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/301
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/301/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/301/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/301/events
|
https://github.com/materialsproject/pymatgen/pull/301
| 128,684,319
|
MDExOlB1bGxSZXF1ZXN0NTcxNTM4MzI=
| 301
|
Fixed chalcogen numbering
|
{
"login": "eantono",
"id": 10929462,
"node_id": "MDQ6VXNlcjEwOTI5NDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/10929462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/eantono",
"html_url": "https://github.com/eantono",
"followers_url": "https://api.github.com/users/eantono/followers",
"following_url": "https://api.github.com/users/eantono/following{/other_user}",
"gists_url": "https://api.github.com/users/eantono/gists{/gist_id}",
"starred_url": "https://api.github.com/users/eantono/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/eantono/subscriptions",
"organizations_url": "https://api.github.com/users/eantono/orgs",
"repos_url": "https://api.github.com/users/eantono/repos",
"events_url": "https://api.github.com/users/eantono/events{/privacy}",
"received_events_url": "https://api.github.com/users/eantono/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 |
[] | 2016-01-26T00:35:52
| 2016-01-26T01:17:58
|
2016-01-26T01:17:58Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The list of Z values for chalcogen elements contained 18 instead of 16.
|
{
"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/301/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/301/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/301",
"html_url": "https://github.com/materialsproject/pymatgen/pull/301",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/301.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/301.patch",
"merged_at": "2016-01-26T01:17:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/302
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/302/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/302/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/302/events
|
https://github.com/materialsproject/pymatgen/pull/302
| 129,641,347
|
MDExOlB1bGxSZXF1ZXN0NTc1OTY3MDE=
| 302
|
Splines
|
{
"login": "blondegeek",
"id": 4080470,
"node_id": "MDQ6VXNlcjQwODA0NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4080470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/blondegeek",
"html_url": "https://github.com/blondegeek",
"followers_url": "https://api.github.com/users/blondegeek/followers",
"following_url": "https://api.github.com/users/blondegeek/following{/other_user}",
"gists_url": "https://api.github.com/users/blondegeek/gists{/gist_id}",
"starred_url": "https://api.github.com/users/blondegeek/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/blondegeek/subscriptions",
"organizations_url": "https://api.github.com/users/blondegeek/orgs",
"repos_url": "https://api.github.com/users/blondegeek/repos",
"events_url": "https://api.github.com/users/blondegeek/events{/privacy}",
"received_events_url": "https://api.github.com/users/blondegeek/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 |
[
"Many thanks Tess!\n"
] | 2016-01-29T02:03:45
| 2016-01-29T02:59:38
|
2016-01-29T02:59:38Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added smooth tolerance and band interpolation failures warnings to get_plot method of BSPlotter.
|
{
"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/302/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/302/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/302",
"html_url": "https://github.com/materialsproject/pymatgen/pull/302",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/302.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/302.patch",
"merged_at": "2016-01-29T02:59:38Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/303
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/303/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/303/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/303/events
|
https://github.com/materialsproject/pymatgen/pull/303
| 130,830,989
|
MDExOlB1bGxSZXF1ZXN0NTgwNTY3NzA=
| 303
|
Added Vasp Interfaces, Examples for same, and unittests for same.
|
{
"login": "dcossey014",
"id": 6851722,
"node_id": "MDQ6VXNlcjY4NTE3MjI=",
"avatar_url": "https://avatars.githubusercontent.com/u/6851722?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dcossey014",
"html_url": "https://github.com/dcossey014",
"followers_url": "https://api.github.com/users/dcossey014/followers",
"following_url": "https://api.github.com/users/dcossey014/following{/other_user}",
"gists_url": "https://api.github.com/users/dcossey014/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dcossey014/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dcossey014/subscriptions",
"organizations_url": "https://api.github.com/users/dcossey014/orgs",
"repos_url": "https://api.github.com/users/dcossey014/repos",
"events_url": "https://api.github.com/users/dcossey014/events{/privacy}",
"received_events_url": "https://api.github.com/users/dcossey014/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 |
[] | 2016-02-02T21:57:21
| 2016-09-25T20:09:54
|
2016-09-25T20:09:53Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Shyue Ping Ong,
We finally got our code through the public release process. We are submitting the VASP Interfaces we demonstrated to you in Summer 2015 with some of your suggestions for auto-populating the dictionaries based on the parameters being set through the command interface. We've also added a simple example as well as a Multi-Firework Workflow example for others to follow. I have also supplied a Unittest Python file for testing the interfaces with future updates of Pymatgen.
Regards,
David Cossey
|
{
"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/303/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/303/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/303",
"html_url": "https://github.com/materialsproject/pymatgen/pull/303",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/303.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/303.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/304
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/304/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/304/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/304/events
|
https://github.com/materialsproject/pymatgen/pull/304
| 132,274,444
|
MDExOlB1bGxSZXF1ZXN0NTg2NzcwMDI=
| 304
|
Merge pull request #2 from materialsproject/master
|
{
"login": "Zhuoying",
"id": 10410019,
"node_id": "MDQ6VXNlcjEwNDEwMDE5",
"avatar_url": "https://avatars.githubusercontent.com/u/10410019?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Zhuoying",
"html_url": "https://github.com/Zhuoying",
"followers_url": "https://api.github.com/users/Zhuoying/followers",
"following_url": "https://api.github.com/users/Zhuoying/following{/other_user}",
"gists_url": "https://api.github.com/users/Zhuoying/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Zhuoying/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Zhuoying/subscriptions",
"organizations_url": "https://api.github.com/users/Zhuoying/orgs",
"repos_url": "https://api.github.com/users/Zhuoying/repos",
"events_url": "https://api.github.com/users/Zhuoying/events{/privacy}",
"received_events_url": "https://api.github.com/users/Zhuoying/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 |
[] | 2016-02-08T22:26:54
| 2016-02-08T22:44:04
|
2016-02-08T22:44:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
update folk pymatgen
|
{
"login": "Zhuoying",
"id": 10410019,
"node_id": "MDQ6VXNlcjEwNDEwMDE5",
"avatar_url": "https://avatars.githubusercontent.com/u/10410019?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Zhuoying",
"html_url": "https://github.com/Zhuoying",
"followers_url": "https://api.github.com/users/Zhuoying/followers",
"following_url": "https://api.github.com/users/Zhuoying/following{/other_user}",
"gists_url": "https://api.github.com/users/Zhuoying/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Zhuoying/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Zhuoying/subscriptions",
"organizations_url": "https://api.github.com/users/Zhuoying/orgs",
"repos_url": "https://api.github.com/users/Zhuoying/repos",
"events_url": "https://api.github.com/users/Zhuoying/events{/privacy}",
"received_events_url": "https://api.github.com/users/Zhuoying/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/304/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/304/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/304",
"html_url": "https://github.com/materialsproject/pymatgen/pull/304",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/304.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/304.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/305
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/305/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/305/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/305/events
|
https://github.com/materialsproject/pymatgen/issues/305
| 132,338,399
|
MDU6SXNzdWUxMzIzMzgzOTk=
| 305
|
breaking change since v3.3.2
|
{
"login": "dwinston",
"id": 1497854,
"node_id": "MDQ6VXNlcjE0OTc4NTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1497854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dwinston",
"html_url": "https://github.com/dwinston",
"followers_url": "https://api.github.com/users/dwinston/followers",
"following_url": "https://api.github.com/users/dwinston/following{/other_user}",
"gists_url": "https://api.github.com/users/dwinston/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dwinston/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dwinston/subscriptions",
"organizations_url": "https://api.github.com/users/dwinston/orgs",
"repos_url": "https://api.github.com/users/dwinston/repos",
"events_url": "https://api.github.com/users/dwinston/events{/privacy}",
"received_events_url": "https://api.github.com/users/dwinston/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 |
[
"Hmm... but in general, sites are serialized from Structure. So this shouldn't have affected the output at all?\n",
"In general, yes, but I was using a `pymatgen.alchemy.materials.TransformedStructure`. :)\n",
"Ah, I see. I think my recent commit f0395cce5fe3e1ba9da76f014c42ced10b5a02f3 may have been a bug-fix and not just cosmetic. Pushing a release with that may fix the regression. Structure passes verbosity=1 by default to the site serializer, but as currently released, the site serializer needs verbosity=2 or higher to do it's thing.\n",
"ok, thanks.\n"
] | 2016-02-09T05:59:48
| 2016-02-11T15:38:16
|
2016-02-11T15:38:10Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This is perhaps only of interest to those using serialized pymatgen structures in database/web applications, but 170a2b0c9dab863ff6f715ddf33f460f600ef5ef introduced a breaking change where two keys ("xyz", "label") usually included in the output of `pymatgen.core.sites.PeriodicSite.as_dict` are now elided in favor of requiring the caller to pass in a non-default `verbosity` kwarg value.
I'm filing this issue so that anyone who needs to make changes to their code downstream (as I did) has the above information for reference.
|
{
"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/305/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/305/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/306
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/306/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/306/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/306/events
|
https://github.com/materialsproject/pymatgen/issues/306
| 135,698,808
|
MDU6SXNzdWUxMzU2OTg4MDg=
| 306
|
Vasprun parsing DOS issue
|
{
"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 |
[
"Thanks for reporting this. I have implemented your suggested fix.\n"
] | 2016-02-23T10:34:40
| 2016-02-23T14:04:16
|
2016-02-23T14:02:51Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
When reporting bugs, please supply the following information:
## System
- pymatgen v3.3.5
- Debian 8.0
## Summary
Vasprun parsing DOS problem in overflow case.
module: pymatgen.io.vasp.outputs
class: Vasprun()
## Example code
``` python
bs = Vasprun('vasprun.xml')
bs.efermi == NoneType
Out: True
bs.get_band_structure().get_vbm()
```
## Error message
```
AttributeError Traceback (most recent call last)
<ipython-input-201-0c1fbcefc18c> in <module>()
----> 1 bs.get_band_structure().get_vbm()
/home/riccif/software/pymatgen-master/pymatgen/electronic_structure/bandstructure.pyc in get_vbm(self)
387
388 list_ind_kpts = []
--> 389 if kpointvbm.label is not None:
390 for i in range(len(self._kpoints)):
391 if self._kpoints[i].label == kpointvbm.label:
AttributeError: 'NoneType' object has no attribute 'label'
```
## Files
[vasprun.xml.tar.gz](https://github.com/materialsproject/pymatgen/files/142272/vasprun.xml.tar.gz)
```
<r> ******** 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 </r>
```
# Suggested Solution
Replace float() function with internal one _vasprun_float() that can manage overflows.
```
def _parse_varray(elem):
- return [[float(i) for i in v.text.split()] for v in elem]
+ return [[_vasprun_float(i) for i in v.text.split()] for v in elem]
```
|
{
"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/306/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/306/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/307
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/307/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/307/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/307/events
|
https://github.com/materialsproject/pymatgen/issues/307
| 137,736,830
|
MDU6SXNzdWUxMzc3MzY4MzA=
| 307
|
Bug in eigenvalue_band_properties()?
|
{
"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": 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 |
[
"Just a quick note that lines 851-854 do try to reverse the eigenvalue notation to (k#, spin) instead of (spin, k#). So in the database, the format is (k#, spin). But that reversal is not reflected back into self.eigenvalues, so the analysis code still works off (spin, k#) notation. It is all a little confusing...\n"
] | 2016-03-02T00:47:10
| 2016-03-03T15:49:08
|
2016-03-03T15:49:08Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: (master, 3.3.5+)
- Python version: 2.7.*
- OS version: OS/X
## Summary
When parsing some output files for basic Si runs, I was surprised to see the "is_gap_direct" field show up as True since Si is clearly an indirect band gap semiconductor. I think this is due to a bug in pymatgen.io.vasp.outputs.Vasprun#eigenvalue_band_properties
Note that this might affect MP database.
## Example code
i) Parse any vasprun.xml using the Vasprun code (one is attached)
[vasprun.xml.gz](https://github.com/materialsproject/pymatgen/files/153880/vasprun.xml.gz)
ii) Look at the generated analysis.is_gap_direct, which will say True, even though it is false.
## Error message
N/A
## Suggested solution (if any)
Where it says k[0] in lines 753 and 756, switch to k[1]. It looks like the eigenvalues k-points are tuples of (Spin, k#). So you want the second index. The existing code considers a band gap direct merely if the CBM and VBM have the same spin.
|
{
"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/307/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/307/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/308
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/308/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/308/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/308/events
|
https://github.com/materialsproject/pymatgen/pull/308
| 138,562,611
|
MDExOlB1bGxSZXF1ZXN0NjE3NTgxNTU=
| 308
|
fix qchem use_pcm method
|
{
"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.\n"
] | 2016-03-04T19:22:42
| 2016-03-04T19:27:02
|
2016-03-04T19:26:56Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- For QChem versions >=4.2 the solvent parameter section is named "solvent" instead "pcm_solvent"
- Fix use_pcm method in QcTask
|
{
"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/308/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/308/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/308",
"html_url": "https://github.com/materialsproject/pymatgen/pull/308",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/308.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/308.patch",
"merged_at": "2016-03-04T19:26:56Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/309
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/309/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/309/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/309/events
|
https://github.com/materialsproject/pymatgen/pull/309
| 138,601,912
|
MDExOlB1bGxSZXF1ZXN0NjE3Nzk3NDg=
| 309
|
Substrate Analyzer
|
{
"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 |
[
"Thanks. But can you also put in the proper doc for all parameters in all public methods. Most of the public methods are not documented with what each parameter means or does.\n"
] | 2016-03-04T22:16:18
| 2016-03-05T15:02:42
|
2016-03-05T14:49:15Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added new substrate analyzer module
- Topology search of matching interfaces for a substrate and film pair using Zur and McGill algorithm
- Calculates multi-layer elastic energy due to super-lattice mismatch from topological search
|
{
"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/309/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/309/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/309",
"html_url": "https://github.com/materialsproject/pymatgen/pull/309",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/309.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/309.patch",
"merged_at": "2016-03-05T14:49:14Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/310
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/310/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/310/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/310/events
|
https://github.com/materialsproject/pymatgen/pull/310
| 139,007,974
|
MDExOlB1bGxSZXF1ZXN0NjE5MzI5NTA=
| 310
|
Additional Documentation on Substrate Analyzer
|
{
"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 |
[
"Many thanks\n"
] | 2016-03-07T15:32:24
| 2016-03-07T16:44:12
|
2016-03-07T16:44:07Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added in documentation for all substrate analyzer methods including full description of argument list.
|
{
"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/310/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/310/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/310",
"html_url": "https://github.com/materialsproject/pymatgen/pull/310",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/310.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/310.patch",
"merged_at": "2016-03-07T16:44:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/311
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/311/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/311/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/311/events
|
https://github.com/materialsproject/pymatgen/pull/311
| 141,719,390
|
MDExOlB1bGxSZXF1ZXN0NjMzMDA0MTI=
| 311
|
add a reciprocal density parameter to vasp sets
|
{
"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 |
[] | 2016-03-17T22:08:05
| 2016-03-17T22:38:35
|
2016-03-17T22:38:35Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Add a "reciprocal_volume" setting for kpoints_settings in vasp sets. This supplements "grid_density" and "length" settings and allows one to set the k-point density using spacing in reciprocal space.
Note that I would suggest also making "force_gamma" one of the kpoints_settings (instead of a constructor to VaspInputSets). I am not sure why this aspect of selecting the kpoint mesh is treated differently than the others.
|
{
"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/311/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/311/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/311",
"html_url": "https://github.com/materialsproject/pymatgen/pull/311",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/311.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/311.patch",
"merged_at": "2016-03-17T22:38:35Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/312
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/312/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/312/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/312/events
|
https://github.com/materialsproject/pymatgen/issues/312
| 141,723,970
|
MDU6SXNzdWUxNDE3MjM5NzA=
| 312
|
several vaspinputset parameters are not serialized
|
{
"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": 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 |
[] | 2016-03-17T22:36:14
| 2016-03-17T23:21:24
|
2016-03-17T23:21:24Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
Latest pymatgen
## Summary
Several DictVaspInputSet parameters are not serialized in the to_dict, so these settings are lost upon serialization / deserialization. This also relates to my suggestion of putting force_gamma inside the kpoints_settings (i.e., inside config_dict).
## Example code
``` python
from pymatgen.io.vasp.sets import MPVaspInputSet, DictVaspInputSet
my_vis = MPVaspInputSet(force_gamma=True)
my_vis_reloaded = DictVaspInputSet.from_dict(my_vis.as_dict())
print my_vis.force_gamma == my_vis_reloaded.force_gamma # should say True
```
## Suggested solution (if any)
Easy fix is to serialize all the different constructor args of DictVaspInputSet. e.g. to add force_gamma to "as_dict" and "from_dict" of DictVaspInputSet.
Suggested fix is to reduce use of constructor args in the first place and put things inside config_dict so they can be set via YAML.
|
{
"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/312/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/312/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/313
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/313/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/313/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/313/events
|
https://github.com/materialsproject/pymatgen/issues/313
| 141,729,628
|
MDU6SXNzdWUxNDE3Mjk2Mjg=
| 313
|
dangerous serialization behavior of many PMG input sets
|
{
"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": 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 |
[
"This is not really a bug, but basically a well-known problem with OOP. We have the same problem when subclassing anything else, e.g., Structure -> Slab. You _have to_ overload the from_dict and preferably as_dict methods as long as your constructor no longer have the exact same signature as the parent class. But this can be mitigated by being explicit about using kwargs in DictVaspInputSet.from_dict. Just pushed a change. See if your code now works. It should. \n",
"The test code now fails for a different reason. What happens is that in the from_dict, the \"name\" is passed as a `**kwarg`. But it also needs to be the first non-optional argument. i.e., try running the following. It fails in the \"super.**init**()\" call because name is both the first argument (\"Test\") and also passed through `**kwargs`.\n\n``` python\nimport os\nfrom monty.serialization import loadfn\nfrom pymatgen.io.vasp.sets import DictVaspInputSet, MODULE_DIR\n\nclass TestVaspInputSet(DictVaspInputSet):\n def __init__(self, reciprocal_density=50, **kwargs):\n super(TestVaspInputSet, self).__init__(\"Test\",\n loadfn(os.path.join(MODULE_DIR, \"MPVaspInputSet.yaml\")), **kwargs)\n\n self.test_var = reciprocal_density\n\nif __name__ == \"__main__\":\n y = TestVaspInputSet()\n y2 = TestVaspInputSet.from_dict(y.as_dict()) # raises error!\n```\n",
"I think this should be solved on the subclass side of things? E.g., if you write\n\n``` python\nd = kwargs\nd[\"name\"] = \"Test\"\nd[\"config_dict\"] = loadfn(os.path.join(MODULE_DIR, \"MPVaspInputSet.yaml\"))\nsuper(TestVaspInputSet, self).__init__(**d)\n```\n\nI am pretty sure this works.\n",
"Works - I will use that for now. I am still thinking in Java where the super() call must be the first line.\n",
"BTW, I point out that subclass in general needs to have the same arg signature as the parent for OOP to work properly. \n\nFor example, let's say we have\n\n``` python\nclass Rectangle:\n def __init__(self, a, b):\n ...\n\nclass Square(Rectangle):\n def __init__(self, a):\n ...\n```\n\nYou will also see that there is no way to code as_dict and from_dict in Rectangle in a general way that works magically for Square. Square has to override those functions.\n\nFor this particular problem, if you want something simpler, we can create an intermediate subclass of DictVaspInputSet say FileVaspInputSet that takes in a config file as a variable, rather than a config dict. That might make it a bit easier.\n"
] | 2016-03-17T23:06:40
| 2016-03-17T23:45:19
|
2016-03-17T23:40:35Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
Latest pymatgen, Mac
## Summary
- Many VaspInputSet objects subclass DictVaspInputSet. For example, MPStaticVaspInputSet is one of many such classes.
- These subclassed VaspInputSet objects also take in constructor parameters. However, I have found that if the first two parameters are not "name" and "config_dict", then there can be deserialization problems.
- The subclassed objects serialize fine to a dict. But on deserialization, the first two parameters given to the object are "name" and "config_dict" (e.g., in DictVaspInputSet). So these must also be the first two parameters given to the objects...
