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/701
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/701/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/701/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/701/events
|
https://github.com/materialsproject/pymatgen/pull/701
| 236,403,085
|
MDExOlB1bGxSZXF1ZXN0MTI1OTc1Mjgy
| 701
|
You can supply max bond distances to recognize dimensionality of NaCl
|
{
"login": "kmu",
"id": 3815357,
"node_id": "MDQ6VXNlcjM4MTUzNTc=",
"avatar_url": "https://avatars.githubusercontent.com/u/3815357?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/kmu",
"html_url": "https://github.com/kmu",
"followers_url": "https://api.github.com/users/kmu/followers",
"following_url": "https://api.github.com/users/kmu/following{/other_user}",
"gists_url": "https://api.github.com/users/kmu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/kmu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/kmu/subscriptions",
"organizations_url": "https://api.github.com/users/kmu/orgs",
"repos_url": "https://api.github.com/users/kmu/repos",
"events_url": "https://api.github.com/users/kmu/events{/privacy}",
"received_events_url": "https://api.github.com/users/kmu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hi @kmu - thanks for this.\r\n\r\nNote that the original code should have allowed you to update the bond lengths by overriding the atomic radii via ```el_radius_updates```, but I forgot to pass the setting to a function. I just pushed a fix for that so that the setting works as intended.\r\n\r\nNote that your proposed PR ```bonds``` operates on atom pairs rather than atoms, so the functionality is slightly different than ```el_radius_updates```.\r\n\r\n@shyuep I think it's good to have both options and this PR is good to go. The only suggested update is to clarify in the docs that ```el_radius_updates``` and ```bonds``` perform similar things and one can do one or the other method, but not both. i.e., if one specifies ```bonds```, the auto-bonding algorithm is turned off and only those bonds are considered.\r\n",
"Can one of you please fix the docs before I merge? THanks.",
"@computron Thank you for the modification and suggestion! \r\n@shyuep I have just fixed the docs.",
"Thanks! I just merged."
] | 2017-06-16T07:32:16
| 2017-06-18T23:54:56
|
2017-06-17T14:02:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* This PR extends the `get_dimensionality` method in `strucuture_analyzer.py`.
* Users can optionally pass max bond distances to correctly recognize the dimensionality of NaCl, which is problematic by default as commented in `get_dimensionality` by the original author.
* If the max bond distances are not supplied, original `get_max_bond_lengths` method works to detect them.
* This can be helpful if users want to ignore specific types of bonds.
* Unit tests are added to verify that
* CsCl is recognized as 1D using `get_max_bond_lengths` (default)
* CsCl is recognized as 3D by passing the max bond distance of Cs-Cl.
* Hope this helps!
## Additional dependencies introduced (if any)
None
## TODO (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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/701/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/701/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/701",
"html_url": "https://github.com/materialsproject/pymatgen/pull/701",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/701.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/701.patch",
"merged_at": "2017-06-17T14:02:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/702
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/702/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/702/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/702/events
|
https://github.com/materialsproject/pymatgen/pull/702
| 237,404,311
|
MDExOlB1bGxSZXF1ZXN0MTI2NjcyMDE2
| 702
|
Sdynamics fix
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-06-21T03:23:13
| 2019-04-04T02:40:46
|
2017-06-21T03:30:10Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Adds selective dynamics parsing to Vasprun. This is necessary if one wants to accurately determine if the max force considered by the optimizer is below the target threshold.
* Vasprun now parses selective dynamics for structures in vasprun.xml
* Associated unittest
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/702/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/702/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/702",
"html_url": "https://github.com/materialsproject/pymatgen/pull/702",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/702.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/702.patch",
"merged_at": "2017-06-21T03:30:10Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/703
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/703/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/703/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/703/events
|
https://github.com/materialsproject/pymatgen/pull/703
| 237,939,236
|
MDExOlB1bGxSZXF1ZXN0MTI3MDYyMDA1
| 703
|
Jhu kpoints
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks. Can you rename the jhu_kpoints to just jhu. Basically, the name of packages in ext will be just the name of the source. E.g., matproj, jhu, oqmd, aflow, ccdb, etc. The jhu module itself can provide kpoints, or whatever else they provide. "
] | 2017-06-22T18:51:01
| 2017-06-22T20:17:47
|
2017-06-22T20:17:47Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
# Summary
Revision of previous PR for JHU servlet k-point grids. See http://muellergroup.jhu.edu/K-Points.html. Also expands user_kpoints_settings functionality of sets.
* Adds JHU servlet interface into a new module ext.jhu_kpoints
* Allows user_kpoints_settings to be supplied a kpoints object directly if desired.
Usage:
```
from pymatgen.ext.jhu import get_kpoints
kpoints = get_kpoints(structure, min_distance=29)
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/703/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/703/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/703",
"html_url": "https://github.com/materialsproject/pymatgen/pull/703",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/703.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/703.patch",
"merged_at": "2017-06-22T20:17:47Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/704
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/704/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/704/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/704/events
|
https://github.com/materialsproject/pymatgen/pull/704
| 237,994,112
|
MDExOlB1bGxSZXF1ZXN0MTI3MTAyODYz
| 704
|
Bug fix for CifWriter with write_magmoms=True
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls add a unittest for this?",
"Thanks. Merged."
] | 2017-06-22T22:41:37
| 2017-06-23T02:22:28
|
2017-06-23T02:22:28Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Now handles float/list magmoms correctly in addition to Magmom class.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/704/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/704/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/704",
"html_url": "https://github.com/materialsproject/pymatgen/pull/704",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/704.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/704.patch",
"merged_at": "2017-06-23T02:22:28Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/705
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/705/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/705/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/705/events
|
https://github.com/materialsproject/pymatgen/pull/705
| 238,323,753
|
MDExOlB1bGxSZXF1ZXN0MTI3MzMzNDgz
| 705
|
Jhu kpoints appveyor fix
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-06-24T15:28:48
| 2019-04-04T02:40:48
|
2017-06-24T16:08:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Should fix the appveyor test. Windows seems to have some issues with the temporary files and monty context manager, so I tried removing the context manager with monty.ScratchDir and that seemed to work. I'm not able to test in my environment yet (don't have Windows), but will set up for the future.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/705/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/705/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/705",
"html_url": "https://github.com/materialsproject/pymatgen/pull/705",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/705.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/705.patch",
"merged_at": "2017-06-24T16:08:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/706
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/706/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/706/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/706/events
|
https://github.com/materialsproject/pymatgen/issues/706
| 238,444,365
|
MDU6SXNzdWUyMzg0NDQzNjU=
| 706
|
Can't copy or pickle pymatgen.io.vasp.inputs.Potcar instance
|
{
"login": "skasamatsu",
"id": 4555912,
"node_id": "MDQ6VXNlcjQ1NTU5MTI=",
"avatar_url": "https://avatars.githubusercontent.com/u/4555912?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/skasamatsu",
"html_url": "https://github.com/skasamatsu",
"followers_url": "https://api.github.com/users/skasamatsu/followers",
"following_url": "https://api.github.com/users/skasamatsu/following{/other_user}",
"gists_url": "https://api.github.com/users/skasamatsu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/skasamatsu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/skasamatsu/subscriptions",
"organizations_url": "https://api.github.com/users/skasamatsu/orgs",
"repos_url": "https://api.github.com/users/skasamatsu/repos",
"events_url": "https://api.github.com/users/skasamatsu/events{/privacy}",
"received_events_url": "https://api.github.com/users/skasamatsu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks. I fixed the class. Usually, we tend not to use pickle as it is highly prone to breakage. The preferred serialization in pymatgen is with json.",
"That was quick! And thank you for recommending json. Unfortunately, the reason I need it to be pickleable is because I want to use pymatgen with multiprocess Queues, which exchanges objects between processes using pickles."
] | 2017-06-26T05:26:26
| 2017-06-26T08:33:05
|
2017-06-26T06:20:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 2017.6.8
* Python version: 2.7.13
* OS version: SUSE Linux Enterprise Server 11
## Summary
* Potcar instances cannot be copied or pickled (not sure if it's a bug or feature limitation)
## Example code
```python
import copy
import cPickle
from pymatgen.io.vasp import Potcar
mypotcar = Potcar(symbols=["Mg"], functional="PBE_54")
#mypotcar_copy = copy.deepcopy(mypotcar)
cPickle.dump(mypotcar, open("mypotcar.pickle","w"))
```
## Error message
```
Traceback (most recent call last):
File "testpotcar_pmg.py", line 8, in <module>
cPickle.dump(mypotcar, open("mypotcar.pickle","w"))
cPickle.PicklingError: Can't pickle <class 'pymatgen.io.vasp.inputs.OrbitalDescription'>: attribute lookup pymatgen.io.vasp.inputs.OrbitalDescription failed
```
If I uncomment the copy line:
```
Traceback (most recent call last):
File "testpotcar_pmg.py", line 7, in <module>
mypotcar_copy = copy.deepcopy(mypotcar)
File "/home/i0009/i000900/tool/python/lib/python2.7/copy.py", line 190, in deepcopy
y = _reconstruct(x, rv, 1, memo)
File "/home/i0009/i000900/tool/python/lib/python2.7/copy.py", line 351, in _reconstruct
item = deepcopy(item, memo)
File "/home/i0009/i000900/tool/python/lib/python2.7/copy.py", line 190, in deepcopy
y = _reconstruct(x, rv, 1, memo)
File "/home/i0009/i000900/tool/python/lib/python2.7/copy.py", line 329, in _reconstruct
y = callable(*args)
File "/home/i0009/i000900/tool/python/lib/python2.7/copy_reg.py", line 93, in __newobj__
return cls.__new__(cls, *args)
File "/home/i0009/i000900/tool/python/lib/python2.7/site-packages/monty/design_patterns.py", line 80, in __new__
inst = klass(*args, **kwargs)
TypeError: __init__() takes exactly 2 arguments (1 given)
```
## Suggested solution (if any)
* The pickling error is due to using namedtuple inside the Potcar class definition. Same issue on stackoverflow:
https://stackoverflow.com/questions/4677012/python-cant-pickle-type-x-attribute-lookup-failed
so it works if I put the namedtuple line at module level, but it isn't pretty.
* The error thrown when trying to copy the instance is due to using the cached_class decoration defined in monty.design_patterns. It seems that copy.deepcopy() at some point calls `__new__ ` without arguments. This is a problem since `__new__` in cached_class calls `__init__`, which throws the TypeError when called without arguments. The example works if I remove the `@cached_class ` decoration line above Potcar class definition, but I'm not sure if there are any side effects (I couldn't find anywhere else in pymatgen that uses the cache made by cached_class).
## Files (if any)
Diff for modified inputs.py:
```
$ diff inputs.py inputs.py.mine
1386c1386,1392
< @cached_class
---
> Orbital = namedtuple('Orbital', ['n', 'l', 'j', 'E', 'occ'])
> Description = namedtuple('Description', ['l', 'E',
> 'Type', "Rcut",
> "Type2", "Rcut2"])
>
>
> #@cached_class
1461,1465c1467,1469
< Orbital = namedtuple('Orbital', ['n', 'l', 'j', 'E', 'occ'])
< Description = namedtuple('OrbitalDescription', ['l', 'E',
< 'Type', "Rcut",
< "Type2", "Rcut2"])
<
---
> #Orbital = Orbital
> #Description = Description
>
1499c1503
< orbitals.append(self.Orbital(int(orbit[0]),
---
> orbitals.append(Orbital(int(orbit[0]),
1514c1518
< descriptions.append(self.Description(int(description[0]),
---
> descriptions.append(Description(int(description[0]),
1658c1662
< elif isinstance(item, (self.Orbital, self.Description)):
---
> elif isinstance(item, (Orbital, Description)):
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/706/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/706/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/707
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/707/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/707/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/707/events
|
https://github.com/materialsproject/pymatgen/issues/707
| 239,035,231
|
MDU6SXNzdWUyMzkwMzUyMzE=
| 707
|
LaTeX errors in BSPlotter and BSDosplotter
|
{
"login": "paulfons",
"id": 6129100,
"node_id": "MDQ6VXNlcjYxMjkxMDA=",
"avatar_url": "https://avatars.githubusercontent.com/u/6129100?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/paulfons",
"html_url": "https://github.com/paulfons",
"followers_url": "https://api.github.com/users/paulfons/followers",
"following_url": "https://api.github.com/users/paulfons/following{/other_user}",
"gists_url": "https://api.github.com/users/paulfons/gists{/gist_id}",
"starred_url": "https://api.github.com/users/paulfons/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/paulfons/subscriptions",
"organizations_url": "https://api.github.com/users/paulfons/orgs",
"repos_url": "https://api.github.com/users/paulfons/repos",
"events_url": "https://api.github.com/users/paulfons/events{/privacy}",
"received_events_url": "https://api.github.com/users/paulfons/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I discovered that this error occurred for an older opensuse version 42.1, I will upgrade to opensuse 42.2 to see if the error still exists and file a new issue if needed."
] | 2017-06-28T02:24:26
| 2017-06-28T03:30:24
|
2017-06-28T03:30:24Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
[Silicon_bandstructure.ipynb.zip](https://github.com/materialsproject/pymatgen/files/1107373/Silicon_bandstructure.ipynb.zip)
<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: v2017.6.24
* Python version: 2.7
* OS version: Open SuSe 42.1 (3.16.7-35-desktop)
## Summary
*Attempting to plot a simple band structure (Silicon) results in a matplot-related LaTeX error and no plot
## Example code
I have attached a self-contained python notebook to this report that reproduces the error (it calculates the band structure of Silicon).
```python
plot = plotter.get_plot(band_structure)
```
## Error message
```
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-187-2455644d0a5f> in <module>()
1 # show the plot
----> 2 plot = plotter.get_plot(band_structure)
/usr/lib64/python2.7/site-packages/pymatgen/electronic_structure/plotter.pyc in get_plot(self, zero_to_efermi, ylim, smooth, vbm_cbm_marker, smooth_tol)
561 plt.ylim(ylim)
562
--> 563 plt.tight_layout()
564
565 return plt
/usr/lib64/python2.7/site-packages/matplotlib/pyplot.pyc in tight_layout(pad, h_pad, w_pad, rect)
1404
1405 fig = gcf()
-> 1406 fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
1407
1408
/usr/lib64/python2.7/site-packages/matplotlib/figure.pyc in tight_layout(self, renderer, pad, h_pad, w_pad, rect)
1751 renderer,
1752 pad=pad, h_pad=h_pad, w_pad=w_pad,
-> 1753 rect=rect)
1754
1755 self.subplots_adjust(**kwargs)
/usr/lib64/python2.7/site-packages/matplotlib/tight_layout.pyc in get_tight_layout_figure(fig, axes_list, subplotspec_list, renderer, pad, h_pad, w_pad, rect)
351 subplot_list=subplot_list,
352 ax_bbox_list=ax_bbox_list,
--> 353 pad=pad, h_pad=h_pad, w_pad=w_pad)
354
355 if rect is not None:
/usr/lib64/python2.7/site-packages/matplotlib/tight_layout.pyc in auto_adjust_subplotpars(fig, renderer, nrows_ncols, num1num2_list, subplot_list, ax_bbox_list, pad, h_pad, w_pad, rect)
128
129 tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
--> 130 if ax.get_visible()])
131 tight_bbox = TransformedBbox(tight_bbox_raw,
132 fig.transFigure.inverted())
/usr/lib64/python2.7/site-packages/matplotlib/axes/_base.pyc in get_tightbbox(self, renderer, call_axes_locator)
3821 bb.append(self._right_title.get_window_extent(renderer))
3822
-> 3823 bb_xaxis = self.xaxis.get_tightbbox(renderer)
3824 if bb_xaxis:
3825 bb.append(bb_xaxis)
/usr/lib64/python2.7/site-packages/matplotlib/axis.pyc in get_tightbbox(self, renderer)
1093 ticks_to_draw = self._update_ticks(renderer)
1094 ticklabelBoxes, ticklabelBoxes2 = self._get_tick_bboxes(ticks_to_draw,
-> 1095 renderer)
1096
1097 self._update_label_position(ticklabelBoxes, ticklabelBoxes2)
/usr/lib64/python2.7/site-packages/matplotlib/axis.pyc in _get_tick_bboxes(self, ticks, renderer)
1076 for tick in ticks:
1077 if tick.label1On and tick.label1.get_visible():
-> 1078 extent = tick.label1.get_window_extent(renderer)
1079 ticklabelBoxes.append(extent)
1080 if tick.label2On and tick.label2.get_visible():
/usr/lib64/python2.7/site-packages/matplotlib/text.pyc in get_window_extent(self, renderer, dpi)
965 raise RuntimeError('Cannot get window extent w/o renderer')
966
--> 967 bbox, info, descent = self._get_layout(self._renderer)
968 x, y = self.get_unitless_position()
969 x, y = self.get_transform().transform_point((x, y))
/usr/lib64/python2.7/site-packages/matplotlib/text.pyc in _get_layout(self, renderer)
351 tmp, lp_h, lp_bl = renderer.get_text_width_height_descent('lp',
352 self._fontproperties,
--> 353 ismath=False)
354 offsety = (lp_h - lp_bl) * self._linespacing
355
/usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in get_text_width_height_descent(self, s, prop, ismath)
228 fontsize = prop.get_size_in_points()
229 w, h, d = texmanager.get_text_width_height_descent(s, fontsize,
--> 230 renderer=self)
231 return w, h, d
232
/usr/lib64/python2.7/site-packages/matplotlib/texmanager.pyc in get_text_width_height_descent(self, tex, fontsize, renderer)
674 else:
675 # use dviread. It sometimes returns a wrong descent.
--> 676 dvifile = self.make_dvi(tex, fontsize)
677 dvi = dviread.Dvi(dvifile, 72 * dpi_fraction)
678 try:
/usr/lib64/python2.7/site-packages/matplotlib/texmanager.pyc in make_dvi(self, tex, fontsize)
421 'string:\n%s\nHere is the full report generated by '
422 'LaTeX: \n\n' % repr(tex.encode('unicode_escape')) +
--> 423 report))
424 else:
425 mpl.verbose.report(report, 'debug')
RuntimeError: LaTeX was not able to process the following string:
'lp'
Here is the full report generated by LaTeX:
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
The attached zip archive contains a python notebook that carries out a simple band structure calculation on Silicon that generates the (matplotlib related) LaTeX errors.
```
|
{
"login": "paulfons",
"id": 6129100,
"node_id": "MDQ6VXNlcjYxMjkxMDA=",
"avatar_url": "https://avatars.githubusercontent.com/u/6129100?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/paulfons",
"html_url": "https://github.com/paulfons",
"followers_url": "https://api.github.com/users/paulfons/followers",
"following_url": "https://api.github.com/users/paulfons/following{/other_user}",
"gists_url": "https://api.github.com/users/paulfons/gists{/gist_id}",
"starred_url": "https://api.github.com/users/paulfons/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/paulfons/subscriptions",
"organizations_url": "https://api.github.com/users/paulfons/orgs",
"repos_url": "https://api.github.com/users/paulfons/repos",
"events_url": "https://api.github.com/users/paulfons/events{/privacy}",
"received_events_url": "https://api.github.com/users/paulfons/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/707/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/707/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/708
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/708/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/708/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/708/events
|
https://github.com/materialsproject/pymatgen/issues/708
| 239,467,957
|
MDU6SXNzdWUyMzk0Njc5NTc=
| 708
|
anonymous fit and mapping for subsets of structures
|
{
"login": "yifeimichelle",
"id": 4400142,
"node_id": "MDQ6VXNlcjQ0MDAxNDI=",
"avatar_url": "https://avatars.githubusercontent.com/u/4400142?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yifeimichelle",
"html_url": "https://github.com/yifeimichelle",
"followers_url": "https://api.github.com/users/yifeimichelle/followers",
"following_url": "https://api.github.com/users/yifeimichelle/following{/other_user}",
"gists_url": "https://api.github.com/users/yifeimichelle/gists{/gist_id}",
"starred_url": "https://api.github.com/users/yifeimichelle/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/yifeimichelle/subscriptions",
"organizations_url": "https://api.github.com/users/yifeimichelle/orgs",
"repos_url": "https://api.github.com/users/yifeimichelle/repos",
"events_url": "https://api.github.com/users/yifeimichelle/events{/privacy}",
"received_events_url": "https://api.github.com/users/yifeimichelle/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@wmdrichards Can you comment on whether this can be done?",
"Seems like this issue has been defunct for many years. Closing.... Feel free to reopen if still valid."
] | 2017-06-29T12:50:35
| 2023-08-08T21:19:52
|
2023-08-08T21:19:52Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Feature Request
## System
* Pymatgen version: 2017.6.8
* Python version: 3.6.1
* OS version: Ubuntu 14.04 LTS
## Summary
* fit_anonymous(struct1, struct2) and get_all_anonymous_mappings(struct1, struct2) in the module pymatgen.analysis.structure_matcher do not allow for fitting a subset, as the equivalent non-anonymous fit(struct1, struct2) and get_mapping(struct1, struct2) do. Instead fit_anonymous() returns False and get_all_anonymous_mappings() returns None.
## Suggested solution (if any)
* Implement the anonymous fit and mapping functions the same way as the species-specific ones do, to account for fitting and mapping a subset.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/708/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/708/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/709
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/709/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/709/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/709/events
|
https://github.com/materialsproject/pymatgen/issues/709
| 239,854,005
|
MDU6SXNzdWUyMzk4NTQwMDU=
| 709
|
Possible bug in Chgcar.write_file()
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"It is rare you want to write a Chgcar for VASP reading. The purpose of writefile is to generate volumetric data for reading by VESTA.",
"Admittedly a rare issue, but I encountered this today (it's a bit off-topic for this bug report, but I'm trying to find a suitable smaller file format so we can visualize CHGCARs interactively on the web, and was trying conversions to/from this alternative format to see how bad the information loss was, when I realized that even just loading/writing a Chgcar with no changes with pymatgen wasn't working).",
"Though the good news with the compression is that I'm getting compressed Chgcars of the order of 50-150 kB (100-1000x compression ratio), which will be more than good enough for visualization purposes. I very much doubt they'll be good enough for VASP inputs though but I was curious to try.",
"What kind of compression? Honestly, if you want to compress CHGCARs, the easiest way is to reduce res. E.g., if you have a 40x40x40 resolution CHGCAR, you coarse grain it to 20x20x20. That will immediately gain 7/8 reduction. ",
"Well, I was trying to find a format that would already work with [NGL Viewer](https://github.com/arose/ngl) (or 3Dmol/JSmol etc.) to save any additional development time -- the author of NGL recommended an 8 bit per voxel binary format, which would be fine, ~ 1/2 MB or so, though we do lose a lot of information.\r\n\r\n~~~More for fun, I thought I'd slicing the CHGCAR, encoding each slice as an image, and compressing the whole CHGCAR as a movie, which is quite straight forward. It's surprisingly robust (given that the distribution of charge is basically the ideal case for something like wavelet compression) and gives 24 bits per voxel and tiny tiny file sizes, since they're just 40px images. It's a bit of a crazy format but it would work well for the web (could render the frames to an off-screen canvas element to reconstruct the array), plus you get to 'see' your CHGCARs, which is cool. At 24-bits, it's an error of about 5e-8 electrons per voxel.~~~ (edit: this had other issues not worth getting into)\r\n\r\nThe problem with coarse-graining and visualization is that you already have to do interpolation/smoothing to construct a smooth iso-surface, and throwing away spatial resolution makes that a lot worse -- purely for visualization purposes, I think spatial resolution is more important, and voxel bit depth less so."
] | 2017-06-30T18:21:17
| 2017-07-29T02:48:28
|
2017-07-29T02:48:28Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: 2017.06.08
* Python version: 3.6.1
* OS version: macOS 10.12.5
## Summary
Reading a CHGCAR and then writing that same CHGCAR results in a CHGCAR that can not be read by VASP.
## Example code
Tested with an `MPStaticSet` and `mpr.get_structures('NaCl')[0]` as the input structure, vasp.5.4.1
## Error message
CHGCAR reading fails with error:
```
RD_RHO_PAW: ion 1 data corrupt
WARNING: PAW occupancies are missing on CHGCAR
```
## Suggested solution (if any)
It looks like this information is missing from the end (and middle) of the CHGCAR:
```
augmentation occupancies 1 33
0.2512469E-04 0.2601868E-21 0.1316082E-11 -0.3207091E-12 0.1861221E-11
-0.1679365E-11 0.5137741E-04 0.5645359E-21 0.2691253E-11 -0.6558170E-12
[...]
augmentation occupancies 2 33
0.6668695E-04 -0.1982265E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00
0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1180570E-02 0.0000000E+00
[...]
```
However, manually adding this information to the pymatgen-generated file results in VASP getting stuck on reading the CHGCAR with this message:
` magnetization density of overlapping atoms calculated`
Not sure what's going on here, but we should fix it to make sure `write_file` does actually produce a VASP-readable CHGCAR.
