentional since it wasn't mentioned in the commit log)",
"Sorry, Duecredit is for another PR. I think I fixed that indentation."
] | 2019-01-31T01:17:20 | 2020-05-12T15:47:24 | 2019-01-31T19:44:09Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Few odd fixes
* Add Metagga types to run_type in Vasprun
* Compatability shouldn't index error for weird elements like Americium. | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1383/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1383/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1383",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1383",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1383.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1383.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1384 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1384/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1384/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1384/events | https://github.com/materialsproject/pymatgen/issues/1384 | 406,191,764 | MDU6SXNzdWU0MDYxOTE3NjQ= | 1,384 | Bug in StructureGraph.remove_nodes method | {
"login": "lan496",
"id": 7272505,
"node_id": "MDQ6VXNlcjcyNzI1MDU=",
"avatar_url": "https://avatars.githubusercontent.com/u/7272505?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/lan496",
"html_url": "https://github.com/lan496",
"followers_url": "https://api.github.com/users/lan496/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-02-04T06:00:04 | 2019-02-06T03:35:48 | 2019-02-06T03:35:48Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
StructrureGraph.remove_nodes method do not seem to change attributes of a graph.
**Environments**
python 3.6.4
pymatgen==2019.1.24
networkx==2.2
**To Reproduce**
```
structure = Structure(Lattice.tetragonal(5.0, 50.0), ['H'], [[0, 0, 0]])
square_sg = StructureGraph.with_empty_graph(st... | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1384/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1384/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1385 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1385/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1385/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1385/events | https://github.com/materialsproject/pymatgen/pull/1385 | 406,194,825 | MDExOlB1bGxSZXF1ZXN0MjQ5OTQ4MTIx | 1,385 | fix relabel_nodes parameter in StructureGraph.remove_nodes | {
"login": "lan496",
"id": 7272505,
"node_id": "MDQ6VXNlcjcyNzI1MDU=",
"avatar_url": "https://avatars.githubusercontent.com/u/7272505?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/lan496",
"html_url": "https://github.com/lan496",
"followers_url": "https://api.github.com/users/lan496/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Pls add a unit test to ensure this bug does not recur. Thanks.",
"I've added tests for checking if (StructureGraph|MoleculeGraph).(remove_nodes|insert_node) correctly update a graph.\r\n\r\nIn writing these tests, I also noticed that insert_node method also may have a bug about networkx:\r\n(1) networkx.relabel.... | 2019-02-04T06:17:15 | 2020-08-14T13:16:39 | 2019-02-06T03:35:48Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Fix https://github.com/materialsproject/pymatgen/issues/1384 | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1385/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1385/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1385",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1385",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1385.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1385.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1386 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1386/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1386/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1386/events | https://github.com/materialsproject/pymatgen/issues/1386 | 406,469,578 | MDU6SXNzdWU0MDY0Njk1Nzg= | 1,386 | netcdf4 should be declared as a dependency | {
"login": "yurivict",
"id": 271906,
"node_id": "MDQ6VXNlcjI3MTkwNg==",
"avatar_url": "https://avatars.githubusercontent.com/u/271906?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yurivict",
"html_url": "https://github.com/yurivict",
"followers_url": "https://api.github.com/users/yurivic... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"What were you importing? Just pymatgen?",
"Yes. Once it is directly required by pymatgen, it should depend on it.",
"I don't think pymatgen requires it. Pls provide the version of pymatgen you are using. ",
"> pymatgen-2019.1.24/pymatgen/io/abinit/netcdf.py:`import netCDF4` failed with the following error:",... | 2019-02-04T18:55:08 | 2019-02-06T00:50:36 | 2019-02-04T20:26:06Z | NONE | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Simple import of this module fails:
```
No module named netCDF4
Please install netcdf4 with `conda install netcdf4`
If the conda version does not work, uninstall it with `conda uninstall hdf4 hdf5 netcdf4`
and use `pip install netcdf4`
and use `pip install netcdf4`""" % str(exc))
```
You need to add netcd... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1386/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1386/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1387 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1387/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1387/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1387/events | https://github.com/materialsproject/pymatgen/pull/1387 | 406,933,184 | MDExOlB1bGxSZXF1ZXN0MjUwNTIwMDE5 | 1,387 | Misc fixes for lammps data | {
"login": "adengz",
"id": 5439300,
"node_id": "MDQ6VXNlcjU0MzkzMDA=",
"avatar_url": "https://avatars.githubusercontent.com/u/5439300?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/adengz",
"html_url": "https://github.com/adengz",
"followers_url": "https://api.github.com/users/adengz/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-02-05T19:14:16 | 2019-02-05T19:32:51 | 2019-02-05T19:32:51Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
* Fix rotation operation for orthogonal box **not** originally aligned with Cartesian axes.