- See example code for more details
## Example code
``` python
import os
from monty.serialization import loadfn
from pymatgen.io.vasp.sets import DictVaspInputSet, MODULE_DIR
class TestVaspInputSet(DictVaspInputSet):
def __init__(self, reciprocal_density=50, **kwargs):
super(TestVaspInputSet, self).__init__("Test",
loadfn(os.path.join(MODULE_DIR, "MPVaspInputSet.yaml")), **kwargs)
self.test_var = reciprocal_density
class TestVaspInputSetRevised(DictVaspInputSet):
def __init__(self, name="Test", config_dict=None, reciprocal_density=50, **kwargs):
super(TestVaspInputSetRevised, self).__init__(name,
loadfn(os.path.join(MODULE_DIR, "MPVaspInputSet.yaml")), **kwargs)
self.test_var = reciprocal_density
if __name__ == "__main__":
x = TestVaspInputSetRevised()
x2 = TestVaspInputSetRevised.from_dict(x.as_dict()) # OK!
print x.as_dict() == x2.as_dict() # True = proper serialization and deserialization
y = TestVaspInputSet()
y2 = TestVaspInputSet.from_dict(y.as_dict()) # raises error!
```
## Error message
The "normal" TestVaspInputSet should give an error at the indicated line.
## Suggested solution (if any)
Possible solutions are:
- subclasses of DictVaspInputSet should make sure the first two parameters are name and config_dict.
- subclasses of DictVaspInputSet should overload the from_dict() function.
There might be other solutions. My main goal here is to raise a flag.
|
{
"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
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/313/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/313/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/314
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/314/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/314/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/314/events
|
https://github.com/materialsproject/pymatgen/issues/314
| 141,849,601
|
MDU6SXNzdWUxNDE4NDk2MDE=
| 314
|
pymatgen.io.vasp.inputs.Potcar can't read file POTCAR.z
|
{
"login": "hlyang1992",
"id": 2081913,
"node_id": "MDQ6VXNlcjIwODE5MTM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2081913?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hlyang1992",
"html_url": "https://github.com/hlyang1992",
"followers_url": "https://api.github.com/users/hlyang1992/followers",
"following_url": "https://api.github.com/users/hlyang1992/following{/other_user}",
"gists_url": "https://api.github.com/users/hlyang1992/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hlyang1992/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hlyang1992/subscriptions",
"organizations_url": "https://api.github.com/users/hlyang1992/orgs",
"repos_url": "https://api.github.com/users/hlyang1992/repos",
"events_url": "https://api.github.com/users/hlyang1992/events{/privacy}",
"received_events_url": "https://api.github.com/users/hlyang1992/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 there, I am not sure what you mean. The Potcar class definitely supports gzip. Can you post a file for us where this fails so taht we can work on it?\n",
"I think the problem is gzip module. [POTCAR.z](https://drive.google.com/file/d/0B7DapXLbWsRKc0ljb3lxWjV3aWM/view?usp=sharing) \n",
"Oh, that's a problem with python's gzip class. I don't think it is a bug per se, but rather the Z format is not strictly the same as the gzip format. There's really nothing much we can do on this front.\n"
] | 2016-03-18T12:14:24
| 2016-03-18T16:12:17
|
2016-03-18T16:12:17Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: 3.3.5
- Python version: Python 2.7.11 :: Anaconda 2.5.0 (64-bit)
- OS version: Ubuntu 14.04
## Summary
if the format of the POTCAR is gzip, Potcar cannot read it. But zcat and uncompress can use to
decompression the file.
## Example code
``` python
import os
from pymatgen.io.vasp.inputs import Potcar
import pymatgen.io.vasp as vaspio
os.environ['VASP_PSP_DIR'] = r"/home/vagrant/workspace/potpaw"
Potcar(symbols=['Co', 'Cu'], functional='LDA')
```
## Error message
```
Traceback (most recent call last):
File "potcar.py", line 9, in <module>
Potcar(symbols=['Co', 'Cu'], functional='LDA')
File "/home/vagrant/apps/anaconda2/lib/python2.7/site-packages/pymatgen/io/vasp/inputs.py", line 1610, in __init__
self.set_symbols(symbols, functional, sym_potcar_map)
File "/home/vagrant/apps/anaconda2/lib/python2.7/site-packages/pymatgen/io/vasp/inputs.py", line 1690, in set_symbols
p = PotcarSingle.from_symbol_and_functional(el, functional)
File "/home/vagrant/apps/anaconda2/lib/python2.7/site-packages/pymatgen/io/vasp/inputs.py", line 1491, in from_symbol_and_functional
return PotcarSingle.from_file(p)
File "/home/vagrant/apps/anaconda2/lib/python2.7/site-packages/pymatgen/io/vasp/inputs.py", line 1474, in from_file
return PotcarSingle(f.read())
File "/home/vagrant/apps/anaconda2/lib/python2.7/gzip.py", line 261, in read
self._read(readsize)
File "/home/vagrant/apps/anaconda2/lib/python2.7/gzip.py", line 303, in _read
self._read_gzip_header()
File "/home/vagrant/apps/anaconda2/lib/python2.7/gzip.py", line 197, in _read_gzip_header
raise IOError, 'Not a gzipped file'
IOError: Not a gzipped 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/314/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/314/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/315
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/315/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/315/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/315/events
|
https://github.com/materialsproject/pymatgen/pull/315
| 142,105,603
|
MDExOlB1bGxSZXF1ZXN0NjM0ODAyNzc=
| 315
|
Refactor the Brillouin zone plotting
|
{
"login": "gpetretto",
"id": 8665734,
"node_id": "MDQ6VXNlcjg2NjU3MzQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8665734?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gpetretto",
"html_url": "https://github.com/gpetretto",
"followers_url": "https://api.github.com/users/gpetretto/followers",
"following_url": "https://api.github.com/users/gpetretto/following{/other_user}",
"gists_url": "https://api.github.com/users/gpetretto/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gpetretto/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gpetretto/subscriptions",
"organizations_url": "https://api.github.com/users/gpetretto/orgs",
"repos_url": "https://api.github.com/users/gpetretto/repos",
"events_url": "https://api.github.com/users/gpetretto/events{/privacy}",
"received_events_url": "https://api.github.com/users/gpetretto/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 |
[] | 2016-03-19T22:09:42
| 2016-03-21T02:58:10
|
2016-03-21T02:58:10Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
The different functions plotting the Brillouin zone now refer to a common implementation based on a few basic functions. These functions can be combined to plot multiple graphical elements in the Brillouin zone (Wigner-Seize cell, paths, labels, k points grids, ellipsoid representing the extrema of the valence and conduction bands).
Reference to pyhull has been removed, fixing issue #282.
|
{
"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/315/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/315/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/315",
"html_url": "https://github.com/materialsproject/pymatgen/pull/315",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/315.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/315.patch",
"merged_at": "2016-03-21T02:58:10Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/316
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/316/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/316/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/316/events
|
https://github.com/materialsproject/pymatgen/issues/316
| 143,424,629
|
MDU6SXNzdWUxNDM0MjQ2Mjk=
| 316
|
error about "%matplotlib inline"
|
{
"login": "QiWen0110",
"id": 17944307,
"node_id": "MDQ6VXNlcjE3OTQ0MzA3",
"avatar_url": "https://avatars.githubusercontent.com/u/17944307?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/QiWen0110",
"html_url": "https://github.com/QiWen0110",
"followers_url": "https://api.github.com/users/QiWen0110/followers",
"following_url": "https://api.github.com/users/QiWen0110/following{/other_user}",
"gists_url": "https://api.github.com/users/QiWen0110/gists{/gist_id}",
"starred_url": "https://api.github.com/users/QiWen0110/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/QiWen0110/subscriptions",
"organizations_url": "https://api.github.com/users/QiWen0110/orgs",
"repos_url": "https://api.github.com/users/QiWen0110/repos",
"events_url": "https://api.github.com/users/QiWen0110/events{/privacy}",
"received_events_url": "https://api.github.com/users/QiWen0110/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 bug. %matplotlib inline is only used in the ipython notebook. Take out the line and it should be fine.\n",
"Hi,Shyue Ping Ong,I tried on ipython,but it still doesn`t work!\nthank you for your help!\n\n> 在 2016年3月25日，下午10:36，Shyue Ping Ong notifications@github.com 写道：\n> \n> This is not a bug. %matplotlib inline is only used in the ipython notebook. Take out the line and it should be fine.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly or view it on GitHub https://github.com/materialsproject/pymatgen/issues/316#issuecomment-201315701\n",
"Ipython Notebook. Just remove that line.\n\nShyue Ping\nOn Mar 25, 2016 08:25, \"QiWen\" notifications@github.com wrote:\n\n> Hi,Shyue Ping Ong,I tried on ipython,but it still doesn`t work!\n> thank you for your help!\n> \n> > 在 2016年3月25日，下午10:36，Shyue Ping Ong notifications@github.com 写道：\n> > \n> > This is not a bug. %matplotlib inline is only used in the ipython\n> > notebook. Take out the line and it should be fine.\n> > \n> > —\n> > You are receiving this because you authored the thread.\n> > Reply to this email directly or view it on GitHub <\n> > https://github.com/materialsproject/pymatgen/issues/316#issuecomment-201315701\n> \n> —\n> You are receiving this because you modified the open/close state.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/316#issuecomment-201332430\n"
] | 2016-03-25T05:07:14
| 2016-03-25T16:20:12
|
2016-03-25T14:36:35Z
|
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.>:3.3.5
- Python version: <Only 2.7.* and 3.* supported.>:python2.7.11
- OS version: <If you are writing Windows here, you are on your own.> OS EI Capitan 10.11.4
## Summary
- <Short 1-2 bullet points stating the problem.>The command "%matplotlib" can`t run
## Example code
from pymatgen.matproj.rest import MPRester
from pymatgen.electronic_structure.core import Spin
# This initiliazes the Rest connection to the Materials Project db. Put your own API key.
a=MPRester("YOUR_API_KEY")
# load the band structure from mp-3748, CuAlO2 from the MP db
bs=a.get_bandstructure_by_material_id("mp-3748")
%matplotlib inline
from pymatgen.electronic_structure.plotter import BSPlotter
plotter=BSPlotter(bs)
plotter.get_plot().show()
``` python
<Example code generating error>
```
## Error message
File "<stdin>", line 1
%matplotlib inline
^
SyntaxError: invalid syntax
[Basic functionality.pdf](https://github.com/materialsproject/pymatgen/files/189082/Basic.functionality.pdf)
[Analyze and plot band structures.pdf](https://github.com/materialsproject/pymatgen/files/189087/Analyze.and.plot.band.structures.pdf)
```
<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/316/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/316/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/317
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/317/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/317/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/317/events
|
https://github.com/materialsproject/pymatgen/pull/317
| 144,969,454
|
MDExOlB1bGxSZXF1ZXN0NjQ4Mjk1OTU=
| 317
|
Substrate Analyzer clean up and refactor for DB building
|
{
"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 |
[] | 2016-03-31T17:42:15
| 2016-04-01T22:42:52
|
2016-04-01T22:42:52Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Cleaned up some of the code
Changed match dict to be more suitable for large DBs
No further changes expected.
|
{
"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/317/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/317/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/317",
"html_url": "https://github.com/materialsproject/pymatgen/pull/317",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/317.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/317.patch",
"merged_at": "2016-04-01T22:42:52Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/318
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/318/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/318/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/318/events
|
https://github.com/materialsproject/pymatgen/issues/318
| 145,213,850
|
MDU6SXNzdWUxNDUyMTM4NTA=
| 318
|
Structure object inefficiency
|
{
"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": 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"
},
{
"id": 5414010766,
"node_id": "LA_kwDOACgets8AAAABQrM_jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20discussion",
"name": "needs discussion",
"color": "D96543",
"default": false,
"description": "Needs discussion to agree on actionable next steps"
}
] |
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 |
[
"Before you refactor, look at the solution I did. I think overloading is difficult. But we can cheat by simply initializing an empty structure (no site creation) and assigning self._sites. This works and doesn't break anything.\n",
"In general, I am not a fan of _args, *_kwargs. It makes it very difficult to know what parameters to supply. The solution I wrote basically speeds up basic structure copying by ~100x. I tested that fast_copy takes 2.7 us per loop, while normal copy or santize takes 200 us per loop.\n",
"Ew. Looks like it could work though.\n\nI think long-term it would be cleaner to refactor to have __init__ take arguments closer to the internal representation. A bunch of weird bugs cropped up with these commits since there's still no way to quickly make a Structure from an IStructure. There would be some side-benefits including speeding up from_dict slightly as well. The args, kwargs would just be a temporary hack to avoid breaking peoples code before they refactor.\n",
"Yep. I agree. Let's think about it a little. I will reopen this issue so that it is on our radar. But otherwise, the solution basically now works. In general, IStructure is an anachronism. Structure should be the default for most things. I have half a mind to remove IStructure completely in pmg 4.0. Though that might break a lot of stuff.\n",
"> IStructure is an anachronism. Structure should be the default for most things. I have half a mind to remove IStructure completely in pmg 4.0.\r\n\r\n@shyuep What's your current thinking on `IStructure`? Should we drop it in `v2024.*.*`?",
"Closing this issue."
] | 2016-04-01T15:44:55
| 2023-08-08T21:15:57
|
2023-08-08T21:15:57Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Structure objects take a long time to copy (long here is relative, but at this point even StructureMatcher spends almost 90% of its time copying structures in the cython_utils branch). They are essentially just lists of periodic sites (which are immutable), so the copy should be able to just copy the list without copying the underlying Site objects. Unfortunately, since Structure.__init__ takes lists of species and coords, this is not currently possible.
## Suggested solution (if any)
- Refactor Structure and Molecule objects, switching Structure.__init__ and Structure.from_sites. I think it's possible to have a temporarily overloaded Structure.__init__ to avoid breaking any code and properly show deprecation warnings.
|
{
"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/318/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/318/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/319
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/319/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/319/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/319/events
|
https://github.com/materialsproject/pymatgen/issues/319
| 145,359,358
|
MDU6SXNzdWUxNDUzNTkzNTg=
| 319
|
get_entries_in_chemsys does not seem to work any more
|
{
"login": "hyllios",
"id": 18228397,
"node_id": "MDQ6VXNlcjE4MjI4Mzk3",
"avatar_url": "https://avatars.githubusercontent.com/u/18228397?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hyllios",
"html_url": "https://github.com/hyllios",
"followers_url": "https://api.github.com/users/hyllios/followers",
"following_url": "https://api.github.com/users/hyllios/following{/other_user}",
"gists_url": "https://api.github.com/users/hyllios/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hyllios/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hyllios/subscriptions",
"organizations_url": "https://api.github.com/users/hyllios/orgs",
"repos_url": "https://api.github.com/users/hyllios/repos",
"events_url": "https://api.github.com/users/hyllios/events{/privacy}",
"received_events_url": "https://api.github.com/users/hyllios/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 |
[
"Your pymatgen version is rather out-dated. There have been some recent changes on the Materials Project side of things to clean up some urls. Pls upgrade your pymatgen to the latest version and it should work. I just tested it.\n",
" Hi,\n\n It works. Thanks a lot!\n\n cheers,\n Miguel\n\nOn 04/02/2016 03:15 PM, Shyue Ping Ong wrote:\n\n> Your pymatgen version is rather out-dated. There have been some recent \n> changes on the Materials Project side of things to clean up some urls. \n> Pls upgrade your pymatgen to the latest version and it should work. I \n> just tested it.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly or view it on GitHub \n> https://github.com/materialsproject/pymatgen/issues/319#issuecomment-204714974\n"
] | 2016-04-02T10:20:39
| 2016-04-02T15:55:36
|
2016-04-02T13:15:11Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: 3.0.10
- Python version: 2.7.6
- OS version: Ubuntu 12.04 LTS
## Summary
- get_entries_in_chemsys does not seem to work any more
I have been using pymatgen to calculate the distance to the convex hull for several months now. A couple of weeks ago, the script stop working, complaining that it did not find come terminal compounds. The same happened in several machines at the same time. Digging a bit I found that get_entries_in_chemsys is only returning a couple of entries from the database, and not all available structures.
## Example code
from pymatgen.matproj.rest import MPRester
a = MPRester('AxxMD49p6cCDmcy9')
e = a.get_entries_in_chemsys(['Ca','Cs','O'])
for i in e:
print i.composition
## Output
Cs2
Cs1
Cs8
Cs4
Cs8
Cs8
Cs2
O8
O2
O2
O24
O2
O8
Cs1 Ca3
Cs2 O1
Cs1 O2
Cs4 O2
Cs21 O3
Cs2 O2
Cs2 O4
Cs6 O2
Cs44 O12
Cs8 O4
Cs1 Ca1 O3
Cs8 Ca4 O8
(No Ca, for example).