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/709/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/709/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/710
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/710/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/710/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/710/events
|
https://github.com/materialsproject/pymatgen/issues/710
| 239,956,730
|
MDU6SXNzdWUyMzk5NTY3MzA=
| 710
|
Inconsistencies in AnionCorrection
|
{
"login": "wmdrichards",
"id": 1108541,
"node_id": "MDQ6VXNlcjExMDg1NDE=",
"avatar_url": "https://avatars.githubusercontent.com/u/1108541?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/wmdrichards",
"html_url": "https://github.com/wmdrichards",
"followers_url": "https://api.github.com/users/wmdrichards/followers",
"following_url": "https://api.github.com/users/wmdrichards/following{/other_user}",
"gists_url": "https://api.github.com/users/wmdrichards/gists{/gist_id}",
"starred_url": "https://api.github.com/users/wmdrichards/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/wmdrichards/subscriptions",
"organizations_url": "https://api.github.com/users/wmdrichards/orgs",
"repos_url": "https://api.github.com/users/wmdrichards/repos",
"events_url": "https://api.github.com/users/wmdrichards/events{/privacy}",
"received_events_url": "https://api.github.com/users/wmdrichards/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 3576027,
"node_id": "MDU6TGFiZWwzNTc2MDI3",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/critical",
"name": "critical",
"color": "e10c02",
"default": false,
"description": ""
},
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
}
] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I fixed it by adding oxide_type by default to the entry.data queried from MP. I retained the fallback to special formulas, but added a warning. \r\n\r\nAs for DB rebuild, this has to be done by @tschaume and @kristinpersson, and I strongly recommend an additional check in the build validators (@computron and Co.) as well as changing the REST interface by default (@dwinston) to add oxide_type to entry queries.",
"P.S. I closed this issue because after the fix, the issue no longer pertains to pymatgen, but rather the DB and website. Those should be Issues on the correct repos, not pymatgen."
] | 2017-07-01T15:49:05
| 2017-07-01T23:39:40
|
2017-07-01T23:33:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The application of the anion energy correction is extremely inconsistent when correct_peroxide=True, making it very difficult to tell what is going on.
The correction applied by AnionCorrection depends on whether or not a structure is present in the entry, and whether the oxide_type parameter is present. If neither of these are included in the ComputedEntry, no peroxide/superoxide/ozonide correction is applied unless the composition happens to fall into one of the 'common' peroxide/superoxide/ozonide formulas.
As a result of this confusion, the corrections are often not correctly applied. For example, https://materialsproject.org/materials/mp-2310/ does not have the peroxide correction on the website energy, though if you pass an entry including a structure it correctly recognizes it as a peroxide. It appears as though the only entries on MP that have the peroxide corrections are those in the common formulas list.
## Summary
* AnionCorrection application is inconsistent
## Example code
```python
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.matproj.rest import MPRester
for e in MPRester('XXXX').get_entries('CdO2', inc_structure=True):
print MaterialsProjectCompatibility().process_entry(e).correction
for e in MPRester('XXXX').get_entries('CdO2', inc_structure=False):
print MaterialsProjectCompatibility().process_entry(e).correction
```
## Suggested solution (if any)
* Get rid of the fallback to using common formulas to identify peroxides
* Raise an error when trying to apply a peroxide/superoxide/ozonide correction when no structure or oxide_type attribute is present
* Rebuild the database (since corrected energies will change)
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/710/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/710/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/711
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/711/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/711/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/711/events
|
https://github.com/materialsproject/pymatgen/issues/711
| 240,373,873
|
MDU6SXNzdWUyNDAzNzM4NzM=
| 711
|
Error when compile docs
|
{
"login": "renpj",
"id": 11707719,
"node_id": "MDQ6VXNlcjExNzA3NzE5",
"avatar_url": "https://avatars.githubusercontent.com/u/11707719?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/renpj",
"html_url": "https://github.com/renpj",
"followers_url": "https://api.github.com/users/renpj/followers",
"following_url": "https://api.github.com/users/renpj/following{/other_user}",
"gists_url": "https://api.github.com/users/renpj/gists{/gist_id}",
"starred_url": "https://api.github.com/users/renpj/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/renpj/subscriptions",
"organizations_url": "https://api.github.com/users/renpj/orgs",
"repos_url": "https://api.github.com/users/renpj/repos",
"events_url": "https://api.github.com/users/renpj/events{/privacy}",
"received_events_url": "https://api.github.com/users/renpj/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"You have to compile pymatgen first before running the docs generation. In any case, all docs are available at pymatgen.org. There is really no need to build it yourself.",
"@shyuep Is there a offline version of docs? ",
"Hmmm.... I am happy to attach it. But is there a reason you need an offline version? \r\n[pymatgen-doc.zip](https://github.com/materialsproject/pymatgen/files/1123423/pymatgen-doc.zip)\r\n",
"@shyuep Thanks very much. The connection is not well here, especially for visiting website abroad. So, it would be more convenient by using a offline docs."
] | 2017-07-04T10:04:33
| 2017-07-05T03:37:36
|
2017-07-04T13:53:50Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: v2017.6.24
* Python version: 2.7.12
* OS version: Mint Linux 18.1
## Summary
* Error when compile docs by "make html"
## Error message
```
Running Sphinx v1.5.2
Exception occurred:
File "../pymatgen/util/coord_utils.py", line 11, in <module>
from . import coord_utils_cython as cuc
ImportError: cannot import name coord_utils_cython
The full traceback has been saved in /tmp/sphinx-err-ENm77V.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Makefile:45: recipe for target 'html' failed
make: *** [html] Error 1
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/711/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/711/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/712
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/712/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/712/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/712/events
|
https://github.com/materialsproject/pymatgen/pull/712
| 240,781,850
|
MDExOlB1bGxSZXF1ZXN0MTI5MDU5Mzkw
| 712
|
Dev elastic
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"It's a Lebedev quadrature for integrating the Grüneisen tensor over the surface of a sphere.\r\n\r\nI generated it from quadpy.sphere.Lebedev, but wasn't able to use their integration tools directly because of the way I'm using numpy's einsum functionality. I figured just having the raw data for the default was better than having a new dependency for just one function.",
"Ok thanks for the clarification."
] | 2017-07-05T21:30:13
| 2019-04-04T02:40:53
|
2017-07-05T21:43:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## New TOEC functionality
This PR includes several updates to the elasticity package which extends many of the third and higher-order elastic constant functionality, in addition to refactoring several elements of prior functionality.
* Tensors
- Einstein summation is simplified with einsum_sequence, which enables quick einstein notation inner and outer products
- Tensors may be constructed from values and indices, with an option to populate the tensor from structure symmetry, e. g. creating the elastic tensor for Cu from c11, c12, and c44.
- Tensor population from structure symmetry occurs via an initial step in which zero entries are revised for each symmetry operation and then the entire tensor updated until self-consistent.
* Strains
- Deformation gradients from Strains are constructed via either cholesky decomposition (by default) or the sqrtm method in the convert_strain_to_deformation function
- DeformedStructureSets are constructed from actual independent strains, rather than independent deformations
- Removes IndependentStrain object. All MP-legacy functionality should now be removed.
* Elastic Tensors
- ComplianceTensor is now an object in order to allow for its proper voigt conversion
- directional Poisson's ratios, Green-Kristoffel Tensor, directional Young's modulus
- Gruneisen parameters from third-order elastic tensors, including GGT, TGT, and linear expansion coefficients. Note that the spherical integration functionality introduces a dataset (e. g. points and weights) for Lebedev quadrature.
- Initial implementations of yield stress and Wallace tensor determination
## TODO:
- Will eventually expand yield stress functionality (e. g. to enable yield surfaces, etc.).
- Am thinking an example notebook with an exploration of this functionality will be useful.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/712/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/712/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/712",
"html_url": "https://github.com/materialsproject/pymatgen/pull/712",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/712.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/712.patch",
"merged_at": "2017-07-05T21:43:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/713
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/713/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/713/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/713/events
|
https://github.com/materialsproject/pymatgen/pull/713
| 241,169,676
|
MDExOlB1bGxSZXF1ZXN0MTI5MzM3NTM5
| 713
|
add charge_balance_combos to Composition
|
{
"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/computron/followers",
"following_url": "https://api.github.com/users/computron/following{/other_user}",
"gists_url": "https://api.github.com/users/computron/gists{/gist_id}",
"starred_url": "https://api.github.com/users/computron/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/computron/subscriptions",
"organizations_url": "https://api.github.com/users/computron/orgs",
"repos_url": "https://api.github.com/users/computron/repos",
"events_url": "https://api.github.com/users/computron/events{/privacy}",
"received_events_url": "https://api.github.com/users/computron/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Ok, so:\r\n\r\n1. Done\r\n2. Done\r\n3. As far as I can tell, this is the same thing as 2? i.e. target_charge. Let me know if not.\r\n4. This one is tricky. The way the algorithm works, you lose the history of how the balance was generated unless you really change everything about it. Note that you also can't really \"post-check\" solutions since it might be an average of multiple common oxidation states. What I did was just add an option for using all oxidation states. The user can choose to try common_oxidation_states first, and if they don't get a result, try it with all_oxi_states to get the behavior you describe. (technically, to really get exactly what you want, you filter entries from the first list from the second list and then concatenate the lists together)\r\n5. I added this ranking. I do think it will help on average (especially if one restricts to common oxidation states) but there will of course be problems. e.g., the famous Li2MnNiO4 where it's Ni2+ and Mn4+ rather than 3/3. If you do all oxidation states, you'll likely get non-sensical results.\r\n\r\nBtw, to demonstrate why I didn't include the all_oxi_states option in the first PR (only common oxidation states), take a look at what you get back for Mn2O3 with all_oxi_states on:\r\n\r\n```\r\nprint(Composition(\"Mn2O3\").oxi_state_guesses(all_oxi_states=True))\r\n\r\n[{u'Mn': 0.0, u'O': 0.0}, {u'Mn': 0.5, u'O': -0.3333333333333333}, {u'Mn': -0.5, u'O': 0.3333333333333333}, {u'Mn': 1.0, u'O': -0.6666666666666666}, {u'Mn': -1.0, u'O': 0.6666666666666666}, {u'Mn': 1.5, u'O': -1.0}, {u'Mn': -1.5, u'O': 1.0}, {u'Mn': 2.0, u'O': -1.3333333333333333}, {u'Mn': -2.0, u'O': 1.3333333333333333}, {u'Mn': 2.5, u'O': -1.6666666666666667}, {u'Mn': -2.5, u'O': 1.6666666666666667}, {u'Mn': 3.0, u'O': -2.0}, {u'Mn': -3.0, u'O': 2.0}]\r\n```\r\n\r\nA lot of these are just silly (Mn: -3, O: +2)?\r\n\r\nYou can try a bunch of other compositions and see that it just produces non-helpful results.",
"Thanks. I think the current implementation is fine. I agree the all oxidation states sound a bit silly. \r\n\r\nFor the ranking, I agree it is a bit arbitrary. But honestly, we cannot expect better accuracy than that. NMC is well known to be Ni2+, Co3+, Mn4+. The current ranking will return 3+, 3+, 3+. But really, there is no way of knowing whether the former or latter is better. For the longest time, no one really knew what the oxidation states for NMC is likely to be, even with the wisdom of far better chemists with hundred years of accumulated chemistry knowledge. So ultimately, we just have to return both and choose one of them to be ahead of the other based on some criteria. \r\n\r\nWill merge now."
] | 2017-07-07T06:29:14
| 2017-07-21T00:41:51
|
2017-07-21T00:41:51Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Adds a new feature to a composition to see if a possible charge-balanced solution can be found. Note that you don't need to assign oxidation states a priori - the algorithm will figure out whether the composition can possibly be charge balanced using either pymatgen common oxidation states or user-specified oxidation states. Will return back a list of all possible charge-balance solutions, with each element of the list being a dict of element->avg_oxidation_state.
Likely helpful to detect ionic compounds as well as exclude compositions that are say S6+ instead of S2- based on the composition alone.
* Add method charge_balance_combos() to Composition.
* Add unit tests for that method
## Additional dependencies introduced (if any)
None
## TODO (if any)
* Note that the name "charge_balance_combos" may not be ideal. Feel free to rename if you come up with something better.
* The list of pymatgen Element.common_oxidation_states, used as default oxidation state possibilities, is not really complete. e.g., the common oxidation states of V are only 5+ and not 2+,3+,4+,5+. I initially had an option to use Element.oxidation_states if desired, which is much more inclusive, but found it to be much too inclusive and had all sorts of very uncommon oxidation states. Something in between the two oxidation state tables would be more desirable. For now, the user can use the oxidation_override parameter to set their desired oxidation state preferences.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/713/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/713/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/713",
"html_url": "https://github.com/materialsproject/pymatgen/pull/713",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/713.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/713.patch",
"merged_at": "2017-07-21T00:41:51Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/714
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/714/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/714/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/714/events
|
https://github.com/materialsproject/pymatgen/pull/714
| 241,411,177
|
MDExOlB1bGxSZXF1ZXN0MTI5NTA5MjY0
| 714
|
Minor reconfiguring of IEEE conversion and helper function for tensor mapping
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Found an issue with symmetry reduction algorithm that I'd like to resolve before merging, so going to close for now.",
"Nevermind, issue I thought was in pymatgen code was elsewhere. This should be good to go."
] | 2017-07-08T00:31:02
| 2017-07-10T04:46:26
|
2017-07-10T04:46:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Reconfigures IEEE conversion to generate the rotation and explicitly convert the tensor separately, so structures can be set into the IEEE basis if desired (e. g. with a primitive cell). Also adds a function that's useful for looking up values in tensor-keyed dictionaries (like the ones generated in symmetry reduction) and a corresponding unittest.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/714/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/714/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/714",
"html_url": "https://github.com/materialsproject/pymatgen/pull/714",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/714.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/714.patch",
"merged_at": "2017-07-10T04:46:26Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/715
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/715/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/715/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/715/events
|
https://github.com/materialsproject/pymatgen/pull/715
| 241,635,769
|
MDExOlB1bGxSZXF1ZXN0MTI5NjI0Njkx
| 715
|
add chgcar_ref args to bader calculation
|
{
"login": "renpj",
"id": 11707719,
"node_id": "MDQ6VXNlcjExNzA3NzE5",
"avatar_url": "https://avatars.githubusercontent.com/u/11707719?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/renpj",
"html_url": "https://github.com/renpj",
"followers_url": "https://api.github.com/users/renpj/followers",
"following_url": "https://api.github.com/users/renpj/following{/other_user}",
"gists_url": "https://api.github.com/users/renpj/gists{/gist_id}",
"starred_url": "https://api.github.com/users/renpj/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/renpj/subscriptions",
"organizations_url": "https://api.github.com/users/renpj/orgs",
"repos_url": "https://api.github.com/users/renpj/repos",
"events_url": "https://api.github.com/users/renpj/events{/privacy}",
"received_events_url": "https://api.github.com/users/renpj/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls add a unittest for the new functionality. Thanks.",
"Does this require manual construction of chgcar_ref? Might be better to have AECCAR arguments in pymatgen and calculate chgcar_ref internally.\r\n\r\nMost of the functionality necessary should be in `pymatgen.io.vasp.outputs.VolumetricData` and the `linear_add` function.",
"@shyuep Sure, I can modify the test file. I need generate a new CHGCAR and AECCAR0, AECCAR2.\r\n@mkhorton Yes, you're right. The defect is we should add one more arg to the function. I prefer less args.",
"Let me know when this is reasdy to merge.",
"@shyuep All modifications were passed the test, pls merge it."
] | 2017-07-10T08:25:42
| 2017-07-12T15:49:49
|
2017-07-12T15:49:49Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The CHGCAR files from the VASP only contain the valance charge density, which may give the wrong bader charge. This can be overcome by using:
> bader CHGCAR -ref CHGCAR_sum
where CHGCAR_sum is calculated by AECCAR0 + AECCAR2.
(See http://theory.cm.utexas.edu/henkelman/code/bader/ for more details.)
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/715/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/715/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/715",
"html_url": "https://github.com/materialsproject/pymatgen/pull/715",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/715.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/715.patch",
"merged_at": "2017-07-12T15:49:49Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/716
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/716/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/716/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/716/events
|
https://github.com/materialsproject/pymatgen/issues/716
| 241,839,095
|
MDU6SXNzdWUyNDE4MzkwOTU=
| 716
|
independentstrain not defined
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"see https://github.com/hackingmaterials/atomate/issues/133",
"That's a different issue",
"Sorry, my mistake :)"
] | 2017-07-10T20:33:23
| 2017-07-10T21:12:35
|
2017-07-10T21:12:35Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* @montoyjh on line https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/strain.py#L162
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/716/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/716/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/717
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/717/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/717/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/717/events
|
https://github.com/materialsproject/pymatgen/pull/717
| 241,845,437
|
MDExOlB1bGxSZXF1ZXN0MTI5NzcxNTkw
| 717
|
Remove old function
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-10T20:54:56
| 2017-07-10T21:12:35
|
2017-07-10T21:12:35Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Deletes legacy as_strain_dict method. Should resolve #716 .
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/717/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/717/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/717",
"html_url": "https://github.com/materialsproject/pymatgen/pull/717",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/717.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/717.patch",
"merged_at": "2017-07-10T21:12:35Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/718
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/718/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/718/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/718/events
|
https://github.com/materialsproject/pymatgen/pull/718
| 241,864,615
|
MDExOlB1bGxSZXF1ZXN0MTI5NzgzMTc3
| 718
|
Update of Specie
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Closing for now, the species and structure tests are passing fine, but I want to take a look at the failing Voronoi test ... (Update: all fixed)",
"I don't quite understand the purpose for this. Can you provide an example usage? My problem with this is that it is confusing if the same property can be part of both. There is a reason why oxi state is a Specie property. A site can be disordered with different species of different oxidation states. The idea of having a site oxidation state only makes sense in the standpoint of a completely ordered site.\r\n\r\nIf the intent is to simply pass through Species properties to site properties, that can be easily done by suitable additions to getattr of Site.",
"I implemented the passthrough. Check it out first. So you cna now do something like structure[0].oxi_state. As for setting Specie properties, taht is not allowed. Specie is immutable (for very good reason). When oxidation states are changed, you do not actually modify specie but rather create a new Specie to replace the old one. ",
"Regarding use cases, I agree it's confusing that there are two separate places to store properties. To be clear, I wasn't suggesting oxidation state should be *both* a site and a Specie property, because I agree that it belongs in Specie.\r\n\r\nHere are two illustrative uses to explain where this is useful:\r\n\r\n* Magnetic moment is currently a site property. Arguably, it might make more sense as a species property instead. It's been convenient to 'convert' a Structure to have the magnetic moment on a Specie spin property instead of the site property: this way, two Specie with different magnetic moments are not treated as equal. Also, disordered magnetic structures are not possible with magnetic moments as site properties.\r\n\r\n* There are lots of algorithms that output a value for each site, and so site_properties is a useful store for the outputs of these algorithms. We have several different structures in the MP database, e.g. a bv_structure, a Bader structure, a 'canonical' structure which has forces and co-ordination as site properties, etc. To minimize confusion, we were thinking about tidying this up, and returning a structure that had, say, both a `bv_oxi_state`, `bader_oxi_state` as site properties. But when you decide which oxidation state to use, you have to have a way to apply them to the structure. The existing method `add_oxidation_state_by_site` basically does this, but doesn't address the question of where we store these oxidation states.\r\n\r\nThere might be better ways of doing this, I'm not sure? At the very least, having `oxidation_state` on an equal basis with `spin` would be useful, so that you can have a Specie with a defined spin without inventing a fictitious oxidation state.",
"For a specific example, consider:\r\n\r\n```\r\ns = mpr.get_structures('NiO')[0]\r\ns.get_primitive_structure() # doesn't respect magmom site props, returns primitive NiO\r\ns.site_property_to_specie_property('magmom', 'spin')\r\ns.get_primitive_structure() # now returns correct AFM primitive NiO\r\n```\r\n\r\nSo for this specific example we could just 'fix' `get_primitive_structure()` to respect magmoms, if that's what we wanted it to do, but more broadly it's this kind of case where it's useful. I could probably fix the implementation so it doesn't try to mutate Specie though.",
"The design principle is that the core Element/Specie encapsulates physical information that rarely changes (if ever). Hence, supported properties on Specie is highly restricted. This also makes it logical for Element to be an Enum type and Specie to be a cached type for memory efficiency. Electron spin is a hard definition that takes on integer multiples and is based on a hard definition of an oxidation state and the number of electrons in the Specie (granted that these are not strictly defined).\r\n\r\nThe properties on Site/PeriodicSite are looser definitions that accounts for the combination of a Specie with a local environment. Hence, there is no definition of supported_properties on Site. Here, anything goes. Magnetic moment, which is different from spin, is given by the specie and the hybridization with the local environment. It takes on non-integer values, usually supplied from a calculation.\r\n\r\nAs far as I know, there is nothing preventing you from adding a site_property bv_oxidation_state or any other site related property.\r\n\r\nFor now, I think the best solution is to just add a \"add_spin_by_specie\" or \"add_spin_by_site\" method to Structure.",
"I am not sure your example is correct. The following code:\r\n\r\n```\r\nfrom pymatgen import MPRester\r\nm = MPRester()\r\ns = m.get_structures(\"NiO\")[0]\r\nprim = s.get_primitive_structure()\r\nprint(prim)\r\n```\r\n\r\nreturns \r\n```\r\nFull Formula (Ni1 O1)\r\nReduced Formula: NiO\r\nabc : 2.970454 2.970454 2.970453\r\nangles: 60.107168 60.107170 60.107175\r\nSites (2)\r\n # SP a b c coordination_no forces magmom\r\n--- ---- --- --- --- ----------------- ------------------------------------- --------\r\n 0 Ni 0 0 0 6 [0.0, 0.0, 0.0] 1.724\r\n 1 O 0.5 0.5 0.5 6 [0.00022106, 0.00015631, -0.00038288] 0\r\n```\r\n\r\nQuite clearly site properties are respected. Here also illustrates the danger of transmitting properties to Specie. Site properties are not accounted for in determining primitive cell and symmetries. So site properties when reducing to primitive cells make very little sense. You have an AFM NiO but after reducing to a primitive cell, it is FM only. The magmom being selected is arbitrary based on grouping.",
"> You have an AFM NiO but after reducing to a primitive cell, it is FM only. \r\n\r\nSo what would be the suggested method for obtaining the primitive magnetic cell? That is, for the case where you have a magnetically-ordered non-primitive cell (e.g. supercell or alternative setting), and you want the primitive cell that retains the magnetic ordering.\r\n\r\nThat was the intent of my example, to show that `get_primitive_cell()` doesn't respect magnetic ordering -- which is presumably correct and by design, but there are cases where you do want to respect the magnetic ordering when trying to calculate a primitive cell.\r\n\r\nAnnotating Specie with the relevant spin in this case seems to work, and seems like a sensible option.\r\n\r\n> Site properties are not accounted for in determining primitive cell and symmetries. ... The magmom being selected is arbitrary based on grouping.\r\n\r\nI'd argue that it's potentially misleading to retain an arbitrary site property when producing the primitive cell, *if* site properties differ from otherwise symmetrically-equivalent sites? That's essentially ignoring whatever meaning is present on those site properties.\r\n\r\nUpdate: Sorry, I missed your earlier comment!\r\n\r\n> For now, I think the best solution is to just add a \"add_spin_by_specie\" or \"add_spin_by_site\" method to Structure.\r\n\r\nThis sounds useful, I can implement this (and their corresponding `remove` methods) instead.",
"I just implemented use_site_props option in get_primitive_cell. I recognize there are instances (rare in my view) you do not want the primitive cell to be reduced and some arbitrary site property is retained.\r\n\r\nCertainly, we can extend this to symmetry as well, but I don't think people usually consider symmetries based on site properties, unless it is magnetic symmetries. In that case, it is better to be explicit and cast your calculated magmom to a spin. This is because magmom is a float, which makes it prone to tolerance issues, e.g., is 6.999 the same as 7 for magnetic symmetry purposes? \r\n\r\nYou can do the add_spin methods.",
"Okay, thanks very much!\r\n\r\n> I recognize there are instances (rare in my view) you do not want the primitive cell to be reduced and some arbitrary site property is retained.\r\n\r\nYeah, I think it probably is quite rare, but it seems to be causing unintended behavior the existing non-FM structures on MP -- this is probably not the place to discuss that though.\r\n\r\n> This is because magmom is a float, which makes it prone to tolerance issues, e.g., is 6.999 the same as 7 for magnetic symmetry purposes?\r\n\r\nAnd very true... purely for symmetry, I've been normalizing the orderings (e.g. retain direction of the magnetic moment vector, but normalize to unity) when comparing cells for magnetic symmetry purposes. This is in a MagneticSymmetryAnalyzer for a future PR..."
] | 2017-07-10T21:58:55
| 2017-07-11T18:01:27
|
2017-07-11T17:51:58Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
All changes are backwards compatible/non-breaking.
**Change:** Oxidation state is now optional
**Motivation:** There's a difference between an oxidation state of 0 and `None`/unknown. Currently, if we want to assign a `spin` property and we do not know an oxidation state, we have to invent a fictious one. This causes problems if the Structure is then serialized, because people might think the oxidation state is 'real' (e.g. from BVAnalyzer or Bader etc.)
**Change:** `Structure` now has `with_specie_property_as_site_property` and `with_site_property_as_specie_property` methods. This allows general switching between `Specie` and `site` properties.