* Fix `Topology` serialization caused by numpy data type.
## Additional dependencies introduced (if any)
None | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1387/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1387/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1387",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1387",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1387.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1387.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1388 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1388/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1388/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1388/events | https://github.com/materialsproject/pymatgen/issues/1388 | 407,927,559 | MDU6SXNzdWU0MDc5Mjc1NTk= | 1,388 | Consider renaming `stress` to `negative_stress` in VASP output parsing | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Given no one else has commented, I suggest you proceed and implement the change.\r\n\r\nMy principle for pymatgen is ask for forgiveness, not permission. If it breaks something elsewhere, we can revert it later.",
"Yeah, I'll go ahead and do this -- it will almost certainly break some things in atomate and/or ou... | 2019-02-07T22:32:37 | 2023-08-10T14:56:22 | 2023-08-10T14:56:22Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
Consider rename the parsed stress from a vasprun.xml/OUTCAR from `stress` to `negative_stress` to more explicitly communicate what is actually being parsed, e.g. consider the following (thanks @montoyjh):
```
FORCE on cell =-STRESS in cart. coord. units (eV/reduce length):
Direction X Y Z ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1388/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1388/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1389 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1389/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1389/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1389/events | https://github.com/materialsproject/pymatgen/pull/1389 | 409,048,198 | MDExOlB1bGxSZXF1ZXN0MjUyMTIxMTk4 | 1,389 | Interface reaction app revision | {
"login": "yihanxiao92",
"id": 25351305,
"node_id": "MDQ6VXNlcjI1MzUxMzA1",
"avatar_url": "https://avatars.githubusercontent.com/u/25351305?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yihanxiao92",
"html_url": "https://github.com/yihanxiao92",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@yihanxiao92 There are test failures. See https://circleci.com/gh/materialsproject/pymatgen/8304 . Pls fix and submit a new PR."
] | 2019-02-12T00:30:29 | 2019-02-12T14:33:50 | 2019-02-12T13:23:45Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Modified the equation normalization, and added convexity tests for the reaction energy plot.
* The returned equations for the interface app are now normalized in such a way that the coefficients of reactants reflect their molar ratios during the mixing.
* Add rigorous tests for the convexity of the re... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1389/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1389/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1389",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1389",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1389.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1389.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1390 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1390/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1390/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1390/events | https://github.com/materialsproject/pymatgen/pull/1390 | 409,078,747 | MDExOlB1bGxSZXF1ZXN0MjUyMTQ0NzYx | 1,390 | Extend PWOutput implementation | {
"login": "zooks97",
"id": 8887252,
"node_id": "MDQ6VXNlcjg4ODcyNTI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8887252?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/zooks97",
"html_url": "https://github.com/zooks97",
"followers_url": "https://api.github.com/users/zooks97/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-02-12T02:03:08 | 2019-02-12T05:05:22 | 2019-02-12T05:05:22Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | I've written a large set of (hopefully working this time) regular expressions for the PWOutput parser class, supporting the following properties:
- Energy
- Final energy
- Enthalpy (new enthalpy)
- Final enthalpy
- Density
- Warnings
- Total stress
- Stress tensor
- Total force
- Force on each atom with sit... | {
"login": "zooks97",
"id": 8887252,
"node_id": "MDQ6VXNlcjg4ODcyNTI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8887252?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/zooks97",
"html_url": "https://github.com/zooks97",
"followers_url": "https://api.github.com/users/zooks97/... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1390/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1390/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1390",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1390",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1390.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1390.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1391 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1391/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1391/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1391/events | https://github.com/materialsproject/pymatgen/pull/1391 | 409,386,905 | MDExOlB1bGxSZXF1ZXN0MjUyMzgzMzIx | 1,391 | fixed bug in test_interface_reactions file | {
"login": "yihanxiao92",
"id": 25351305,
"node_id": "MDQ6VXNlcjI1MzUxMzA1",
"avatar_url": "https://avatars.githubusercontent.com/u/25351305?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yihanxiao92",
"html_url": "https://github.com/yihanxiao92",
"followers_url": "https://api.github.com/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-02-12T16:27:49 | 2019-02-12T17:11:37 | 2019-02-12T17:11:37Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Fixed bug in test_interface_reactions.py file.
(Note: the other error from the tests are not from this pull request.) | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1391/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1391/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1391",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1391",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1391.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1391.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1392 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1392/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1392/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1392/events | https://github.com/materialsproject/pymatgen/pull/1392 | 409,470,002 | MDExOlB1bGxSZXF1ZXN0MjUyNDQ3NTUx | 1,392 | DLS predictor - add limits | {
"login": "computron",
"id": 986759,
"node_id": "MDQ6VXNlcjk4Njc1OQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/986759?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/computron",
"html_url": "https://github.com/computron",
"followers_url": "https://api.github.com/users/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 2019-02-12T19:47:12 | 2019-02-12T20:00:08 | 2019-02-12T20:00:08Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Issue #1295 mentions that DLSVolumePredictor can have very large errors in rare (but important) instances.