|
{
"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/319/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/319/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/320
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/320/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/320/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/320/events
|
https://github.com/materialsproject/pymatgen/pull/320
| 146,723,894
|
MDExOlB1bGxSZXF1ZXN0NjU2ODc3NTc=
| 320
|
Adding in Piezo Tensor to Pymatgen
|
{
"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 |
[
"Great. but instead of having Operations.transform_r2, transform_r3, and transform_r4, isn't it better to simply have one transform method that works for all dimensions?\n\n``` python\ndim = tensor.shape\nrank = dim[0]\nassert all([i == rank for i in dim])\n\nind1 = \"abcdefgh\"\nind2 = \"ijklmnop\"\n\nn = [\"%s%s\" % (i,j) for i, j in zip(ind1[:rank], ind2[:rank]]\nm = \",\".join(n) + \",\" + ind1[:rank] +\"->\"+ ind2[:rank] \nargs = [self.rotation_matrix] * rank + [tensor]\nreturn np.einsum(m, *args)\n```\n\nThis is the rough @concept.\n",
"Joey had the same idea. I've committed his code in. I think we might have to assert that each dimension is size 3, since the rotation matrix is a 3x3. It technically doesn't make sense in any other form. \n"
] | 2016-04-07T19:44:04
| 2016-04-07T20:24:57
|
2016-04-07T20:24:57Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added in Piezotensor
Updated Outcar to automatically parse piezo and dielectric tensors
Added in symmetry operations for rank 3 and rank 4 tensors
|
{
"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/320/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/320/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/320",
"html_url": "https://github.com/materialsproject/pymatgen/pull/320",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/320.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/320.patch",
"merged_at": "2016-04-07T20:24:57Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/321
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/321/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/321/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/321/events
|
https://github.com/materialsproject/pymatgen/issues/321
| 146,775,030
|
MDU6SXNzdWUxNDY3NzUwMzA=
| 321
|
major issue in get_primitive_standard_structure()
|
{
"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": 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 |
[
"@hautierg can you look into this? We are using this code for tens of thousands of band structures, and a structure change would obviously be disastrous. In the case I posted, the new primitive standard structure even has positive energy even though the initial structure is correct.\n",
"Also, the error appears to be somewhere between line 454-470 of analyzer.py.\n\ni.e., starting with conventational_standard_structure() and refined_structure() is correct. But modifying the refined_structure() has an error somewhere.\n",
"A further hint - \n- The code starts with the refined structure (correct) and makes further changes.\n- The changes attempt to modify the refined lattice matrix into a new setting.\n- But, this modification code seems to only use a single lattice vector length of the old setting in the calculation of the new matrix. Thus, the new lattice only has a single lattice vector length.\n- _But_ the rhombohedral cell has 2 unique lattice vector lengths. It looks like this is not preserved...\n\nProbably the transformation needs to take into account the 2nd lattice vector length\n",
"OK. I have looked more into this.\n\nI think the problem comes from the refined structure for a rhombohedral cell being returned as hexagonal settings.\nIn fact, while for cubic systems the conventional cell is clearly and uniquely defined, the rhombohedral systems can have both a rhombohedral or hexagonal representation.\nAs far as I understood the IUCr did not choose one (see table of crystallography p. 14-15 http://ahrenkiel.sdsmt.edu/courses/Spring2016/NANO704/International_Tables_For_Crystallography_A.pdf http://ahrenkiel.sdsmt.edu/courses/Spring2016/NANO704/International_Tables_For_Crystallography_A.pdf)\n\nIn itself, this is fine. It is just a definition from spglib. BUT the convention we took (for band structures) from Setyawan assumes a rhombohedral (and not hexagonal) representation. The mess comes from the code expecting a rhombohedral cell and getting an hexagonal one.\n\nIf it had been like this directly when we coded this, we would have seen it. In fact, we have some rhombohedral runs in the MP data that look perfectly fine (meaning their primitive standard, static run is exactly what we expect). So, my guess is that the convention to give the hexagonal cell changed with time in spglib. Although I cannot formally prove it this seems the most likely explanation at the moment.\n\nWhat I suggest to do:\n\n-keep the conventional to be the hexagonal in our crystal symmetry analysis package as in spglib\n-change the code generating primitive standard cell to take this into account and to solve the mismatch we have now. This should be pretty easy.\n-add some checks as you suggested on volume for instance\n\nFollow-up on how this affect the MP.\n\nBest,\n\nGeoffroy\n\n> On 08 Apr 2016, at 19:45, Anubhav Jain notifications@github.com wrote:\n> \n> A further hint -\n> \n> The code starts with the refined structure (correct) and makes further changes.\n> The changes attempt to modify the refined lattice matrix into a new setting.\n> But, this modification code seems to only use a single lattice vector length of the old setting in the calculation of the new matrix. Thus, the new lattice only has a single lattice vector length.\n> But the rhombohedral cell has 2 unique lattice vector lengths. It looks like this is not preserved...\n> Probably the transformation needs to take into account the 2nd lattice vector length\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub https://github.com/materialsproject/pymatgen/issues/321#issuecomment-207533707\n",
"Hi all,\n\nI'm not sure if this is related, but I have witnessed a very strange error\non the MaterialsProject when doing the primitive unit cell function on some\nrhombohedral unit cells. Consider the following:\n\nhttps://materialsproject.org/materials/mp-674478/\n\nThe conventional standard shows a rhombohedral R-3c structure. But if you\nclick on Primitive, it returns a cubic structure, with completely messed up\ninternal coordinates.\n\nI showed this to Shyue Ping a while back and he tried to reproduce in\nPymatgen, but got the correct primitive cell. I didn't pursue the issue,\nbut perhaps it is related to the bug discussed here.\n\nBest,\nWenhao Sun\n\nOn Sun, Apr 10, 2016 at 2:09 PM, Geoffroy Hautier notifications@github.com\nwrote:\n\n> OK. I have looked more into this.\n> \n> I think the problem comes from the refined structure for a rhombohedral\n> cell being returned as hexagonal settings.\n> In fact, while for cubic systems the conventional cell is clearly and\n> uniquely defined, the rhombohedral systems can have both a rhombohedral or\n> hexagonal representation.\n> As far as I understood the IUCr did not choose one (see table of\n> crystallography p. 14-15\n> http://ahrenkiel.sdsmt.edu/courses/Spring2016/NANO704/International_Tables_For_Crystallography_A.pdf\n> <\n> http://ahrenkiel.sdsmt.edu/courses/Spring2016/NANO704/International_Tables_For_Crystallography_A.pdf\n> \n> > )\n> \n> In itself, this is fine. It is just a definition from spglib. BUT the\n> convention we took (for band structures) from Setyawan assumes a\n> rhombohedral (and not hexagonal) representation. The mess comes from the\n> code expecting a rhombohedral cell and getting an hexagonal one.\n> \n> If it had been like this directly when we coded this, we would have seen\n> it. In fact, we have some rhombohedral runs in the MP data that look\n> perfectly fine (meaning their primitive standard, static run is exactly\n> what we expect). So, my guess is that the convention to give the hexagonal\n> cell changed with time in spglib. Although I cannot formally prove it this\n> seems the most likely explanation at the moment.\n> \n> What I suggest to do:\n> \n> -keep the conventional to be the hexagonal in our crystal symmetry\n> analysis package as in spglib\n> -change the code generating primitive standard cell to take this into\n> account and to solve the mismatch we have now. This should be pretty easy.\n> -add some checks as you suggested on volume for instance\n> \n> Follow-up on how this affect the MP.\n> \n> Best,\n> \n> Geoffroy\n> \n> > On 08 Apr 2016, at 19:45, Anubhav Jain notifications@github.com wrote:\n> > \n> > A further hint -\n> > \n> > The code starts with the refined structure (correct) and makes further\n> > changes.\n> > The changes attempt to modify the refined lattice matrix into a new\n> > setting.\n> > But, this modification code seems to only use a single lattice vector\n> > length of the old setting in the calculation of the new matrix. Thus, the\n> > new lattice only has a single lattice vector length.\n> > But the rhombohedral cell has 2 unique lattice vector lengths. It looks\n> > like this is not preserved...\n> > Probably the transformation needs to take into account the 2nd lattice\n> > vector length\n> > \n> > —\n> > You are receiving this because you were mentioned.\n> > Reply to this email directly or view it on GitHub <\n> > https://github.com/materialsproject/pymatgen/issues/321#issuecomment-207533707\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/321#issuecomment-208071686\n\n## \n\nCeder Research Group http://web.mit.edu/ceder/ | Massachusetts Institute\nof Technology\nDepartment of Materials Science and Engineering\n77 Massachusetts Ave | Room 13-5065 | Cambridge, MA, 02139\n",
"I would recommend a more robust solution that assuming either rhom or hex setting. In general, the code should validate what latttice it is getting, before standardizing it. If it is in rhom, it applies a rhom conversion. If it is a hex, it applies a hex conversion. Validating isn't difficult since it is pretty clear from the lattice lengths and angles. \n\nIn fact, the rest of the cells should have a similar validation.\n",
"For me version 3.0.13 works as expected. The bug is introduced in the next version 3.1.0, which is where spglib was updated to version 1.7.3.\n"
] | 2016-04-07T23:57:21
| 2016-04-17T15:24:04
|
2016-04-17T15:24:04Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
- Python version: 2.7.*
- OS version: Mac
## Summary
The structure changes _very_ drastically upon calling "get_primitive_standard_structure".
## Example code
``` python
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.io.vasp import Poscar
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
old_structure = Poscar.from_file("CONTCAR.gz").structure
sym_finder = SpacegroupAnalyzer(old_structure)
new_structure = sym_finder.get_primitive_standard_structure()
# easy sanity check
print("Is the volume per atom the same in old and new structures?")
print(old_structure.volume/old_structure.num_sites, new_structure.volume/new_structure.num_sites)
print("No! Clearly these are very different structures...")
print("")
print("Does the structurematcher think these structures are the same?")
sm = StructureMatcher()
print(sm.fit(old_structure, new_structure))
```
## Error message
This is what is printed out when running the above code:
```
Is the volume per atom the same in old and new structures?
(10.64341518083199, 4.561477853966009)
No! Clearly these are very different structures...
Does the structurematcher think these structures are the same?
False
```
## Suggested solution (if any)
I didn't debug the underlying code, but this is probably the 2nd or 3rd time there has been a problem in this method. I would strongly recommend adding an `assert` statement at the end of the code that asserts that volume per atom is the same in the original and final structures. This should not affect performance and will help us find errors. In this case, I thought the error was stemming from a new workflow code but it looks like the culprit is probably this structure change. It would have been much easier debug if I had seen an assertion failure at this step.
## Files (if any)
[CONTCAR.gz](https://github.com/materialsproject/pymatgen/files/209410/CONTCAR.gz)
|
{
"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/321/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/321/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/322
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/322/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/322/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/322/events
|
https://github.com/materialsproject/pymatgen/pull/322
| 146,841,801
|
MDExOlB1bGxSZXF1ZXN0NjU3NDY4OTk=
| 322
|
Make Kpoints init convert style string to enum
|
{
"login": "dwinston",
"id": 1497854,
"node_id": "MDQ6VXNlcjE0OTc4NTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1497854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dwinston",
"html_url": "https://github.com/dwinston",
"followers_url": "https://api.github.com/users/dwinston/followers",
"following_url": "https://api.github.com/users/dwinston/following{/other_user}",
"gists_url": "https://api.github.com/users/dwinston/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dwinston/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dwinston/subscriptions",
"organizations_url": "https://api.github.com/users/dwinston/orgs",
"repos_url": "https://api.github.com/users/dwinston/repos",
"events_url": "https://api.github.com/users/dwinston/events{/privacy}",
"received_events_url": "https://api.github.com/users/dwinston/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 |
[] | 2016-04-08T07:31:07
| 2016-04-08T12:51:44
|
2016-04-08T12:51:44Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
`Kpoints.__init__` now sets `self.style`, thus using a setter method to automatically convert a given string `style` to the proper enum type if possible.
- `Kpoints.__init__` is more lenient about its input `style`
- `Kpoints.from_dict` is shortened
Alternative solution:
In `Kpoints.from_dict`, could change `Kpoints.supported_modes[generation_style]` to `Kpoints.supported_modes.from_string(generation_style)`, but it seems cleaner to remove that spot conversion entirely and delegate to `Kpoints.__init__`.
|
{
"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/322/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/322/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/322",
"html_url": "https://github.com/materialsproject/pymatgen/pull/322",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/322.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/322.patch",
"merged_at": "2016-04-08T12:51:44Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/323
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/323/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/323/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/323/events
|
https://github.com/materialsproject/pymatgen/pull/323
| 146,923,370
|
MDExOlB1bGxSZXF1ZXN0NjU3ODI0NTM=
| 323
|
Integration of ChemEnv into pymatgen
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/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!\n",
"Is there a Readme or any documentation on this package? I was trying to search for a utility that calculates coordination numbers for a structure...\n",
"The plan is to write a few examples of usage in the pymatgen examples.\n\n> On 11 Apr 2016, at 00:55, Saurabh Bajaj notifications@github.com wrote:\n> \n> Is there a Readme or any documentation on this package? I was trying to search for a utility that calculates coordination numbers for a structure...\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub https://github.com/materialsproject/pymatgen/pull/323#issuecomment-208087322\n"
] | 2016-04-08T13:00:20
| 2016-04-11T06:54:10
|
2016-04-08T13:40:14Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
The ChemEnv package has been integrated into pymatgen
- Fast, robust and automatic identification of coordination environments of structures
- Visualization of coordination environments with structure_vtk
- Script get_environments.py to get environments of a given structure from a Cif file or from a MP id
- Unit tests
## TODO
Improve the strategies
|
{
"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/323/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/323/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/323",
"html_url": "https://github.com/materialsproject/pymatgen/pull/323",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/323.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/323.patch",
"merged_at": "2016-04-08T13:40:14Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/324
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/324/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/324/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/324/events
|
https://github.com/materialsproject/pymatgen/pull/324
| 147,018,195
|
MDExOlB1bGxSZXF1ZXN0NjU4MzYwODQ=
| 324
|
handle disordered species
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[] | 2016-04-08T19:32:51
| 2016-04-08T19:49:12
|
2016-04-08T19:49:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Error faced: "AttributeError: specie" when running get_voronoi_polyhedra() for a site that has as its nearest neighbor (nn) a disorderd site.
- Proposed fix: separate handling of disordered nn, get elements contained on the site, check if present in structure, and update the weighted polyhedra.
- Attachment: example structure (as a dictionary) tested with
[structure_sd_1615854.json.zip](https://github.com/materialsproject/pymatgen/files/210750/structure_sd_1615854.json.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/324/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/324/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/324",
"html_url": "https://github.com/materialsproject/pymatgen/pull/324",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/324.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/324.patch",
"merged_at": "2016-04-08T19:49:12Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/325
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/325/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/325/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/325/events
|
https://github.com/materialsproject/pymatgen/issues/325
| 147,309,603
|
MDU6SXNzdWUxNDczMDk2MDM=
| 325
|
Predictor-corrector parsing, and storage in Structure
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/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 |
[] | 2016-04-11T03:55:17
| 2016-04-12T13:21:04
|
2016-04-12T13:21:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
- Python version: 2.7.\* and 3.*
- OS version: OS X & Linux
## Summary
For the predictor-corrector data, currently pymatgen looks for a chunk after reading the velocities from CONTCAR, and stores them as "site_properties" in the Structure. There are two issues here:
(1) There is a 3-line-long preamble in the "predictor-corrector" chunk, listing a "key", POTIM, and a set of thermostat parameters. Since site_property stores an array of N data points, upon parsing, these 3 lines spuriously occupy the "site_properties" of the first 3 sites. Consequently, the correct correspondence between a site and the "predictor-corrector" data is lost, and more importantly the predictor-corrector information for the last 3 atoms are not stored. Therefore when a POSCAR is generated from this Structure, the missing information causes VASP to complain and halt.
(2) The "predictor-corrector" chunk consists of 3 sets of 3 x N data points corresponding to positions and derivatives. Currently pymatgen only stores 1 set as site_properties (and as I mention in item (1), that isn't done correctly either).
## Example code
``` python
p = Poscar.from_file("test_files/CONTCAR.MD", check_for_POTCAR=False)
```
## Error message
The predictor corrector information in the Structure is wrong. For exampe for the above CONTCAR.MD read from test_files, the regenerated Poscar ends with the following predictor corrector chunk, where the predictor-corrector coordinates of last three atoms are missing.
1
2.0
1.291972 0.009838 0.000000 0.000000
0.333878 0.772915 0.367011
0.030832 0.042070 0.287438
..
0.202082 0.545512 0.332244
0.209706 0.018853 0.630065
0.042787 0.718967 0.808148
missing predictor-corrector coordinates:
> > 0.98321567E+00 0.32246042E+00 0.83616357E+00
> > 0.97678703E+00 0.70638938E+00 0.12546431E+00
> > 0.15997023E-01 0.29204035E+00 0.15797571E+00
Besides, the following two 3xN size additional sets of predictor-corrector information is missing too. VASP cannot read the new POSCAR due to missing data:
> > lib-4001 : UNRECOVERABLE library error
> > A READ operation tried to read past the end-of-file
> > ...
## Suggested solution (if any)
Please see the pull request I submitted for details. In a nut shell:
- Fixing item (2) is straightforward as it is simply a parsing issue. My suggested solution is for each site, bundling all 3 predictor-corrector parameters into a list, and storing that list as the site_property. When generating a Poscar from Structure, the output is also accordingly generated.
- To fix item (2), we need to store the "preamble" of predictor-corrector data in some way in Structure. Not to muddle up Structure, I suggest adding a "structure_properties" dict attribute to Structure, which can store arbitrary information about the structure. We can use that in this case to store the "predictor_corrector_preamble". My pull request also implements this suggestion. As this suggestion modifies a core pymatgen object, I felt this may be a point needed to be discussed further.
```
```
|
{
"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/325/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/325/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/326
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/326/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/326/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/326/events
|
https://github.com/materialsproject/pymatgen/pull/326
| 147,312,950
|
MDExOlB1bGxSZXF1ZXN0NjU5Mzg2MTA=
| 326
|
Suggested fix for the parsing issues related with the predictor-corrector data in VASP output
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/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 think the new parsing is great. But I think there is really no reason to add a structure_property field. Structure is mutable by default. So you can simply set any new properties as Structure.thermostat = X for example. Also, I think things like thermostat etc. are not really Structure related but rather POSCAR related. So they should actually be stored in POSCAR itself rather than Structure?\n",
"Thanks for the comments. I will isolate the parsing and submit a new pull request. \n\nFor the preamble storage (key, time-step and thermostat parameters), I agree that the proper place would be Poscar since they are specific to it. But the reason why I suggested storing them in Structure was, because they are tied with the predictor corrector coordinates and derivatives (e.g. those are valid for only the time-step given in the preamble) so I wasn't sure about separating them. Because in that sense, having them together in Structure ensures that when a Structure parsed from a CONTCAR is stored, it is self-sufficient to generate a new Poscar in future, without needing access to the CONTCAR it was generated from (or a stored Poscar object). I hope my point is clear. What do you think? Would you prefer the \"Structure.thermostat\" style or storing in the Poscar? \n",
"Thanks. I agree it is strange that the predictor_corrector are stored in site properties. There is actually a good reason for that. When the properties are related to an overall structure, there is no issue with storing them in the Poscar itself. When there are properties that relates to sites, the problem is that people may sometimes manipulate the structure e.g., swapping atomic ordering etc., after parsing a Poscar and then regenerating that Poscar. Those properties have to be linked to each site so that any ordering works. \n\nIn general, core objects like Site and Structure should be kept free from DFT code specific things. I don't see the site_properties as a major deviation because site_properties was there to begin with. Things like Poscar related parameters should site within the Poscar object itself.\n",
"Ok, I got it. I'll put the those parameters in Poscar. Thanks.\n"
] | 2016-04-11T04:17:50
| 2016-04-12T03:59:17
|
2016-04-12T03:59:17Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This is a suggested solution for the Issue #325, mostly for code review purposes. I can work on a new pull request based on the comments on this one.
- Predictor corrector data is now correctly parsed.
- These 3 sets of 3 xN parameters are stored properly for each site as a site_property.
- inputs.Poscar is modified to now generate the the correct string for POSCAR's with predictor_corrector information.
- A generic "structure_properties" attribute is added to Structure to store any arbitrary structure information that is not site-specific.
- Using that, predictor corrector preamble (key, potim, thermostat params...) is stored as a structure_property
- Structure and IStructure were modified to accommodate "structure_properties" (e.g. addition of properties, structure generation, copying etc.)
- Changes are tested, no errors generated.
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/326/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/326/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/326",
"html_url": "https://github.com/materialsproject/pymatgen/pull/326",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/326.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/326.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/327
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/327/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/327/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/327/events
|
https://github.com/materialsproject/pymatgen/pull/327
| 147,337,873
|
MDExOlB1bGxSZXF1ZXN0NjU5NDk3NTY=
| 327
|
Small fix of the test_orthonormal_vectors
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/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 |
[] | 2016-04-11T07:23:20
| 2016-04-11T13:17:41
|
2016-04-11T13:17:41Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fixed test of orthogonal vectors in Plane (was working on my workstation, machine-precision error). I hope it now works on the Ci
|
{
"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/327/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/327/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/327",
"html_url": "https://github.com/materialsproject/pymatgen/pull/327",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/327.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/327.patch",
"merged_at": "2016-04-11T13:17:41Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/328
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/328/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/328/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/328/events
|
https://github.com/materialsproject/pymatgen/pull/328
| 147,587,229
|
MDExOlB1bGxSZXF1ZXN0NjYwODAxMTM=
| 328
|
Predictor-corrector parsing and storage
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/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!\n"
] | 2016-04-11T23:39:11
| 2016-04-12T02:35:14
|
2016-04-12T02:35:05Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request addresses [Issue #325](https://github.com/materialsproject/pymatgen/issues/325).
- Fixed the parsing of predictor-corrector data from an MD CONTCAR.