**Motivation:** This is along similar lines as `add_oxidation_state_by_site` except more general, and using site_properties as a store. There have been several instances where these methods have been useful, for example to convert from a Specie Spin property to a magnetic moment on a Site property. Also, we have different Structures in the MP database with e.g. an oxidation state from BVAnalyzer and also an oxidation state from Bader, and it's been useful to swap between them, or store them both in one canonical Structure with both sets of information annotated in site_properties.
**Change:** Oxidation state is now a property
**Motivation:** This follows from above. This is only an internal change, specie constructor and to/from dict remain the same for compatibility.
## Additional dependencies introduced (if any)
None
## TODO (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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/718/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/718/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/718",
"html_url": "https://github.com/materialsproject/pymatgen/pull/718",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/718.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/718.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/719
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/719/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/719/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/719/events
|
https://github.com/materialsproject/pymatgen/pull/719
| 241,891,582
|
MDExOlB1bGxSZXF1ZXN0MTI5ODAyMjAw
| 719
|
Get latest version of pymatgen and move all changes to a new branch
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pull request not ready to merge, please close. My apologies for the mistake."
] | 2017-07-11T00:42:16
| 2017-07-11T00:57:25
|
2017-07-11T00:48:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
<Short few sentences, and summary of the major changes in bullet
points>
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
<List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. If you are putting anything here, you should
provide a justification why that dependency is needed. Especially
frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.>
## TODO (if any)
<If this is a work-in-progress, write something about what else needs
to be done>
* Feature 1 supports a, but not b.
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/719/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/719/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/719",
"html_url": "https://github.com/materialsproject/pymatgen/pull/719",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/719.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/719.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/720
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/720/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/720/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/720/events
|
https://github.com/materialsproject/pymatgen/pull/720
| 242,431,157
|
MDExOlB1bGxSZXF1ZXN0MTMwMTc1NDc3
| 720
|
PbsProAdapter compatible with zenobe cluster
|
{
"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/followers",
"following_url": "https://api.github.com/users/gmatteo/following{/other_user}",
"gists_url": "https://api.github.com/users/gmatteo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gmatteo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gmatteo/subscriptions",
"organizations_url": "https://api.github.com/users/gmatteo/orgs",
"repos_url": "https://api.github.com/users/gmatteo/repos",
"events_url": "https://api.github.com/users/gmatteo/events{/privacy}",
"received_events_url": "https://api.github.com/users/gmatteo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-12T15:57:24
| 2017-07-12T15:58:42
|
2017-07-12T15:58:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* New method of XRDCalculator to plot xrd for multiple structures on the same figure
* New version of PbsPro adapter for zenobe
* Wrapper for fold2bloch
* Minor bugs fixed
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/720/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/720/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/720",
"html_url": "https://github.com/materialsproject/pymatgen/pull/720",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/720.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/720.patch",
"merged_at": "2017-07-12T15:58:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/721
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/721/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/721/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/721/events
|
https://github.com/materialsproject/pymatgen/pull/721
| 242,579,575
|
MDExOlB1bGxSZXF1ZXN0MTMwMjgyMzk5
| 721
|
lammps_log parser update
|
{
"login": "wood-b",
"id": 11530209,
"node_id": "MDQ6VXNlcjExNTMwMjA5",
"avatar_url": "https://avatars.githubusercontent.com/u/11530209?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/wood-b",
"html_url": "https://github.com/wood-b",
"followers_url": "https://api.github.com/users/wood-b/followers",
"following_url": "https://api.github.com/users/wood-b/following{/other_user}",
"gists_url": "https://api.github.com/users/wood-b/gists{/gist_id}",
"starred_url": "https://api.github.com/users/wood-b/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/wood-b/subscriptions",
"organizations_url": "https://api.github.com/users/wood-b/orgs",
"repos_url": "https://api.github.com/users/wood-b/repos",
"events_url": "https://api.github.com/users/wood-b/events{/privacy}",
"received_events_url": "https://api.github.com/users/wood-b/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There is a failing py27 test. https://circleci.com/gh/materialsproject/pymatgen/6476\r\nPls fix."
] | 2017-07-13T04:04:36
| 2017-07-13T13:43:37
|
2017-07-13T04:35:52Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
I added more fields to be parsed (simulation info and # of dangerous builds). Additionally, I changed the structure of thermo_data from a numpy array to a dictionary.
## TODO (if any)
We need to write a parser for the one and multi thermo_styles. At the moment only thermo_style custom is supported
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/721/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/721/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/721",
"html_url": "https://github.com/materialsproject/pymatgen/pull/721",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/721.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/721.patch",
"merged_at": "2017-07-13T04:35:52Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/722
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/722/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/722/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/722/events
|
https://github.com/materialsproject/pymatgen/issues/722
| 242,801,445
|
MDU6SXNzdWUyNDI4MDE0NDU=
| 722
|
`pymatgen.io.vasp.Vasprun` fails to parse `other_dielectric`
|
{
"login": "alchem0x2A",
"id": 6829706,
"node_id": "MDQ6VXNlcjY4Mjk3MDY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6829706?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/alchem0x2A",
"html_url": "https://github.com/alchem0x2A",
"followers_url": "https://api.github.com/users/alchem0x2A/followers",
"following_url": "https://api.github.com/users/alchem0x2A/following{/other_user}",
"gists_url": "https://api.github.com/users/alchem0x2A/gists{/gist_id}",
"starred_url": "https://api.github.com/users/alchem0x2A/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/alchem0x2A/subscriptions",
"organizations_url": "https://api.github.com/users/alchem0x2A/orgs",
"repos_url": "https://api.github.com/users/alchem0x2A/repos",
"events_url": "https://api.github.com/users/alchem0x2A/events{/privacy}",
"received_events_url": "https://api.github.com/users/alchem0x2A/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-13T19:11:32
| 2017-07-14T00:14:37
|
2017-07-14T00:14:37Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The class `Vasprun` fails to parse the `other_dielectric` for GW type vasprun.xml.
## System
* Pymatgen version: 2017.06.24
* Python version: 3.5.4
## Summary
* When parsing vasprun.xml with multiple dielectricfunction elements, it gives error of `KeyError: 'comment'`.
* Possibly due to line 448 in `outputs.py`
* Adding one line for `str_tmp = elem.attrib["comment"]` and change line 448 to `self.other_dielectric[str_tmp] = self._parse_diel(elem)` will work.
* Don't know exactly if this is due to Python grammar rules or only for certain python versions
[vasprun.GW0.xml.zip](https://github.com/materialsproject/pymatgen/files/1146345/vasprun.GW0.xml.zip)
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/722/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/722/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/723
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/723/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/723/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/723/events
|
https://github.com/materialsproject/pymatgen/issues/723
| 243,055,416
|
MDU6SXNzdWUyNDMwNTU0MTY=
| 723
|
SpagegroupAnalyzer.get_conventional_standard_structure().
|
{
"login": "Djordje117",
"id": 13387824,
"node_id": "MDQ6VXNlcjEzMzg3ODI0",
"avatar_url": "https://avatars.githubusercontent.com/u/13387824?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Djordje117",
"html_url": "https://github.com/Djordje117",
"followers_url": "https://api.github.com/users/Djordje117/followers",
"following_url": "https://api.github.com/users/Djordje117/following{/other_user}",
"gists_url": "https://api.github.com/users/Djordje117/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Djordje117/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Djordje117/subscriptions",
"organizations_url": "https://api.github.com/users/Djordje117/orgs",
"repos_url": "https://api.github.com/users/Djordje117/repos",
"events_url": "https://api.github.com/users/Djordje117/events{/privacy}",
"received_events_url": "https://api.github.com/users/Djordje117/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I can't reproduce this error.\r\n\r\n```\r\nfrom pymatgen import Structure\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\ns = Structure.from_file(\"POSCAR\")\r\na = SpacegroupAnalyzer(s, 0.1)\r\nss = a.get_conventional_standard_structure()\r\nss.to(filename=\"conv.cif\")\r\ns.to(filename=\"orig.cif\")\r\n```\r\n\r\nI opened both cifs in VESTA and they look exactly the same.",
"It works fine when you increase symprec by 100 times (from 0.001 to 0.1). It also works when symprec increased to 0.01. I only increased up to 3 times. Thank you for the help.",
"Yes, symmetry detection is based on tolerances. 0.001 is fine if you have a very well defined structure. If you have a DFT relaxed structure, tolerances have to be set lower. Usually we stick to 0.1 as a default."
] | 2017-07-14T17:08:08
| 2017-07-14T17:48:09
|
2017-07-14T17:48:09Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: 2017.7.4
* Python version: 2.7.13
* OS version: Linux
## Summary
When a Structure object of nicely layered material is passed to the SpagegroupAnalyzer.get_conventional_standard_structure(), it returns a molecular structure.
Figure 1 shown a staring structure, while Figure 2 shows a returned structure. POSCAR of a problematic structure is:
Mo2 Cl6
1.0
0.000000 6.260814 0.007832
-5.422831 3.130407 0.003916
0.000000 0.000000 6.307389
Cl Mo
6 2
direct
0.148065 0.999913 0.277579 Cl
0.499843 0.648557 0.721695 Cl
0.851935 0.000087 0.722421 Cl
0.852063 0.648113 0.277949 Cl
0.147937 0.351887 0.722050 Cl
0.500157 0.351443 0.278308 Cl
0.166623 0.666720 0.500071 Mo
0.833377 0.333280 0.499928 Mo
Figure 1
Figure 2
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/723/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/723/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/724
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/724/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/724/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/724/events
|
https://github.com/materialsproject/pymatgen/issues/724
| 243,184,032
|
MDU6SXNzdWUyNDMxODQwMzI=
| 724
|
Bug: VASP INCAR option EINT not parsed as a list
|
{
"login": "andreaslinscheid",
"id": 11784858,
"node_id": "MDQ6VXNlcjExNzg0ODU4",
"avatar_url": "https://avatars.githubusercontent.com/u/11784858?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/andreaslinscheid",
"html_url": "https://github.com/andreaslinscheid",
"followers_url": "https://api.github.com/users/andreaslinscheid/followers",
"following_url": "https://api.github.com/users/andreaslinscheid/following{/other_user}",
"gists_url": "https://api.github.com/users/andreaslinscheid/gists{/gist_id}",
"starred_url": "https://api.github.com/users/andreaslinscheid/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/andreaslinscheid/subscriptions",
"organizations_url": "https://api.github.com/users/andreaslinscheid/orgs",
"repos_url": "https://api.github.com/users/andreaslinscheid/repos",
"events_url": "https://api.github.com/users/andreaslinscheid/events{/privacy}",
"received_events_url": "https://api.github.com/users/andreaslinscheid/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I just fixed this. We do not know the comprehensive list of types. But it is strange that it is being parsed as a int type. Usually for unspecified types, the default goes to a string.",
"Thank you for this immediate response.\r\nLooking at the code, I guess unspecified types goes to a string unless they match ^-?\\d+ in the beginning. In that case line 817 matches and return this match which in my case (\"-0.85 0.85\") was -0. Is that what you want? My guess is not because it alters the input parameters.",
"Ok, I fixed this bad logic in the latest commit ."
] | 2017-07-15T16:08:41
| 2017-07-15T17:18:56
|
2017-07-15T16:16:49Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Dear pymatgen developers,
I am using Custodian with pymatgen to perform VASP STM runs.
Thank you for providing this well developed piece of software to the community.
The incar option "EINT" is not in the list of parameters specified in pymatgen/vasp/io/inputs.py so it gets parsed in line 817 as a signed int and in=Incar.read_file("INCAR");in.write_file("INCAR") magically resets EINT to a single integer number.
It can be a list of two or one real number so when I append this option to pymatgen/vasp/io/inputs.py line 748 the problem is solved.
A different way of interpreting the error is that you don't implement a default conversion for unknown list parameters (it is understandable that EINT is not common ...).
One could maybe solve this and similar issues with unknown list options by inserting after line 808
try:
output = []
toks = re.findall( r"(-?\d+\.?\d*)\*?(-?\d+\.?\d*)?\*?(-?\d+\.?\d*)?", val)
//similar logic as above for list options
if len(output) == 0:
raise ValueError
return output
except ValueError:
pass
I have not tested that but I guess you get the idea.
Thank you very much,
Andy
P.s. an INCAR file that triggers this problem is
ALGO = Fast
ECUT = 510
EDIFF = 1e-07
EINT = -0.85 0.85
IBRION = -1
ICHARG = 11
ISIF = 3
ISMEAR = 1
ISPIN = 1
LPARD = True
NBMOD = -3
PREC = Accurate
SIGMA = 0.1
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/724/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/724/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/725
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/725/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/725/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/725/events
|
https://github.com/materialsproject/pymatgen/pull/725
| 243,491,075
|
MDExOlB1bGxSZXF1ZXN0MTMwOTI1MjM2
| 725
|
Slight changes in StructureMotifInterstitial class
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There are failing tests. And I am not clear why tet is renamed tetalt.",
"There are now variants of tetrahedral and octahedral order parameters (tetalt and octalt) that cannot become negative.",
"The current pull request should be successfully passing the tests. At least, the unit tests didn't make any trouble on my system. I apologize for not having run the tests before issuing the pull request. My bad.",
"I'm not sure \"tetalt\" will be clear to people. Maybe \"tet_v2\"?",
"In general, I think an enum type would work better. I have no idea what kind of order parameters are available without looking at the code. This is generally a bad design from a user perspective. Always assume that the user is going to try to use your method without looking at the body of the code to figure out what parameters are accepted. People need to be able to work it out from purely the method signature alone",
"Thanks for the suggestions, Anubhav and Shyue.\r\n\r\nI just observed that I forgot to update the documentation of the constructor to reflect the definition of alternative qtet and qoct. So, if I added something like below, does that help?\r\n\r\n\"tetalt\": alternative Peters-style OP recognizing tetrahedral coordination which importantly avoids negative values.\r\n\r\nI thought that it would be good to keep the original OPs. Another way around it is to call the new OPs qtet and qoct and the old ones qtet_orig and qoct_orig. Does that sound better/more clear?\r\n\r\nThe types argument (list) is the only required argument for the constructor. All other arguments are optional and have default values. I could make the description of the types argument more concise if you think that helps increasing clarity.\r\n",
"My personal preference is that if users are expected to use the \"revised\" parameters, to rename the old ones to _legacy or _orig - i.e., to make things clear for new users by just having the new ones be \"tet\". But that breaks backwards compatibility with any existing code that's out in the wild that references the current \"tet\". Since the order parameters code is still pretty new it might be OK, but up to @shyuep ",
"For keeping older OPs, I'd vote for '_legacy' over '_orig'. For 'tetalt' specificly, why not 'tet_peters'? But as long as it's properly described in the method docstring, I'm sure either is fine and won't cause too much confusion.",
"Thanks, guys, for the great feedback and suggestions. I'll go ahead and rename the original qtet and qoct to qtet_legacy and qoct_legacy as well as updating the documentation to explain the issue and change things in StructureMotifInterstitial and other code (e.g., matminer and pycdt).\r\n",
"BTW, Matt, I like your profile picture. :-)"
] | 2017-07-17T18:51:59
| 2017-07-18T16:52:37
|
2017-07-17T19:46:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
1) Using new definitions of tetrahedral and octahedral order parameters now, which cannot become negative.
2) Added a function to obtain OP value associated with a given interstitial site.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/725/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/725/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/725",
"html_url": "https://github.com/materialsproject/pymatgen/pull/725",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/725.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/725.patch",
"merged_at": "2017-07-17T19:46:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/726
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/726/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/726/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/726/events
|
https://github.com/materialsproject/pymatgen/issues/726
| 243,900,054
|
MDU6SXNzdWUyNDM5MDAwNTQ=
| 726
|
Hello guys
|
{
"login": "Francisenujekwu",
"id": 30256792,
"node_id": "MDQ6VXNlcjMwMjU2Nzky",
"avatar_url": "https://avatars.githubusercontent.com/u/30256792?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Francisenujekwu",
"html_url": "https://github.com/Francisenujekwu",
"followers_url": "https://api.github.com/users/Francisenujekwu/followers",
"following_url": "https://api.github.com/users/Francisenujekwu/following{/other_user}",
"gists_url": "https://api.github.com/users/Francisenujekwu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Francisenujekwu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Francisenujekwu/subscriptions",
"organizations_url": "https://api.github.com/users/Francisenujekwu/orgs",
"repos_url": "https://api.github.com/users/Francisenujekwu/repos",
"events_url": "https://api.github.com/users/Francisenujekwu/events{/privacy}",
"received_events_url": "https://api.github.com/users/Francisenujekwu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-19T01:52:02
| 2017-07-30T14:38:05
|
2017-07-30T14:38:05Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <Write "branch_name" if it is development version.>
* Python version: <Only 2.7.* and 3.* supported.>
* OS version: <If you are writing Windows here, you are on your own.>
## Summary
* <Short 1-2 bullet points stating the problem.>
## Example code
```python
<Example code generating error>
```
## Error message
```
<Error message>
```
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/726/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/726/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/727
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/727/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/727/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/727/events
|
https://github.com/materialsproject/pymatgen/pull/727
| 244,275,223
|
MDExOlB1bGxSZXF1ZXN0MTMxNDkwNjQy
| 727
|
ingore pymatgen[matproj.snl] warning when use python3
|
{
"login": "specter119",
"id": 8768524,
"node_id": "MDQ6VXNlcjg3Njg1MjQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8768524?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/specter119",
"html_url": "https://github.com/specter119",
"followers_url": "https://api.github.com/users/specter119/followers",
"following_url": "https://api.github.com/users/specter119/following{/other_user}",
"gists_url": "https://api.github.com/users/specter119/gists{/gist_id}",
"starred_url": "https://api.github.com/users/specter119/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/specter119/subscriptions",
"organizations_url": "https://api.github.com/users/specter119/orgs",
"repos_url": "https://api.github.com/users/specter119/repos",
"events_url": "https://api.github.com/users/specter119/events{/privacy}",
"received_events_url": "https://api.github.com/users/specter119/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-20T07:55:14
| 2017-07-20T13:43:49
|
2017-07-20T13:43:49Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
ingore pymatgen[matproj.snl] warning when use python3
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/727/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/727/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/727",
"html_url": "https://github.com/materialsproject/pymatgen/pull/727",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/727.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/727.patch",
"merged_at": "2017-07-20T13:43:49Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/728
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/728/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/728/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/728/events
|
https://github.com/materialsproject/pymatgen/pull/728
| 244,533,966
|
MDExOlB1bGxSZXF1ZXN0MTMxNjc3NjEy
| 728
|
Elastic module cleanup
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-21T00:37:42
| 2017-07-21T00:42:04
|
2017-07-21T00:42:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Cleanup and docstring editing in elasticity module
Minor changes in elasticity module, mostly to docstrings and formatting.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/728/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/728/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/728",
"html_url": "https://github.com/materialsproject/pymatgen/pull/728",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/728.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/728.patch",
"merged_at": "2017-07-21T00:42:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/729
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/729/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/729/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/729/events
|
https://github.com/materialsproject/pymatgen/issues/729
| 244,731,223
|
MDU6SXNzdWUyNDQ3MzEyMjM=
| 729
|
Bug in Kpoints.automatic_density creates lattice symmetry breaking k mesh
|
{
"login": "andreaslinscheid",
"id": 11784858,
"node_id": "MDQ6VXNlcjExNzg0ODU4",
"avatar_url": "https://avatars.githubusercontent.com/u/11784858?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/andreaslinscheid",
"html_url": "https://github.com/andreaslinscheid",
"followers_url": "https://api.github.com/users/andreaslinscheid/followers",
"following_url": "https://api.github.com/users/andreaslinscheid/following{/other_user}",
"gists_url": "https://api.github.com/users/andreaslinscheid/gists{/gist_id}",
"starred_url": "https://api.github.com/users/andreaslinscheid/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/andreaslinscheid/subscriptions",
"organizations_url": "https://api.github.com/users/andreaslinscheid/orgs",
"repos_url": "https://api.github.com/users/andreaslinscheid/repos",
"events_url": "https://api.github.com/users/andreaslinscheid/events{/privacy}",
"received_events_url": "https://api.github.com/users/andreaslinscheid/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Can anybody confirm this or is there a misunderstanding on my end?",
"Thanks. I have implemented your fix and pushed the changes."
] | 2017-07-21T17:15:25
| 2017-08-10T02:48:11
|
2017-08-10T02:48:05Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Dear pymatgen developers,
I encountered the following problem:
For fcc Al, setting the k point density to 1000kpts/atom, I obtain the k mesh 10x10x9 which breaks the lattice symmetry. The POSCAR is from the materials project:
Al1
1.0
2.473329 0.000000 1.427977
0.824443 2.331877 1.427977
0.000000 0.000000 2.855955
Al
1
direct
0.000000 0.000000 0.000000 Al
Looking at the code, the problem appears to be that I chose by accident a density that has an integer 3rd root.
If that is the case, rounding errors in the length of each lattice vector will tip the scale to be above or below the integer value. Since 'mult' in line 1053 takes these vectors into account, I figure the respective longest of these vectors will get 10 points assigned, while the shortest 9 kpts/direction because of the integer cast 'floor' in line 1055.
The logic also applies when I choose a density of 729 (9^3) in which case the code sets a grid of 9x9x8 where it should be 9x9x9
The easiest solution I can think of is simply checking if kppa is the third power of an integer, e.g. like this, added in line 1052
if math.fabs((math.floor(kppa**(1/3)+0.5))**3 - kppa) < 1:
kppa = kppa + kppa*0.01
If this is the case, we simply add 1% (or subtract) to kppa.
This solved the problem for me.
Cheers,
Andy
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/729/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/729/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/730
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/730/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/730/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/730/events
|
https://github.com/materialsproject/pymatgen/issues/730
| 244,885,437
|
MDU6SXNzdWUyNDQ4ODU0Mzc=
| 730
|
Bug in parse_oxide Method
|
{
"login": "QiWen77",
"id": 22218737,
"node_id": "MDQ6VXNlcjIyMjE4NzM3",
"avatar_url": "https://avatars.githubusercontent.com/u/22218737?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/QiWen77",
"html_url": "https://github.com/QiWen77",
"followers_url": "https://api.github.com/users/QiWen77/followers",
"following_url": "https://api.github.com/users/QiWen77/following{/other_user}",
"gists_url": "https://api.github.com/users/QiWen77/gists{/gist_id}",
"starred_url": "https://api.github.com/users/QiWen77/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/QiWen77/subscriptions",
"organizations_url": "https://api.github.com/users/QiWen77/orgs",
"repos_url": "https://api.github.com/users/QiWen77/repos",
"events_url": "https://api.github.com/users/QiWen77/events{/privacy}",
"received_events_url": "https://api.github.com/users/QiWen77/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This is not a pymatgen bug. Pls post on the right Github Issues page. Thanks."