As no long-term solution is likely forthcoming, this PR allows the user to set bounds on how much the volume can change from the initial structure, with defaults of 50% to 150% of the original cel... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1392/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1392/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1392",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1392",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1392.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1392.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1393 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1393/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1393/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1393/events | https://github.com/materialsproject/pymatgen/issues/1393 | 409,483,649 | MDU6SXNzdWU0MDk0ODM2NDk= | 1,393 | Bug in VoronoiConnectivity. | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | [] | closed | false | {
"login": "computron",
"id": 986759,
"node_id": "MDQ6VXNlcjk4Njc1OQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/986759?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/computron",
"html_url": "https://github.com/computron",
"followers_url": "https://api.github.com/users/comp... | [
{
"login": "computron",
"id": 986759,
"node_id": "MDQ6VXNlcjk4Njc1OQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/986759?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/computron",
"html_url": "https://github.com/computron",
"followers_url": "https://api.g... | null | [
"Why assigned to me? This is Will Richards's method AFAIK?",
"Anyway maybe @utf from my team can look into it, and if no solution within an hour, to figure out what to do next",
"Nvm. I fixed it."
] | 2019-02-12T20:22:32 | 2019-02-12T21:20:41 | 2019-02-12T21:20:41Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Describe the bug**
There are failing tests with VoronoiConnectivity with new numpy version.
See https://circleci.com/gh/materialsproject/pymatgen/8309
**Desktop (please complete the following information):**
- Master | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1393/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1393/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1394 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1394/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1394/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1394/events | https://github.com/materialsproject/pymatgen/issues/1394 | 409,569,931 | MDU6SXNzdWU0MDk1Njk5MzE= | 1,394 | Dash offline docs not being deployed | {
"login": "dwinston",
"id": 1497854,
"node_id": "MDQ6VXNlcjE0OTc4NTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1497854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dwinston",
"html_url": "https://github.com/dwinston",
"followers_url": "https://api.github.com/users/dwins... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I have submitted a fix. "
] | 2019-02-13T00:44:31 | 2019-02-13T04:19:10 | 2019-02-13T04:19:10Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | **Description**
It seems that building/deploying of [Dash](http://kapeli.com/dash) docsets is not longer happening properly. The last version available is for the 2018.12.12 release.
To reproduce, one needs to have the Dash app for OSX.
| {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1394/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1394/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1395 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1395/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1395/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1395/events | https://github.com/materialsproject/pymatgen/pull/1395 | 409,730,367 | MDExOlB1bGxSZXF1ZXN0MjUyNjM2NDIy | 1,395 | New/adapted method for handling COHPs/ICOHPs | {
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I have included the suggestions and also renamed the method get_summed_icohp_by_labellist to get_summed_cohp_by_label_list etc. I will update the corresponding tutorial as soon as possible."
] | 2019-02-13T10:23:11 | 2019-02-13T15:44:35 | 2019-02-13T15:44:35Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
I have added a method to CompleteCohp that allows to plot summed COHPs easily (get_summed_cohps_by_labellist). And, I have included a new parameter in the method get_icohp_dict_of_certain_site of IcohpCollection that allows to filter for certain bonding partners. Of course, I have also added new unit tes... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1395/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1395/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1395",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1395",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1395.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1395.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1396 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1396/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1396/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1396/events | https://github.com/materialsproject/pymatgen/pull/1396 | 411,081,367 | MDExOlB1bGxSZXF1ZXN0MjUzNjQ3OTkz | 1,396 | fix json serialization for Molecule with DummySpecie | {
"login": "gpetretto",
"id": 8665734,
"node_id": "MDQ6VXNlcjg2NjU3MzQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8665734?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gpetretto",
"html_url": "https://github.com/gpetretto",
"followers_url": "https://api.github.com/users/gp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks"
] | 2019-02-16T15:13:20 | 2019-02-16T15:39:49 | 2019-02-16T15:39:45Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
The current implementation of `from_dict` in `Molecule` fails if a `DummySpecie` is present:
```
from pymatgen import Molecule
m = Molecule(species=["X"], coords=[[0,0,0]])
Molecule.from_dict(m.as_dict())
```
leads to the following error:
>
> /pymatgen/pymatgen/core/structure.py in from_dict(cls... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1396/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1396/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1396",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1396",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1396.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1396.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1397 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1397/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1397/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1397/events | https://github.com/materialsproject/pymatgen/issues/1397 | 412,037,487 | MDU6SXNzdWU0MTIwMzc0ODc= | 1,397 | wrong magmom using MPSOCSet | {
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fra... | [] | closed | false | {
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhor... | [
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.gi... | null | [
"This line should already be there in MPSOCSet:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/5904d5e00aa5d8300404f82af9f4c0e01cb65479/pymatgen/io/vasp/sets.py#L1048\r\n\r\nIt's not clear to me why that wouldn't be working just by looking at it. If you can upload your example (or email me it directly), I... | 2019-02-19T17:22:30 | 2023-08-10T14:56:48 | 2023-08-10T14:56:48Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | Hello,
I noticed that using MPSOCSet on a magnetic previous calculation,
it does not write the proper MAGMOM in the incar.