- Preamble (key, POTIM, thermostat parameters) for the predictor-corrector data is stored in Poscar.
|
{
"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/328/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/328/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/328",
"html_url": "https://github.com/materialsproject/pymatgen/pull/328",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/328.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/328.patch",
"merged_at": "2016-04-12T02:35:05Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/329
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/329/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/329/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/329/events
|
https://github.com/materialsproject/pymatgen/pull/329
| 147,665,956
|
MDExOlB1bGxSZXF1ZXN0NjYxMTQ5OTU=
| 329
|
Correction of the tests in chemenv
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/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 |
[] | 2016-04-12T07:58:26
| 2016-04-12T13:15:30
|
2016-04-12T13:15:30Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Corrected tests in chemenv.
|
{
"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/329/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/329/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/329",
"html_url": "https://github.com/materialsproject/pymatgen/pull/329",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/329.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/329.patch",
"merged_at": "2016-04-12T13:15:30Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/330
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/330/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/330/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/330/events
|
https://github.com/materialsproject/pymatgen/issues/330
| 148,024,937
|
MDU6SXNzdWUxNDgwMjQ5Mzc=
| 330
|
get_reduced_structure method of IStructure not work
|
{
"login": "hlyang1992",
"id": 2081913,
"node_id": "MDQ6VXNlcjIwODE5MTM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2081913?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hlyang1992",
"html_url": "https://github.com/hlyang1992",
"followers_url": "https://api.github.com/users/hlyang1992/followers",
"following_url": "https://api.github.com/users/hlyang1992/following{/other_user}",
"gists_url": "https://api.github.com/users/hlyang1992/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hlyang1992/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hlyang1992/subscriptions",
"organizations_url": "https://api.github.com/users/hlyang1992/orgs",
"repos_url": "https://api.github.com/users/hlyang1992/repos",
"events_url": "https://api.github.com/users/hlyang1992/events{/privacy}",
"received_events_url": "https://api.github.com/users/hlyang1992/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 problem with get_reduced_structure. When you use from_file, it does not reduce your structure to a primitive cell by default. If you add primitive=True, it should work as intended.\n",
"Fixed in https://github.com/materialsproject/pymatgen/commit/0cfa800a56c850edfa6084ac9656db532de3639a\n",
"I think this is a problem with get_reduced_structure @shyuep . If I don't reduce structure when use from_file, I will not able to use structure.get_reduced_structure method to get a reduced structure. It will affect VaspInputSet, such as in DictVaspInputSet of sets.py:\n[get_poscar](https://github.com/materialsproject/pymatgen/blob/d0aa4166e14164f23f782892679f7a9eb3626698/pymatgen/io/vasp/sets.py#L316-L321)\n\nIf I use from_file without primitive=True and give this structure to DictVaspInputSet with reduce_structure=\"niggli\", I can't get reduce structure by using write_input method.\n",
"This is not a problem with get_reduced_structure. You misunderstand what \"reduced\" means. \"Reduced\" is lattice vector reduction, which means that the shortest vectors are found. It does not mean primitive cell reduction. If you want to do primitive cell, you should call structure.get_primitive_structure() first.\n",
"Thank you very much. \n"
] | 2016-04-13T11:09:02
| 2016-05-12T08:13:07
|
2016-04-13T16:03:41Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: u'3.4.0'
- Python version: python 2.7
- OS version: ubuntu14.04
## Summary
get_reduced_structure method of IStructure not work,
``` python
fn = "Si-51688.cif"
si = mg.IStructure.from_file(fn)
p = Poscar(si.get_reduced_structure())
print(p)
```
output is:
```
Si8
1.0
5.430530 -0.000000 0.000000
0.000000 5.430530 0.000000
-0.000000 -0.000000 5.430530
Si
8
direct
0.250000 0.250000 0.250000 Si0+
0.000000 0.000000 0.000000 Si0+
0.250000 0.750000 0.750000 Si0+
0.750000 0.250000 0.750000 Si0+
0.750000 0.750000 0.250000 Si0+
0.000000 0.500000 0.500000 Si0+
0.500000 0.000000 0.500000 Si0+
0.500000 0.500000 1.000000 Si0+
```
but when use `read_structure` read structure file, get_reduced_structure will work:
``` python
from pymatgen.io.smart import read_structure
fn = "Si-51688.cif"
si = read_structure(fn)
p = Poscar(si.get_reduced_structure())
print(p)
```
output is:
```
Si2
1.0
2.715265 2.715265 0.000000
2.715265 0.000000 -2.715265
0.000000 2.715265 -2.715265
Si
2
direct
0.750000 0.750000 0.750000 Si0+
0.000000 0.000000 0.000000 Si0+
```
|
{
"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/330/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/330/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/331
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/331/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/331/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/331/events
|
https://github.com/materialsproject/pymatgen/issues/331
| 148,066,688
|
MDU6SXNzdWUxNDgwNjY2ODg=
| 331
|
UnicodeEncodeError in IStructure.from_file
|
{
"login": "hlyang1992",
"id": 2081913,
"node_id": "MDQ6VXNlcjIwODE5MTM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2081913?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hlyang1992",
"html_url": "https://github.com/hlyang1992",
"followers_url": "https://api.github.com/users/hlyang1992/followers",
"following_url": "https://api.github.com/users/hlyang1992/following{/other_user}",
"gists_url": "https://api.github.com/users/hlyang1992/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hlyang1992/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hlyang1992/subscriptions",
"organizations_url": "https://api.github.com/users/hlyang1992/orgs",
"repos_url": "https://api.github.com/users/hlyang1992/repos",
"events_url": "https://api.github.com/users/hlyang1992/events{/privacy}",
"received_events_url": "https://api.github.com/users/hlyang1992/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 looks like an error related to environmental variable settings. Try to\nset\n\nexport LC_ALL=en_US.UTF-8\n\n export LANG=en_US.UTF-8\n\nLet's know whether it works. Thanks\n\nOn Wednesday, April 13, 2016, lzuyanghl notifications@github.com wrote:\n\n> when use IStructure.from_file read some cif file such as test\n> https://drive.google.com/open?id=0B7DapXLbWsRKcWdyVDk3REJPTEU will\n> raise UnicodeEncodeError.\n> \n> ```\n> si = mg.IStructure.from_file(filename)\n> ```\n> \n> File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py\", line 1531, in from_file\n> primitive=primitive, sort=sort)\n> File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py\", line 1477, in from_str\n> parser = CifParser.from_string(input_string)\n> File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/io/cif.py\", line 292, in from_string\n> stream = cStringIO(cif_string)\n> UnicodeEncodeError: 'ascii' codec can't encode character u'\\ufeff' in position 0: ordinal not in range(128)\n> \n> I find the error may be in monty.io.zopen, follow code can raise\n> UnicodeEncodeError.\n> \n> with zopen(\"test.cif\", \"r\") as f:\n> data = f.read()\n> stream = cStringIO(data)\n> \n> However, follow code works fine, no error.\n> \n> with open(\"test.cif\", 'r') as f1:\n> data = f1.read()\n> stream = cStringIO(data)\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/331\n",
"The file itself also has a binary symbol at the beginning. This is a bad file. \n"
] | 2016-04-13T13:48:19
| 2016-04-13T16:08:45
|
2016-04-13T16:08:45Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
when use IStructure.from_file read some cif file such as [test](https://drive.google.com/open?id=0B7DapXLbWsRKcWdyVDk3REJPTEU) will raise UnicodeEncodeError.
```
si = mg.IStructure.from_file(filename)
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py", line 1531, in from_file
primitive=primitive, sort=sort)
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/core/structure.py", line 1477, in from_str
parser = CifParser.from_string(input_string)
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/pymatgen/io/cif.py", line 292, in from_string
stream = cStringIO(cif_string)
UnicodeEncodeError: 'ascii' codec can't encode character u'\ufeff' in position 0: ordinal not in range(128)
```
I find the error may be in monty.io.zopen, follow code can raise `UnicodeEncodeError`.
```
with zopen("test.cif", "r") as f:
data = f.read()
stream = cStringIO(data)
```
However, follow code works fine, no error.
```
with open("test.cif", 'r') as f1:
data = f1.read()
stream = cStringIO(data)
```
|
{
"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/331/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/331/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/332
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/332/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/332/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/332/events
|
https://github.com/materialsproject/pymatgen/pull/332
| 148,191,851
|
MDExOlB1bGxSZXF1ZXN0NjYzOTY4MTY=
| 332
|
add a safe guard to monitor whether ion phase appear when requesting a Pourbaix Diagram
|
{
"login": "xhqu1981",
"id": 4646623,
"node_id": "MDQ6VXNlcjQ2NDY2MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/4646623?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xhqu1981",
"html_url": "https://github.com/xhqu1981",
"followers_url": "https://api.github.com/users/xhqu1981/followers",
"following_url": "https://api.github.com/users/xhqu1981/following{/other_user}",
"gists_url": "https://api.github.com/users/xhqu1981/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xhqu1981/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xhqu1981/subscriptions",
"organizations_url": "https://api.github.com/users/xhqu1981/orgs",
"repos_url": "https://api.github.com/users/xhqu1981/repos",
"events_url": "https://api.github.com/users/xhqu1981/events{/privacy}",
"received_events_url": "https://api.github.com/users/xhqu1981/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 |
[
"Lighting fast. I am just talking to Donny. ^_^. Thanks a lot.\n\nOn Wed, Apr 13, 2016 at 2:51 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Merged #332 https://github.com/materialsproject/pymatgen/pull/332.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/332#event-626484794\n"
] | 2016-04-13T21:44:05
| 2016-04-13T21:52:33
|
2016-04-13T21:51:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
add a safe guard to monitor whether ion phase appear when requesting a Pourbaix Diagram
|
{
"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/332/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/332/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/332",
"html_url": "https://github.com/materialsproject/pymatgen/pull/332",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/332.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/332.patch",
"merged_at": "2016-04-13T21:51:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/333
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/333/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/333/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/333/events
|
https://github.com/materialsproject/pymatgen/pull/333
| 148,378,761
|
MDExOlB1bGxSZXF1ZXN0NjY0OTMyOTg=
| 333
|
Fix important problem with get_primitive_standard affecting rhombohed…
|
{
"login": "hautierg",
"id": 910839,
"node_id": "MDQ6VXNlcjkxMDgzOQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/910839?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hautierg",
"html_url": "https://github.com/hautierg",
"followers_url": "https://api.github.com/users/hautierg/followers",
"following_url": "https://api.github.com/users/hautierg/following{/other_user}",
"gists_url": "https://api.github.com/users/hautierg/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hautierg/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hautierg/subscriptions",
"organizations_url": "https://api.github.com/users/hautierg/orgs",
"repos_url": "https://api.github.com/users/hautierg/repos",
"events_url": "https://api.github.com/users/hautierg/events{/privacy}",
"received_events_url": "https://api.github.com/users/hautierg/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.\n"
] | 2016-04-14T14:26:32
| 2016-04-14T21:11:33
|
2016-04-14T21:11:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Fix important problem with rhombohedral cells in get_primitive_standard
- Fix a unittest related to get_primitive_standard
- Add a new unites for get_primitive_standard (rhombohedral)
## TODO (if any)
*add more unittests
|
{
"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/333/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/333/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/333",
"html_url": "https://github.com/materialsproject/pymatgen/pull/333",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/333.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/333.patch",
"merged_at": "2016-04-14T21:11:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/334
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/334/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/334/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/334/events
|
https://github.com/materialsproject/pymatgen/issues/334
| 148,384,537
|
MDU6SXNzdWUxNDgzODQ1Mzc=
| 334
|
SPGlib segfault
|
{
"login": "sdacek",
"id": 2327718,
"node_id": "MDQ6VXNlcjIzMjc3MTg=",
"avatar_url": "https://avatars.githubusercontent.com/u/2327718?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sdacek",
"html_url": "https://github.com/sdacek",
"followers_url": "https://api.github.com/users/sdacek/followers",
"following_url": "https://api.github.com/users/sdacek/following{/other_user}",
"gists_url": "https://api.github.com/users/sdacek/gists{/gist_id}",
"starred_url": "https://api.github.com/users/sdacek/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/sdacek/subscriptions",
"organizations_url": "https://api.github.com/users/sdacek/orgs",
"repos_url": "https://api.github.com/users/sdacek/repos",
"events_url": "https://api.github.com/users/sdacek/events{/privacy}",
"received_events_url": "https://api.github.com/users/sdacek/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 posted to spglib. In future, you might want to directly post to spglib's Github Issues so that Togo can help take a look.\n",
"@wmdrichards @sdacek You might want to note the different answers with different tolerances at https://github.com/atztogo/spglib/issues/9#issuecomment-210404808.\n"
] | 2016-04-14T14:44:46
| 2016-04-17T15:22:48
|
2016-04-17T15:22:48Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
SPGlib 1.9.1 segaults on nosetests when compiled with GCC (4.8.4, 4.4.6)
SPGlib 1.7.4 also segfaults on nosetests when compiled with GCC ( 4.8.4 )
It could be that some spglib outputs (e.g. empty lists of rotations) that we use as new inputs aren't always valid
|
{
"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/334/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/334/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/335
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/335/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/335/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/335/events
|
https://github.com/materialsproject/pymatgen/issues/335
| 148,521,727
|
MDU6SXNzdWUxNDg1MjE3Mjc=
| 335
|
parse floats and units from Element attributes
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 now implemented. But there are some properties where parsing is more complicated. Use with care.\n",
"Thanks Shyue! \n\nIt still leaves out \"10^-8\" (and similar exponentials) in the electrical_resistivity, which may be important. Let me see if I can deal with this.\n"
] | 2016-04-15T00:39:13
| 2016-04-15T20:47:33
|
2016-04-15T02:57:21Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: 3.4
- Python version: 2.7.10
- OS version: Mac OS X
## Requested feature
- Change the return type for some attribute properties of Element from strings (currently) to perhaps a float/unit or a FloatWithUnit object
## Example code
``` python
from pymatgen import Element, FloatWithUnit
el = Element('Al')
print el.thermal_conductivity
print FloatWithUnit.from_string(el.thermal_conductivity)
print FloatWithUnit.from_string(el.thermal_conductivity).real
print FloatWithUnit.from_string(el.thermal_conductivity).unit
print el.electrical_resistivity
print FloatWithUnit.from_string(el.electrical_resistivity)
print FloatWithUnit.from_string(el.electrical_resistivity).real
print FloatWithUnit.from_string(el.electrical_resistivity).unit
```
gives the following unit,
235 W m<sup>-1</sup> K<sup>-1</sup>
235.0 sup^4 K W m
235.0
sup^4 K W m
2.7 10<sup>-8</sup> Ω m
2.7 sup^2 Omega m
2.7
sup^2 Omega m
## Suggested solution
*Replacing all "<sup>"with "^" and removing all "</sup>" gives the following output,
235 W m^-1 K^-1
235.0 W K^-1 m^-1
235.0
W K^-1 m^-1
2.7 10^-8 Ω m
2.7 Omega m
2.7
Omega m
The electrical resistivity is still missing 10^-8, so perhaps further suggested parsing?
|
{
"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/335/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/335/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/336
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/336/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/336/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/336/events
|
https://github.com/materialsproject/pymatgen/pull/336
| 148,764,844
|
MDExOlB1bGxSZXF1ZXN0NjY3MDIxNDE=
| 336
|
handle bracketed data in attribute data for Elememt
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[] | 2016-04-15T20:44:02
| 2016-04-15T20:44:43
|
2016-04-15T20:44:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Some attribute data contains brackets, which raises an error when converting to a FloatWithUnit.
- Fix: remove bracketed data
## Example:
Element('P').melting_point = "(white P) 317.3 K"
|
{
"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/336/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/336/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/336",
"html_url": "https://github.com/materialsproject/pymatgen/pull/336",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/336.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/336.patch",
"merged_at": "2016-04-15T20:44:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/337
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/337/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/337/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/337/events
|
https://github.com/materialsproject/pymatgen/pull/337
| 148,796,860
|
MDExOlB1bGxSZXF1ZXN0NjY3MjA0ODY=
| 337
|
handle base 10 powers that exist in two Element attributes
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[] | 2016-04-16T00:06:25
| 2016-04-16T02:03:50
|
2016-04-16T02:03:50Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Base 10 powers occur in "electrical_resistivity" and "coefficient_of_linear_thermal_expansion" which were not handled, thus returning a string instead of a FloatWithUnit object
- Fix: extract the factor and add it to the float, define the unit for the above two attributes (since such factors only seem to be present there), and return a FloatWithUnit object for these attributes.
Example, the code,
from pymatgen import Element, FloatWithUnit
el = Element('Al')
print el.melting_point
print float(el.melting_point)
print el.melting_point.unit
print el.thermal_conductivity
print float(el.thermal_conductivity)
print el.thermal_conductivity.unit
print el.coefficient_of_linear_thermal_expansion
print float(el.coefficient_of_linear_thermal_expansion)
print el.coefficient_of_linear_thermal_expansion.unit
print el.electrical_resistivity
print float(el.electrical_resistivity)
print el.electrical_resistivity.unit
produces the following output,
933.47 K
933.47
K
235.0 W K^-1 m^-1
235.0
W K^-1 m^-1
2.31e-05 K^-1
2.31e-05
K^-1
2.7e-08 m ohm
2.7e-08
m ohm
|
{
"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/337/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/337/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/337",
"html_url": "https://github.com/materialsproject/pymatgen/pull/337",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/337.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/337.patch",
"merged_at": "2016-04-16T02:03:50Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/338
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/338/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/338/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/338/events
|
https://github.com/materialsproject/pymatgen/pull/338
| 148,820,518
|
MDExOlB1bGxSZXF1ZXN0NjY3Mjg5MDc=
| 338
|
correct unit test of periodic_table.py
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[] | 2016-04-16T05:47:19
| 2016-04-16T13:36:36
|
2016-04-16T13:36:36Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Correct unit test of Al's electrical resistivity which should be 2.7e^-8 ohm m, and not 2.7 ohm m.
|
{
"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/338/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/338/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/338",
"html_url": "https://github.com/materialsproject/pymatgen/pull/338",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/338.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/338.patch",
"merged_at": "2016-04-16T13:36:36Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/339
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/339/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/339/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/339/events
|
https://github.com/materialsproject/pymatgen/pull/339
| 148,928,765
|
MDExOlB1bGxSZXF1ZXN0NjY3NjE2NjY=
| 339
|
add LAMMPS io
|
{
"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 |
[] | 2016-04-17T08:16:36
| 2016-04-17T15:14:06
|
2016-04-17T15:14:06Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Basic LAMMPS io
- read/write lammps data files: basic(atom_style=atomic/charge) and from force field and molecular topologies(atom_style=molecular/full)
- write the main input file with the control parameters from dict
- parse the outpufiles(the log file and the dump file) for the thermodynamic data and the trajectory. Provide interface to the pymatgen diffusion_analyzer so that the basic transport properties like diffusivity, conductivuty etc can be evaluated.
- unittests
## TODO (if any)
Complete the forcefiled and topology classes by adding interfaces to the AMBER and CHARMM style force fields and topologies.
|
{
"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/339/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/339/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/339",
"html_url": "https://github.com/materialsproject/pymatgen/pull/339",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/339.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/339.patch",
"merged_at": "2016-04-17T15:14:06Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/340
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/340/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/340/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/340/events
|
https://github.com/materialsproject/pymatgen/issues/340
| 148,964,388
|
MDU6SXNzdWUxNDg5NjQzODg=
| 340
|
Test files for chemenv and lammps need to be in root test_files folder.
|
{
"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 |
[
"@shyuep done\n"
] | 2016-04-17T15:40:26
| 2017-06-03T14:39:42
|
2017-06-03T14:39:42Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
## Summary
- All test data files should be in the root test_files in subfolders. E.g., test_files/lammps or test_files/chemenv. This makes it easier to exclude such files from the distributed version of pymatgen.
@matk86 Pls do it for lammps.
@hautierg Pls ask David to do it for Chemenv. FOr some reason, he is not searchable within my Github account.