] | 2017-07-23T03:09:53
| 2017-07-23T03:56:25
|
2017-07-23T03:56:25Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.>
## System
* Pymatgen version: <Write "branch_name" if it is development version.>
* Python version: <Only 2.7.* and 3.* supported.>
* OS version: <If you are writing Windows here, you are on your own.>
## Summary
There are some issues on the determination of oxide state when running a mpworks workflow.Some cases are fine,while some will fail,the main problem may occurs here https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/structure_analyzer.py#L718L727
* <Short 1-2 bullet points stating the problem.>
## Example code
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Element
from pymatgen.analysis.structure_analyzer import oxide_type
s = Structure.from_file('POSCAR')
print(isinstance(s.composition.elements[0], Element))
oxide_type(s)
-----------POSCAR--------
K1 H85 Pb18 C17 I54 N34
1.0
8.660300 0.000000 0.000000
-12.990450 22.500120 0.000000
0.000000 0.000000 23.706601
K H Pb C I N
1 85 18 17 54 34
direct
0.666670 0.444440 0.551640 K
0.402160 0.199747 0.051643 H
0.402160 0.199747 0.384977 H
0.402160 0.199747 0.718310 H
0.402160 0.533080 0.051643 H
0.402160 0.533080 0.384977 H
0.402160 0.533080 0.718310 H
0.402160 0.866413 0.051643 H
0.402160 0.866413 0.384977 H
0.402160 0.866413 0.718310 H
0.350040 0.298137 0.051747 H
0.350040 0.298137 0.385080 H
0.350040 0.298137 0.718413 H
0.350040 0.631470 0.051747 H
0.350040 0.631470 0.385080 H
0.350040 0.631470 0.718413 H
0.350040 0.964803 0.051747 H
0.350040 0.964803 0.385080 H
0.350040 0.964803 0.718413 H
0.541210 0.299360 0.051827 H
0.541210 0.299360 0.385160 H
0.541210 0.299360 0.718493 H
0.541210 0.632693 0.051827 H
0.541210 0.632693 0.385160 H
0.541210 0.632693 0.718493 H
0.541210 0.966027 0.051827 H
0.541210 0.966027 0.385160 H
0.541210 0.966027 0.718493 H
0.103410 0.153050 0.051643 H
0.103410 0.153050 0.384977 H
0.103410 0.153050 0.718310 H
0.103410 0.486383 0.051643 H
0.103410 0.486383 0.384977 H
0.103410 0.486383 0.718310 H
0.103410 0.819717 0.051643 H
0.103410 0.819717 0.384977 H
0.103410 0.819717 0.718310 H
0.106100 0.216643 0.051643 H
0.106100 0.216643 0.384977 H
0.106100 0.216643 0.718310 H
0.106100 0.549977 0.051643 H
0.106100 0.549977 0.384977 H
0.106100 0.549977 0.718310 H
0.106100 0.883310 0.051643 H
0.106100 0.883310 0.384977 H
0.106100 0.883310 0.718310 H
0.801750 0.133250 0.218310 H
0.801750 0.133250 0.551643 H
0.801750 0.133250 0.884977 H
0.801750 0.466583 0.218310 H
0.801750 0.466583 0.884977 H
0.801750 0.799917 0.218310 H
0.801750 0.799917 0.551643 H
0.801750 0.799917 0.884977 H
0.455720 0.116923 0.218247 H
0.455720 0.116923 0.551580 H
0.455720 0.116923 0.884913 H
0.455720 0.450257 0.218247 H
0.455720 0.450257 0.884913 H
0.455720 0.783590 0.218247 H
0.455720 0.783590 0.551580 H
0.455720 0.783590 0.884913 H
0.645180 0.180123 0.218267 H
0.645180 0.180123 0.551600 H
0.645180 0.180123 0.884933 H
0.645180 0.513457 0.218267 H
0.645180 0.513457 0.884933 H
0.645180 0.846790 0.218267 H
0.645180 0.846790 0.551600 H
0.645180 0.846790 0.884933 H
0.643380 0.034047 0.218310 H
0.643380 0.034047 0.551643 H
0.643380 0.034047 0.884977 H
0.643380 0.367380 0.218310 H
0.643380 0.367380 0.884977 H
0.643380 0.700713 0.218310 H
0.643380 0.700713 0.551643 H
0.643380 0.700713 0.884977 H
0.455780 0.034807 0.218310 H
0.455780 0.034807 0.551643 H
0.455780 0.034807 0.884977 H
0.455780 0.368140 0.218310 H
0.455780 0.368140 0.884977 H
0.455780 0.701473 0.218310 H
0.455780 0.701473 0.551643 H
0.455780 0.701473 0.884977 H
0.000000 0.000000 0.002000 Pb
0.000000 0.000000 0.335333 Pb
0.000000 0.000000 0.668667 Pb
0.000000 0.333333 0.002000 Pb
0.000000 0.333333 0.335333 Pb
0.000000 0.333333 0.668667 Pb
0.000000 0.666667 0.002000 Pb
0.000000 0.666667 0.335333 Pb
0.000000 0.666667 0.668667 Pb
0.000000 0.000000 0.168667 Pb
0.000000 0.000000 0.502000 Pb
0.000000 0.000000 0.835333 Pb
0.000000 0.333333 0.168667 Pb
0.000000 0.333333 0.502000 Pb
0.000000 0.333333 0.835333 Pb
0.000000 0.666667 0.168667 Pb
0.000000 0.666667 0.502000 Pb
0.000000 0.666667 0.835333 Pb
0.333333 0.222222 0.051643 C
0.333333 0.222222 0.384977 C
0.333333 0.222222 0.718310 C
0.333333 0.555556 0.051643 C
0.333333 0.555556 0.384977 C
0.333333 0.555556 0.718310 C
0.333333 0.888889 0.051643 C
0.333333 0.888889 0.384977 C
0.333333 0.888889 0.718310 C
0.666667 0.111111 0.218310 C
0.666667 0.111111 0.551643 C
0.666667 0.111111 0.884977 C
0.666667 0.444444 0.218310 C
0.666667 0.444444 0.884977 C
0.666667 0.777778 0.218310 C
0.666667 0.777778 0.551643 C
0.666667 0.777778 0.884977 C
0.831170 0.056277 0.083667 I
0.831170 0.056277 0.417000 I
0.831170 0.056277 0.750333 I
0.831170 0.389610 0.083667 I
0.831170 0.389610 0.417000 I
0.831170 0.389610 0.750333 I
0.831170 0.722943 0.083667 I
0.831170 0.722943 0.417000 I
0.831170 0.722943 0.750333 I
0.831170 0.220780 0.083667 I
0.831170 0.220780 0.417000 I
0.831170 0.220780 0.750333 I
0.831170 0.554113 0.083667 I
0.831170 0.554113 0.417000 I
0.831170 0.554113 0.750333 I
0.831170 0.887447 0.083667 I
0.831170 0.887447 0.417000 I
0.831170 0.887447 0.750333 I
0.337660 0.056277 0.083667 I
0.337660 0.056277 0.417000 I
0.337660 0.056277 0.750333 I
0.337660 0.389610 0.083667 I
0.337660 0.389610 0.417000 I
0.337660 0.389610 0.750333 I
0.337660 0.722943 0.083667 I
0.337660 0.722943 0.417000 I
0.337660 0.722943 0.750333 I
0.168830 0.277057 0.250333 I
0.168830 0.277057 0.583667 I
0.168830 0.277057 0.917000 I
0.168830 0.610390 0.250333 I
0.168830 0.610390 0.583667 I
0.168830 0.610390 0.917000 I
0.168830 0.943723 0.250333 I
0.168830 0.943723 0.583667 I
0.168830 0.943723 0.917000 I
0.168830 0.112553 0.250333 I
0.168830 0.112553 0.583667 I
0.168830 0.112553 0.917000 I
0.168830 0.445887 0.250333 I
0.168830 0.445887 0.583667 I
0.168830 0.445887 0.917000 I
0.168830 0.779220 0.250333 I
0.168830 0.779220 0.583667 I
0.168830 0.779220 0.917000 I
0.662340 0.277057 0.250333 I
0.662340 0.277057 0.583667 I
0.662340 0.277057 0.917000 I
0.662340 0.610390 0.250333 I
0.662340 0.610390 0.583667 I
0.662340 0.610390 0.917000 I
0.662340 0.943723 0.250333 I
0.662340 0.943723 0.583667 I
0.662340 0.943723 0.917000 I
0.171210 0.195707 0.051643 N
0.171210 0.195707 0.384977 N
0.171210 0.195707 0.718310 N
0.171210 0.529040 0.051643 N
0.171210 0.529040 0.384977 N
0.171210 0.529040 0.718310 N
0.171210 0.862373 0.051643 N
0.171210 0.862373 0.384977 N
0.171210 0.862373 0.718310 N
0.412460 0.276360 0.051657 N
0.412460 0.276360 0.384990 N
0.412460 0.276360 0.718323 N
0.412460 0.609693 0.051657 N
0.412460 0.609693 0.384990 N
0.412460 0.609693 0.718323 N
0.412460 0.943027 0.051657 N
0.412460 0.943027 0.384990 N
0.412460 0.943027 0.718323 N
0.581900 0.056433 0.218310 N
0.581900 0.056433 0.551643 N
0.581900 0.056433 0.884977 N
0.581900 0.389767 0.218310 N
0.581900 0.389767 0.884977 N
0.581900 0.723100 0.218310 N
0.581900 0.723100 0.551643 N
0.581900 0.723100 0.884977 N
0.583020 0.137447 0.218420 N
0.583020 0.137447 0.551753 N
0.583020 0.137447 0.885087 N
0.583020 0.470780 0.218420 N
0.583020 0.470780 0.885087 N
0.583020 0.804113 0.218420 N
0.583020 0.804113 0.551753 N
0.583020 0.804113 0.885087 N
```python
<Example code generating error>
```
## Error message
```
<Error message>
```
ERROR:mpworks.drones.mp_vaspdrone:can get oxide_type
## Suggested solution (if any)
* <If you have a suggestion on how to solve the issue, you may write it
here.>
## Files (if any)
<If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.>
```
<contents of file 1>
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/730/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/730/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/731
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/731/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/731/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/731/events
|
https://github.com/materialsproject/pymatgen/pull/731
| 245,532,216
|
MDExOlB1bGxSZXF1ZXN0MTMyMzc3MzAy
| 731
|
bug fix in lammps output.py
|
{
"login": "mike5603",
"id": 10424186,
"node_id": "MDQ6VXNlcjEwNDI0MTg2",
"avatar_url": "https://avatars.githubusercontent.com/u/10424186?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mike5603",
"html_url": "https://github.com/mike5603",
"followers_url": "https://api.github.com/users/mike5603/followers",
"following_url": "https://api.github.com/users/mike5603/following{/other_user}",
"gists_url": "https://api.github.com/users/mike5603/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mike5603/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mike5603/subscriptions",
"organizations_url": "https://api.github.com/users/mike5603/orgs",
"repos_url": "https://api.github.com/users/mike5603/repos",
"events_url": "https://api.github.com/users/mike5603/events{/privacy}",
"received_events_url": "https://api.github.com/users/mike5603/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-25T20:53:54
| 2017-07-25T20:55:39
|
2017-07-25T20:55:38Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
<Short few sentences, and summary of the major changes in bullet
points>
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
<List all new dependencies needed. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. If you are putting anything here, you should
provide a justification why that dependency is needed. Especially
frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.>
## TODO (if any)
<If this is a work-in-progress, write something about what else needs
to be done>
* Feature 1 supports a, but not b.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/731/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/731/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/731",
"html_url": "https://github.com/materialsproject/pymatgen/pull/731",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/731.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/731.patch",
"merged_at": "2017-07-25T20:55:38Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/732
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/732/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/732/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/732/events
|
https://github.com/materialsproject/pymatgen/pull/732
| 245,533,201
|
MDExOlB1bGxSZXF1ZXN0MTMyMzc4MDM5
| 732
|
Make BoltztrapRunner MSONable
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyamd/following{/other_user}",
"gists_url": "https://api.github.com/users/shyamd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyamd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyamd/subscriptions",
"organizations_url": "https://api.github.com/users/shyamd/orgs",
"repos_url": "https://api.github.com/users/shyamd/repos",
"events_url": "https://api.github.com/users/shyamd/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyamd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Unittest pls..."
] | 2017-07-25T20:57:36
| 2017-07-26T20:09:38
|
2017-07-26T20:09:38Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Made BoltztrapRunner MSONable
Makes it easier to store and pass this object around.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/732/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/732/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/732",
"html_url": "https://github.com/materialsproject/pymatgen/pull/732",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/732.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/732.patch",
"merged_at": "2017-07-26T20:09:38Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/733
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/733/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/733/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/733/events
|
https://github.com/materialsproject/pymatgen/issues/733
| 245,612,777
|
MDU6SXNzdWUyNDU2MTI3Nzc=
| 733
|
Trying to get in touch with people working on VASP. Please is anyone home
|
{
"login": "Francisenujekwu",
"id": 30256792,
"node_id": "MDQ6VXNlcjMwMjU2Nzky",
"avatar_url": "https://avatars.githubusercontent.com/u/30256792?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Francisenujekwu",
"html_url": "https://github.com/Francisenujekwu",
"followers_url": "https://api.github.com/users/Francisenujekwu/followers",
"following_url": "https://api.github.com/users/Francisenujekwu/following{/other_user}",
"gists_url": "https://api.github.com/users/Francisenujekwu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Francisenujekwu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Francisenujekwu/subscriptions",
"organizations_url": "https://api.github.com/users/Francisenujekwu/orgs",
"repos_url": "https://api.github.com/users/Francisenujekwu/repos",
"events_url": "https://api.github.com/users/Francisenujekwu/events{/privacy}",
"received_events_url": "https://api.github.com/users/Francisenujekwu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This is not the forum. Pls do not spam us with this kind of posts."
] | 2017-07-26T05:48:05
| 2017-07-30T14:37:54
|
2017-07-30T14:37:35Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Trying to get in touch with people working on VASP. Please is anyone home
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/733/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/733/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/734
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/734/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/734/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/734/events
|
https://github.com/materialsproject/pymatgen/pull/734
| 245,736,386
|
MDExOlB1bGxSZXF1ZXN0MTMyNTI2MDE4
| 734
|
New functions in BoltztrapAnalyzer/Plotter and minor fixing
|
{
"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/fraricci/followers",
"following_url": "https://api.github.com/users/fraricci/following{/other_user}",
"gists_url": "https://api.github.com/users/fraricci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fraricci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fraricci/subscriptions",
"organizations_url": "https://api.github.com/users/fraricci/orgs",
"repos_url": "https://api.github.com/users/fraricci/repos",
"events_url": "https://api.github.com/users/fraricci/events{/privacy}",
"received_events_url": "https://api.github.com/users/fraricci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There are failing tests related to the new functionality in travis. Pls fix before I merge.",
"There still seem to be failing tests because of the import of a defunct physical constants module.",
"yes exactly. I don't know why in my computer it works.\nAnyway, there a module that replace it?\nOr I have to get the constant inside scipy directly?\n\nThanks\nFR\n\n2017-07-26 17:58 GMT+02:00 Shyue Ping Ong <notifications@github.com>:\n\n> There still seem to be failing tests because of the import of a defunct\n> physical constants module.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/734#issuecomment-318098992>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AQnsPcDLVXEKpDaqSmsTEUaoqNXDYGkkks5sR2I0gaJpZM4Oj-4W>\n> .\n>\n",
"Get it from scipy. scipy is now a req. So it is fine to use theirs.\n\n\nShyue Ping\n\nOn July 26, 2017 at 9:08:17 AM, fraricci (notifications@github.com) wrote:\n\nyes exactly. I don't know why in my computer it works.\nAnyway, there a module that replace it?\nOr I have to get the constant inside scipy directly?\n\nThanks\nFR\n\n2017-07-26 17:58 GMT+02:00 Shyue Ping Ong <notifications@github.com>:\n\n> There still seem to be failing tests because of the import of a defunct\n> physical constants module.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <\nhttps://github.com/materialsproject/pymatgen/pull/734#issuecomment-318098992\n>,\n> or mute the thread\n> <\nhttps://github.com/notifications/unsubscribe-auth/AQnsPcDLVXEKpDaqSmsTEUaoqNXDYGkkks5sR2I0gaJpZM4Oj-4W\n>\n> .\n>\n\n—\nYou are receiving this because you commented.\nReply to this email directly, view it on GitHub\n<https://github.com/materialsproject/pymatgen/pull/734#issuecomment-318102120>,\nor mute the thread\n<https://github.com/notifications/unsubscribe-auth/AAjOU5s1dUOydkunaPrHNfVvKq3ldL86ks5sR2RvgaJpZM4Oj-4W>\n.\n"
] | 2017-07-26T14:13:59
| 2017-07-26T17:42:27
|
2017-07-26T17:42:27Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
- get_seebeck_eff_mass allows to calculate the seebeck effective mass
- get_complexity_factor allows to calculate the complexity factor
It is possible to calculate both quantities w.r.t. the chemical potential
or doping levels, for different temperatures.
The three diagonal components of the tensors or an average are provided.
Correspondent functions to plot these quantities are coded too.
The meaning of these quantities is described in the paper
Gibbs, Z. M. et al., Effective mass and fermi surface complexity factor
from ab initio band structure calculations. npj Computational Materials 3, 8 (2017).
Note: fdint module is required for quick calculation of fermi integrals
Minor fixing:
- symprec set at None disable the symmetries in the BoltztrapRunner.
Useful when a NSCF calculation is performed over a kmesh that cover
the whole BZ.
- edit in the doc of fermi surface plotter. Energy levels are respect to
the VBM set at 0 eV, like in the bandstructure plot
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/734/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/734/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/734",
"html_url": "https://github.com/materialsproject/pymatgen/pull/734",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/734.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/734.patch",
"merged_at": "2017-07-26T17:42:27Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/735
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/735/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/735/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/735/events
|
https://github.com/materialsproject/pymatgen/pull/735
| 245,880,876
|
MDExOlB1bGxSZXF1ZXN0MTMyNjM0MjI5
| 735
|
Mvl slabset update
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-26T23:10:21
| 2017-07-26T23:15:20
|
2017-07-26T23:15:20Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Updates MVLSlabSet to support automatic dipole correction
* Adds a dipole correction to the slab incar params based on the center of mass for MVLSlabSet
* Updated unittest
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/735/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/735/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/735",
"html_url": "https://github.com/materialsproject/pymatgen/pull/735",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/735.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/735.patch",
"merged_at": "2017-07-26T23:15:20Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/736
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/736/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/736/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/736/events
|
https://github.com/materialsproject/pymatgen/pull/736
| 245,887,125
|
MDExOlB1bGxSZXF1ZXN0MTMyNjM4NzE1
| 736
|
fix bug in MVLSlabSet init
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-26T23:48:47
| 2019-04-04T02:40:57
|
2017-07-27T00:13:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Sorry, failed to merge last commit. Should fix bug in CI tests.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/736/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/736/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/736",
"html_url": "https://github.com/materialsproject/pymatgen/pull/736",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/736.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/736.patch",
"merged_at": "2017-07-27T00:13:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/737
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/737/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/737/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/737/events
|
https://github.com/materialsproject/pymatgen/pull/737
| 245,955,241
|
MDExOlB1bGxSZXF1ZXN0MTMyNjg2NjU4
| 737
|
fix inversed oxidation state decoration from bader
|
{
"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/followers",
"following_url": "https://api.github.com/users/adengz/following{/other_user}",
"gists_url": "https://api.github.com/users/adengz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/adengz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/adengz/subscriptions",
"organizations_url": "https://api.github.com/users/adengz/orgs",
"repos_url": "https://api.github.com/users/adengz/repos",
"events_url": "https://api.github.com/users/adengz/events{/privacy}",
"received_events_url": "https://api.github.com/users/adengz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-27T07:51:47
| 2017-07-27T13:10:07
|
2017-07-27T13:10:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Previously, the method used # of electrons as oxidation state, but the two should be opposite to each other.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/737/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/737/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/737",
"html_url": "https://github.com/materialsproject/pymatgen/pull/737",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/737.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/737.patch",
"merged_at": "2017-07-27T13:10:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/738
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/738/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/738/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/738/events
|
https://github.com/materialsproject/pymatgen/issues/738
| 246,290,848
|
MDU6SXNzdWUyNDYyOTA4NDg=
| 738
|
Design question regarding PointgroupAnalyzer
|
{
"login": "mcocdawc",
"id": 15892408,
"node_id": "MDQ6VXNlcjE1ODkyNDA4",
"avatar_url": "https://avatars.githubusercontent.com/u/15892408?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mcocdawc",
"html_url": "https://github.com/mcocdawc",
"followers_url": "https://api.github.com/users/mcocdawc/followers",
"following_url": "https://api.github.com/users/mcocdawc/following{/other_user}",
"gists_url": "https://api.github.com/users/mcocdawc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mcocdawc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mcocdawc/subscriptions",
"organizations_url": "https://api.github.com/users/mcocdawc/orgs",
"repos_url": "https://api.github.com/users/mcocdawc/repos",
"events_url": "https://api.github.com/users/mcocdawc/events{/privacy}",
"received_events_url": "https://api.github.com/users/mcocdawc/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The PointGroup in pymatgen.symmetry.groups are defined based on fractional coordinates and are for use in crystal structures. It is an idealized symmetry class.\r\n\r\nPointGroupOperations on the other hand are a series of operations that are determined on cartesian coordinates based on the detected symmetry operations, and are the actual operations you apply on a Molecule (not a crystal). \r\n\r\nThe two are not the same.",
"Thank you very much for your answer.\r\n\r\nIf there is a slightly distorted molecule and pymatgen was able to detect the correct pointgroups (perhaps with tweaking tolerance settings), is there the possibility to obtain the symmetrised molecule?",
"Well, I think it can be done. You simply need to get all the equivalent atoms, and then choose one of them to be the generating atom, and apply all operations of the point group to get the symmetrized molecule. This functionality is not implemented as yet.",
"Is this planed to be implemented in the near future?\r\n\r\nIn the molecules, I thought of, I would average over the location of the equivalent atoms, but that is a detail question of implementation.",
"I am not planning to do it myself. I cannot speak as to whether the ~100 contributors to pymatgen will be doing so. In general, I would recommend you do it yourself and then submit a pull request. I think it is not too difficult.",
"Ok, I will write an Enhancement issue for it, to avoid double work."
] | 2017-07-28T09:12:05
| 2017-08-02T15:59:27
|
2017-07-28T12:48:14Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: '2017.7.21'
* Python version: 3.6.1
* OS version: Ubuntu 16.04 LTS
## Summary
``get_pointgroup`` returns a ``pymatgen.symmetry.analyzer.PointGroupOperations`` instance.
## Example code
I use fullerene as example molecule for the pointgroup analyzer [xyz-file here](http://www.nanotube.msu.edu/fullerene/fullerene.php?C=60):
```python
analyser = PointGroupAnalyzer(fullerene)
print(type(analyser.get_pointgroup()))
```
Gives:
```
pymatgen.symmetry.analyzer.PointGroupOperations
```
Isn't this a bit redundant, if you already have a class ``pymatgent.symmetry.groups.Pointgroup``?
## Suggested solution (if any)
* ``get_pointgroup`` should return a ``pymatgent.symmetry.groups.Pointgroup`` instance.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/738/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/738/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/739
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/739/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/739/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/739/events
|
https://github.com/materialsproject/pymatgen/pull/739
| 246,494,376
|
MDExOlB1bGxSZXF1ZXN0MTMzMDc3NDgw
| 739
|
Chgcar write_file 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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-29T02:48:16
| 2017-07-29T03:08:27
|
2017-07-29T03:08:27Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Chgcar.from_file(‘…’).write_file(‘…’) should no longer lose
information, stores any additional lines in a .data_aug dict associated with each VolumetricData contained inside a file. Now prints Fortran-style floats for easier visual comparison too.
Includes test. Closes #709
## Additional dependencies introduced (if any)
None
## TODO (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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/739/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/739/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/739",
"html_url": "https://github.com/materialsproject/pymatgen/pull/739",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/739.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/739.patch",
"merged_at": "2017-07-29T03:08:27Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/740
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/740/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/740/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/740/events
|
https://github.com/materialsproject/pymatgen/pull/740
| 246,543,855
|
MDExOlB1bGxSZXF1ZXN0MTMzMTA1NDcw
| 740
|
Bader update + tests for same
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-29T20:35:47
| 2017-07-29T21:01:45
|
2017-07-29T20:53:56Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Can now automatically construct reference file from AECCAR0 and AECCAR2
* Can now calculate magnetic moments using Bader method
* Adds MSONable `BaderResult` to easily save results from Bader analysis
* Now detects version of `bader` binary, and warns if it's too old (there was previously a minor issue with regards to calculating vacuum charge with reference files)
* Adds helper method to automatically run Bader analysis on a typical VASP output directory, or from pymatgen Chgcar objectsa
* Fixes regression in `BaderAnalysis` from #715 where analysis would fail if reference wasn't supplied
* Fixes headers ('min' is now 'min_dist', 'dist' is now 'atomic_vol')
## Additional dependencies introduced (if any)
None
## TODO (if any)
None, though I might have renamed `BaderAnalysis` to `BaderCaller` because I think it makes more sense, but I left it as-is for backwards compatibility.
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/740/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/740/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/740",
"html_url": "https://github.com/materialsproject/pymatgen/pull/740",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/740.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/740.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/741
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/741/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/741/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/741/events
|
https://github.com/materialsproject/pymatgen/pull/741
| 246,545,177
|
MDExOlB1bGxSZXF1ZXN0MTMzMTA2MjU2
| 741
|
Bader update + tests for same (v2)
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Weird, this is passing on my local machine for both py27 and py36, but not in CI, issue is from:\r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"/root/pymatgen/pymatgen/command_line/tests/test_bader_caller.py\", line 71, in test_automatic_runner\r\n self.assertEqual(bader_result.__dict__, summary_ref)\r\nAssertionError: {'min_dist': [0.8358, 0.9295, 0.9295, 0.973,[544 chars]705]} != {'magmom': [4.298761, 4.221997, 4.221997, 3.[647 chars]True}\r\n```\r\n\r\nThis is just comparing two dicts, but in the CI it seems to be treating them as strings?\r\n\r\nEdit: thanks @matk86!",
"use self.assertDictEqual",
"Tests failed. Can you submit a pull request fixing the problem?\r\n\r\nAlso, the tests depend on bader executables in the cmd_line directory. That might be the cause. The versions might be outdated.",
"Looks like the same problem as before, though I'm using `assertDictEqual` now:\r\n\r\n```\r\n======================================================================\r\nFAIL: test_automatic_runner (pymatgen.command_line.tests.test_bader_caller.BaderAnalysisTest)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n File \"/home/travis/build/materialsproject/pymatgen/pymatgen/command_line/tests/test_bader_caller.py\", line 71, in test_automatic_runner\r\n self.assertDictEqual(summary, summary_ref)\r\nAssertionError: {'min_dist': [0.8358, 0.9295, 0.9295, 0.973,[544 chars]705]} != {'magmom': [4.298761, 4.221997, 4.221997, 3.[647 chars]True}\r\nDiff is 4625 characters long. Set self.maxDiff to None to see it.\r\n```\r\n\r\nTests pass locally. Will look into it.",
"Instead of doing dict equal, it is better to just compare the values for each key with a loop. That wya you know exactly where the problem is. It is likely a precision issue. These are floats. You probably need ArrayAlmostEqual or something of that sort.",
"Yeah, they may not be exactly equal if different bader versions are used -- I'll make the test more loose. Generally, `assertDictEqual` should show the keys where the difference is located though, otherwise there's not much point using it over `assertEqual`."