Example:
in: MPSOCSet.from_prev_calc('.').incar['MAGMOM']
out: [0.6, 0.6, 0.6, 0.6, 0.6]
Although, the returned structure contains the right MAGMOM:
in: MPSOCSet.from_prev_calc('.').stru... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1397/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1397/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} | ||
https://api.github.com/repos/materialsproject/pymatgen/issues/1398 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1398/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1398/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1398/events | https://github.com/materialsproject/pymatgen/pull/1398 | 412,126,820 | MDExOlB1bGxSZXF1ZXN0MjU0NDEwODMx | 1,398 | Fix outrageous performance bug in Poscar.get_string | {
"login": "ExpHP",
"id": 1411280,
"node_id": "MDQ6VXNlcjE0MTEyODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/1411280?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ExpHP",
"html_url": "https://github.com/ExpHP",
"followers_url": "https://api.github.com/users/ExpHP/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks. Perhaps you can also highlight where there are othe property abuses, and we can try to fix those."
] | 2019-02-19T21:13:19 | 2019-02-19T22:14:24 | 2019-02-19T22:13:46Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ```python
#!/usr/bin/env python3
import numpy as np
from pymatgen import Structure
from pymatgen.io.vasp import Poscar
N = 100000
s = Structure(np.array([[1,0,0],[0,1,0],[0,0,1]]), ['C']*N, np.zeros((N, 3)))
Poscar(s, velocities=np.zeros((N, 3)).tolist()).get_string()
```
Prepare to wait several millenia.
... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1398/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1398/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1398",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1398",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1398.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1398.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1399 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1399/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1399/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1399/events | https://github.com/materialsproject/pymatgen/pull/1399 | 412,187,382 | MDExOlB1bGxSZXF1ZXN0MjU0NDU4MTEx | 1,399 | How best to handle PointGroupAnalyzer error when list from `_get_smallest_set_not_on_axis` is empty. | {
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I think the way the eigen_zero is tested can be changed. There is no reason for the **3. It is rather arbitrary. I just pushed a fix."
] | 2019-02-20T00:25:13 | 2019-02-20T02:57:57 | 2019-02-20T02:57:42Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | This pull request has a question at the bottom of the post.
For the following Molecule, with the default parameters, PointGroupAnalyzer throws an error from the list returned [`self._get_smallest_set_not_on_axis(axis)` being empty](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/symmetry/analyzer.p... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1399/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1399/timeline | null | true | false | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1399",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1399",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1399.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1399.patch",
"merged_at... | |||
https://api.github.com/repos/materialsproject/pymatgen/issues/1400 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1400/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1400/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1400/events | https://github.com/materialsproject/pymatgen/issues/1400 | 412,510,664 | MDU6SXNzdWU0MTI1MTA2NjQ= | 1,400 | Property abuse | {
"login": "ExpHP",
"id": 1411280,
"node_id": "MDQ6VXNlcjE0MTEyODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/1411280?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ExpHP",
"html_url": "https://github.com/ExpHP",
"followers_url": "https://api.github.com/users/ExpHP/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks for the feedback. Just to address a few points:\r\n\r\ni. The reason why properties are used is that these are indeed attributes. E.g., Structure.cart_coords - these refer to the cartesian coordinates of the Structure. Certainly, one can use the more cumbersome Structure.get_cart_coords() but that makes it ... | 2019-02-20T16:19:19 | 2019-10-02T19:11:10 | 2019-10-02T19:11:10Z | CONTRIBUTOR | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | I alluded to issues of property abuse in #1398. Allow me to describe what I'm talking about.
For better or worse, pymatgen appears to be following some design trend that any method which takes no arguments should be a property. I will argue that this design decision is largely for the worse, resulting in a number ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1400/reactions",
"total_count": 2,
"+1": 2,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
} | https://api.github.com/repos/materialsproject/pymatgen/issues/1400/timeline | null | completed | false | false | {
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.