Pls do this quick. I can't actually release a new version of pymatgen otherwise.
|
{
"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/340/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/340/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/341
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/341/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/341/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/341/events
|
https://github.com/materialsproject/pymatgen/pull/341
| 148,969,105
|
MDExOlB1bGxSZXF1ZXN0NjY3NzM1ODY=
| 341
|
move the lammps test_files to the the root test_files/lammps folder
|
{
"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 |
[
"Many thanks.\n"
] | 2016-04-17T16:48:16
| 2016-04-17T20:08:46
|
2016-04-17T20:08:40Z
|
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/341/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/341/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/341",
"html_url": "https://github.com/materialsproject/pymatgen/pull/341",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/341.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/341.patch",
"merged_at": "2016-04-17T20:08:40Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/342
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/342/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/342/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/342/events
|
https://github.com/materialsproject/pymatgen/pull/342
| 149,001,943
|
MDExOlB1bGxSZXF1ZXN0NjY3ODM1MjA=
| 342
|
py3k fixes
|
{
"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 |
[] | 2016-04-17T22:18:52
| 2016-04-17T22:19:19
|
2016-04-17T22:19:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
tested with python.3.4.3 and 2.7 on ubuntu 14.04
|
{
"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/342/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/342/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/342",
"html_url": "https://github.com/materialsproject/pymatgen/pull/342",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/342.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/342.patch",
"merged_at": "2016-04-17T22:19:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/343
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/343/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/343/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/343/events
|
https://github.com/materialsproject/pymatgen/pull/343
| 149,034,234
|
MDExOlB1bGxSZXF1ZXN0NjY3OTYwOTA=
| 343
|
add parsing of NMR Chemical Shifts and EFG from OUTCAR
|
{
"login": "xhqu1981",
"id": 4646623,
"node_id": "MDQ6VXNlcjQ2NDY2MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/4646623?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xhqu1981",
"html_url": "https://github.com/xhqu1981",
"followers_url": "https://api.github.com/users/xhqu1981/followers",
"following_url": "https://api.github.com/users/xhqu1981/following{/other_user}",
"gists_url": "https://api.github.com/users/xhqu1981/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xhqu1981/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xhqu1981/subscriptions",
"organizations_url": "https://api.github.com/users/xhqu1981/orgs",
"repos_url": "https://api.github.com/users/xhqu1981/repos",
"events_url": "https://api.github.com/users/xhqu1981/events{/privacy}",
"received_events_url": "https://api.github.com/users/xhqu1981/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. But the chemical shift notation class doesn't seem to be right in outputs. I think you need to create a proper NMR analysis class. Parsing can still be in Outcar, but the actual analysis should be in a separate module.\n",
"@shyuep OK. I will refactor it. Where do you prefer to store the nmr conversion code? Please be noted that this class is not a real analyzing module, instead, it just provides the conversion between different notations. It is pretty sad that the notation used by VASP is different than the most popular notation in the literatures.\n",
"Well, just drop it into a pymatgen.analysis.nmr class. Though today you do not have analysis code yet, I am pretty sure you are going to write some in future.\n",
"@shyuep Done. Please check. Thanks for the good suggestions.\n"
] | 2016-04-18T03:57:26
| 2016-04-18T13:35:09
|
2016-04-18T13:35:08Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
NMR chemicals shift and electric field gradient tensor are only available in OUTCAR. I have add the ability to parse them from 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/343/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/343/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/343",
"html_url": "https://github.com/materialsproject/pymatgen/pull/343",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/343.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/343.patch",
"merged_at": "2016-04-18T13:35:08Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/344
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/344/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/344/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/344/events
|
https://github.com/materialsproject/pymatgen/issues/344
| 149,906,266
|
MDU6SXNzdWUxNDk5MDYyNjY=
| 344
|
Vasprun.eigenvalue_band_properties() for metals
|
{
"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 |
[
"Before I do this, I would like to understand why there is a difference between the bandstructure version vs the get_eigenvalue properties version. I need to be convinced that the bandstructure is the correct one.\n",
"@hautierg - do you know the difference and the reason for the two? The biggest difference I noticed is that the band structure one explicitly tests for is_metal() and overrides the data in that case.\n",
"I will not make any judgement on the “best” method… but just clarify what I believe they exactly do:\r\n\r\n-the band structure looks at fermi level and see if the fermi level crosses any bands if yes, it’s a metal and bg=0. we do not use any occupation values. Band structure objects do not have occupations.\r\n\r\n-in the case of the eigenvalue one here we use the occupations computed by vasp (so it will technically depend on the type of smearing used etc…). The tolerance on occupation is 10^-8.\r\n\r\nPlease note that the band structure one has been designed assuming you have a decent k-point sampling. I am not hundred percent sure how it will do if you a loose k-point grid...\r\n\r\nDoes it make sense?",
"Seems like this issue has been defunct for 7 years. Closing...."
] | 2016-04-20T22:38:37
| 2023-08-08T21:16:33
|
2023-08-08T21:16:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: Latest master
- Python version: 2.7
- OS version: Mac
## Summary
- The algorithm used to get CBM, VBM, and band gap is similar but different in Vasprun.eigenvalue_band_properties() and Bandstructure.get_band_gap()
- The former can sometimes give non-zero gaps for metals, e.g. 0.0003 eV for Al
- The latter first checks for metallic behavior and overrides the gap to be exactly 0 in these instances. So Al gives exactly zero gap. Otherwise the algorithm looks very similar.
- The algorithm itself contains a fair amount of duplication between these methods. It is not clear that both are needed and IMO the Bandstructure version is superior.
## Example code
(Can provide upon request)
## Suggested solution (if any)
- The Vasprun.eigenvalue_band_properties() is reimplemented to simply get the band structure object, and then call Bandstructure.get_band_gap() and return values from there. Then the code duplication is removed and the values will be consistent. There might be a small performance hit.
## Files (if any)
(Can provide upon request)
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/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/344/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/344/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/345
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/345/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/345/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/345/events
|
https://github.com/materialsproject/pymatgen/issues/345
| 149,911,272
|
MDU6SXNzdWUxNDk5MTEyNzI=
| 345
|
Outcar.get_dipole_energy method or variable
|
{
"login": "rtrottie",
"id": 8291373,
"node_id": "MDQ6VXNlcjgyOTEzNzM=",
"avatar_url": "https://avatars.githubusercontent.com/u/8291373?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rtrottie",
"html_url": "https://github.com/rtrottie",
"followers_url": "https://api.github.com/users/rtrottie/followers",
"following_url": "https://api.github.com/users/rtrottie/following{/other_user}",
"gists_url": "https://api.github.com/users/rtrottie/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rtrottie/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rtrottie/subscriptions",
"organizations_url": "https://api.github.com/users/rtrottie/orgs",
"repos_url": "https://api.github.com/users/rtrottie/repos",
"events_url": "https://api.github.com/users/rtrottie/events{/privacy}",
"received_events_url": "https://api.github.com/users/rtrottie/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 already possible. Vasprun contains almost all parameters.\n\n``` python\nIn [1]: from pymatgen.io.vasp import Vasprun\nIn [2]: v= Vasprun(\"vasprun.xml\")\nIn [3]: v.parameters[\"IDIPOL\"]\nOut[3]: 0\n```\n",
"Sorry, if you mean you want the actual corrections from the calculations, please provide an example OUTCAR with the corrections.\n",
"Yes, I meant the numerical corrections, glad I wasn't too ambiguous. I've attached the OUTCAR as you requested. \n\nFor your reference:\n\nLine 4650 : Energy used as Vasprun.final_energy\nLine 5688 : Dipole correction\nLine 5958 : Energy with dipole correction included\n\n[OUTCAR.txt](https://github.com/materialsproject/pymatgen/files/230408/OUTCAR.txt)\n",
"This is done. However, to read the dipole corrections, you need to specifically call outcar.read_corrections() and then the data is stored in the outcar.data[\"dipol_quadrupol_corrections\"].\n"
] | 2016-04-20T23:11:10
| 2016-04-25T16:47:34
|
2016-04-25T16:39:59Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
There should be some method of obtaining the dipole correction from IDIPOL = 1/2/3 from the VASP outputs.
|
{
"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/345/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/345/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/346
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/346/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/346/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/346/events
|
https://github.com/materialsproject/pymatgen/pull/346
| 150,307,860
|
MDExOlB1bGxSZXF1ZXN0Njc0NzcyODk=
| 346
|
enable setting 3d MAGMOM in incar for spin-orbit coupling calculations
|
{
"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 |
[] | 2016-04-22T08:40:39
| 2016-04-22T12:43:51
|
2016-04-22T12:43:51Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Allow [x,y,z] values for each ion in MAGMOM when LSORBIT or LNONCOLLINEAR is set.
This makes the "MAGMOM" value a list of lists for spin-orbit coupling calculations. Please see the 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/346/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/346/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/346",
"html_url": "https://github.com/materialsproject/pymatgen/pull/346",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/346.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/346.patch",
"merged_at": "2016-04-22T12:43:51Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/347
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/347/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/347/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/347/events
|
https://github.com/materialsproject/pymatgen/pull/347
| 150,460,096
|
MDExOlB1bGxSZXF1ZXN0Njc1NjU2NTU=
| 347
|
bug fix in incar magmom for soc
|
{
"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 |
[] | 2016-04-22T20:07:08
| 2016-04-22T21:13:53
|
2016-04-22T21:13:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
made a mistake in the conditional statement
|
{
"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/347/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/347/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/347",
"html_url": "https://github.com/materialsproject/pymatgen/pull/347",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/347.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/347.patch",
"merged_at": "2016-04-22T21:13:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/348
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/348/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/348/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/348/events
|
https://github.com/materialsproject/pymatgen/pull/348
| 150,488,101
|
MDExOlB1bGxSZXF1ZXN0Njc1ODI4Mzc=
| 348
|
New tensor base
|
{
"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 |
[] | 2016-04-22T22:42:40
| 2016-04-23T21:26:32
|
2016-04-23T21:26:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR adds a new base class for the tensor-based properties, TensorBase, and provides more consolidated support for tensor transformations. Some additional features added to ElasticTensor and DeformedStructureSet
- TensorBase base class for tensors that implements tensor transformations, symmetrizations, and fits to structures
- DeformedStructure set now allows for symmetry reduction of deformations
- Fixed bug in the index construction of the transformation method in SymmOp.transform_tensor
## TODO (if any)
- Refactoring piezo with new base class
- IEEE conversion
|
{
"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/348/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/348/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/348",
"html_url": "https://github.com/materialsproject/pymatgen/pull/348",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/348.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/348.patch",
"merged_at": "2016-04-23T21:26:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/349
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/349/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/349/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/349/events
|
https://github.com/materialsproject/pymatgen/pull/349
| 150,710,807
|
MDExOlB1bGxSZXF1ZXN0Njc2NTMxNDk=
| 349
|
Add get_pourbaix_plot_colorfill_by_domain_name()
|
{
"login": "xhqu1981",
"id": 4646623,
"node_id": "MDQ6VXNlcjQ2NDY2MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/4646623?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xhqu1981",
"html_url": "https://github.com/xhqu1981",
"followers_url": "https://api.github.com/users/xhqu1981/followers",
"following_url": "https://api.github.com/users/xhqu1981/following{/other_user}",
"gists_url": "https://api.github.com/users/xhqu1981/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xhqu1981/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xhqu1981/subscriptions",
"organizations_url": "https://api.github.com/users/xhqu1981/orgs",
"repos_url": "https://api.github.com/users/xhqu1981/repos",
"events_url": "https://api.github.com/users/xhqu1981/events{/privacy}",
"received_events_url": "https://api.github.com/users/xhqu1981/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 |
[
"Xiaohui - don't pull this to the web master until we have submitted the\npaper and gotten the reviews back, ok?\n\nBest\n\nKristin\n\nOn Sun, Apr 24, 2016 at 4:01 PM, Xiaohui Qu notifications@github.com\nwrote:\n\n> Let the caller be able to specific the color of domain via a dict. Also\n> including the following abilities:\n> \n> 1) more accurate calculation of the text label position, which results in\n> a center closer to human filling. This is implemented by considering the\n> surrounding lines.\n> \n> 2) Avoid overlap the text label with H2O stability lines.\n> \n> 3) Add one more cluster phase which by default uses and in between color\n> of solid and aqueous ions.\n> \n> 4) let the callers able to select which domain text label to be highlight\n> by \"bold\" style.\n> \n> 5) Misc fine tuning of the label text font and line styles.\n> \n> Example plot:\n> \n> [image: no mol pic]\n> \n> ## https://cloud.githubusercontent.com/assets/4646623/14771113/b9ada47c-0a35-11e6-974e-1ef862de83d9.jpg\n> \n> You can view, comment on, or merge this pull request online at:\n> \n> https://github.com/materialsproject/pymatgen/pull/349\n> Commit Summary\n> - fix the sign bug of kappa, the correct order should be sigma_22 -\n> sigma_iso\n> - add get_pourbaix_plot_colorfill_by_domain_name() function\n> - make all the lines antialiased\n> - add parameter to choose line width, use alpha channel to make the\n> domain edge looks smoother\n> - let the user to control whether to plot the benchmark line (H line,\n> O line and center lines)\n> - remove alpha channel in domains\n> - add a new version of get_center() which considers the distribution\n> of vertices\n> - use Times New Roman\n> - also use Times New Roman for X and Y ticks\n> - add one significant floating point number to XY ticks lables\n> - make the ticks outside\n> - use Bold text for selected species\n> - use color scheme of MP\n> - make the default line width of boundaries to be 0.5\n> - slightly move the text if overlapping with H2O stability line\n> - default to plot H2O stability line, use smaller dashes\n> - reduce the fontsize of the axis labels\n> - add docs\n> \n> File Changes\n> - _M_ pymatgen/analysis/nmr.py\n> https://github.com/materialsproject/pymatgen/pull/349/files#diff-0\n> (10)\n> - _M_ pymatgen/analysis/pourbaix/plotter.py\n> https://github.com/materialsproject/pymatgen/pull/349/files#diff-1\n> (220)\n> - _M_ pymatgen/analysis/tests/test_nmr.py\n> https://github.com/materialsproject/pymatgen/pull/349/files#diff-2\n> (22)\n> - _M_ pymatgen/util/plotting_utils.py\n> https://github.com/materialsproject/pymatgen/pull/349/files#diff-3\n> (4)\n> \n> Patch Links:\n> - https://github.com/materialsproject/pymatgen/pull/349.patch\n> - https://github.com/materialsproject/pymatgen/pull/349.diff\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/349\n\n## \n\n## \n\nKristin A Persson\n\nAssistant Professor in Materials Science and Engineering\nUniversity of California at Berkeley\n\nStaff Scientist\nLawrence Berkeley National Laboratory\nWeb: http://eetd.lbl.gov/staff/kristin-persson\n",
"Erm, I already merged it two hours ago. Is there actually something sensitive in there? It seems just a prettifying of the Pourbaix diagram.\n",
"As long as the cluster energies are not presented...I am currently writing\nthe paper on aqueous clusters.\n\nPrettifying is ok :-)\n\nOn Sun, Apr 24, 2016 at 7:08 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> Erm, I already merged it two hours ago. Is there actually something\n> sensitive in there? It seems just a prettifying of the Pourbaix diagram.\n> \n> —\n> You are receiving this because you commented.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/pull/349#issuecomment-214093464\n\n## \n\n## \n\nKristin A Persson\n\nAssistant Professor in Materials Science and Engineering\nUniversity of California at Berkeley\n\nStaff Scientist\nLawrence Berkeley National Laboratory\nWeb: http://eetd.lbl.gov/staff/kristin-persson\n",
"I don't know if the clusters are in there. @xhqu1981 would have to comment. \n"
] | 2016-04-24T23:01:57
| 2016-04-25T02:32:02
|
2016-04-25T00:07:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Let the caller be able to specific the color of domain via a dict. Also including the following abilities:
1) more accurate calculation of the text label position, which results in a center closer to human filling. This is implemented by considering the surrounding lines.
2) Avoid overlap the text label with H2O stability lines.
3) Add one more cluster phase which by default uses and in between color of solid and aqueous ions.
4) let the callers able to select which domain text label to be highlight by "bold" style.
5) Misc fine tuning of the label text font and line styles.
|
{
"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/349/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/349/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/349",
"html_url": "https://github.com/materialsproject/pymatgen/pull/349",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/349.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/349.patch",
"merged_at": "2016-04-25T00:07:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/350
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/350/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/350/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/350/events
|
https://github.com/materialsproject/pymatgen/issues/350
| 150,922,226
|
MDU6SXNzdWUxNTA5MjIyMjY=
| 350
|
Elastic and NMR OUTCAR needs to be refactored
|
{
"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 |
[
"Will do. Thanks.\n",
"@montoyjh @xhqu1981 Can I have a status update pls.\n",
"I will push the solution tonight or tomorrow.\n\nOn Sat, May 7, 2016 at 7:29 AM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> @montoyjh https://github.com/montoyjh @xhqu1981\n> https://github.com/xhqu1981 Can I have a status update pls.\n> \n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/350#issuecomment-217641196\n",
"Done. @shyuep I have to add the read_table_pattern() method. This is because the NMR data are tables and context related. Very hard to defined by a single line pattern. E.g. the chemical shift table have two sections one is without core contribution, another is with core contributions. Only the second one is desired. The rows from both section are matching exactly the same line pattern. As such, I have to add one more function read_table_pattern(). Both chemical shift and EFG parsing are built on it. Concept of of named and unamed regex capturing groups is involved. It increases some complexity, however, it helps users to get the desired field only.\n",
"The read_table_pattern is a lot more flexible than my initial approach to the elastic/piezo, so I'm going to redo my changes using that method.\n",
"@montoyjh Thanks.\n",
"Thanks,\n"
] | 2016-04-25T16:45:33
| 2016-05-13T16:27:37
|
2016-05-13T16:27:37Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
## Summary
- Currently, the Outcar **init** is a big mess with elastic property and NMR reading all bundled in. Note that OUTCAR parsing is by nature very calculation dependent. We cannot cater to ALL kinds of run in the **init** method. Hence, other than the most basic parameters like energies and magmoms, all other special parsing should be done via the read__property_ methods, with the use of read_pattern as a general approach.
- @montoyjh Pls refactor the elastic and piezo parsing.
- @xhqu1981 Pls refactor the NMR parsing.
Thanks.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/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/350/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/350/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/351
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/351/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/351/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/351/events
|
https://github.com/materialsproject/pymatgen/pull/351
| 151,549,465
|
MDExOlB1bGxSZXF1ZXN0NjgxNjM5Njk=
| 351
|
minor bug fix in get_vasprun_outcar
|
{
"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 |
[] | 2016-04-28T04:56:11
| 2016-04-28T13:02:36
|
2016-04-28T13:02:36Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
join the directory name to the filename.
|
{
"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/351/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/351/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/351",
"html_url": "https://github.com/materialsproject/pymatgen/pull/351",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/351.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/351.patch",
"merged_at": "2016-04-28T13:02:36Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/352
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/352/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/352/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/352/events
|
https://github.com/materialsproject/pymatgen/issues/352
| 151,589,604
|
MDU6SXNzdWUxNTE1ODk2MDQ=
| 352
|
can't run unit test
|
{
"login": "hlyang1992",
"id": 2081913,
"node_id": "MDQ6VXNlcjIwODE5MTM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2081913?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hlyang1992",
"html_url": "https://github.com/hlyang1992",
"followers_url": "https://api.github.com/users/hlyang1992/followers",
"following_url": "https://api.github.com/users/hlyang1992/following{/other_user}",
"gists_url": "https://api.github.com/users/hlyang1992/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hlyang1992/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hlyang1992/subscriptions",
"organizations_url": "https://api.github.com/users/hlyang1992/orgs",
"repos_url": "https://api.github.com/users/hlyang1992/repos",
"events_url": "https://api.github.com/users/hlyang1992/events{/privacy}",
"received_events_url": "https://api.github.com/users/hlyang1992/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 |
[
"Nosetests are run in the root directory whre setup.py is. Not the pymatgen directory.\n",
"Thank you, but I first run Nosetests in the directory where setup.py, the error is:\n\n```\nE\n======================================================================\nERROR: Failure: ImportError (No module named coord_utils_cython)\n----------------------------------------------------------------------\nTraceback (most recent call last):\n File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/loader.py\", line 418, in loadTestsFromName\n addr.filename, addr.module)\n File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/importer.py\", line 47, in importFromPath\n return self.importFromDir(dir_path, fqname)\n File \"/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/importer.py\", line 94, in importFromDir\n mod = load_module(part_fqname, fh, filename, desc)\n File \"/home/vagrant/space/pymatgen/pymatgen/__init__.py\", line 14, in <module>\n from .core import *\n File \"/home/vagrant/space/pymatgen/pymatgen/core/__init__.py\", line 17, in <module>\n from .structure import Structure, IStructure, Molecule, IMolecule\n File \"/home/vagrant/space/pymatgen/pymatgen/core/structure.py\", line 40, in <module>\n from pymatgen.core.sites import Site, PeriodicSite\n File \"/home/vagrant/space/pymatgen/pymatgen/core/sites.py\", line 26, in <module>\n from pymatgen.util.coord_utils import pbc_diff\n File \"/home/vagrant/space/pymatgen/pymatgen/util/coord_utils.py\", line 25, in <module>\n import pymatgen.util.coord_utils_cython as cuc\nImportError: No module named coord_utils_cython\n\n----------------------------------------------------------------------\nRan 1 test in 0.374s\n\nFAILED (errors=1)\n```\n",
"You need to run python setup.py develop or install before running the nosetests.\n"
] | 2016-04-28T09:23:18
| 2016-04-28T18:46:21
|
2016-04-28T12:56:15Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: 3.5.0
- Python version: 2.7
- OS version: ubuntu 14.04
## Problem
when run `nosetests` in the pymatgen root directory, the output is:
```
Traceback (most recent call last):
File "/home/vagrant/opt/anaconda2/bin/nosetests", line 4, in <module>
from nose import run_exit
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/__init__.py", line 1, in <module>
from nose.core import collector, main, run, run_exit, runmodule
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/core.py", line 11, in <module>
from nose.config import Config, all_config_files
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/config.py", line 9, in <module>
from nose.plugins.manager import NoPlugins
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/plugins/__init__.py", line 185, in <module>
from nose.plugins.manager import *
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/nose/plugins/manager.py", line 418, in <module>
import pkg_resources
File "/home/vagrant/opt/anaconda2/lib/python2.7/site-packages/setuptools-20.6.7-py2.7.egg/pkg_resources/__init__.py", line 25, in <module>
File "/home/vagrant/opt/anaconda2/lib/python2.7/zipfile.py", line 501, in <module>
class ZipExtFile(io.BufferedIOBase):
AttributeError: 'module' object has no attribute 'BufferedIOBase'
```
|
{
"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/352/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/352/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/353
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/353/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/353/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/353/events
|
https://github.com/materialsproject/pymatgen/issues/353
| 151,760,751
|
MDU6SXNzdWUxNTE3NjA3NTE=
| 353
|
Chemenv should read MAPI_KEY
|
{
"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 |
[] | 2016-04-28T22:51:05
| 2017-06-03T14:38:35
|
2017-06-03T14:38:35Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
## Summary
- The Chemenv `get_environment` script can read structures from MP if the API key is supplied via a configuration file
- I am not completely sure how to set this configuration file. But it seems to me that if I have the `MAPI_KEY` environment variable set, that ChemEnv should detect this and set my Materials API key accordingly (unless overridden by the config file or something). Since the `MAPI_KEY` environment variable is a standard part of pymatgen's MP interaction, this would help make sure that every package does not require its own way of giving the MP API key.