] | 2017-07-29T21:05:28
| 2017-07-29T23:25:34
|
2017-07-29T22:47:57Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Can now automatically construct reference file from AECCAR0 and AECCAR2
* Can now calculate magnetic moments using Bader method
* Adds MSONable `BaderResult` to easily save results from Bader analysis
* Now detects version of `bader` binary, and warns if it's too old (there was previously a minor issue with regards to calculating vacuum charge with reference files)
* Adds helper method to automatically run Bader analysis on a typical VASP output directory, or from pymatgen Chgcar objects
* Fixes regression in `BaderAnalysis` from #715 where analysis would fail if reference wasn't supplied
* Fixes headers ('min' is now 'min_dist', 'dist' is now 'atomic_vol')
## Additional dependencies introduced (if any)
None
## TODO (if any)
None, though I might have renamed `BaderAnalysis` to `BaderCaller` because I think it makes more sense, but I left it as-is for backwards compatibility.
Edit: First PR didn't have tests for MSONable, this has been fixed now.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/741/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/741/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/741",
"html_url": "https://github.com/materialsproject/pymatgen/pull/741",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/741.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/741.patch",
"merged_at": "2017-07-29T22:47:57Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/742
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/742/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/742/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/742/events
|
https://github.com/materialsproject/pymatgen/pull/742
| 246,560,123
|
MDExOlB1bGxSZXF1ZXN0MTMzMTE0OTMw
| 742
|
(Wait for CI before merge) New tests for Bader caller
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-07-30T03:38:31
| 2017-07-30T03:46:15
|
2017-07-30T03:46:15Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Updated tests for Bader caller
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/742/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/742/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/742",
"html_url": "https://github.com/materialsproject/pymatgen/pull/742",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/742.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/742.patch",
"merged_at": "2017-07-30T03:46:15Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/743
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/743/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/743/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/743/events
|
https://github.com/materialsproject/pymatgen/issues/743
| 246,587,825
|
MDU6SXNzdWUyNDY1ODc4MjU=
| 743
|
Overflow errors in elastic
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Fixed via 52b3c05."
] | 2017-07-30T14:40:01
| 2018-12-17T16:58:42
|
2018-12-17T16:58:42Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: master
* Python version: 3.6.2
* OS version: Linux
## Summary
* Tests are showing overflow errors. Looking at the equations, it seems that there should be some special handling if t is very small.
```
/root/pymatgen/pymatgen/analysis/elasticity/elastic.py:644: RuntimeWarning: overflow encountered in double_scalars
c *= np.exp(hbar_w / kt) / (np.exp(hbar_w / kt) - 1)**2
/root/pymatgen/pymatgen/analysis/elasticity/elastic.py:644: RuntimeWarning: overflow encountered in exp
c *= np.exp(hbar_w / kt) / (np.exp(hbar_w / kt) - 1)**2
/root/pymatgen/pymatgen/analysis/elasticity/elastic.py:644: RuntimeWarning: invalid value encountered in double_scalars
c *= np.exp(hbar_w / kt) / (np.exp(hbar_w / kt) - 1)**2
```
Though the code may actually work, it is best to explicitly handle such cases to avoid ambiguity.
@montoyjh Can you fix pls?
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyamd/following{/other_user}",
"gists_url": "https://api.github.com/users/shyamd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyamd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyamd/subscriptions",
"organizations_url": "https://api.github.com/users/shyamd/orgs",
"repos_url": "https://api.github.com/users/shyamd/repos",
"events_url": "https://api.github.com/users/shyamd/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyamd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/743/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/743/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/744
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/744/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/744/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/744/events
|
https://github.com/materialsproject/pymatgen/pull/744
| 246,916,397
|
MDExOlB1bGxSZXF1ZXN0MTMzMzYxMzI0
| 744
|
(Wait for CI) Various magmom handling fixes, improvements for SOC calculations + 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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There seems to be *a lot* of test failures. As a general rule, changes to core classes (those in pymatgen.core) needs to be thought through very carefully. You can run the tests on your local machine to make sure they pass first). \r\n\r\nWhat is magmom supposed to be? A scalar or a vector?",
"Magmom's already in electronic_structure.core.\n\nAgreed re. test failures, I tested all the tests for the modules that were changed and they passed, but I suspected there could be failures in unrelated modules, which is why I wanted to see the CI results (I haven't got my own CI set up yet, but will do soon hopefully).",
"Will close it for now until test failures are resolved.",
"You don't need to do your own CI setup. You just need to cd into the pymatgen/core directory, and then run \"nosetest\". At the minimum, all the errors on the core classes will pop up.",
"Have reverted the problematic change (the explicit magmom site attr, I think this was a bad idea!). The other changes should be non-breaking, but let's see...\r\n\r\nMy nosetests are passing in pymatgen/core, but I often have nosetests fail even on the master branch, and I haven't had time to debug it yet. I think it may be because of an old enumlib."
] | 2017-07-31T23:48:17
| 2017-08-01T02:57:59
|
2017-08-01T02:57:59Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This touches a lot of files, so I'd like to wait for CI results before merging + read them carefully.
* `Outcar` now detects vector magmoms from SOC calculations (previously would only detect x component)
* `Chgcar` now properly handles charge density from SOC calculations
* for SOC calculations, `.data` will have `.data['diff_x']`, `.data['diff_y']`, `.data['diff_z']` as the canonical magnetization densities, but will also try to construct a `.data['diff']` referenced to an arbitrary direction to give a scalar density (this uses the same approach as `float(Magmom)`)
* has new `net_magnetization` property and `is_soc` property
* `Structure` `to`/`from_file` now detects `.mcif`
* `Structure` implements `add_spin_by_site`, `remove_spin` (c.f. `add_oxidation_state_by_site`, `remove_oxidation_state`), which was suggested in #718
* Had to include the minor change to `Specie` that makes oxidation state optional, so we can have Specie with spin even if oxidation state is unknown, also added comma to str representation (so `Ni,spin=5`, `Ni2+,spin=5` vs old `Nispin=5`, `Ni2+spin=5`)
* `CifWriter` and `Incar` includes better handling of Magmom class, more tests
* `Magmom` has minor bug fix to define equality between floats and Magmoms
* ~~~**`Site` now has explicit `magmom` attr**, this follows the same logic as in `io.vasp.sets`, which is to look for site property first and then spin property if not, and will always returns a instance of `Magmom` if magmom is defined~~~ (this was a bad idea, reverted)
* ~~~this makes reasoning about magmoms a lot easier since it provides a uniform interface to magmom; if we do want to change this behavior in future, it'll be much easier to change it here than hunting everywhere magmoms are handled in pymatgen (I have a few ideas to improve this later)~~~
* ~~~I think this is probably the most controversial change here, do we want to keep this?~~~
## Additional dependencies introduced (if any)
None
## TODO (if any)
* (In future) Improvements to handling of the spin quantization axis, in particular processing it from `Outcar`, setting the `SAXIS` variable in `Incar`, and smarter handling in `MPSOCSet` (and, by extension, atomate's SOC powerups too), and better tests for non-standard `SAXIS` throughout
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/744/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/744/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/744",
"html_url": "https://github.com/materialsproject/pymatgen/pull/744",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/744.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/744.patch",
"merged_at": "2017-08-01T02:57:59Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/745
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/745/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/745/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/745/events
|
https://github.com/materialsproject/pymatgen/issues/745
| 247,283,914
|
MDU6SXNzdWUyNDcyODM5MTQ=
| 745
|
Error when using BSPlotter under python 3.6.2
|
{
"login": "Hugo-Leung",
"id": 20005167,
"node_id": "MDQ6VXNlcjIwMDA1MTY3",
"avatar_url": "https://avatars.githubusercontent.com/u/20005167?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Hugo-Leung",
"html_url": "https://github.com/Hugo-Leung",
"followers_url": "https://api.github.com/users/Hugo-Leung/followers",
"following_url": "https://api.github.com/users/Hugo-Leung/following{/other_user}",
"gists_url": "https://api.github.com/users/Hugo-Leung/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Hugo-Leung/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Hugo-Leung/subscriptions",
"organizations_url": "https://api.github.com/users/Hugo-Leung/orgs",
"repos_url": "https://api.github.com/users/Hugo-Leung/repos",
"events_url": "https://api.github.com/users/Hugo-Leung/events{/privacy}",
"received_events_url": "https://api.github.com/users/Hugo-Leung/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I think this has been fixed in recent versions. Pls upgrade your pymatgen to 2017.7.21 and try again.",
"Closing this issue for now. Pls reopen if you still encounter the same issue in more recent versions."
] | 2017-08-02T06:16:00
| 2017-08-03T15:33:52
|
2017-08-03T15:33:52Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: <2017.06.08>
* Python version: <3.6.2>
* OS version: <SL7.3>
## Summary
I got an error when I try to plot the projected band structure
## Example code
```import matplotlib
matplotlib.use("pdf")
from pymatgen.io.vasp import BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotterProjected
v=BSVasprun("vasprun.xml",parse_projected_eigen=True)
bs=v.get_band_structure(kpoints_filename="KPOINTS",line_mode=True)
plt=BSPlotterProjected(bs)
fig=plt.get_plot()
fig.savefig("bandstructure.pdf")
dic={"Ga":["s"]}
fig=plt.get_projected_plots_dots(dic)
fig.savefig("Ga_s.pdf")
matplotlib.pyplot.close("all")
# Example code generating error
```
## Error message
```
/opt/anaconda3/lib/python3.6/site-packages/matplotlib/tight_layout.py:226: UserWarning: tight_layout : falling back to Agg renderer
warnings.warn("tight_layout : falling back to Agg renderer")
Traceback (most recent call last):
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/mathtext.py", line 2517, in parse
result = self._expression.parseString(s)
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1216, in parseString
raise exc
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1206, in parseString
loc, tokens = self._parse( instring, 0 )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2801, in parseImpl
return self.expr._parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2544, in parseImpl
loc, exprtokens = e._parse( instring, loc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2970, in parseImpl
return super(ZeroOrMore, self).parseImpl(instring, loc, doActions)
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2923, in parseImpl
loc, tokens = self_expr_parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2527, in parseImpl
loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1098, in _parseNoCache
tokens = fn( instring, tokensStart, retTokens )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 819, in wrapper
ret = func(*args[limit[0]:])
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/mathtext.py", line 2588, in math_string
return self._math_expression.parseString(toks[0][1:-1])
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1216, in parseString
raise exc
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1206, in parseString
loc, tokens = self._parse( instring, 0 )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2801, in parseImpl
return self.expr._parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2923, in parseImpl
loc, tokens = self_expr_parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2801, in parseImpl
return self.expr._parse( instring, loc, doActions, callPreParse=False )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1072, in _parseNoCache
loc,tokens = self.parseImpl( instring, preloc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 2658, in parseImpl
ret = e._parse( instring, loc, doActions )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1137, in _parseCache
value = self._parseNoCache( instring, loc, doActions, callPreParse )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 1098, in _parseNoCache
tokens = fn( instring, tokensStart, retTokens )
File "/opt/anaconda3/lib/python3.6/site-packages/pyparsing.py", line 819, in wrapper
ret = func(*args[limit[0]:])
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/mathtext.py", line 2694, in unknown_symbol
raise ParseFatalException(s, loc, "Unknown symbol: %s" % c)
pyparsing.ParseFatalException: Unknown symbol: \ (at char 0), (line:1, col:1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/hleung/vasptools/bandstructure.py", line 11, in <module>
fig.savefig("bandstructure.pdf")
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py", line 697, in savefig
res = fig.savefig(*args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/figure.py", line 1573, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2252, in print_figure
**kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_pdf.py", line 2527, in print_pdf
self.figure.draw(renderer)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/figure.py", line 1144, in draw
renderer, self, dsu, self.suppressComposite)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 2426, in draw
mimage._draw_list_compositing_images(renderer, self, dsu)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/axis.py", line 1150, in draw
self.label.draw(renderer)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/text.py", line 802, in draw
ismath=ismath, mtext=mtext)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_pdf.py", line 1953, in draw_text
return self.draw_mathtext(gc, x, y, s, prop, angle)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_pdf.py", line 1779, in draw_mathtext
self.mathtext_parser.parse(s, 72, prop)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/mathtext.py", line 3286, in parse
box = self._parser.parse(s, font_output, fontsize, dpi)
File "/opt/anaconda3/lib/python3.6/site-packages/matplotlib/mathtext.py", line 2523, in parse
six.text_type(err)]))
ValueError:
\\mathrm{Wave\ Vector}
^
Unknown symbol: \ (at char 0), (line:1, col:1)
# Error message
```
## Suggested solution
I've read that it could be due to the `r` in `plt.xlabel(r'$\mathrm{Wave\ Vector}$', fontsize=30)` in the BSPlotter class.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/745/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/745/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/746
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/746/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/746/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/746/events
|
https://github.com/materialsproject/pymatgen/issues/746
| 247,440,912
|
MDU6SXNzdWUyNDc0NDA5MTI=
| 746
|
ENH: Obtain symmetrised molecule from PointGroupAnalyzer
|
{
"login": "mcocdawc",
"id": 15892408,
"node_id": "MDQ6VXNlcjE1ODkyNDA4",
"avatar_url": "https://avatars.githubusercontent.com/u/15892408?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mcocdawc",
"html_url": "https://github.com/mcocdawc",
"followers_url": "https://api.github.com/users/mcocdawc/followers",
"following_url": "https://api.github.com/users/mcocdawc/following{/other_user}",
"gists_url": "https://api.github.com/users/mcocdawc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mcocdawc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mcocdawc/subscriptions",
"organizations_url": "https://api.github.com/users/mcocdawc/orgs",
"repos_url": "https://api.github.com/users/mcocdawc/repos",
"events_url": "https://api.github.com/users/mcocdawc/events{/privacy}",
"received_events_url": "https://api.github.com/users/mcocdawc/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-02T16:03:56
| 2017-08-15T14:36:26
|
2017-08-15T14:36:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This Issue exists just to avoid double work.
I plan to write a ``get_symmetrized`` method for the PointGroupAnalyzer class, to obtain the symmetrised molecule.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/746/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/746/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/747
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/747/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/747/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/747/events
|
https://github.com/materialsproject/pymatgen/pull/747
| 247,829,906
|
MDExOlB1bGxSZXF1ZXN0MTM0MDM3Mzc2
| 747
|
Support gzipped files for BaderAnalysis
|
{
"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/followers",
"following_url": "https://api.github.com/users/adengz/following{/other_user}",
"gists_url": "https://api.github.com/users/adengz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/adengz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/adengz/subscriptions",
"organizations_url": "https://api.github.com/users/adengz/orgs",
"repos_url": "https://api.github.com/users/adengz/repos",
"events_url": "https://api.github.com/users/adengz/events{/privacy}",
"received_events_url": "https://api.github.com/users/adengz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-03T20:44:07
| 2017-08-03T20:57:37
|
2017-08-03T20:57:37Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
BaderAnalysis is able to process all input files if they are gzipped
## TODO (if any)
A classmethod similar to current `bader_analysis_from_path` to instantiate the class with given path
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/747/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/747/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/747",
"html_url": "https://github.com/materialsproject/pymatgen/pull/747",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/747.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/747.patch",
"merged_at": "2017-08-03T20:57:37Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/748
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/748/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/748/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/748/events
|
https://github.com/materialsproject/pymatgen/pull/748
| 247,909,314
|
MDExOlB1bGxSZXF1ZXN0MTM0MDk1MTY4
| 748
|
`BaderAnalysis.from_path`
|
{
"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/followers",
"following_url": "https://api.github.com/users/adengz/following{/other_user}",
"gists_url": "https://api.github.com/users/adengz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/adengz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/adengz/subscriptions",
"organizations_url": "https://api.github.com/users/adengz/orgs",
"repos_url": "https://api.github.com/users/adengz/repos",
"events_url": "https://api.github.com/users/adengz/events{/privacy}",
"received_events_url": "https://api.github.com/users/adengz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-04T05:51:48
| 2017-08-04T13:42:02
|
2017-08-04T13:42:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added a Convenient constructor that takes in the path name of VASP run to perform Bader analysis.
## TODO (if any)
code cleanup in `bader_caller.py`, I'll leave this for @mkhorton to decide.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/748/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/748/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/748",
"html_url": "https://github.com/materialsproject/pymatgen/pull/748",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/748.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/748.patch",
"merged_at": "2017-08-04T13:42:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/749
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/749/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/749/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/749/events
|
https://github.com/materialsproject/pymatgen/pull/749
| 248,046,216
|
MDExOlB1bGxSZXF1ZXN0MTM0MTk3NzQ2
| 749
|
Refactor io.lammps
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-04T15:52:10
| 2017-08-04T17:37:23
|
2017-08-04T17:37:23Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* set input from templates instead of rigid key/values pairs
* forcefield data settings for atoms with custom labels
* updated packmolrunner: added capability to restore the site properties in the final packed system
* added input set = input+data
* more general dump/trajectory parsing
* made all classes msonable
* added more tests
* cleanedup the test_files/lammps folder
* misc bug fixes
* Thanks to @rishigurnani and @wood-b for the feedback and helping with the tests.
## TODO (if any)
* make the output parsing more robust and fast by using https://github.com/MDAnalysis/mdanalysis. @wood-b will be in charge of that.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/749/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/749/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/749",
"html_url": "https://github.com/materialsproject/pymatgen/pull/749",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/749.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/749.patch",
"merged_at": "2017-08-04T17:37:23Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/750
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/750/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/750/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/750/events
|
https://github.com/materialsproject/pymatgen/pull/750
| 248,277,267
|
MDExOlB1bGxSZXF1ZXN0MTM0MzQzNzUx
| 750
|
Substrate analyzer refactor
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyamd/following{/other_user}",
"gists_url": "https://api.github.com/users/shyamd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyamd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyamd/subscriptions",
"organizations_url": "https://api.github.com/users/shyamd/orgs",
"repos_url": "https://api.github.com/users/shyamd/repos",
"events_url": "https://api.github.com/users/shyamd/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyamd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-06T22:49:32
| 2017-08-06T23:07:34
|
2017-08-06T23:07:34Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Refactored the substrate analyzer code to be clearer and fixed some bugs along the way.
* ZSLGenerator now only implements the ZSL algorithm. It can be used for any sort of topological matching
* SubstrateAnalyzer takes on the brunt of generating different slabs of various miller indicies and feeding them to ZSLGenerator
* Fixed elastic energy being off by a factor of 10 due to units by using the units class
Note this still assumes the elastic tensor is in units of GPa.
* Fixed bug where the elastic tensor and the strain orientation might have been different by putting the strain in the IEEE orientation. Docs have been updated to state the elastic tensor should already be in the IEEE orientation.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/750/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/750/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/750",
"html_url": "https://github.com/materialsproject/pymatgen/pull/750",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/750.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/750.patch",
"merged_at": "2017-08-06T23:07:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/751
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/751/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/751/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/751/events
|
https://github.com/materialsproject/pymatgen/pull/751
| 248,443,946
|
MDExOlB1bGxSZXF1ZXN0MTM0NDYyMzky
| 751
|
minor bug fix in lammspinput
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-07T15:17:14
| 2017-08-07T15:45:11
|
2017-08-07T15:45:11Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* parsing issue
* added test
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/751/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/751/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/751",
"html_url": "https://github.com/materialsproject/pymatgen/pull/751",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/751.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/751.patch",
"merged_at": "2017-08-07T15:45:11Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/752
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/752/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/752/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/752/events
|
https://github.com/materialsproject/pymatgen/pull/752
| 248,534,470
|
MDExOlB1bGxSZXF1ZXN0MTM0NTI5MTA4
| 752
|
Bug fixes in deformation and heat capacity
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-07T21:18:09
| 2017-08-07T21:22:52
|
2017-08-07T21:22:52Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fixes to elastic tensor from deformation application and overflow errors in heat capacity.
* Deformation.apply_to_structure method was previously defined incorrectly in such a way that could cause large shear deformations to be incorrectly applied to structures. This is fixed and the unittests have been made more robust to ensure that cartesian lattice vectors and site positions are properly transformed by the application of the deformation gradient. Should not affect normal deformations or shear deformations in the differential limit. Thanks to @shyamd for pointing this out.
* Conditional to protect against overflow errors in heat capacity functionality of ElasticTensorExpansion.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/752/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/752/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/752",
"html_url": "https://github.com/materialsproject/pymatgen/pull/752",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/752.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/752.patch",
"merged_at": "2017-08-07T21:22:52Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/753
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/753/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/753/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/753/events
|
https://github.com/materialsproject/pymatgen/pull/753
| 248,543,735
|
MDExOlB1bGxSZXF1ZXN0MTM0NTM1OTg2
| 753
|
Added unit tests & missing helper functions in point_defects.py
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-07T22:00:30
| 2017-08-07T22:04:30
|
2017-08-07T22:04:29Z
|
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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/753/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/753/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/753",
"html_url": "https://github.com/materialsproject/pymatgen/pull/753",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/753.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/753.patch",
"merged_at": "2017-08-07T22:04:29Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/754
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/754/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/754/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/754/events
|
https://github.com/materialsproject/pymatgen/issues/754
| 248,571,012
|
MDU6SXNzdWUyNDg1NzEwMTI=
| 754
|
Possible error reading user_incar_settings in DictSet
|
{
"login": "iicurtis",
"id": 29741521,
"node_id": "MDQ6VXNlcjI5NzQxNTIx",
"avatar_url": "https://avatars.githubusercontent.com/u/29741521?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/iicurtis",
"html_url": "https://github.com/iicurtis",
"followers_url": "https://api.github.com/users/iicurtis/followers",
"following_url": "https://api.github.com/users/iicurtis/following{/other_user}",
"gists_url": "https://api.github.com/users/iicurtis/gists{/gist_id}",
"starred_url": "https://api.github.com/users/iicurtis/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/iicurtis/subscriptions",
"organizations_url": "https://api.github.com/users/iicurtis/orgs",
"repos_url": "https://api.github.com/users/iicurtis/repos",
"events_url": "https://api.github.com/users/iicurtis/events{/privacy}",
"received_events_url": "https://api.github.com/users/iicurtis/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I am not quite sure what you are intending here. But the format of the LDAUU and LDAUJ is not correct. This is a dict of a dict. The right formation should be:\r\n\r\n```\r\n \"LDAUL\": {\"S\": {\"Sm\": 3}},\r\n \"LDAUU\": {\"S\": {\"Sm\": 7.1}}, \r\n \"LDAUJ\": {\"S\": {\"Sm\": 1.0}},\r\n```\r\n\r\nU values are set based on the anion (most_electroneg). Also, there should be no U value on S. There is therefore no need to set a value there.",
"My apologies, I misunderstood how these values are set using pymatgen. If I wanted to set multiple species, how would this be done? E.g. for SmLaS, would I apply:\r\n```python\r\n\"LDAUL\": {\"S\": {\"Sm\": 3, \"La\": 3}}\r\n\"LDAUU\": {\"S\": {\"Sm\": 7.1, \"La\": 6.5}}, \r\n\"LDAUJ\": {\"S\": {\"Sm\": 1.0, \"La\": 1.0}},\r\n```\r\n",
"I think this is actually a subtle bug ...\r\n\r\nThis [line](https://github.com/materialsproject/pymatgen/blob/7ec9509e543bd84268d21b893e8a0c879f2343e4/pymatgen/io/vasp/sets.py#L290):\r\n\r\n```\r\n elif most_electroneg in v.keys():\r\n if isinstance(v[most_electroneg], dict):\r\n```\r\n\r\nshould read\r\n\r\n```\r\n elif (most_electroneg in v.keys()) and \\\r\n (isinstance(v[most_electroneg], dict):\r\n```\r\n\r\nI'll submit a PR to fix\r\n",
"@iicurtis the origin of this bug is a bit complicated, but basically when running in high-throughput calculations, it's useful to define anion-specific LDAU values, which is why `user_incar_settings` has this nested dict structure (e.g. `\"LDAUU\": {\"S\": {\"Sm\": 7.1, \"La\": 6.5}}`), and it attempts to detect the anion first so that the appropriate LDAU value is used.\r\n\r\nBut if you're just doing an individual calculation, it's often much more convenient to set your LDAU values directly (e.g. with your original example `\"LDAUU\": {\"S\": 0, \"Sm\": 7.1}`), and pymatgen also supports this. However, since your structure contained an S anion, pymatgen was expecting this nested dict structure and wouldn't accept your example, which caused the bug to be triggered."
] | 2017-08-08T00:55:46
| 2017-08-08T03:01:50
|
2017-08-08T02:04:54Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: master
* Python version: 3.6.2
* OS version: Linux 4.12.4-1-ARCH
## Summary
* Passing `{'LDAU': True, 'LDAUU': {'S': 0.0, 'Sm': 1.0}} to MPStaticSet, the run crashes with KeyError("LDAUU")
* In pymatgen/io/vasp/sets.py: line 291:
```python
if isinstance(v[most_electroneg], dict):
incar[k] = [v[most_electroneg].get(sym, 0)
for sym in poscar.site_symbols]
```
* `v` is a dict in my case (`{'S': 0.0, 'Sm': 1.0}`). Testing a value to check if it is a dict does not make sense to me.
* `v[most_electroneg]` should be a float, right? (`0.0`)
* Modifying as follows allows the run to go through:
```python
if isinstance(v, dict):
incar[k] = [v.get(sym, 0)
for sym in poscar.site_symbols]
```
## Example code
```python
uis_elastic = {
"ISPIN": 2,
"LDAU": True,
"LDAUL": {"S": -1, "Sm": 3},
"LDAUU": {"S": 0, "Sm": 7.1},
"LDAUJ": {"S": 0, "Sm": 1.0},
"LDAUTYPE": 2,
"LMAXMIX": 6,
"LASPH": True}
vis_input = MPStaticSet(structure, # Crashes
user_incar_settings=uis_elastic)
```
## Error message
```
Traceback (most recent call last):
File "../runit_default.py", line 35, in <module>
print(vis_input.incar)
File "/zdata/icurtis/atomate/codes/pymatgen/pymatgen/io/vasp/sets.py", line 492, in incar
parent_incar = super(MPStaticSet, self).incar
File "/zdata/icurtis/atomate/codes/pymatgen/pymatgen/io/vasp/sets.py", line 311, in incar
has_u = hubbard_u and sum(incar['LDAUU']) > 0
KeyError: 'LDAUU'
```
## Suggested solution (if any)
* Change line 291 in pymatgen/io/vasp/sets.py from:
```python
if isinstance(v[most_electroneg], dict):
incar[k] = [v[most_electroneg].get(sym, 0)
for sym in poscar.site_symbols]
```
to
```python
if isinstance(v, dict):
incar[k] = [v.get(sym, 0)
for sym in poscar.site_symbols]
```
(removing the `[most_electroneg]` index from our value dict)
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/754/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/754/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/755
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/755/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/755/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/755/events
|
https://github.com/materialsproject/pymatgen/pull/755
| 248,586,900
|
MDExOlB1bGxSZXF1ZXN0MTM0NTY2NzI1
| 755
|
Fix for #754
|
{
"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/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-08T02:58:57
| 2017-08-08T03:02:40
|
2017-08-08T03:02:40Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
See issue page / commit message for details.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/755/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/755/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/755",
"html_url": "https://github.com/materialsproject/pymatgen/pull/755",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/755.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/755.patch",
"merged_at": "2017-08-08T03:02:40Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/756
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/756/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/756/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/756/events
|
https://github.com/materialsproject/pymatgen/pull/756
| 248,882,895
|
MDExOlB1bGxSZXF1ZXN0MTM0Nzg2MTEx
| 756
|
Changed order parameter labels & added motif recognition function
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-09T00:18:07
| 2017-08-09T00:22:50
|
2017-08-09T00:22:50Z
|
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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/756/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/756/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/756",
"html_url": "https://github.com/materialsproject/pymatgen/pull/756",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/756.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/756.patch",
"merged_at": "2017-08-09T00:22:50Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/757
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/757/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/757/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/757/events
|
https://github.com/materialsproject/pymatgen/pull/757
| 249,225,007
|
MDExOlB1bGxSZXF1ZXN0MTM1MDM2MDIz
| 757
|
MSONable Compatability
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyamd/following{/other_user}",
"gists_url": "https://api.github.com/users/shyamd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyamd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyamd/subscriptions",
"organizations_url": "https://api.github.com/users/shyamd/orgs",
"repos_url": "https://api.github.com/users/shyamd/repos",
"events_url": "https://api.github.com/users/shyamd/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyamd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-10T03:47:13
| 2017-08-16T14:22:49
|
2017-08-16T14:22:49Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This makes the compatibility objects MSONable and adds the appropriate test
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/757/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/757/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/757",
"html_url": "https://github.com/materialsproject/pymatgen/pull/757",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/757.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/757.patch",
"merged_at": "2017-08-16T14:22:49Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/758
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/758/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/758/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/758/events
|
https://github.com/materialsproject/pymatgen/issues/758
| 249,312,467
|
MDU6SXNzdWUyNDkzMTI0Njc=
| 758
|
Need add ruamel.yaml to matsci channel as dependency of pymatgen
|
{
"login": "specter119",
"id": 8768524,
"node_id": "MDQ6VXNlcjg3Njg1MjQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8768524?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/specter119",
"html_url": "https://github.com/specter119",
"followers_url": "https://api.github.com/users/specter119/followers",
"following_url": "https://api.github.com/users/specter119/following{/other_user}",
"gists_url": "https://api.github.com/users/specter119/gists{/gist_id}",
"starred_url": "https://api.github.com/users/specter119/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/specter119/subscriptions",
"organizations_url": "https://api.github.com/users/specter119/orgs",
"repos_url": "https://api.github.com/users/specter119/repos",
"events_url": "https://api.github.com/users/specter119/events{/privacy}",
"received_events_url": "https://api.github.com/users/specter119/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Done.",
"@shyuep Thanks!"
] | 2017-08-10T11:12:02
| 2017-08-10T14:21:51
|
2017-08-10T14:15:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: v2017.8.4
* Python version: 3.6
* OS version: windows
## Summary
pymatgen add ruamel.yaml>=0.15.6 to requirement in v2017.8.4.
But ruamel.yaml is named as ruamel_yaml in conda default channel, and its current version is 0.11.14.
It's better to include ruamel.yaml to matsci channel to solve the dependency of pymatgen.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/758/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/758/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/759
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/759/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/759/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/759/events
|
https://github.com/materialsproject/pymatgen/pull/759
| 249,765,705
|
MDExOlB1bGxSZXF1ZXN0MTM1NDMyNDI5
| 759
|
Parsing charge densities for each atom
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyamd/following{/other_user}",
"gists_url": "https://api.github.com/users/shyamd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyamd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyamd/subscriptions",
"organizations_url": "https://api.github.com/users/shyamd/orgs",
"repos_url": "https://api.github.com/users/shyamd/repos",
"events_url": "https://api.github.com/users/shyamd/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyamd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-11T22:51:03
| 2017-08-12T15:16:36
|
2017-08-12T15:16:36Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added parsing of charge densities from Bader partitioned Chgcars
Cuts out extra 0's from the atomic charge densities to save space
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/759/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/759/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/759",
"html_url": "https://github.com/materialsproject/pymatgen/pull/759",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/759.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/759.patch",
"merged_at": "2017-08-12T15:16:36Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/760
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/760/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/760/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/760/events
|
https://github.com/materialsproject/pymatgen/pull/760
| 250,043,877
|
MDExOlB1bGxSZXF1ZXN0MTM1NjA2NjQx
| 760
|
ENH: Implemented get_symmetrised_molecule + helper functions; Improved performance of generate_full_symmops
|
{
"login": "mcocdawc",
"id": 15892408,
"node_id": "MDQ6VXNlcjE1ODkyNDA4",
"avatar_url": "https://avatars.githubusercontent.com/u/15892408?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mcocdawc",
"html_url": "https://github.com/mcocdawc",
"followers_url": "https://api.github.com/users/mcocdawc/followers",
"following_url": "https://api.github.com/users/mcocdawc/following{/other_user}",
"gists_url": "https://api.github.com/users/mcocdawc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mcocdawc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mcocdawc/subscriptions",
"organizations_url": "https://api.github.com/users/mcocdawc/orgs",
"repos_url": "https://api.github.com/users/mcocdawc/repos",
"events_url": "https://api.github.com/users/mcocdawc/events{/privacy}",
"received_events_url": "https://api.github.com/users/mcocdawc/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks! Do you mind adding a simple unittest? E.g., give it a slightly distorted methane molecule and symmetrize it.",
"The tests are not yet finished. I will finish them tomorrow",
"Tests are finished and I added some more functionality:\r\nAdded public function:\r\n``iterative_symmetrize`` applies ``PointGroupAnalyzer.symmetrize_molecule`` in a self consistent manner.\r\nSince this requires the creation of new ``PointGroupAnalyzer`` instances, I didn't make it a method, but a function.\r\nI used only pytest before and don't know, if the code in the test suite is idiomatic. So if you could have a look there, it would be great.",
"Thanks a lot!",
"Thanks a lot for the project. ;)",
"@shyuep May I ask, how often the PyPi package gets updated, because I would like to use ``iterative_symmetrize`` as dependency in a package of mine.",
"Ah, ok. I can release a version today. There is usually no fixed timeframe to releases. I use my judgment on when a collection of bug fixes or features have reached a critical mass for a release.",
"Thank you very much.\r\nFrom my side there is definetely no hurry to update it in the timeframe of days.\r\nI just wanted to make sure, that you don't have release cycles of half a year.",
"Ok, I just released a new version.\r\n\r\nOh, don't worry. Releases definitely happen more than once a month typically. Scientific research cannot wait half a year for releases! ;-)",
"Yeah makes sense. ;)"
] | 2017-08-14T14:15:08
| 2017-08-16T14:44:17
|
2017-08-15T14:36:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
# Summary
Closes materialsproject/pymatgen#746
New public functions:
* ``PointGroupAnalyzer.symmetrize_molecule``
* ``PointGroupAnalyzer.get_equivalent_atoms``
Changes in public functions:
* ``analyzer.cluster_sites`` now supports an optional boolean keyword argument ``give_only_index``, which defaults to ``False`` (previous behaviour)
* ``analyze.generate_full_symmops`` was optimised numerically and does not use recursion anymore. In the case of icosahedral point groups (tested on fullerene) the new implementation is 72 times faster.
New private functions (helper functions for ``PointGroupAnalyzer.get_equivalent_atoms``)
* ``PointGroupAnalyzer._get_eq_sets``
* ``PointGroupAnalyzer._combine_eq_sets``
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/760/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/760/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/760",
"html_url": "https://github.com/materialsproject/pymatgen/pull/760",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/760.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/760.patch",
"merged_at": "2017-08-15T14:36:26Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/761
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/761/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/761/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/761/events
|
https://github.com/materialsproject/pymatgen/pull/761
| 250,147,852
|
MDExOlB1bGxSZXF1ZXN0MTM1NjgyMzYy
| 761
|
QuasiharmonicDebyeApprox: Consider anaharmonic contribution to Debye temperature.
|
{
"login": "bocklund",
"id": 7681751,
"node_id": "MDQ6VXNlcjc2ODE3NTE=",
"avatar_url": "https://avatars.githubusercontent.com/u/7681751?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/bocklund",
"html_url": "https://github.com/bocklund",
"followers_url": "https://api.github.com/users/bocklund/followers",
"following_url": "https://api.github.com/users/bocklund/following{/other_user}",
"gists_url": "https://api.github.com/users/bocklund/gists{/gist_id}",
"starred_url": "https://api.github.com/users/bocklund/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/bocklund/subscriptions",
"organizations_url": "https://api.github.com/users/bocklund/orgs",
"repos_url": "https://api.github.com/users/bocklund/repos",
"events_url": "https://api.github.com/users/bocklund/events{/privacy}",
"received_events_url": "https://api.github.com/users/bocklund/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"looks good, could you add a test with anharmonic_contribution=True?",
"also for backward compatibility set the default value for anharmonic_contribution to be False ",
"This is ready for another look",
":+1: "
] | 2017-08-14T20:41:13
| 2017-08-16T14:22:35
|
2017-08-16T14:22:35Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The Debye temperature can have anharmonic contributions which can be calculated through the Gruneisen parameter.
This change implements the anharmonic contribution by default (can be turned off) with updates to documentation to reflect the change.
Previous tests were updated to reflect the anharmonic contribution option.
For theoretical details see:
Moruzzi et al. Phys. Rev. B 37, 790–799 (1988). (Eq 20)
Shang et al. Comput. Mater. Sci. 47, 1040–1048 (2010). (Eq 18)
Result:
@matk86 please take a look
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/761/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/761/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/761",
"html_url": "https://github.com/materialsproject/pymatgen/pull/761",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/761.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/761.patch",
"merged_at": "2017-08-16T14:22:35Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/762
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/762/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/762/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/762/events
|
https://github.com/materialsproject/pymatgen/issues/762
| 250,369,614
|
MDU6SXNzdWUyNTAzNjk2MTQ=
| 762
|
'@' operator not python2 compatible
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I just pushed a fix."
] | 2017-08-15T16:40:49
| 2017-08-15T17:02:01
|
2017-08-15T17:02:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/48b7a8b390c02fe6d8fbee96f137dc0526502f76/pymatgen/symmetry/analyzer.py#L1375
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/762/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/762/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/763
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/763/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/763/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/763/events
|
https://github.com/materialsproject/pymatgen/pull/763
| 250,503,068
|
MDExOlB1bGxSZXF1ZXN0MTM1OTM1NDU1
| 763
|
Interface
|
{
"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/users/yihanxiao92/followers",
"following_url": "https://api.github.com/users/yihanxiao92/following{/other_user}",
"gists_url": "https://api.github.com/users/yihanxiao92/gists{/gist_id}",
"starred_url": "https://api.github.com/users/yihanxiao92/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/yihanxiao92/subscriptions",
"organizations_url": "https://api.github.com/users/yihanxiao92/orgs",
"repos_url": "https://api.github.com/users/yihanxiao92/repos",
"events_url": "https://api.github.com/users/yihanxiao92/events{/privacy}",
"received_events_url": "https://api.github.com/users/yihanxiao92/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There are a lot of failing tests. Pls fix before I merge.",
"Dear Prof. Ong,\r\n\r\nThe errors in test files during the Travis CI build check all come from plot functions using matplotlib. I am not sure it is a failing test. Not only the newly_added \"test_interface_reactons.py\" suffered from the error, but also the existing test codes such as test_get_plot (pymatgen.phasediagram.tests.test_plotter.PDPlotterTest) and test_bz_plot (pymatgen.electronic_structure.tests.test_plotter.PlotBZTest). In this case, should I remove the test of plot function in my test file, or is anything could be fixed in the Travis CI build check?\r\n\r\nThanks,\r\nYihan",
"@yihanxiao92 if you read the [Travis CI logs](https://travis-ci.org/materialsproject/pymatgen/builds/264996086#L2278), it looks like all the interface reaction tests are failing with this error from [this line](https://github.com/materialsproject/pymatgen/pull/763/files#diff-c4a0a20f0c27251532b028f5b1c2895bR70):\r\n\r\n`'Please provide grand phase diagram to compute no_mixing_energy for reactants!`\r\n\r\nI suspect something might be going wrong in your test `setUp`?",
"For tests that use plot, you need to implement matplotlib.use(\"pdf\"). There is no DISPLAY on travis CI. If the backend is not switched to a non-display version, there will be an error.",
"@mkhorton Yes, you are correct. I was trying to test AssertionError with the code in the following format:\r\n```\r\nwith self.assertRaises(Exception) as context:\r\n #Do something that create AssertionError\r\n self.assertTrue('Error message' in context.exception)\r\n```\r\nThis worked as expected in the nosetests. But it seems the Travis CI misunderstood context.exception to be an iterable and then reported the error. So I modified the line to:\r\n```\r\nwith self.assertRaises(Exception) as context:\r\n #Do something that create AssertionError\r\n self.assertTrue('Error message' == str(context.exception))\r\n```\r\nHope that could fix the problem.",
"@yihanxiao92 I looked at the interface code in greater detail. Unfortunately, the docstrings do not conform to pymatgen standards, and also, the style is definitely not pep8. \r\n\r\nPls fix all these changes in a pull request. Otherwise, I will need to revert the entire commit until they are fixed.",
"Sorry about that. I will fix them as soon as I can. Expect to finish in 1-2 days."
] | 2017-08-16T03:45:02
| 2017-09-01T21:42:58
|
2017-08-17T05:20:23Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Add interface_reactions.py and its test file to pymatgen/analysis library. This module does analysis for interfacial reactions between two reactants, and plots reaction energy vs. mixing ratio x. The "Interfacial reaction" web app on Materials Project website will use this module for calculations.
* Gets critical mixing ratio where the composition tie lie intersects with phase diagram facets.
* Gets reaction energy and balanced reaction equation for each critical mixing ratio.
* Finds maximum driving force for interface reaction, which is a measure of the reactivity.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/763/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/763/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/763",
"html_url": "https://github.com/materialsproject/pymatgen/pull/763",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/763.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/763.patch",
"merged_at": "2017-08-17T05:20:22Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/764
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/764/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/764/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/764/events
|
https://github.com/materialsproject/pymatgen/pull/764
| 250,635,766
|
MDExOlB1bGxSZXF1ZXN0MTM2MDMwODcx
| 764
|
lammps updates
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-16T13:55:18
| 2017-08-16T14:16:12
|
2017-08-16T14:16:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* fix forcefield serialization: ensure it plays nicely with fireworks/pymongo
* minor fixes and updates in the lammps/packmol runners
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/764/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/764/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/764",
"html_url": "https://github.com/materialsproject/pymatgen/pull/764",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/764.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/764.patch",
"merged_at": "2017-08-16T14:16:12Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/765
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/765/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/765/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/765/events
|
https://github.com/materialsproject/pymatgen/issues/765
| 250,716,458
|
MDU6SXNzdWUyNTA3MTY0NTg=
| 765
|
LAMMPS io to be improved to support 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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "chc273",
"id": 22353204,
"node_id": "MDQ6VXNlcjIyMzUzMjA0",
"avatar_url": "https://avatars.githubusercontent.com/u/22353204?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chc273",
"html_url": "https://github.com/chc273",
"followers_url": "https://api.github.com/users/chc273/followers",
"following_url": "https://api.github.com/users/chc273/following{/other_user}",
"gists_url": "https://api.github.com/users/chc273/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chc273/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chc273/subscriptions",
"organizations_url": "https://api.github.com/users/chc273/orgs",
"repos_url": "https://api.github.com/users/chc273/repos",
"events_url": "https://api.github.com/users/chc273/events{/privacy}",
"received_events_url": "https://api.github.com/users/chc273/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"login": "chc273",
"id": 22353204,
"node_id": "MDQ6VXNlcjIyMzUzMjA0",
"avatar_url": "https://avatars.githubusercontent.com/u/22353204?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chc273",
"html_url": "https://github.com/chc273",
"followers_url": "https://api.github.com/users/chc273/followers",
"following_url": "https://api.github.com/users/chc273/following{/other_user}",
"gists_url": "https://api.github.com/users/chc273/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chc273/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chc273/subscriptions",
"organizations_url": "https://api.github.com/users/chc273/orgs",
"repos_url": "https://api.github.com/users/chc273/repos",
"events_url": "https://api.github.com/users/chc273/events{/privacy}",
"received_events_url": "https://api.github.com/users/chc273/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
] | null |
[] | 2017-08-16T18:22:33
| 2017-08-19T15:43:30
|
2017-08-19T15:43:30Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
LAMMPs io is primarily coded for molecules/polymers. Need to support periodic structures, e.g., for MD simulations and descriptor 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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/765/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/765/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/766
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/766/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/766/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/766/events
|
https://github.com/materialsproject/pymatgen/issues/766
| 250,717,057
|
MDU6SXNzdWUyNTA3MTcwNTc=
| 766
|
Core spectra objects to be moved from pyxas to pymatgen
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@czhengsci @shyamd @matk86 I have completely refactored the Spectrum object. See pymatgen.core.spectum for the core object. Then look at pymatgen.analysis.xas for the XANES subclass.\r\n\r\nHere are a few things I would like @czhengsci to follow-up on:\r\n\r\ni. Document EVERYTHING. You write code that has no documentation. Even when they exist, they are not the Google-style that pymatgen uses. I want you to write good documentation for both the core spectra class as well as the XANES class.\r\n\r\nii. Implement EXAFS.\r\n\r\niii. At some point, I want to start to move the Phonon DOS to subclass Spectrum. And eventually, the DOS itself.\r\n\r\nFor now, do (i) and (ii). \r\n"
] | 2017-08-16T18:24:41
| 2018-04-24T16:04:48
|
2018-04-24T16:04:48Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Pyxas spectra objects are general and usable by many others. These should be moved to pymatgen.analysis. In fact, consider integrating existing XRD and NMR spectra on same footing. Right now it is the Wild West.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/766/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/766/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/767
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/767/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/767/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/767/events
|
https://github.com/materialsproject/pymatgen/issues/767
| 250,717,447
|
MDU6SXNzdWUyNTA3MTc0NDc=
| 767
|
Workfunction analysis
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-16T18:25:58
| 2023-08-08T21:20:03
|
2023-08-08T21:20:03Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
These should be made publicly available. @richardtran415 to take charge.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/767/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/767/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/768
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/768/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/768/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/768/events
|
https://github.com/materialsproject/pymatgen/issues/768
| 250,720,641
|
MDU6SXNzdWUyNTA3MjA2NDE=
| 768
|
Feature request: Surface properties to MAPI
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 3576072,
"node_id": "MDU6TGFiZWwzNTc2MDcy",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/feature%20request",
"name": "feature request",
"color": "f3fcae",
"default": false,
"description": "Request for a new feature"
}
] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-16T18:37:59
| 2023-08-08T21:20:13
|
2023-08-08T21:20:13Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Add recent data from:
Tran, R., Xu, Z., Radhakrishnan, B., Winston, D., Sun, W., Persson, K. A., & Ong, S. P. (2016). Data Descripter: Surface energies of elemental crystals. Scientific Data, 3(160080), 1–13. https://doi.org/10.1038/cgt.2016.38
to the Materials Project API and corresponding documentation to mapidoc
@richardtran415 will take charge
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/768/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/768/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/769
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/769/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/769/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/769/events
|
https://github.com/materialsproject/pymatgen/issues/769
| 250,724,292
|
MDU6SXNzdWUyNTA3MjQyOTI=
| 769
|
Periodic heatmap
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 3576072,
"node_id": "MDU6TGFiZWwzNTc2MDcy",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/feature%20request",
"name": "feature request",
"color": "f3fcae",
"default": false,
"description": "Request for a new feature"
}
] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This is a good idea. But I am assigning this to @johnson1228 since he just implemented this for a paper.",
"+1 for this, almost implemented it myself ... will look forward to testing this",
"@johnson1228 Note that the heatmap should support empty values. E.g., people can provide a dict of {\"Li\": value, ..}. If no value is provided, a default greyed out thing should be used. The first version does not need to support color scheme choices. The subsequent versions should allow for it. ",
"@johnson1228 it should also have a parameter that allows the user to choose whichever color scheme they want for the heatmap, eg. 'PuBu' or 'plasma'",
"Regarding color scheme choices, it should be fairly easy just to use the standard matplotlib colormap objects (e.g. `from matplotlib.cm import viridis`) these objects take an int from 0-255 and return a color. (@richardtran415 beat me to this!)\r\n\r\nAlso, would be useful if the class had an `as_dict()` method which would return a dict of elements and their associated color values, in case we want to use custom renderers in future (e.g. on the web).",
"I will leave @johnson1228 to do this. Don't worry about this. This will be implemented at the MAVRL weekly hackathon tomorrow.",
"How about\r\nhttp://bokeh.pydata.org/en/latest/docs/gallery/periodic.html\r\n\r\nOr\r\nhttps://github.com/wolverton-research-group/periodic-table-plotter/tree/master/examples",
"Ours will be better.",
"I have moved this to pymatgen.util.plotting as I think it is more appropriate there. This is good enough for further finetuning."
] | 2017-08-16T18:50:28
| 2017-08-18T00:28:16
|
2017-08-18T00:28:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
New feature to util, a function to plot a publication quality periodic table with user input values for each table entry. The table will be a heatmap to easily discern some periodic trends related to a specific property eg surface energy, work function, Young's modulus etc. See:
Lejaeghere, K., Van Speybroeck, V., Van Oost, G., & Cottenier, S. (2014). Error Estimates for Solid-State Density-Functional Theory Predictions: An Overview by Means of the Ground-State Elemental Crystals. Critical Reviews in Solid State and Materials Sciences, 39(1), 1–24. https://doi.org/10.1080/10408436.2013.772503
as an example.
@richardtran415 will take charge
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/769/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/769/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/770
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/770/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/770/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/770/events
|
https://github.com/materialsproject/pymatgen/issues/770
| 250,728,992
|
MDU6SXNzdWUyNTA3Mjg5OTI=
| 770
|
check for Laue symmetry
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls make sure to reference this issue in future pull requests and commits, and also to close the issue when done."
] | 2017-08-16T19:08:22
| 2017-08-17T17:53:46
|
2017-08-17T17:53:28Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Add simple method on SpacegroupAnalyzer to check if structure has Laue pointgroup symmetry.
@richardtran415 will handle this
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/770/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/770/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/771
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/771/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/771/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/771/events
|
https://github.com/materialsproject/pymatgen/pull/771
| 250,795,901
|
MDExOlB1bGxSZXF1ZXN0MTM2MTQ5MzU5
| 771
|
updates to oxi_state_guesses and valence table
|
{
"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/computron/followers",
"following_url": "https://api.github.com/users/computron/following{/other_user}",
"gists_url": "https://api.github.com/users/computron/gists{/gist_id}",
"starred_url": "https://api.github.com/users/computron/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/computron/subscriptions",
"organizations_url": "https://api.github.com/users/computron/orgs",
"repos_url": "https://api.github.com/users/computron/repos",
"events_url": "https://api.github.com/users/computron/events{/privacy}",
"received_events_url": "https://api.github.com/users/computron/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Tests not passing on py3. Pls fix.",
"\n[](https://coveralls.io/builds/12871204)\n\nChanges Unknown when pulling **28083a4750cff9828dd394f695b339ffd6ffeb14 on structure_analysis** into ** on master**.\n",
"\n[](https://coveralls.io/builds/12898542)\n\nChanges Unknown when pulling **28083a4750cff9828dd394f695b339ffd6ffeb14 on structure_analysis** into ** on master**.\n"
] | 2017-08-17T00:15:01
| 2018-08-10T11:13:48
|
2017-08-17T03:14:44Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR adds many new functionalities and improvements regarding oxidation states
* The periodic table "Element" class has a new attribute called icsd_oxidation_states. These are oxidation states found in ICSD that have at least 10 examples *and* at least 1% of entries for that element. I have found this to be much superior to the current oxidation state tables, which are either too restrictive or too loose.