## Example code
Just set your MAPI_KEY environment variable, run `get_environment.py` and notice that if you haven't configured things that the MAPI_KEY is not detected.
## Suggested solution (if any)
The ChemEnv config should check for os.environ["MAPI_KEY"] and use that as the Materials API key if not given otherwise
|
{
"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/353/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/353/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/354
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/354/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/354/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/354/events
|
https://github.com/materialsproject/pymatgen/pull/354
| 151,795,058
|
MDExOlB1bGxSZXF1ZXN0NjgzMjU4OTE=
| 354
|
parse force constants from vasprun
|
{
"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 |
[] | 2016-04-29T05:21:02
| 2016-04-29T13:10:53
|
2016-04-29T13:10:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Parse vasprun.xml file for force constants in a phonon DFPT run.
- The data, `vasprun.force_constants` is a 4D numpy array of shape (natoms, natoms, 3, 3).
- `vasprun.force_constants` can be subsequently used with the [phonopy](http://atztogo.github.io/phonopy/phonopy-module.html) to compute the phonon bandstructure and other thermal properties.
- Also parse the normal mode eigenvalues and eigenvectors.
|
{
"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/354/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/354/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/354",
"html_url": "https://github.com/materialsproject/pymatgen/pull/354",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/354.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/354.patch",
"merged_at": "2016-04-29T13:10:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/355
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/355/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/355/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/355/events
|
https://github.com/materialsproject/pymatgen/pull/355
| 151,861,634
|
MDExOlB1bGxSZXF1ZXN0NjgzNjg2MDM=
| 355
|
Bztricci
|
{
"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 |
[
"The tests are failing because of the ASE import. See https://circleci.com/gh/materialsproject/pymatgen/4405 . Can you pls make sure you do not introduce new dependencies unless absolutely necessary, especially dependencies that cannot be installed easily via pip? read_cube can be easily written without using ASE. \n"
] | 2016-04-29T13:08:15
| 2016-04-29T17:54:33
|
2016-04-29T13:11:36Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- different convergence method in Runner, only based on searching the first couple of lpfac and energy_grid parameters that gives a fermi level for each doping level.
- DOS mode added but it needs a custom BZT version. An error is raised in case that std version is used. It works correctly with partial eigenvalues and for spin polarized cases (get_complete_dos() in Analyzer)
- BANDS, FERMI modes work properly with std v. of BoltzTrap
- BANDS mode gives a complete BS on sym line (get_symm_bands() in Analyzer). It's also possible to specify any k-point line to have interpolated bands along them.
- accuracy check on sym-line-bands for materials with gap (check_acc_bzt_bands() in Analyzer)
- energy_span_around_fermi auto selected for DOS and BANDS mode
- fermi surface data read from fort.30 file (std version of Boltztrap) or from boltztrap_BZ.cube (custom version of Boltztrap) and stored as a property of Analyzer.
- experimental plot_fermi_surface() in BoltztrapPlotter. skimage package required (ImportError raised in case it's not installed)
- small fix in the procedure that create the boltztrap folder
- test_files folder reorganized to separate each boltztrap mode. New tests added for BANDS, FERMI, DOS modes.
## TODO
- x_trans script of std Boltztrap overwrite .def file written by boltztrap.py
Hence, _make_def_file() and _make_proj_files() functions don't works properly
- extend the accuracy band check to metals
- plot_fermi_surface works well only with loose points grid. A better implementation could be done using mayavi (although it's a huge package)
|
{
"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/355/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/355/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/355",
"html_url": "https://github.com/materialsproject/pymatgen/pull/355",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/355.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/355.patch",
"merged_at": "2016-04-29T13:11:36Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/356
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/356/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/356/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/356/events
|
https://github.com/materialsproject/pymatgen/pull/356
| 152,011,072
|
MDExOlB1bGxSZXF1ZXN0Njg0NTg4NzI=
| 356
|
Structure analysis methods for liquid and amorphous structures
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/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 |
[
"RDF is already implemented in pymatgen-diffusion package. Does the Voronoi analysis overlap with the chemenv that David recently added to pymatgen?\n",
"Re: RDF, do you mean the Van Hove analysis? I agree that Van-Hove reduces to static RDF for t = 0. But given the simplicity of RDFs, I feel like accessing them through a “Van Hove” type dynamic analysis class may be a bit complicated (e.g. initialize a VanHove instance for each MD frame and specie, get G’s for delta_t=0, and then average all G’s at the end). Also this route may not be necessarily obvious to all pymatgen users; and means extra work. In my opinion, considering RDF is a pretty common, preliminary structural analysis for any work involving amorphous or liquid structures, allowing access to them through pymatgen with a simpler route in a dedicated class can come in handy for many users. Up to you.\n\nRe: Voronoi: I checked chemenv. It is pretty comprehensive. But I don’t see any straightforward way of obtaining the same type of Voronoi analysis through that, so I would say overlap is not obvious. I think I named the class too broadly for its purpose; it's actually focused on a certain polyhedron tessellation from glass literature; obtained directly by post-processing qhull output. Maybe refactoring VoronoiAnalysis to a more specific name; e.g. VoronoiAnalysisForGlasses might be helpful in differentiating? \nThanks.\n",
"My postdoc will push the RDF to pymatgen-diffusion in a short while. I'd rather not have two pieces of code oding the same thing.\n\nAs for Voronoi, it's fine. I will merge after you remove the RDF.\n",
"Sounds great.\n",
"Ready to merge.\n",
"Thanks!\n"
] | 2016-04-30T05:24:47
| 2016-05-02T21:09:16
|
2016-05-02T21:09:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Structural analysis methods relevant for liquid and amorphous structures are added.
- Class for Voronoi Analysis: statistical distribution of polyhedra
- Class for Radial distribution function
- Helper function to get ensemble average coordination numbers
|
{
"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/356/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/356/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/356",
"html_url": "https://github.com/materialsproject/pymatgen/pull/356",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/356.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/356.patch",
"merged_at": "2016-05-02T21:09:16Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/357
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/357/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/357/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/357/events
|
https://github.com/materialsproject/pymatgen/pull/357
| 152,043,948
|
MDExOlB1bGxSZXF1ZXN0Njg0NzQ1MzE=
| 357
|
update Derived input sets.
|
{
"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 |
[] | 2016-04-30T18:02:31
| 2016-04-30T18:08:54
|
2016-04-30T18:08:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- make reciprocal_density the default option to set kpoints
- add more checks for structure standardizations.
- add small_gap multiply
## TODO
update prev incar with structure dependent lda+u params. magmom seems ok.
|
{
"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/357/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/357/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/357",
"html_url": "https://github.com/materialsproject/pymatgen/pull/357",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/357.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/357.patch",
"merged_at": "2016-04-30T18:08:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/358
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/358/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/358/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/358/events
|
https://github.com/materialsproject/pymatgen/pull/358
| 152,045,007
|
MDExOlB1bGxSZXF1ZXN0Njg0NzUxNTc=
| 358
|
remove the old stuff(marked to delete) from vasp.tests.test_sets.py
|
{
"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 |
[] | 2016-04-30T18:26:41
| 2016-04-30T20:53:43
|
2016-04-30T20:53:43Z
|
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/358/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/358/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/358",
"html_url": "https://github.com/materialsproject/pymatgen/pull/358",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/358.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/358.patch",
"merged_at": "2016-04-30T20:53:43Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/359
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/359/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/359/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/359/events
|
https://github.com/materialsproject/pymatgen/pull/359
| 152,187,330
|
MDExOlB1bGxSZXF1ZXN0Njg0OTA0MzI=
| 359
|
enable writing ldau params from site_properties
|
{
"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 |
[] | 2016-05-01T08:14:14
| 2016-05-01T13:22:56
|
2016-05-01T13:22:56Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- add ldau params to the structure site_properties in `vasp.sets.get_structure_from_prev_run`
- enable writing ldau params from site_properties in `vasp.sets.DictVaspInputSet.get_incar`
- unittests
|
{
"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/359/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/359/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/359",
"html_url": "https://github.com/materialsproject/pymatgen/pull/359",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/359.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/359.patch",
"merged_at": "2016-05-01T13:22:56Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/360
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/360/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/360/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/360/events
|
https://github.com/materialsproject/pymatgen/pull/360
| 152,621,695
|
MDExOlB1bGxSZXF1ZXN0Njg2MDUyMjE=
| 360
|
minor bug fix: missing import in vasp.sets.py
|
{
"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 |
[] | 2016-05-02T19:09:17
| 2016-05-02T19:37:36
|
2016-05-02T19:37:36Z
|
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/360/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/360/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/360",
"html_url": "https://github.com/materialsproject/pymatgen/pull/360",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/360.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/360.patch",
"merged_at": "2016-05-02T19:37:36Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/361
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/361/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/361/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/361/events
|
https://github.com/materialsproject/pymatgen/pull/361
| 152,697,888
|
MDExOlB1bGxSZXF1ZXN0Njg2NTY4MDU=
| 361
|
Minor fix in vaso.io.inputs
|
{
"login": "aykol",
"id": 7274088,
"node_id": "MDQ6VXNlcjcyNzQwODg=",
"avatar_url": "https://avatars.githubusercontent.com/u/7274088?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/aykol",
"html_url": "https://github.com/aykol",
"followers_url": "https://api.github.com/users/aykol/followers",
"following_url": "https://api.github.com/users/aykol/following{/other_user}",
"gists_url": "https://api.github.com/users/aykol/gists{/gist_id}",
"starred_url": "https://api.github.com/users/aykol/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/aykol/subscriptions",
"organizations_url": "https://api.github.com/users/aykol/orgs",
"repos_url": "https://api.github.com/users/aykol/repos",
"events_url": "https://api.github.com/users/aykol/events{/privacy}",
"received_events_url": "https://api.github.com/users/aykol/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 |
[] | 2016-05-03T04:34:24
| 2016-05-03T04:58:52
|
2016-05-03T04:58:52Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Revision to properly handle the specific case when a _Structure_ that has predictor_corrector site_properties (e.g. obtained from a _Poscar_ parsed from MD CONTCAR) is reused to generate a new _Poscar_ and write inputs.
- Fix: Rather than raising a ValueError for missing predictor_corrector_preamble, a warning is raised and POSCAR is properly written excluding the entire predictor corrector chunk.
- This fix ensures that; for example, the existing MITMDVasp input sets work as before, with a Structure obtained from a previous MD run, without raising a "No predictor corrector preamble" error.
|
{
"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/361/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/361/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/361",
"html_url": "https://github.com/materialsproject/pymatgen/pull/361",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/361.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/361.patch",
"merged_at": "2016-05-03T04:58:52Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/362
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/362/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/362/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/362/events
|
https://github.com/materialsproject/pymatgen/pull/362
| 153,347,951
|
MDExOlB1bGxSZXF1ZXN0NjkwODYwNjk=
| 362
|
Boltztrap
|
{
"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 |
[] | 2016-05-05T23:24:07
| 2016-05-05T23:27:06
|
2016-05-05T23:27:05Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Part 1 of Boltztrap changes. I've only made my through about 5% of the code...not sure how much I can actually do but there will likely be more parts later. This should be enough to at least get a little start.
Changes:
- Move some plotting methods to plotting package (rather than inside boltztrap.py or bandstructure.py)
- Add ability to set temperature range and grid
- Clean up and reorganize quite a lot of code (this was the bulk of changes)
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/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/362/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/362/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/362",
"html_url": "https://github.com/materialsproject/pymatgen/pull/362",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/362.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/362.patch",
"merged_at": "2016-05-05T23:27:05Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/363
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/363/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/363/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/363/events
|
https://github.com/materialsproject/pymatgen/pull/363
| 153,672,814
|
MDExOlB1bGxSZXF1ZXN0NjkyNzY4NjU=
| 363
|
Add read_table_pattern() method. Refactor NMR parsing code.
|
{
"login": "xhqu1981",
"id": 4646623,
"node_id": "MDQ6VXNlcjQ2NDY2MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/4646623?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xhqu1981",
"html_url": "https://github.com/xhqu1981",
"followers_url": "https://api.github.com/users/xhqu1981/followers",
"following_url": "https://api.github.com/users/xhqu1981/following{/other_user}",
"gists_url": "https://api.github.com/users/xhqu1981/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xhqu1981/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xhqu1981/subscriptions",
"organizations_url": "https://api.github.com/users/xhqu1981/orgs",
"repos_url": "https://api.github.com/users/xhqu1981/repos",
"events_url": "https://api.github.com/users/xhqu1981/events{/privacy}",
"received_events_url": "https://api.github.com/users/xhqu1981/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 |
[] | 2016-05-08T19:23:10
| 2016-05-08T21:51:03
|
2016-05-08T21:51:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
refactor NMR parsing code to read property scheme.
|
{
"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/363/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/363/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/363",
"html_url": "https://github.com/materialsproject/pymatgen/pull/363",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/363.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/363.patch",
"merged_at": "2016-05-08T21:51:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/364
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/364/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/364/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/364/events
|
https://github.com/materialsproject/pymatgen/pull/364
| 153,681,265
|
MDExOlB1bGxSZXF1ZXN0NjkyODE4NjE=
| 364
|
Refactor outcar
|
{
"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. I guess the epsilon bits would be useful, though this info is already available in the vasprun.xml.\n"
] | 2016-05-08T22:35:07
| 2016-05-09T01:57:57
|
2016-05-09T01:57:57Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Uses @xhqu1981's table parser for the elastic and piezo tensors.
- Elastic and piezo tensors read in separate methods using read_table_pattern
- Elastic and piezo tensors are stored in outcar.data, rather than as attributes of outcar
## TODO (if any)
It looks like some parts of the lepsilon parsing methods should be refactored as well using the table_parsing method. I can go ahead and refactor these as seems prudent from the code, but I don't know much about how these methods are used.
|
{
"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/364/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/364/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/364",
"html_url": "https://github.com/materialsproject/pymatgen/pull/364",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/364.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/364.patch",
"merged_at": "2016-05-09T01:57:57Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/365
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/365/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/365/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/365/events
|
https://github.com/materialsproject/pymatgen/issues/365
| 153,875,854
|
MDU6SXNzdWUxNTM4NzU4NTQ=
| 365
|
get_publication_quality_plot broken
|
{
"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 |
[
"Update your matplotlib version.\n",
"1.5.1\nalready up-to-date. \n"
] | 2016-05-09T21:37:00
| 2016-05-09T21:43:57
|
2016-05-09T21:43:57Z
|
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: master
- Python version: 2.7.9
- OS version: OS X 10.11.4
## Summary
- get_publication_quality_plot broken due to ax.set_prop_cycle(palettable.colorbrewer.qualitative.Set1_9.mpl_colors)
## Example code
``` python
%matplotlib inline
from pymatgen.util.plotting_utils import get_publication_quality_plot
import numpy as np
plt = get_publication_quality_plot(8,6)
plt.plot(np.random.uniform(size=10), np.random.uniform(size=10))
```
## Error message
```
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-1-b31405f6f6f9> in <module>()
3 import numpy as np
4
----> 5 plt = get_publication_quality_plot(8,6)
6 plt.plot(np.random.uniform(size=10), np.random.uniform(size=10))
/Users/zhideng/repos/pymatgen/pymatgen/util/plotting_utils.pyc in get_publication_quality_plot(width, height, plt, dpi)
47 plt.figure(figsize=(width, height), facecolor="w", dpi=dpi)
48 ax = plt.gca()
---> 49 ax.set_prop_cycle(palettable.colorbrewer.qualitative.Set1_9.mpl_colors)
50 else:
51 fig = plt.gcf()
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes/_base.pyc in set_prop_cycle(self, *args, **kwargs)
1110 prop_cycle = None
1111 else:
-> 1112 prop_cycle = cycler(*args, **kwargs)
1113 self._get_lines.set_prop_cycle(prop_cycle)
1114 self._get_patches_for_fill.set_prop_cycle(prop_cycle)
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/rcsetup.pyc in cycler(*args, **kwargs)
703 if len(args) == 1:
704 if not isinstance(args[0], Cycler):
--> 705 raise TypeError("If only one positional argument given, it must "
706 " be a Cycler instance.")
707
TypeError: If only one positional argument given, it must be a Cycler instance.
```
## 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/365/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/365/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/366
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/366/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/366/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/366/events
|
https://github.com/materialsproject/pymatgen/issues/366
| 154,131,859
|
MDU6SXNzdWUxNTQxMzE4NTk=
| 366
|
Why two parameters?
|
{
"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 |
[
"This has actually be carefully thought through. You are missing one scenario - where you actually have a sym_prec, e.g., for BS kpoint purposes, but you do **not** want to standardize the cell.\n",
"But in the code I referred to (which is a well defined function) there seems to be no effect of standardize=False and sym_prec>0 (i.e., the sym_prec does nothing).\n\nI also looked at the \"from_prev_run()\" method in both MPStaticSet and MPNonSCFSet (which both have the two parameters), and both of them also seem to assume that if you have standardize=False, that sym_prec does nothing no matter what you set it to (I didn't test it, just looking at the code). However in these latter two cases, if you were to pass on the \"sym_prec\" parameter to the \"init()\" function at the end of the method, it should have the behavior you say - i.e. kpoints use symprec but structure remains the same.\n",
"Ok, I pushed a changed to set it to just one parameter.\n"
] | 2016-05-10T23:52:15
| 2016-05-11T04:02:53
|
2016-05-11T04:02:38Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
pymatgen.io.vasp.sets.get_structure_from_prev_run() has both "standardize" and "sym_prec" parameters. The "standardize" parameter seems redundant. i.e. if you set sym_prec = 0 then it would not standardize the cell. If you set standardize=True but sym_prec=0 it will also not standardize the cell. So why have the standardize parameter at all - why not just use sym_prec? Is it for added clarity?
Note that many downstream objects also use two parameters in this way.
|
{
"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/366/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/366/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/367
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/367/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/367/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/367/events
|
https://github.com/materialsproject/pymatgen/pull/367
| 154,140,149
|
MDExOlB1bGxSZXF1ZXN0Njk2MDE4NzI=
| 367
|
Removed glitch
|
{
"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 |
[] | 2016-05-11T01:12:53
| 2016-05-11T03:49:39
|
2016-05-11T03:49:39Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Removed glitch when attempting to (unsuccessfully) multiply a float carrying a length unit with a non-units carrying matrix in lattice.py.