* oxi_state_guesses() uses the icsd_oxidation_states by default (not common_oxidation_states, e.g., the latter only has V5+ whereas the new version has V2+,3+,4+,5+)
* the ranking of solutions in oxi_state_guesses() is much improved. Instead of min sum squared of the oxidation states, which can lead to bad solutions, solutions are ranked based on prior probabilities from the bond valence table.
* Structure has a new convenience method called "add_oxidation_states_by_guess". Just give it a Structure and it will decorate it with reasonable oxidation states. Note that it may add fractional / float oxidation states to a site, though.
## TODO (if any)
The loading of prior probabilities is done every time one calls Composition.oxi_state_guesses(). I'd prefer to do this at the top of the composition.py module, but didn't want to slow down the load of this common module for this one feature. So for now, things are a little slower than they could be.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/771/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/771/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/771",
"html_url": "https://github.com/materialsproject/pymatgen/pull/771",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/771.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/771.patch",
"merged_at": "2017-08-17T03:14:44Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/772
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/772/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/772/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/772/events
|
https://github.com/materialsproject/pymatgen/issues/772
| 250,809,366
|
MDU6SXNzdWUyNTA4MDkzNjY=
| 772
|
A tiny problem in class Composition
|
{
"login": "YunxingZuo",
"id": 20294764,
"node_id": "MDQ6VXNlcjIwMjk0NzY0",
"avatar_url": "https://avatars.githubusercontent.com/u/20294764?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/YunxingZuo",
"html_url": "https://github.com/YunxingZuo",
"followers_url": "https://api.github.com/users/YunxingZuo/followers",
"following_url": "https://api.github.com/users/YunxingZuo/following{/other_user}",
"gists_url": "https://api.github.com/users/YunxingZuo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/YunxingZuo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/YunxingZuo/subscriptions",
"organizations_url": "https://api.github.com/users/YunxingZuo/orgs",
"repos_url": "https://api.github.com/users/YunxingZuo/repos",
"events_url": "https://api.github.com/users/YunxingZuo/events{/privacy}",
"received_events_url": "https://api.github.com/users/YunxingZuo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The anon formula is ABCD4. Your regular expression is wrong. It should be ([A-Z][a-z]*)(\\d*)."
] | 2017-08-17T02:03:57
| 2017-08-17T03:05:46
|
2017-08-17T03:05:46Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: 2017.8.14
* Python version: 3.6
* OS version: OSX 10.12.5
## Summary
According to the Jupyter Notebook about getting data from Materials Projects in matgenb, if I use the chemical formula like "Li1Fe1P1O4", the getting process don't work.
## Example code
```python
from pymatgen import MPRester, Composition
import re
comp = Composition("Li1Fe1P1O4")
anon_formula = comp.anonymized_formula
anon_formula = {m.group(1): int(m.group(2))
for m in re.finditer(r"([A-Z]+)(\d+)", anon_formula)}
```
## Error message
```
# Error message
```
## Suggested solution (if any)
Here the variable "anon_formula" should be a dict: {'A':1, 'B':1, 'C': 1, 'D':4}, instead it comes {'ABCD': 1}. It is because in the Composition class in pymatgen.core.composition, when it comes to 1, the property "anon_formula" automatically deletes the number 1 and gives an empty string.
## Files (if any)
* If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.
```
<contents of file 1>
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/772/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/772/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/773
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/773/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/773/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/773/events
|
https://github.com/materialsproject/pymatgen/issues/773
| 250,837,742
|
MDU6SXNzdWUyNTA4Mzc3NDI=
| 773
|
ReplaceSiteSpeciesTransform disordering map input fails
|
{
"login": "paulfons",
"id": 6129100,
"node_id": "MDQ6VXNlcjYxMjkxMDA=",
"avatar_url": "https://avatars.githubusercontent.com/u/6129100?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/paulfons",
"html_url": "https://github.com/paulfons",
"followers_url": "https://api.github.com/users/paulfons/followers",
"following_url": "https://api.github.com/users/paulfons/following{/other_user}",
"gists_url": "https://api.github.com/users/paulfons/gists{/gist_id}",
"starred_url": "https://api.github.com/users/paulfons/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/paulfons/subscriptions",
"organizations_url": "https://api.github.com/users/paulfons/orgs",
"repos_url": "https://api.github.com/users/paulfons/repos",
"events_url": "https://api.github.com/users/paulfons/events{/privacy}",
"received_events_url": "https://api.github.com/users/paulfons/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The documentation here is wrong. ReplaceSiteSpecies only replaces a single site. The right syntax should be \r\n\r\n```\r\ntrans = ReplaceSiteSpeciesTransformation({0: {\"Li\": 0.5, \"Na\":0.5}})\r\ntrans.apply_transformation(s)\r\n```\r\n\r\nIn other words, the key needs to be a numerical index.\r\n\r\nUnless you have a good reason to use a transformation (e.g., you need to keep track of provenance), the easiest way is to simply directly modify the structure.\r\n\r\n```\r\n# Modify a single site\r\ns[0] = {\"Li\": 0.5, \"Na\": 0.5}\r\n\r\n# Modify all sites containing Li\r\ns[\"Li\"] = {\"Li\": 0.5, \"Na\": 0.5}\r\n```",
"Dear Shyue Ping,\n\n Thank you for your note. Even for a Python amateur like myself, it was clear that the source code only took numerical indices, but I was confused by the documentation. Your alternative \n\n> s[0] = {\"Li\": 0.5, \"Na\": 0.5}\n\nis a good solution for randomizing a lattice. On the same thread, if I wish to run a VASP calculation on a disordered lattice, is there a way to get pymatgen to “throw the dice” and assign a specific specie or is this something I would have to code myself?\n\nBest wishes,\n Paul\n\n\n\n> On Aug 17, 2017, at 23:06, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> The documentation here is wrong. ReplaceSiteSpecies only replaces a single site. The right syntax should be\n> \n> trans = ReplaceSiteSpeciesTransformation({0: {\"Li\": 0.5, \"Na\":0.5}})\n> trans.apply_transformation(s)\n> In other words, the key needs to be a numerical index.\n> \n> Unless you have a good reason to use a transformation (e.g., you need to keep track of provenance), the easiest way is to simply directly modify the structure.\n> \n> # Modify a single site\n> s[0] = {\"Li\": 0.5, \"Na\": 0.5}\n> \n> # Modify all sites containing Li\n> s[\"Li\"] = {\"Li\": 0.5, \"Na\": 0.5}\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/773#issuecomment-323084235>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF2FzIaWAoiGQmEl-ScMPgYUP9JaJirgks5sZEj_gaJpZM4O50Dy>.\n> \n\n",
"> On the same thread, if I wish to run a VASP calculation on a disordered lattice, is there a way to get pymatgen to “throw the dice” and assign a specific specie or is this something I would have to code myself?\r\n\r\n`OrderDisorderedStructureTransformation` can help with this, see example notebook here: http://pymatgen.org/_static/Ordering%20Disordered%20Structures.html\r\n\r\nThis will give an ordered approximation of your disordered structure. I don't believe pymatgen has functionality for giving a random approximation ('throwing the dice' for each site), though maybe @shyuep can correct me on that.",
"No random version. But you can get a list from the apply_transformation and set return_rank_list = whatever number and then just do a random.shuffle if you wish."
] | 2017-08-17T06:02:33
| 2017-08-17T23:07:18
|
2017-08-17T14:08:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
When reporting bugs/issues, please supply the following information. If
this is a feature request, please simply state the requested feature.
## System
* Pymatgen version: pymatgen-2017.8.16
* Python version: Python 2.7
* OS version: CentOS 7
## Summary
* The documentation for ReplaceSiteSpeciesTransform states that it will replace site species with new sites according to a user provided dictionary. It states that operator overloading is enabled such that a mapping of the form {"Si":{"Si":0.75,"Ge":0.25}} will allow disordering of sites (in this case Si sites). It does not work as the code casts the dictionary key into an integer.
## Example code
In [79]: s1 = mg.Structure(lattice, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
In [80]: s1
Out[80]:
Structure Summary
Lattice
abc : 4.2000000000000002 4.2000000000000002 4.2000000000000002
angles : 90.0 90.0 90.0
volume : 74.088000000000008
A : 4.2000000000000002 0.0 0.0
B : 0.0 4.2000000000000002 0.0
C : 0.0 0.0 4.2000000000000002
PeriodicSite: Cs (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: Cl (2.1000, 2.1000, 2.1000) [0.5000, 0.5000, 0.5000]
In [85]: mymap = {"Cs":{"Si":0.75,"Ge":0.25}}
In [86]: transform = ReplaceSiteSpeciesTransformation(mymap)
In [87]: transformed = transform.apply_transformation(s1)
```python
# Example code generating error
```
## Error message
```
ValueError Traceback (most recent call last)
<ipython-input-87-02f99378f276> in <module>()
----> 1 transformed = transform.apply_transformation(s1)
/usr/lib64/python2.7/site-packages/pymatgen/transformations/site_transformations.pyc in apply_transformation(self, structure)
100 s = structure.copy()
101 for i, sp in self.indices_species_map.items():
--> 102 s[int(i)] = sp
103 return s
104
ValueError: invalid literal for int() with base 10: 'Cs'
```
## Suggested solution (if any)
* If you have a suggestion on how to solve the issue, you may write it
here.
The source code for the ReplaceSiteSpeciesTransform
def apply_transformation(self, structure):
s = structure.copy()
for i, sp in self.indices_species_map.items():
s[int(i)] = sp <----------- casts string dictionary key ("Cs" in this case) into an int and fails
return s
## Files (if any)
* If input files are needed to reproduce the error, please provide
either links (e.g., Dropbox or GDrive) for large files or simply paste
the file below for small files.
```
<contents of file 1>
```
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/773/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/773/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/774
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/774/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/774/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/774/events
|
https://github.com/materialsproject/pymatgen/issues/774
| 251,013,991
|
MDU6SXNzdWUyNTEwMTM5OTE=
| 774
|
VaspInputSet should have user_potcar_settings
|
{
"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/computron/followers",
"following_url": "https://api.github.com/users/computron/following{/other_user}",
"gists_url": "https://api.github.com/users/computron/gists{/gist_id}",
"starred_url": "https://api.github.com/users/computron/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/computron/subscriptions",
"organizations_url": "https://api.github.com/users/computron/orgs",
"repos_url": "https://api.github.com/users/computron/repos",
"events_url": "https://api.github.com/users/computron/events{/privacy}",
"received_events_url": "https://api.github.com/users/computron/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 3576072,
"node_id": "MDU6TGFiZWwzNTc2MDcy",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/feature%20request",
"name": "feature request",
"color": "f3fcae",
"default": false,
"description": "Request for a new feature"
}
] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-17T17:20:02
| 2017-08-17T17:28:20
|
2017-08-17T17:28:20Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Similar to user_incar_settings and user_kpoints_settings, VaspInputSet should have user_potcar_settings.
See https://github.com/hackingmaterials/atomate/issues/146 for more details.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/774/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/774/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/775
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/775/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/775/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/775/events
|
https://github.com/materialsproject/pymatgen/pull/775
| 251,014,780
|
MDExOlB1bGxSZXF1ZXN0MTM2MzEwMjMw
| 775
|
very simple change to SpacegroupAnalyzer, added is_laue().
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-17T17:23:10
| 2017-08-17T17:30:58
|
2017-08-17T17:30:58Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added a simple method to SpaceGroupAnalyzer to check if a structure has Laue class symmetry (centrosymmetric). Also renamed symmetrize_slab() in the SlabGenerator class to nonstoichiometric_symmetrized_slab().
* added is_laue to SpaceGroupAnalyzer
* renamed symmetrize_slab() in the SlabGenerator class to nonstoichiometric_symmetrized_slab()
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/775/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/775/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/775",
"html_url": "https://github.com/materialsproject/pymatgen/pull/775",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/775.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/775.patch",
"merged_at": "2017-08-17T17:30:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/776
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/776/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/776/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/776/events
|
https://github.com/materialsproject/pymatgen/pull/776
| 251,053,233
|
MDExOlB1bGxSZXF1ZXN0MTM2MzM5MTM3
| 776
|
Initialization of spectrum module
|
{
"login": "czhengsci",
"id": 7264656,
"node_id": "MDQ6VXNlcjcyNjQ2NTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/7264656?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/czhengsci",
"html_url": "https://github.com/czhengsci",
"followers_url": "https://api.github.com/users/czhengsci/followers",
"following_url": "https://api.github.com/users/czhengsci/following{/other_user}",
"gists_url": "https://api.github.com/users/czhengsci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/czhengsci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/czhengsci/subscriptions",
"organizations_url": "https://api.github.com/users/czhengsci/orgs",
"repos_url": "https://api.github.com/users/czhengsci/repos",
"events_url": "https://api.github.com/users/czhengsci/events{/privacy}",
"received_events_url": "https://api.github.com/users/czhengsci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Is this ready for merging or are you still working on it? The tests are failing. Also, Spectrum should be MSONAble, not XANES. That way, all subclasses of Spectrum are MSONAble.",
"Hi Shyue Ping, I fixed the code and make the Spectrum class MSONAble. All tests passed. I am working on the rest on the todo list now. Thanks a lot ",
"Would it make more sense to have spectrum_data be abstract in the Spectrum class and then XANES can just construct the data on the fly? \r\n\r\nAlso, there should be some sort of concat method for XANES that lets you easily add them together, since it's possible to have multiple unique sites for one species that contribute differently to the overall spectrum. ",
"It will be like DOS. There are __add__ methods etc. that allows adding of spectra.",
"Ok, I will merge and make a few changes. "
] | 2017-08-17T19:52:48
| 2017-08-25T15:50:02
|
2017-08-25T15:50:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Initial commit of pymatgen.analysis.spectra module
* Add Spectrum base abstract class
* Add Xanes class
* Add unittest for Xane
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/776/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/776/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/776",
"html_url": "https://github.com/materialsproject/pymatgen/pull/776",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/776.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/776.patch",
"merged_at": "2017-08-25T15:50:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/777
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/777/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/777/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/777/events
|
https://github.com/materialsproject/pymatgen/pull/777
| 251,069,577
|
MDExOlB1bGxSZXF1ZXN0MTM2MzUxNDEx
| 777
|
add read fermi contact shift
|
{
"login": "random-var-x",
"id": 6107838,
"node_id": "MDQ6VXNlcjYxMDc4Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/6107838?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/random-var-x",
"html_url": "https://github.com/random-var-x",
"followers_url": "https://api.github.com/users/random-var-x/followers",
"following_url": "https://api.github.com/users/random-var-x/following{/other_user}",
"gists_url": "https://api.github.com/users/random-var-x/gists{/gist_id}",
"starred_url": "https://api.github.com/users/random-var-x/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/random-var-x/subscriptions",
"organizations_url": "https://api.github.com/users/random-var-x/orgs",
"repos_url": "https://api.github.com/users/random-var-x/repos",
"events_url": "https://api.github.com/users/random-var-x/events{/privacy}",
"received_events_url": "https://api.github.com/users/random-var-x/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This is fine, but do not use a gzipped OUTCAR. Just a normal outcar. Git can handle file compression.",
"Also, paste here a sample output for the fermi contact shift data."
] | 2017-08-17T20:55:27
| 2017-08-21T16:48:21
|
2017-08-21T16:48:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Add read_fermi_contact_shift. (Currently Pymatgen can only do: read_chemical_shifts.)
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/777/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/777/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/777",
"html_url": "https://github.com/materialsproject/pymatgen/pull/777",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/777.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/777.patch",
"merged_at": "2017-08-21T16:48:21Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/778
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/778/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/778/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/778/events
|
https://github.com/materialsproject/pymatgen/pull/778
| 251,077,775
|
MDExOlB1bGxSZXF1ZXN0MTM2MzU3NzM0
| 778
|
Added local_env.py for near-neighbor finding
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Great. Can you put deprecation messages on the relevant classes in structure_analyzer? Say they will be removed with pymatgen > 2018. ",
"Will do.",
"Maybe pymatgen > 2017 (so, in 2018)?",
"Ok... forgive my lack of precision. pmg >= 2018.",
"OK. :-)"
] | 2017-08-17T21:28:48
| 2017-08-17T22:05:30
|
2017-08-17T22:05:29Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
In the future, the OrderParameter class from structure_analyzer.py will be moved to this module under the proposed name LocalStructOrderParas to avoid confusion with order parameters in a more global materials science-related sense. Is that desirable, @shyuep?
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/778/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/778/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/778",
"html_url": "https://github.com/materialsproject/pymatgen/pull/778",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/778.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/778.patch",
"merged_at": "2017-08-17T22:05:29Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/779
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/779/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/779/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/779/events
|
https://github.com/materialsproject/pymatgen/pull/779
| 251,085,967
|
MDExOlB1bGxSZXF1ZXN0MTM2MzY0MDc3
| 779
|
Added deprecation warnings.
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-17T22:06:24
| 2017-08-17T22:06:55
|
2017-08-17T22:06:55Z
|
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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/779/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/779/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/779",
"html_url": "https://github.com/materialsproject/pymatgen/pull/779",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/779.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/779.patch",
"merged_at": "2017-08-17T22:06:55Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/780
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/780/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/780/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/780/events
|
https://github.com/materialsproject/pymatgen/pull/780
| 251,091,166
|
MDExOlB1bGxSZXF1ZXN0MTM2MzY3OTMw
| 780
|
Removed bug in local_env.py
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I cannot merge this. Pls pull the latest pymatgen master and merge properly first and commit.",
"Sorry."
] | 2017-08-17T22:34:04
| 2017-08-17T23:20:33
|
2017-08-17T23:19:25Z
|
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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/780/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/780/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/780",
"html_url": "https://github.com/materialsproject/pymatgen/pull/780",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/780.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/780.patch",
"merged_at": "2017-08-17T23:19:25Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/781
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/781/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/781/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/781/events
|
https://github.com/materialsproject/pymatgen/pull/781
| 251,104,897
|
MDExOlB1bGxSZXF1ZXN0MTM2Mzc4MDk0
| 781
|
minor bugfix
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-18T00:00:12
| 2017-08-18T00:01:03
|
2017-08-18T00:01:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Not sure why, but this import line has been causing problems for me. Doesn't appear to be used in the module.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/781/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/781/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/781",
"html_url": "https://github.com/materialsproject/pymatgen/pull/781",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/781.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/781.patch",
"merged_at": "2017-08-18T00:01:03Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/782
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/782/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/782/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/782/events
|
https://github.com/materialsproject/pymatgen/pull/782
| 251,105,282
|
MDExOlB1bGxSZXF1ZXN0MTM2Mzc4MzQ5
| 782
|
Static method that makes the periodic heatmap
|
{
"login": "johnson1228",
"id": 4379950,
"node_id": "MDQ6VXNlcjQzNzk5NTA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4379950?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/johnson1228",
"html_url": "https://github.com/johnson1228",
"followers_url": "https://api.github.com/users/johnson1228/followers",
"following_url": "https://api.github.com/users/johnson1228/following{/other_user}",
"gists_url": "https://api.github.com/users/johnson1228/gists{/gist_id}",
"starred_url": "https://api.github.com/users/johnson1228/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/johnson1228/subscriptions",
"organizations_url": "https://api.github.com/users/johnson1228/orgs",
"repos_url": "https://api.github.com/users/johnson1228/repos",
"events_url": "https://api.github.com/users/johnson1228/events{/privacy}",
"received_events_url": "https://api.github.com/users/johnson1228/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-18T00:02:43
| 2017-08-18T00:04:29
|
2017-08-18T00:04:29Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
New static method in Element class that plots periodic heatmap (credit to Richard Tran). This is to address Issue #769.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/782/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/782/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/782",
"html_url": "https://github.com/materialsproject/pymatgen/pull/782",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/782.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/782.patch",
"merged_at": "2017-08-18T00:04:29Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/783
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/783/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/783/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/783/events
|
https://github.com/materialsproject/pymatgen/pull/783
| 251,114,885
|
MDExOlB1bGxSZXF1ZXN0MTM2Mzg0OTUw
| 783
|
Minor bugfix for periodic heatmap plotting
|
{
"login": "johnson1228",
"id": 4379950,
"node_id": "MDQ6VXNlcjQzNzk5NTA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4379950?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/johnson1228",
"html_url": "https://github.com/johnson1228",
"followers_url": "https://api.github.com/users/johnson1228/followers",
"following_url": "https://api.github.com/users/johnson1228/following{/other_user}",
"gists_url": "https://api.github.com/users/johnson1228/gists{/gist_id}",
"starred_url": "https://api.github.com/users/johnson1228/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/johnson1228/subscriptions",
"organizations_url": "https://api.github.com/users/johnson1228/orgs",
"repos_url": "https://api.github.com/users/johnson1228/repos",
"events_url": "https://api.github.com/users/johnson1228/events{/privacy}",
"received_events_url": "https://api.github.com/users/johnson1228/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"You need to merge the master first. Right now, you are reintroducing the code in the periodic_table.py",
"Look at the files changed. THer should only be one file, but there are three."
] | 2017-08-18T01:19:52
| 2017-08-18T03:21:55
|
2017-08-18T03:21:55Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request fixes the bug when max_val becomes negative or min_val becomes positive.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/783/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/783/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/783",
"html_url": "https://github.com/materialsproject/pymatgen/pull/783",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/783.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/783.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/784
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/784/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/784/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/784/events
|
https://github.com/materialsproject/pymatgen/issues/784
| 251,118,746
|
MDU6SXNzdWUyNTExMTg3NDY=
| 784
|
Query conventional unit cell with MPRester
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hmmm... I think the query method might be able to do that. You need to check the mapidoc to see if the conventional structure is stored in one of the keys.",
"I see, OK, thank you for the info",
"Just checked the mapidoc, and there's a `cifs.conventional_standard` key that can give this, but no actual Structure object I can see. You can then use `Structure.from_str(..., fmt='cif')` on the returned string to get back your Structure object. Whether it's worth using this over just using SpacegroupAnalyzer I wouldn't know."
] | 2017-08-18T01:53:50
| 2017-08-18T17:34:24
|
2017-08-18T06:14:18Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Is there a method in in MPRester that can return the conventional standard structure from Materials Project instead of just the primitive unit cell, I know the SpacegroupAnalyzer has such a tool for getting this structure, but I think it would be more convenient to just have a way to quickly get it from MPRester instead of querying for the primitive structure and then converting it with SpacegroupAnalyzer everytime.
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/784/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/784/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/785
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/785/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/785/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/785/events
|
https://github.com/materialsproject/pymatgen/pull/785
| 251,129,830
|
MDExOlB1bGxSZXF1ZXN0MTM2Mzk1Mjkz
| 785
|
add vasp input sets for BSE calc
|
{
"login": "zbwang",
"id": 8037294,
"node_id": "MDQ6VXNlcjgwMzcyOTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8037294?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/zbwang",
"html_url": "https://github.com/zbwang",
"followers_url": "https://api.github.com/users/zbwang/followers",
"following_url": "https://api.github.com/users/zbwang/following{/other_user}",
"gists_url": "https://api.github.com/users/zbwang/gists{/gist_id}",
"starred_url": "https://api.github.com/users/zbwang/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/zbwang/subscriptions",
"organizations_url": "https://api.github.com/users/zbwang/orgs",
"repos_url": "https://api.github.com/users/zbwang/repos",
"events_url": "https://api.github.com/users/zbwang/events{/privacy}",
"received_events_url": "https://api.github.com/users/zbwang/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@setten @hautierg @gmatteo @computron (this is a somewhat random list of people I think might be interested in this)\r\n\r\nPls note that I intend to delete the current pymatgen.io.vasp.GWvaspinputsets.py and the corresponding yaml. That file is extremely out of date, and also, there are methods in there which writes SLURM job submission scripts. Such things really shouldn't be in pymatgen. If necessary, they should be in FireWorks.\r\n\r\nSo pls take the opportunity to review these inputs sets that Zhenbin has written, and if you have comments, pls say them now. You can also help improve on these new sets if you wish. Also, note that the default POTCAR for GW is switched to the PBE_54 series for VASP, not the standard PBE. These are necessary to make sure the calculations work as intended."
] | 2017-08-18T03:27:33
| 2017-08-18T20:20:52
|
2017-08-18T20:20:52Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Add GW/BSE vasp input sets with the newest GW psp (PBE_54) as default.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/785/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/785/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/785",
"html_url": "https://github.com/materialsproject/pymatgen/pull/785",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/785.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/785.patch",
"merged_at": "2017-08-18T20:20:52Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/786
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/786/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/786/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/786/events
|
https://github.com/materialsproject/pymatgen/pull/786
| 251,131,297
|
MDExOlB1bGxSZXF1ZXN0MTM2Mzk2MzA2
| 786
|
Adding GB input set
|
{
"login": "Tinaatucsd",
"id": 22058433,
"node_id": "MDQ6VXNlcjIyMDU4NDMz",
"avatar_url": "https://avatars.githubusercontent.com/u/22058433?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Tinaatucsd",
"html_url": "https://github.com/Tinaatucsd",
"followers_url": "https://api.github.com/users/Tinaatucsd/followers",
"following_url": "https://api.github.com/users/Tinaatucsd/following{/other_user}",
"gists_url": "https://api.github.com/users/Tinaatucsd/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Tinaatucsd/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Tinaatucsd/subscriptions",
"organizations_url": "https://api.github.com/users/Tinaatucsd/orgs",
"repos_url": "https://api.github.com/users/Tinaatucsd/repos",
"events_url": "https://api.github.com/users/Tinaatucsd/events{/privacy}",
"received_events_url": "https://api.github.com/users/Tinaatucsd/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Note that there are failing tests. Instead of introducing a new Mo structure, I suggest you just change it to a Li structure instead since the POTCAR for Li is already available."
] | 2017-08-18T03:40:24
| 2017-08-18T12:51:19
|
2017-08-18T12:51:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This is to address the issue #12 GB input set.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/786/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/786/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/786",
"html_url": "https://github.com/materialsproject/pymatgen/pull/786",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/786.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/786.patch",
"merged_at": "2017-08-18T12:51:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/787
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/787/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/787/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/787/events
|
https://github.com/materialsproject/pymatgen/pull/787
| 251,182,312
|
MDExOlB1bGxSZXF1ZXN0MTM2NDMxODg3
| 787
|
Added tag_surface_sites and surface_sites_equal
|
{
"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/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@richardtran415 There are failing tests. Pls fix."
] | 2017-08-18T08:58:12
| 2017-08-19T10:45:03
|
2017-08-19T10:45:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request partially adresses issue #767
Added the tag_surface_sites and surface_sites_equal class methods to the Slab class. These methods will be useful later on for further analysis of surface properties such as work function and surface energy as well as finding viable adsorbate sites.
* Feature 1: tag_surface_sites is a class method of Slab, it finds surface sites based on undercoordination relative to the bulk and then adds site properties indicating whether a site is on the surface.
* Feature 2: surface_sites_equal checks if the sites on both surfaces are equivalent. This is useful for defining equal surfaces in slabs that do not have Laue symmetry.
* All functions that looks for Laue symmetry in the surface.py and its test file uses is_laue() method in SpaceGroupAnalyzer class.
## TODO
An algorithm is needed to find sites in a slab equivalent to sites in the bulk.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/787/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/787/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/787",
"html_url": "https://github.com/materialsproject/pymatgen/pull/787",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/787.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/787.patch",
"merged_at": "2017-08-19T10:45:03Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/788
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/788/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/788/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/788/events
|
https://github.com/materialsproject/pymatgen/issues/788
| 251,243,829
|
MDU6SXNzdWUyNTEyNDM4Mjk=
| 788
|
missing imports + no unit tests?
|
{
"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/computron/followers",
"following_url": "https://api.github.com/users/computron/following{/other_user}",
"gists_url": "https://api.github.com/users/computron/gists{/gist_id}",
"starred_url": "https://api.github.com/users/computron/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/computron/subscriptions",
"organizations_url": "https://api.github.com/users/computron/orgs",
"repos_url": "https://api.github.com/users/computron/repos",
"events_url": "https://api.github.com/users/computron/events{/privacy}",
"received_events_url": "https://api.github.com/users/computron/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@nisse3000 Pls fix. I think yu and Bharat were co-authors on this class? And pls add unittests.",
"Sorry, I forgot to put in the unit tests for the other neighbor-finding methods (i.e., the non-min_dist ones). Will come shortly.",
"@nisse3000 Is this resolved?",
"Yes, I'll issue a pull request shortly in which the last remaining unit tests are added. I didn't add tests for solid_angle, get_okeeffe_params, get_okeeffe_distance_prediction because those are called from the class tests. Is that acceptable, @shyuep?",
"That's fine for now. "
] | 2017-08-18T13:23:13
| 2017-08-23T23:17:47
|
2017-08-23T23:17:47Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
There are multiple functions in
pymatgen.analysis.defects.point_defects
that seem to be missing key imports to work.
e.g.
pymatgen.analysis.defects.point_defects.get_okeeffe_params is missing BV_PARAMS
get_okeeffe_distance_prediction is missing math
I am pretty sure these functions are not even going be runnable. Are there no unit tests at all?
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/788/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/788/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/789
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/789/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/789/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/789/events
|
https://github.com/materialsproject/pymatgen/pull/789
| 251,297,109
|
MDExOlB1bGxSZXF1ZXN0MTM2NTE4NDkw
| 789
|
io.lammps updates
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I want to discuss this code. @chc273 is supposed to implement the Structure version. In general, I don't understand why LAMMPSData needs to take in molecules. It should just take in a structure and have a static method that takes in a molecule with box sizes. As far as I can tell, the LAMMPS input file is also periodic, for which a structure is the de facto object.\r\n\r\n@chc273 @adengz Discuss with Kiran properly and merge the one that you have in our internal code base to the one in pymatgen. In future, this kind of thing should be done in pymatgen. I don't understand why you implemented it in pymacy in the first place.",
"doesnt LammpsData.from_structure do what you are suggesting? i wasnt aware of your group working on it..anyway i would rather do it myself than wait for someone...",
"I am not asking you to wait. I am saying you need to coordinate so that the needs of you and others are handled. I don't care who implements it. But I do care that it is implemented in a way that does not box us into one specific mode of operation.",
"I'm not involved in this at all, but have used LAMMPS before. Just a comment on:\r\n\r\n> As far as I can tell, the LAMMPS input file is also periodic, for which a structure is the de facto object.\r\n\r\nLAMMPS can have a variety of boundary conditions, including mixed boundary conditions (some periodic, some non-periodic), though I don't know how often people use these. http://lammps.sandia.gov/doc/boundary.html",
"@matk86 Pls check that the merged file is correct in the resolution of conflict. Once it is done, I will merge the complete file. At some point, I want a unified LAMMPSData. ",
"checked, no merge conflicts ..looping in @wood-b too"
] | 2017-08-18T16:32:30
| 2017-08-18T22:17:54
|
2017-08-18T22:17:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* added more general lammps data file parser
* enable data file generation for periodic structures. fixes issue #765
* added from_structure method to inputset
* tests for all new additions
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/789/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/789/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/789",
"html_url": "https://github.com/materialsproject/pymatgen/pull/789",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/789.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/789.patch",
"merged_at": "2017-08-18T22:17:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/790
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/790/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/790/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/790/events
|
https://github.com/materialsproject/pymatgen/pull/790
| 251,325,237
|
MDExOlB1bGxSZXF1ZXN0MTM2NTM5NDQ1
| 790
|
Cleaned-up point_defects.py and local_env.py
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-18T18:34:23
| 2017-08-18T18:42:29
|
2017-08-18T18:42:29Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
- Added deprecation warning to ValenceIonicRadiusEvaluator in point_defects.py (is now also in local_env.py where it belongs most naturally in my opinion).
- Got entirely rid of get_neighbors_of_site_with_index because we have now the NearNeighbors class in local_env.py. Therefore, also moved the O'Keeffe helper function into local_env.py
- Moved site_is_of_motif function to local_env.py
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/790/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/790/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/790",
"html_url": "https://github.com/materialsproject/pymatgen/pull/790",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/790.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/790.patch",
"merged_at": "2017-08-18T18:42:29Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/791
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/791/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/791/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/791/events
|
https://github.com/materialsproject/pymatgen/pull/791
| 251,349,066
|
MDExOlB1bGxSZXF1ZXN0MTM2NTU3MzUy
| 791
|
Reinserted high-level neighbor-finding function
|
{
"login": "nisse3000",
"id": 11105218,
"node_id": "MDQ6VXNlcjExMTA1MjE4",
"avatar_url": "https://avatars.githubusercontent.com/u/11105218?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nisse3000",
"html_url": "https://github.com/nisse3000",
"followers_url": "https://api.github.com/users/nisse3000/followers",
"following_url": "https://api.github.com/users/nisse3000/following{/other_user}",
"gists_url": "https://api.github.com/users/nisse3000/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nisse3000/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nisse3000/subscriptions",
"organizations_url": "https://api.github.com/users/nisse3000/orgs",
"repos_url": "https://api.github.com/users/nisse3000/repos",
"events_url": "https://api.github.com/users/nisse3000/events{/privacy}",
"received_events_url": "https://api.github.com/users/nisse3000/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-18T20:21:10
| 2017-08-18T21:01:17
|
2017-08-18T21:01:17Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Because it is used in both pymatgen and matminer.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/791/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/791/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/791",
"html_url": "https://github.com/materialsproject/pymatgen/pull/791",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/791.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/791.patch",
"merged_at": "2017-08-18T21:01:17Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/792
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/792/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/792/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/792/events
|
https://github.com/materialsproject/pymatgen/pull/792
| 251,354,591
|
MDExOlB1bGxSZXF1ZXN0MTM2NTYxNDI5
| 792
|
Add LMPData class to convert a pymatgen structure into a charge-type lammps input data.
|
{
"login": "chc273",
"id": 22353204,
"node_id": "MDQ6VXNlcjIyMzUzMjA0",
"avatar_url": "https://avatars.githubusercontent.com/u/22353204?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chc273",
"html_url": "https://github.com/chc273",
"followers_url": "https://api.github.com/users/chc273/followers",
"following_url": "https://api.github.com/users/chc273/following{/other_user}",
"gists_url": "https://api.github.com/users/chc273/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chc273/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chc273/subscriptions",
"organizations_url": "https://api.github.com/users/chc273/orgs",
"repos_url": "https://api.github.com/users/chc273/repos",
"events_url": "https://api.github.com/users/chc273/events{/privacy}",
"received_events_url": "https://api.github.com/users/chc273/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"other than setting the charge = oxidation state i dont see the new LMDdata class doing anything different from LammpsData",
"The old version idd not support non-orthogonal cells. Since the new one that you pushed today did, I have deleted the new LMPData."
] | 2017-08-18T20:46:15
| 2017-08-19T03:28:40
|
2017-08-18T21:01:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Read periodic pymatgen structure and convert it to lammps data
* The cell box size is calculated from pymatgen structure
* Enable non-orthogonal cells
## TODO (if any)
LMPData supports only the specific "atom_type charge" lammps input data and are for crystal structures. It perhaps can be merged with the molecule-specific input data class in the same data.py file.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/792/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/792/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/792",
"html_url": "https://github.com/materialsproject/pymatgen/pull/792",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/792.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/792.patch",
"merged_at": "2017-08-18T21:01:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/793
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/793/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/793/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/793/events
|
https://github.com/materialsproject/pymatgen/pull/793
| 251,386,349
|
MDExOlB1bGxSZXF1ZXN0MTM2NTg0NzYw
| 793
|
Add Haven ratio-related attributes to DiffusionAnalyzer
|
{
"login": "johnson1228",
"id": 4379950,
"node_id": "MDQ6VXNlcjQzNzk5NTA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4379950?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/johnson1228",
"html_url": "https://github.com/johnson1228",
"followers_url": "https://api.github.com/users/johnson1228/followers",
"following_url": "https://api.github.com/users/johnson1228/following{/other_user}",
"gists_url": "https://api.github.com/users/johnson1228/gists{/gist_id}",
"starred_url": "https://api.github.com/users/johnson1228/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/johnson1228/subscriptions",
"organizations_url": "https://api.github.com/users/johnson1228/orgs",
"repos_url": "https://api.github.com/users/johnson1228/repos",
"events_url": "https://api.github.com/users/johnson1228/events{/privacy}",
"received_events_url": "https://api.github.com/users/johnson1228/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-19T00:17:17
| 2017-08-19T00:18:35
|
2017-08-19T00:18:35Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Add Haven ratio, charge diffusivity, etc. as new attributes in DiffusionAnalyzer.
- Add unittests for the new additions (for both NpT and NVT simulations).
- Minor bugfix in periodic heatmap (when vmin = vmax).
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/793/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/793/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/793",
"html_url": "https://github.com/materialsproject/pymatgen/pull/793",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/793.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/793.patch",
"merged_at": "2017-08-19T00:18:35Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/794
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/794/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/794/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/794/events
|
https://github.com/materialsproject/pymatgen/pull/794
| 251,457,512
|
MDExOlB1bGxSZXF1ZXN0MTM2NjI1ODU1
| 794
|
Implement set_charge for structure
|
{
"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/followers",
"following_url": "https://api.github.com/users/adengz/following{/other_user}",
"gists_url": "https://api.github.com/users/adengz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/adengz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/adengz/subscriptions",
"organizations_url": "https://api.github.com/users/adengz/orgs",
"repos_url": "https://api.github.com/users/adengz/repos",
"events_url": "https://api.github.com/users/adengz/events{/privacy}",
"received_events_url": "https://api.github.com/users/adengz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-20T00:15:07
| 2017-08-20T00:16:16
|
2017-08-20T00:16:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
`LammpsData` now supports charged structure from oxidation states.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/794/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/794/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/794",
"html_url": "https://github.com/materialsproject/pymatgen/pull/794",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/794.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/794.patch",
"merged_at": "2017-08-20T00:16:16Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/795
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/795/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/795/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/795/events
|
https://github.com/materialsproject/pymatgen/issues/795
| 251,503,727
|
MDU6SXNzdWUyNTE1MDM3Mjc=
| 795
|
BSPlotterProjected does not work
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I have nothing to do with this. I coded BSDOSPlotter only. I'm happy to support the plotter I wrote but that does not put me on the hook for fixing previous plotting codes that I had no hand in writing (and frankly never use).\r\n\r\nHonestly pymatgen should just encourage use of BSDOSPlotter...",
"@computron Ok. In that case, unless anyone has objections in the next one week or so and/or fixes BSPlotterProjected, I will just completely delete the old BS plotter.",
"A few notes:\r\n\r\n- The BSDOSPlotter requires both a bs and dos. Before deleting the old plotter, we should change BSDOSPlotter so that the DOS is optional and you can only plot the BS if desired (or perhaps only the dos if the bs is None). I don't think this would be difficult to do.\r\n- The projections that BSDOSPlotter can plot are limited to \"by element\" and \"by orbital\" only. There is no function to project by both element and orbital or by anything more complicated (e.g. by site). If this is there in BSPlotterProjected, then you would lose functionality by having BSDOSPlotter only unless the latter was modified to include more complex projections.",
"I will let you figure out (i). For (ii), as far as I can tell, BSPlotterProjected does allow you to specify sites, but given that it does not work right now, it is not a relevant consideration. I would suggest making BSDOSPlotter more flexible to allow those kind of projections, which I don't think is difficult at all. \r\n\r\nThe current BSPlotterProjected takes in a complicated list of orbitals and site numbers, which does not even seem to be zero-index based. Unless someone takes the effort to fix this, I am inclined to delete it because it is unusable at the moment anyway.",
"Ok I don't see any problems with finishing (i) this week. For the site projections, I'll code it when I need it but would certainly be happy to see it happen w/o my involvement.\r\n",
"I’ll look at this.\n\nOn the long-term, merging all in BSDOSPlotter could be a good move but we have to make sure we do not loose functionality.\n\nGeoffroy\n\n> On 21 Aug 2017, at 02:16, Anubhav Jain <notifications@github.com> wrote:\n> \n> Ok I don't see any problems with finishing (i) this week. For the site projections, I'll code it when I need it but would certainly be happy to see it happen w/o my involvement.\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/795#issuecomment-323621151>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA3l935i_b5CKsVHOcIUTBxZNXMgPMt8ks5saMxBgaJpZM4O8rnG>.\n> \n\n",
"Dear all,\r\n\r\nI coded the \"get_projected_plots_dots_patom_pmorb\" method. I cloned the newest pymatgen and checked it. From my first look it works. I think the point might be at the incorrect site-numbers of \"Cu\" and \"O\" you supported ({'Cu': [3, 5], 'O': [1]}). These numbers should be complied with structure computed. Actually, if you give wrong site numbers, you will get error and notification (_number_of_subfigures method deals with this). When I check on my own computer, for instance, I put {'Cu': [3, 5], 'O': [1]} and get \r\n\r\nValueError: You put wrong site numbers in 'dictpa[O]': 1.\r\n\r\nI do not know why you did not see something like that. Could you start with change in line 136 of \"~/pymatgen/electronic_structure/tests/test_plotter.py\", for example, {'Cu': [2], 'O': [3,4]}, and recheck again.\r\n\r\nBest regards,\r\nViet-Anh HA. ",
"I am not sure what you are referring to. I tried \r\n```\r\nplotter.get_projected_plots_dots_patom_pmorb(\r\n {'Cu': ['dxy', 's', 'px'], 'O': ['px', 'py', 'pz']},\r\n {'Cu': [2], 'O': [3, 4]}\r\n )\r\n```\r\n\r\nand I get the wrong site numbers error.\r\n\r\nThe original version gave me the error I wrote above.\r\n\r\nNote that I am running Python 3.6, not 2.7. What I noticed is that you used some calls to map. In python 3.6, map returns a generator, not a list. A generator has no len.",
"I just pushed something which I think will fix it.",
"I should note that the structure in the BS object is O O Cu Cu Cu Cu species order. I am not sure why you think Cu is 2 and O is 3 and 4. In any case, does it work with zero indexing or is it 1 index? I tried 0 and it didn't work.",
"@shyuep I checked with AlCuO2 structure, thus, the orders of O and Cu are different. The index should be >=1. I am running with python 2.7. I will continue to check.",
"@shyuep The errors are at map call as you said. I used this twice and now I correct by putting \"map\" as an argument of \"list\" function, list(map(...)). For sure, I checked and it works for both python 2.x and python 3.x. I pushed my changes to my pymatgen version on github and asked for merging."
] | 2017-08-20T17:51:38
| 2017-08-24T14:57:13
|
2017-08-23T15:59:24Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
* Pymatgen version: master
* Python version: 3.6.2
* OS version: Mac
## Summary
* @hautierg @computron Basically, a simple supply of the BSPlotterProjected, especially the get_projected_plots_dots_patom_pmorb generates errors. E.g.,
```
ERROR: test_methods (__main__.BSPlotterProjectedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/units.py", line 145, in get_converter
if not np.all(xravel.mask):
AttributeError: 'numpy.ndarray' object has no attribute 'mask'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/shyue/repos/pymatgen/pymatgen/electronic_structure/tests/test_plotter.py", line 136, in test_methods
{'Cu': [3, 5], 'O': [1]}
File "/Users/shyue/repos/pymatgen/pymatgen/electronic_structure/plotter.py", line 1474, in get_projected_plots_dots_patom_pmorb
'b-', linewidth=band_linewidth)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/pyplot.py", line 3317, in plot
ret = ax.plot(*args, **kwargs)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/__init__.py", line 1898, in inner
return func(ax, *args, **kwargs)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 1406, in plot
for line in self._get_lines(*args, **kwargs):
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 407, in _grab_next_args
for seg in self._plot_args(remaining, kwargs):
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 385, in _plot_args
x, y = self._xy_from_xy(x, y)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 217, in _xy_from_xy
bx = self.axes.xaxis.update_units(x)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/axis.py", line 1413, in update_units
converter = munits.registry.get_converter(data)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/units.py", line 158, in get_converter
converter = self.get_converter(next_item)
File "/Users/shyue/miniconda3/lib/python3.6/site-packages/matplotlib/units.py", line 161, in get_converter
if converter is None and iterable(x) and (len(x) > 0):
TypeError: object of type 'map' has no len()
```
## Example code
See code in the corresponding test.
## Suggested solution (if any)
* Pls fix the plotter with unittests. Unfortunately, I do have to insist that this is accompanied by unittests this time. It has been 5 years since the last change. Because there are no unittests, this has gone unfixed.
* Pls get this done soon, i.e., within the next week or so.
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/795/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/795/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/796
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/796/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/796/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/796/events
|
https://github.com/materialsproject/pymatgen/pull/796
| 251,716,954
|
MDExOlB1bGxSZXF1ZXN0MTM2ODAyOTcy
| 796
|
read_fermi_contact_shift
|
{
"login": "random-var-x",
"id": 6107838,
"node_id": "MDQ6VXNlcjYxMDc4Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/6107838?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/random-var-x",
"html_url": "https://github.com/random-var-x",
"followers_url": "https://api.github.com/users/random-var-x/followers",
"following_url": "https://api.github.com/users/random-var-x/following{/other_user}",
"gists_url": "https://api.github.com/users/random-var-x/gists{/gist_id}",
"starred_url": "https://api.github.com/users/random-var-x/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/random-var-x/subscriptions",
"organizations_url": "https://api.github.com/users/random-var-x/orgs",
"repos_url": "https://api.github.com/users/random-var-x/repos",
"events_url": "https://api.github.com/users/random-var-x/events{/privacy}",
"received_events_url": "https://api.github.com/users/random-var-x/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-21T16:55:47
| 2017-08-21T16:56:56
|
2017-08-21T16:56:56Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
add read_fermi_contact_shift with example output and change to Li2O OUTCAR
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/796/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/796/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/796",
"html_url": "https://github.com/materialsproject/pymatgen/pull/796",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/796.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/796.patch",
"merged_at": "2017-08-21T16:56:56Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/797
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/797/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/797/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/797/events
|
https://github.com/materialsproject/pymatgen/pull/797
| 252,035,563
|
MDExOlB1bGxSZXF1ZXN0MTM3MDM5MTc4
| 797
|
dos is optional in BSDOSPlotter. Pertains to #795
|
{
"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/computron/followers",
"following_url": "https://api.github.com/users/computron/following{/other_user}",
"gists_url": "https://api.github.com/users/computron/gists{/gist_id}",
"starred_url": "https://api.github.com/users/computron/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/computron/subscriptions",
"organizations_url": "https://api.github.com/users/computron/orgs",
"repos_url": "https://api.github.com/users/computron/repos",
"events_url": "https://api.github.com/users/computron/events{/privacy}",
"received_events_url": "https://api.github.com/users/computron/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2017-08-22T17:41:20
| 2017-08-22T18:07:46
|
2017-08-22T18:07:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
BSDOSPlotter now has dos as an optional (instead of required) parameter. See Issue #795
## Additional dependencies introduced (if any)
none
## TODO (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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/797/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/797/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/797",
"html_url": "https://github.com/materialsproject/pymatgen/pull/797",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/797.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/797.patch",
"merged_at": "2017-08-22T18:07:46Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/798
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/798/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/798/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/798/events
|
https://github.com/materialsproject/pymatgen/pull/798
| 252,289,966
|
MDExOlB1bGxSZXF1ZXN0MTM3MjIzMjY4
| 798
|
minor io.lammps updates
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I will merge first. But I will make some changes."
] | 2017-08-23T13:49:06
| 2017-08-23T14:31:48
|
2017-08-23T14:10:57Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* some code simplifications and cleanup
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/798/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/798/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/798",
"html_url": "https://github.com/materialsproject/pymatgen/pull/798",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/798.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/798.patch",
"merged_at": "2017-08-23T14:10:57Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/799
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/799/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/799/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/799/events
|
https://github.com/materialsproject/pymatgen/issues/799
| 252,330,134
|
MDU6SXNzdWUyNTIzMzAxMzQ=
| 799
|
Missing unit tests for LammpsForceFieldData
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"test_forcefield_data.py has LammpsForceFieldData tests",
"Ok. Can you move these to test_data? The idea here is for test_*name* to correspond to the tests for *name*.py module. That way, people don't need to think that they need to find another test file to ensure the module works."
] | 2017-08-23T15:47:13
| 2017-08-23T17:42:39
|
2017-08-23T17:42:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Right now, there is no test for LammpsForceFieldData in test_data.py. This caused changes to LammpsData, which is the subclass to break unittests in sets.py, but not break tests in test_data.py.
A basic test should be implemented for LammpsForceFieldData to ensure that refactoring change errors get caught in a granular level. @matk86
|
{
"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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/799/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/799/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/800
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/800/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/800/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/800/events
|
https://github.com/materialsproject/pymatgen/pull/800
| 252,336,142
|
MDExOlB1bGxSZXF1ZXN0MTM3MjU4MDg2
| 800
|
refactor lammps test modules
|
{
"login": "matk86",
"id": 8696276,
"node_id": "MDQ6VXNlcjg2OTYyNzY=",
"avatar_url": "https://avatars.githubusercontent.com/u/8696276?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matk86",
"html_url": "https://github.com/matk86",
"followers_url": "https://api.github.com/users/matk86/followers",
"following_url": "https://api.github.com/users/matk86/following{/other_user}",
"gists_url": "https://api.github.com/users/matk86/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matk86/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matk86/subscriptions",
"organizations_url": "https://api.github.com/users/matk86/orgs",
"repos_url": "https://api.github.com/users/matk86/repos",
"events_url": "https://api.github.com/users/matk86/events{/privacy}",
"received_events_url": "https://api.github.com/users/matk86/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
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": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks for the quick update."
] | 2017-08-23T16:05:39
| 2017-08-23T16:19:21
|
2017-08-23T16:18:02Z
|
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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/800/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/800/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/800",
"html_url": "https://github.com/materialsproject/pymatgen/pull/800",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/800.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/800.patch",
"merged_at": "2017-08-23T16:18:02Z"
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.