The weird part was that for some structures that I'm currently testing the issue resulted in a true error and sometimes not.
|
{
"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/367/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/367/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/367",
"html_url": "https://github.com/materialsproject/pymatgen/pull/367",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/367.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/367.patch",
"merged_at": "2016-05-11T03:49:39Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/368
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/368/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/368/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/368/events
|
https://github.com/materialsproject/pymatgen/pull/368
| 154,364,908
|
MDExOlB1bGxSZXF1ZXN0Njk3NTgzMzI=
| 368
|
Removed a bug in OrderParameters class of structure_analyzer.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 |
[] | 2016-05-11T23:23:46
| 2016-05-11T23:37:43
|
2016-05-11T23:37:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
There were inconsistencies regarding unsuccessful set-up of the spherical coordinate system.
|
{
"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/368/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/368/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/368",
"html_url": "https://github.com/materialsproject/pymatgen/pull/368",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/368.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/368.patch",
"merged_at": "2016-05-11T23:37:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/369
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/369/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/369/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/369/events
|
https://github.com/materialsproject/pymatgen/issues/369
| 154,426,017
|
MDU6SXNzdWUxNTQ0MjYwMTc=
| 369
|
Vasprun get ParseError
|
{
"login": "hlyang1992",
"id": 2081913,
"node_id": "MDQ6VXNlcjIwODE5MTM=",
"avatar_url": "https://avatars.githubusercontent.com/u/2081913?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hlyang1992",
"html_url": "https://github.com/hlyang1992",
"followers_url": "https://api.github.com/users/hlyang1992/followers",
"following_url": "https://api.github.com/users/hlyang1992/following{/other_user}",
"gists_url": "https://api.github.com/users/hlyang1992/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hlyang1992/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hlyang1992/subscriptions",
"organizations_url": "https://api.github.com/users/hlyang1992/orgs",
"repos_url": "https://api.github.com/users/hlyang1992/repos",
"events_url": "https://api.github.com/users/hlyang1992/events{/privacy}",
"received_events_url": "https://api.github.com/users/hlyang1992/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 |
[
"Your file contains binary characters. It is usually either a bad vasp calculation or a bad compilation of VASP. This is not a problem with pymatgen.\n"
] | 2016-05-12T08:32:44
| 2016-05-12T13:37:42
|
2016-05-12T13:37:42Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
When use Vasprun("vasprun.xml") with follow file, will get "ParesError: not well-defined(invaild token).
## Files
[vasprun.xml](https://drive.google.com/file/d/0B7DapXLbWsRKUHBVSU1iWVFwS1k/view?usp=sharing)
|
{
"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/369/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/369/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/370
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/370/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/370/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/370/events
|
https://github.com/materialsproject/pymatgen/pull/370
| 154,522,864
|
MDExOlB1bGxSZXF1ZXN0Njk4NjUwOTU=
| 370
|
proper serialization/deserialization for lammps input and data
|
{
"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 |
[] | 2016-05-12T16:14:23
| 2016-05-12T16:37:36
|
2016-05-12T16:37:36Z
|
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/370/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/370/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/370",
"html_url": "https://github.com/materialsproject/pymatgen/pull/370",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/370.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/370.patch",
"merged_at": "2016-05-12T16:37:36Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/371
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/371/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/371/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/371/events
|
https://github.com/materialsproject/pymatgen/issues/371
| 154,546,070
|
MDU6SXNzdWUxNTQ1NDYwNzA=
| 371
|
problem installing pymatgen
|
{
"login": "asb130",
"id": 16896070,
"node_id": "MDQ6VXNlcjE2ODk2MDcw",
"avatar_url": "https://avatars.githubusercontent.com/u/16896070?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/asb130",
"html_url": "https://github.com/asb130",
"followers_url": "https://api.github.com/users/asb130/followers",
"following_url": "https://api.github.com/users/asb130/following{/other_user}",
"gists_url": "https://api.github.com/users/asb130/gists{/gist_id}",
"starred_url": "https://api.github.com/users/asb130/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/asb130/subscriptions",
"organizations_url": "https://api.github.com/users/asb130/orgs",
"repos_url": "https://api.github.com/users/asb130/repos",
"events_url": "https://api.github.com/users/asb130/events{/privacy}",
"received_events_url": "https://api.github.com/users/asb130/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 seems to be an old version of the script. The new version should use **version** for pip. \nIn any case, you can easily install pymatgen just using pip install pymatgen nowadays. There is no need to use this script, which was more for old days when some of the dependencies are more difficult to install.\n",
"I am using the version which is currently available at pymatgen website. At the website it is written that\n\"This installation script requires only basic Python 2.7+, setuptools, and a working version of gcc as prerequisites. Click to download the pmg_install.py script. Move the script to an empty directory and then run:\n\npython pmg_install.py\"\n\non using python pmg_install.py, I am getting error written in my last mail. Now on using pip install pymatgen or by using pip install pymatgen --user. I am getting the following error.\nI am very new to python and linux. Kindly let me know how to install this software.\n\nerror: Command \"/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/lapack_lite/python_xerbla.o -L/usr/local/lib -L/usr/lib64 -L/opt/sam/epd/epd-7.2-2-rh5-x86_64/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -llapack -lblas -lblas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so\" failed with exit status 1\n\n---\n\n Rolling back uninstall of numpy\nCommand /opt/sam/epd/epd-7.2-2-rh5-x86_64/bin/python -c \"import setuptools;**file**='/ihome/kjohnson/asb130/pymtagen/build/numpy/setup.py';exec(compile(open(**file**).read().replace('\\r\\n', '\\n'), **file**, 'exec'))\" install --single-version-externally-managed --record /tmp/pip-PGeswR-record/install-record.txt --user failed with error code 1\nStoring complete log in /ihome/kjohnson/asb130/.pip/pip.log\n",
"If you have a linux operating system, it is best you do a `sudo apt-get install python-numpy python-scipy` first, then just do pip install pymatgen. That should already work without doing anything else.\n"
] | 2016-05-12T18:09:43
| 2016-05-13T13:41:38
|
2016-05-13T13:41:38Z
|
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: <5.3.2.>
- OS version: <I am connected to supercomputer through my windows 10 pc>
## Summary
I am getting the following error while installing pymatgen
when I type python pmg_install.py in the directory where I have .py script. I get this error.
Detected Python version 2.7.2.final.0
Detected setuptools version 5.4.1
Traceback (most recent call last):
File "pmg_install.py", line 125, in <module>
print("Detected pip version {}".format(pip.**version**))
AttributeError: 'module' object has no attribute '**version**'
## Example code
``` python
<Example code generating error>
```
## Error message
Detected Python version 2.7.2.final.0
Detected setuptools version 5.4.1
Traceback (most recent call last):
File "pmg_install.py", line 125, in <module>
print("Detected pip version {}".format(pip.**version**))
AttributeError: 'module' object has no attribute '**version**'
```
<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>
Ashish Bhatnagar
```
|
{
"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/371/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/371/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/372
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/372/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/372/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/372/events
|
https://github.com/materialsproject/pymatgen/pull/372
| 154,579,083
|
MDExOlB1bGxSZXF1ZXN0Njk5MDUxNTc=
| 372
|
fix lammps input serialization
|
{
"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 |
[] | 2016-05-12T20:54:22
| 2016-05-12T20:55:08
|
2016-05-12T20:55:08Z
|
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/372/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/372/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/372",
"html_url": "https://github.com/materialsproject/pymatgen/pull/372",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/372.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/372.patch",
"merged_at": "2016-05-12T20:55:08Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/373
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/373/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/373/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/373/events
|
https://github.com/materialsproject/pymatgen/issues/373
| 154,604,913
|
MDU6SXNzdWUxNTQ2MDQ5MTM=
| 373
|
parsing of Born effective charges chokes database insertion
|
{
"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 |
[
"jsanitizing the output is another option...\n",
"I am pretty sure I tried this exact solution but got some different serialization error since there was numpy arrays embedded in the dict. The jsanitize() would surely clear it up, but the raw dict still had errors.\n",
"(I also made an attempt to turn the numpy matrices into lists - but again hit some error which is when I stopped working on it).\n",
"Not quite sure what's the problem with turning numpy matrices into lists. Isn't it just array.tolist()? That always works. \n\nI didn't bother to convert the numpy array in the class itself because there are a lot of instances where you actually prefer the numpy array (e.g., to do mass manipulation effficiently). For insertion into DBs, try the tolist() method.\n",
"I didn't use to_list(), but I did try avoiding the numpy array entirely for the Born charges by having it natively be parsed as a list. I ended up getting an int index error for db insertion like before, which didn't make much sense to me but I also didn't try looking into it more.\n\nAnyway, since you have made the new jsanitize() and fixed the format of this, I will just work with that for now and speak up if I run into any more issues.\n"
] | 2016-05-12T23:39:58
| 2016-05-13T17:57:34
|
2016-05-13T13:35:17Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
- Python version: 2.7
## Summary
- The parsing of the born effective charges takes place around lines: pymatgen/io/vasp/outputs.py:1833
- The format is a dictionary, where keys are _int_ of atom index, and values are the BEC matrix
- For example it looks like this:
```
u'born': {0: array([[ -9.58400000e-02, 5.50000000e-04, 3.90000000e-04],
[ 0.00000000e+00, -9.52700000e-02, 6.00000000e-05],
[ -0.00000000e+00, -0.00000000e+00, -9.60900000e-02]]), 1: array([[ -9.58400000e-02, -5.50000000e-04, -3.90000000e-04],
[ 0.00000000e+00, -9.64400000e-02, -7.00000000e-05],
[ 0.00000000e+00, -0.00000000e+00, -9.56000000e-02]])}
```
- This chokes any Drone that tries to enter this data into the database, since MongoDB does not allow int keys (only str)
## Suggested solution (if any)
- Either use string keys, or change the format entirely - e.g. array of tensor rather than dict of tensor, or array of dict where each member sub-dict has an ion_idx and born keys.
More information available if needed...
|
{
"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/373/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/373/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/374
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/374/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/374/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/374/events
|
https://github.com/materialsproject/pymatgen/issues/374
| 154,710,544
|
MDU6SXNzdWUxNTQ3MTA1NDQ=
| 374
|
Spacegroup symbol compatibility for orthorhombic systems
|
{
"login": "gpetretto",
"id": 8665734,
"node_id": "MDQ6VXNlcjg2NjU3MzQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8665734?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gpetretto",
"html_url": "https://github.com/gpetretto",
"followers_url": "https://api.github.com/users/gpetretto/followers",
"following_url": "https://api.github.com/users/gpetretto/following{/other_user}",
"gists_url": "https://api.github.com/users/gpetretto/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gpetretto/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gpetretto/subscriptions",
"organizations_url": "https://api.github.com/users/gpetretto/orgs",
"repos_url": "https://api.github.com/users/gpetretto/repos",
"events_url": "https://api.github.com/users/gpetretto/events{/privacy}",
"received_events_url": "https://api.github.com/users/gpetretto/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "hautierg",
"id": 910839,
"node_id": "MDQ6VXNlcjkxMDgzOQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/910839?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hautierg",
"html_url": "https://github.com/hautierg",
"followers_url": "https://api.github.com/users/hautierg/followers",
"following_url": "https://api.github.com/users/hautierg/following{/other_user}",
"gists_url": "https://api.github.com/users/hautierg/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hautierg/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hautierg/subscriptions",
"organizations_url": "https://api.github.com/users/hautierg/orgs",
"repos_url": "https://api.github.com/users/hautierg/repos",
"events_url": "https://api.github.com/users/hautierg/events{/privacy}",
"received_events_url": "https://api.github.com/users/hautierg/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"login": "hautierg",
"id": 910839,
"node_id": "MDQ6VXNlcjkxMDgzOQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/910839?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hautierg",
"html_url": "https://github.com/hautierg",
"followers_url": "https://api.github.com/users/hautierg/followers",
"following_url": "https://api.github.com/users/hautierg/following{/other_user}",
"gists_url": "https://api.github.com/users/hautierg/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hautierg/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hautierg/subscriptions",
"organizations_url": "https://api.github.com/users/hautierg/orgs",
"repos_url": "https://api.github.com/users/hautierg/repos",
"events_url": "https://api.github.com/users/hautierg/events{/privacy}",
"received_events_url": "https://api.github.com/users/hautierg/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
] | null |
[
"@hautierg will need to fix this. In general, the bandstructure code should not depend on specific crystallographic settings for centered lattices. Cm2m and Amm2 are perfectly valid representations of spacegroup 38.\n",
"Seems like this issue has been defunct for 7 years. Closing...."
] | 2016-05-13T13:22:35
| 2023-08-08T21:16:53
|
2023-08-08T21:16:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version:3.5.3
- Python version: 2.7
## Summary
With the new version of spglib (I am not sure starting from which one) the spacegroup symbol for orthorhombic systems seems to have changed. Taking for example mp-569450 the symbol in the materials project db is Cm2m, while the SpacegroupAnalyzer returns Amm2. Based on a quick test the problem seems to be there for several space groups with number between 16 and 75.
Apart from the compatibility with the information previously obtained, this change leads to an error when trying to obtain the high symmetry path for some of these materials.
## Example code
```
from pymatgen import MPRester, Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.symmetry.bandstructure import HighSymmKpath
data = MPRester().get_data('mp-569450')[0]
s = Structure.from_str(data['cif'], fmt='cif')
print SpacegroupAnalyzer(s).get_spacegroup_symbol(), data['spacegroup']['symbol']
HighSymmKpath(s)
```
## Error message
pymatgen/symmetry/bandstructure.py:99: UserWarning: Unexpected value for spg_symbol: Amm2
## Suggested solution (if any)
At least for HighSymmPath, as it seems that in some cases symbols containing a C has been consistently replaced with symbols containing an A, a simple solution could be to replace line 96 of symmetry/bandstucture.py with
`elif "C" in spg_symbol or "A" in spg_symbol:`
but maybe it would be necessary to verify explicitly that this will be the intended behaviour for all the modified symbols.
|
{
"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/374/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/374/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/375
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/375/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/375/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/375/events
|
https://github.com/materialsproject/pymatgen/pull/375
| 154,728,240
|
MDExOlB1bGxSZXF1ZXN0NzAwMDY5OTM=
| 375
|
add read_velocities option in Poscar
|
{
"login": "gVallverdu",
"id": 5417018,
"node_id": "MDQ6VXNlcjU0MTcwMTg=",
"avatar_url": "https://avatars.githubusercontent.com/u/5417018?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gVallverdu",
"html_url": "https://github.com/gVallverdu",
"followers_url": "https://api.github.com/users/gVallverdu/followers",
"following_url": "https://api.github.com/users/gVallverdu/following{/other_user}",
"gists_url": "https://api.github.com/users/gVallverdu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gVallverdu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gVallverdu/subscriptions",
"organizations_url": "https://api.github.com/users/gVallverdu/orgs",
"repos_url": "https://api.github.com/users/gVallverdu/repos",
"events_url": "https://api.github.com/users/gVallverdu/events{/privacy}",
"received_events_url": "https://api.github.com/users/gVallverdu/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.\n"
] | 2016-05-13T14:43:34
| 2016-05-13T16:18:18
|
2016-05-13T16:18:14Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- add read_velocities option in Poscar class method from_file
- check velocities when write a POSCAR file
## Comment
I write a comment in case of there is a better way to solve the problem. The pull request solve the error of the example at the end of this message.
Actually, the problem comes from the site_properties property of the Structure class (see below).
``` py
@property
def site_properties(self):
"""
Returns the site properties as a dict of sequences. E.g.,
{"magmom": (5,-5), "charge": (-4,4)}.
"""
props = {}
prop_keys = set()
for site in self:
prop_keys.update(site.properties.keys())
for k in prop_keys:
props[k] = [site.properties.get(k, None) for site in self]
return props
```
That property returns the value None if you ask for a property which does not exist for the given site of the structure. Thus if you are working on a structure where sites have specific properties, you have to manually update them. For example in the case of POSCAR files, if you add or remove atoms and velocities is a property of the site of the strucutre, when you try to write the POSCAR file, velocities of added atom is None and thus you obtain an error message.
Maybe the follwing exampel is clearer :
```
In [1]: import pymatgen as mg
In [2]: poscar = mg.io.vasp.inputs.Poscar.from_file("CONTCAR")
In [3]: poscar.structure.insert(0, "O", [0.2, 0.3, 0.4])
In [4]: poscar.velocities
Out[4]: [None, [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]
In [5]: poscar.write_file("test.vasp")
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-5-5972e896ad38> in <module>()
----> 1 poscar.write_file("test.vasp")
/home/r/user/g/gvallver/git/pymatgen/pymatgen/io/vasp/inputs.py in write_file(self, filename, **kwargs)
443 """
444 with zopen(filename, "wt") as f:
--> 445 f.write(self.get_string(**kwargs))
446
447 def as_dict(self):
/home/r/user/g/gvallver/git/pymatgen/pymatgen/io/vasp/inputs.py in get_string(self, direct, vasp4_compatible, significant_figures)
417 lines.append("")
418 for v in self.velocities:
--> 419 lines.append(" ".join([format_str.format(i) for i in v]))
420
421 if self.predictor_corrector:
TypeError: 'NoneType' object is not iterable
```
|
{
"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/375/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/375/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/375",
"html_url": "https://github.com/materialsproject/pymatgen/pull/375",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/375.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/375.patch",
"merged_at": "2016-05-13T16:18:14Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/376
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/376/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/376/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/376/events
|
https://github.com/materialsproject/pymatgen/issues/376
| 154,772,066
|
MDU6SXNzdWUxNTQ3NzIwNjY=
| 376
|
'list index out of range' in PotcarCorrection.get_correction of pymatgen.entries.compatibility.py
|
{
"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 |
[
"This is not a problem with pymatgen. If you are using pymatgen-db to construct the database, there is a specific method to reconstruct entries from db entries.\n",
"In fact, i haven't used pymatgen-db. Perhaps there a better way in pymatgen-db to reconstruct entries from db entries? Then, i will go and learn it. Thank you.\n"
] | 2016-05-13T18:21:47
| 2016-05-15T13:28:03
|
2016-05-15T13:16:44Z
|
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: 3.5.3(pip) <Write "branch_name" if it is development version.>
- Python version: 2.7.11<Only 2.7.* and 3.* supported.>
- OS version: OSX 10.11.4<If you are writing Windows here, you are on your own.>
## Summary
Gets an IndexError when i set `parameters["potcar_symbols"]` in the class `ComputedStructureEntry`
## Example code
``` python
structure = Structure.from_dict(compound['output']['crystal'])
energy = compound['output']['final_energy']
parameters = {\
"hubbards":compound['hubbards'],\
"potcar_symbols":compound['pseudo_potential']['labels']\
}
data = {\
... : ...
}
mg_entries.append(ComputedStructureEntry(structure, energy, \
parameters = parameters, data = data)\
)
```
## Error message
```
Traceback (most recent call last):
File "/Users/Home/Documents/Research/YCuTe2/analyze/test.py", line 10, in <module>
entery = muti_entery(query)
File "/Users/Home/Documents/Research/YCuTe2/analyze/AnalyzeMongo.py", line 119, in muti_entery
entries[key] = compat.process_entries(mg_entries + mp_entries)
File "/usr/local/lib/python2.7/site-packages/pymatgen/entries/compatibility.py", line 437, in process_entries
return list(filter(None, map(self.process_entry, entries)))
File "/usr/local/lib/python2.7/site-packages/pymatgen/entries/compatibility.py", line 403, in process_entry
corrections = self.get_corrections_dict(entry)
File "/usr/local/lib/python2.7/site-packages/pymatgen/entries/compatibility.py", line 421, in get_corrections_dict
val = c.get_correction(entry)
File "/usr/local/lib/python2.7/site-packages/pymatgen/entries/compatibility.py", line 153, in get_correction
"potcar_symbols"] if sym])
IndexError: list index out of range
```
## Suggested solution (if any)
In the [line 150~158 of pymatgen.entries.compatibility.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/entries/compatibility.py#L150), which is already listed below:
``` python
else:
psp_settings = set([sym.split()[1]
for sym in entry.parameters[
"potcar_symbols"] if sym])
if {self.valid_potcars[str(el)] for el in
entry.composition.elements} != psp_settings:
raise CompatibilityError('Incompatible potcar')
return 0
```
It seems to aim to compare the equality of `entry.composition.elements` and `psp_settings`.
But in my dbs, the value of ['pseudo_potential']['labels'] is formated as `Cu_pv` or `H`. Therefore `sym.split()` will have no effect. Even `.split("_")` will get a list of `["Cu","pv"]` or `["H"]`, and the index `[1]` will point to `["pv"]` or IndexError.
I am not sure if the `psp_settings` is intended to obtain `"Cu"` from `"Cu_pv"`, maybe the line 151 shoud be:
``` python
psp_settings = set([sym.split("_")[0]
```
I am a novice to DFT, if there is something wrong in my words, please forgive me.
|
{
"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/376/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/376/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/377
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/377/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/377/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/377/events
|
https://github.com/materialsproject/pymatgen/issues/377
| 154,874,374
|
MDU6SXNzdWUxNTQ4NzQzNzQ=
| 377
|
Zr is written as "r" in vasprun.xml hence exception is raised by Vasprun
|
{
"login": "albalu",
"id": 14810408,
"node_id": "MDQ6VXNlcjE0ODEwNDA4",
"avatar_url": "https://avatars.githubusercontent.com/u/14810408?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/albalu",
"html_url": "https://github.com/albalu",
"followers_url": "https://api.github.com/users/albalu/followers",
"following_url": "https://api.github.com/users/albalu/following{/other_user}",
"gists_url": "https://api.github.com/users/albalu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/albalu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/albalu/subscriptions",
"organizations_url": "https://api.github.com/users/albalu/orgs",
"repos_url": "https://api.github.com/users/albalu/repos",
"events_url": "https://api.github.com/users/albalu/events{/privacy}",
"received_events_url": "https://api.github.com/users/albalu/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 don't think this is a standard bug. We have extensively worked with Zr based systems and this issue has never come up. Can you check your VASP compilation? Thanks.\n",
"Ok I just ran the same system on Edison on 5.3.3 (attached) and got the same error. Have you used Zr_sv in those materials?\n[self.zip](https://github.com/materialsproject/pymatgen/files/264734/self.zip)\n",
"I too faced this issue many times.\nOn May 14, 2016 2:51 PM, \"Shyue Ping Ong\" notifications@github.com wrote:\n\n> I don't think this is a standard bug. We have extensively worked with Zr\n> based systems and this issue has never come up. Can you check your VASP\n> compilation? Thanks.\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/377#issuecomment-219253556\n",
"As far as I can see, the standard MP input set uses Zr_sv. There are plenty of Zr compounds on the MP website. If such a bug exists, it would have been detected some time ago.\n\nWhat version of the PSP are you using? MP is using a pretty old one.\n",
"This is the heading of POTCAR for Zr:\n\n PAW_PBE Zr_sv 04Jan2005 \n 12.0000000000000 \n parameters from PSCTR are:\n VRHFIN =r: 4s4p5s4d\n LEXCH = PE\n EATOM = 1284.2219 eV, 94.3876 Ry\n\n TITEL = PAW_PBE Zr_sv 04Jan2005\n LULTRA = F use ultrasoft PP ?\n IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no\n RPACOR = 2.200 partial core radius\n POMASS = 91.224; ZVAL = 12.000 mass and valenz\n RCORE = 2.500 outmost cutoff radius\n RWIGS = 3.070; RWIGS = 1.625 wigner-seitz radius (au A)\n ENMAX = 229.898; ENMIN = 172.424 eV\n ICORE = 3 local potential\n LCOR = T correct aug charges\n LPAW = T paw PP\n EAUG = 461.257\n DEXC = 0.000\n RMAX = 2.561 core radius for proj-oper\n RAUG = 1.300 factor for augmentation sphere\n RDEP = 2.597 radius for radial grids\n RDEPT = 2.007 core radius for aug-charge\n\nI agree that this is strange. I do not understand why VASP would print '>r' in vasprun.xml instead of '>Zr' which seems like the part pymatgen use to read the symbols.\n",
"I am pretty sure MP is using\n PAW_PBE Zr_sv 07Sep2000\n\nIt would need to be confirmed, but this could be the reason for the\ndifference\n\nOn Sun, May 15, 2016 at 10:12 AM, Alireza Faghanina <\nnotifications@github.com> wrote:\n\n> This is the heading of POTCAR for Zr:\n> \n> PAW_PBE Zr_sv 04Jan2005\n> \n> 12.0000000000000\n> \n> parameters from PSCTR are:\n> VRHFIN =r: 4s4p5s4d\n> LEXCH = PE\n> EATOM = 1284.2219 eV, 94.3876 Ry\n> \n> TITEL = PAW_PBE Zr_sv 04Jan2005\n> LULTRA = F use ultrasoft PP ?\n> IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no\n> RPACOR = 2.200 partial core radius\n> POMASS = 91.224; ZVAL = 12.000 mass and valenz\n> RCORE = 2.500 outmost cutoff radius\n> RWIGS = 3.070; RWIGS = 1.625 wigner-seitz radius (au A)\n> ENMAX = 229.898; ENMIN = 172.424 eV\n> ICORE = 3 local potential\n> LCOR = T correct aug charges\n> LPAW = T paw PP\n> EAUG = 461.257\n> DEXC = 0.000\n> RMAX = 2.561 core radius for proj-oper\n> RAUG = 1.300 factor for augmentation sphere\n> RDEP = 2.597 radius for radial grids\n> RDEPT = 2.007 core radius for aug-charge\n> \n> I agree that this is strange. I do not understand why VASP would print\n> '>r' in vasprun.xml instead of '>Zr' which seems like the part pymatgen use\n> to read the symbols. This is what I get when I do 'grep \">r\" vasprun.xml':\n> r 3\n> 1r 91.22400000 12.00000000 PAW_PBE Zr_sv 04Jan2005\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/377#issuecomment-219298027\n",
"I faced this issue two years ago at LBNL.\nIf I remember correctly, I was not using MP's psp. I was using one of the\nnewer ones.\n\nOn Sat, May 14, 2016 at 10:37 PM, Shyue Ping Ong notifications@github.com\nwrote:\n\n> As far as I can see, the standard MP input set uses Zr_sv. There are\n> plenty of Zr compounds on the MP website. If such a bug exists, it would\n> have been detected some time ago.\n> \n> What version of the PSP are you using? MP is using a pretty old one.\n> \n> —\n> You are receiving this because you commented.\n> Reply to this email directly or view it on GitHub\n> https://github.com/materialsproject/pymatgen/issues/377#issuecomment-219267580\n\n## \n\nBharat Medasani\nPostdoctoral Associate,\nPacific Northwest National Lab\nRichland, WA 99354\nUSA\n",
"Ok. Pls implement a solution with a unittest and send a pull request. I will merge. Thanks. \n",
"Apologies for reviving this nearly 10 year old issue, but since this is one of the first hits on a google search for relevant keywords, I thought I would comment here. After running into this issue myself (granted not using pymatgen or any MP packages), I spent too long digging into it and found the cause. I believe this is caused by a typo in the latest pseudo52 Zr_sv pseudopotential as hinted above. The VASP code that generates vasprun.xml determines the element symbol from the line \"VRHFIN\" in the POTCAR file, which for the Jan 4, 2005 Zr_sv POTPAW_PBE POTCAR file is erroneously labeled \"r\" rather than \"Zr\". Adjusting the text in this POTCAR file seems to resolve the issue. Hoping this will save anyone trying to resolve this problem in the future some time."
] | 2016-05-14T20:35:50
| 2024-10-03T15:56:09
|
2016-05-14T21:51:48Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: 3.5.3 <Write "branch_name" if it is development version.>
- Python version: 2.7.8 <Only 2.7.* and 3.* supported.>
- OS version: Linux version 2.6.32-431.17.1.el6.x86_64 (mockbuild@sl6.fnal.gov) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) <If you are writing Windows here, you are on your own.>
## Summary
- Zr is written as "r" in vasprun hence exception is raised by Vasprun
## Example code
<Example code generating error>
``` python
from pymatgen.io.vasp.outputs import Vasprun
run = Vasprun("vasprun.xml")
```
## Error message
```
Traceback (most recent call last):
File "test_Vasprun.py", line 5, in <module>
run = Vasprun("vasprun.xml")
File "/home/research/alireza/.local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 378, in __init__
parse_projected_eigen=parse_projected_eigen)
File "/home/research/alireza/.local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 417, in _parse
self._parse_atominfo(elem)
File "/home/research/alireza/.local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 964, in _parse_atominfo
sym in atomic_symbols], potcar_symbols
File "/home/research/alireza/.local/lib/python2.7/site-packages/pymatgen/io/vasp/outputs.py", line 960, in parse_atomic_symbol
raise e
ValueError: r is not a valid Element
```
## Suggested solution (if any)
- contacting VASP is a good idea but may take long.
- similar to Xe add a condition:
``` python
# ensure atomic symbols are valid elements
def parse_atomic_symbol(symbol):
try:
return str(Element(symbol))
# vasprun.xml uses X instead of Xe for xenon
except ValueError as e:
if symbol == "X":
return "Xe"
elif symbol == "r":
return "Zr"
raise e
```
## Files
```
The following example is for ZrSnO3 self consistent vasprun.xml ran on VASP 5.3.3
[ZrSnO3_Vasprun-test.zip](https://github.com/materialsproject/pymatgen/files/264679/ZrSnO3_Vasprun-test.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/377/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/377/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/378
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/378/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/378/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/378/events
|
https://github.com/materialsproject/pymatgen/issues/378
| 154,912,603
|
MDU6SXNzdWUxNTQ5MTI2MDM=
| 378
|
test_dilute_solution is monstrously slow
|
{
"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 |
[
"One suggestion is to skip the test for the time being because the underlying function incorporates a large amount of functionality. I am in the process of rewriting the dilute solution formalism with lots of smaller functions. The new code will make it easier to write a good test suite."
] | 2016-05-15T14:55:01
| 2017-06-03T14:30:51
|
2017-06-03T14:30:51Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: master
## Summary
- test_dilute_solution is way too slow. It takes at least a few minutes to complete.
## Suggested solution (if any)
- Unittests should be designed on model systems that complete reasnoably quickly.
- @mbkumar Can you pls fix this. It slows down releases and tests considerably.
|
{
"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/378/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/378/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/379
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/379/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/379/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/379/events
|
https://github.com/materialsproject/pymatgen/pull/379
| 154,946,244
|
MDExOlB1bGxSZXF1ZXN0NzAxNDEwNjU=
| 379
|
added an exception for unknown "r" element to be read as "Zr". Added …
|
{
"login": "albalu",
"id": 14810408,
"node_id": "MDQ6VXNlcjE0ODEwNDA4",
"avatar_url": "https://avatars.githubusercontent.com/u/14810408?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/albalu",
"html_url": "https://github.com/albalu",
"followers_url": "https://api.github.com/users/albalu/followers",
"following_url": "https://api.github.com/users/albalu/following{/other_user}",
"gists_url": "https://api.github.com/users/albalu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/albalu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/albalu/subscriptions",
"organizations_url": "https://api.github.com/users/albalu/orgs",
"repos_url": "https://api.github.com/users/albalu/repos",
"events_url": "https://api.github.com/users/albalu/events{/privacy}",
"received_events_url": "https://api.github.com/users/albalu/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 |
[
"@albalu looks like the automated tests fail? Please click details and debug. It might just be that some tests need updating since you added a new vasprun.xml to the folder, which affects tests that are trying to automatically parse all the vasprun.xml\n"
] | 2016-05-16T01:41:56
| 2016-06-26T21:29:38
|
2016-06-26T21:29:38Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Added an exception in outputs.py to return "Zr" if "r" element is mistakenly detected.
- Also, added a test in test_files. Please excuse me if I didn't do the test right; in this case I'd appreciate your help regarding the correct place of this test and whether or not it is necessary.
|
{
"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/379/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/379/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/379",
"html_url": "https://github.com/materialsproject/pymatgen/pull/379",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/379.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/379.patch",
"merged_at": "2016-06-26T21:29:38Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/380
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/380/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/380/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/380/events
|
https://github.com/materialsproject/pymatgen/pull/380
| 155,060,473
|
MDExOlB1bGxSZXF1ZXN0NzAyMTc4MzQ=
| 380
|
refactor eos.py. move from io.abinit to analysis
|
{
"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 |
[
"done\n",
"Thanks\n"
] | 2016-05-16T15:57:51
| 2016-05-16T16:42:31
|
2016-05-16T15:58:37Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Move the eos.py module from io.abinit to analysis. Its usage is more general.
Content in eos.py untouched.
|
{
"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/380/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/380/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/380",
"html_url": "https://github.com/materialsproject/pymatgen/pull/380",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/380.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/380.patch",
"merged_at": "2016-05-16T15:58:37Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/381
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/381/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/381/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/381/events
|
https://github.com/materialsproject/pymatgen/pull/381
| 155,064,639
|
MDExOlB1bGxSZXF1ZXN0NzAyMjA3MzU=
| 381
|
add io.abinit.eos stub with deprecation warning
|
{
"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 |
[] | 2016-05-16T16:17:37
| 2016-05-16T16:59:05
|
2016-05-16T16:59:04Z
|
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/381/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/381/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/381",
"html_url": "https://github.com/materialsproject/pymatgen/pull/381",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/381.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/381.patch",
"merged_at": "2016-05-16T16:59:04Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/382
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/382/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/382/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/382/events
|
https://github.com/materialsproject/pymatgen/pull/382
| 155,323,121
|
MDExOlB1bGxSZXF1ZXN0NzA0MDIxNzM=
| 382
|
vaspinput set for spinorbit coupling
|
{
"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 |
[] | 2016-05-17T18:01:12
| 2016-05-17T19:05:52
|
2016-05-17T19:05:51Z
|
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/382/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/382/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/382",
"html_url": "https://github.com/materialsproject/pymatgen/pull/382",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/382.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/382.patch",
"merged_at": "2016-05-17T19:05:51Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/383
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/383/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/383/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/383/events
|
https://github.com/materialsproject/pymatgen/pull/383
| 155,338,042
|
MDExOlB1bGxSZXF1ZXN0NzA0MTI5Njk=
| 383
|
Boltztrap
|
{
"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 |
[] | 2016-05-17T19:10:42
| 2016-05-17T19:35:26
|
2016-05-17T19:35:26Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Part 2 of Boltztrap changes - cleanup of BoltztrapRunner runner.
- mostly just code cleanup
- a few minor bugfixes, e.g. writing Boltztrap.def to the correct directory
- some additional parameters for controlling convergence
- make some file writing methods public in case you want to use them outside of the given run() method
## TODO
Have not started cleaning up BoltztrapAnalyzer yet (that will be part 3 and maybe part 4, depending on if I feel like dragging it out like the Hunger Games movies)
|
{
"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/383/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/383/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/383",
"html_url": "https://github.com/materialsproject/pymatgen/pull/383",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/383.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/383.patch",
"merged_at": "2016-05-17T19:35:26Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/384
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/384/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/384/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/384/events
|
https://github.com/materialsproject/pymatgen/pull/384
| 155,588,680
|
MDExOlB1bGxSZXF1ZXN0NzA1ODk4ODQ=
| 384
|
example notebook for plotting phonon bandstructure
|
{
"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 |
[] | 2016-05-18T20:01:32
| 2016-05-18T20:39:32
|
2016-05-18T20:39:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Shows how to use vasp dfpt output and phonopy interface to plot phonon bandstructure.
|
{
"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/384/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/384/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/384",
"html_url": "https://github.com/materialsproject/pymatgen/pull/384",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/384.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/384.patch",
"merged_at": "2016-05-18T20:39:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/385
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/385/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/385/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/385/events
|
https://github.com/materialsproject/pymatgen/pull/385
| 155,616,485
|
MDExOlB1bGxSZXF1ZXN0NzA2MTAzMTY=
| 385
|
Added "DIPOL" to list_keys in incar
|
{
"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 |
[] | 2016-05-18T22:30:45
| 2016-05-18T22:44:50
|
2016-05-18T22:44:50Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Minor fix to INCAR that allows file parsing to read DIPOL key.
Fixes an issue where Incar.from_file was reading only first number in 3-tuple of DIPOL.
|
{
"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/385/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/385/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/385",
"html_url": "https://github.com/materialsproject/pymatgen/pull/385",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/385.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/385.patch",
"merged_at": "2016-05-18T22:44:50Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/386
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/386/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/386/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/386/events
|
https://github.com/materialsproject/pymatgen/issues/386
| 155,861,491
|
MDU6SXNzdWUxNTU4NjE0OTE=
| 386
|
Increase tolerance for is_valid()?
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 you just implement a tolerance factor to be added as an arg. Thanks.\n",
"It is already an argument, but with a default of 0.01 A. Should the default be increased?\n",
"No. You set the value to something you need. H is a special case.\n\nShyue Ping\n\nOn May 19, 2016 at 5:45:03 PM, Saurabh Bajaj (notifications@github.com) wrote:\n\nIt is already an argument, but with a default of 0.01 A. Should the default be increased?\n\n—\nYou are receiving this because you commented.\nReply to this email directly or view it on GitHub\n",
"Okay thanks\n",
"Let me just a bit more context here -\n\nSaurabh and I parsed the Pauling file database, which is full of bad structures for various reasons. We relied on the default \"is_valid()\" method to help in avoiding some of the bad structures. However, we noticed that there are many bad structures that pass through this method, i.e., structures where O-O bonds are 0.2 Angstroms in length. We feel that:\n- <0.01 Angstrom atom distance = certainly wrong structure, and is_valid() correctly marks as false\n- 0.01-0.5 Angstrom distance = also certainly wrong structure, but default is_valid() marks as valid. We are saying _certainly_ wrong because the smallest bond distance should be about 0.73 Angstrom which is a hydrogen-hydrogen bond. There will be no smaller bonds than that. Taking a little bit of safety tolerance, we reduce that down to 0.5 Angstrom (Saurabh wrote 0.75 Angstrom, but 0.5 Angstrom is probably a safer bet to ensure that _zero_ valid structures pass through)\n- 0.5 Angstrom - 0.72 Angstrom - extremely likely to be invalid structure, but maybe be on the cautious side and have default is_valid() mark them as valid (retain current behavior)\n- >0.72 Angstrom - should be valid, i.e. retain current behavior\n\nBasically, we are saying there is significant room to crank up the default tolerance for is_valid() such that _zero_ valid structures are filtered out, while doing a better job of filtering out invalid structures. Of course, if there are any valid structures with atom distances in the 0.01 Angstrom - 0.5 Angstrom range, this is null and void. We just don't think are any.\n",
"Ok, I will crank it up to 0.5.\n"
] | 2016-05-20T00:02:26
| 2016-05-20T03:40:23
|
2016-05-20T03:40:23Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Should the tolerance distance for SiteCollection.is_valid() in pymatgen/pymatgen/core/structure.py be higher than the default 0.01 A?
## Example
For a H atom, atomic_radius = 0.25 A, atomic_radius_calculated = 0.53 A and van der Waal's radius = 1.2 A. I have a structure that has atoms within 0.05 A which should be invalid.
## Suggested solution (if any)
Increase tolerance to 0.75 A?
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/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/386/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/386/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/387
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/387/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/387/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/387/events
|
https://github.com/materialsproject/pymatgen/pull/387
| 156,057,726
|
MDExOlB1bGxSZXF1ZXN0NzA5MjIyMTQ=
| 387
|
Noble gas species and no atomic_radius in ValenceIonicRadiusEvaluator
|
{
"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 |
[] | 2016-05-20T21:51:17
| 2016-05-20T22:22:26
|
2016-05-20T22:22:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Addressed problems in ValenceIonicRadiusEvaluator related to noble gas species (don't have common_oxidation_states) and elements which have no atomic_radius (using calculated one now instead).
|
{
"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/387/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/387/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/387",
"html_url": "https://github.com/materialsproject/pymatgen/pull/387",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/387.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/387.patch",
"merged_at": "2016-05-20T22:22:26Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/388
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/388/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/388/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/388/events
|
https://github.com/materialsproject/pymatgen/pull/388
| 156,062,592
|
MDExOlB1bGxSZXF1ZXN0NzA5MjU4NTI=
| 388
|
Refactor piezo
|
{
"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 |
[] | 2016-05-20T22:30:24
| 2016-05-20T22:38:05
|
2016-05-20T22:38:05Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This PR refactors PiezoTensor to subclass TensorBase primarily so that it inherits the fit_to_structure and is_fit_to_structure methods, rather than implementing the symmetrization methods explicitly. Note that, like ElasticTensor, PiezoTensor's default constructor now takes the 3x3x3 true tensor notation as input, and uses PiezoTensor.from_voigt to construct from the Voigt-notation 3x6 matrix.
- PiezoTensor subclasses TensorBase
- Removed PiezoTensor-specific symmetrization operations
- Fixed some typos in documentation of elasticity
- Updated Piezo unittests accordingly
## TODO (if any)
PiezoTensor needs a few more methods associated with calculations on the MP website, i. e. maximum piezoelectric modulus and direction.
|
{
"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/388/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/388/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/388",
"html_url": "https://github.com/materialsproject/pymatgen/pull/388",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/388.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/388.patch",
"merged_at": "2016-05-20T22:38:05Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/389
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/389/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/389/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/389/events
|
https://github.com/materialsproject/pymatgen/pull/389
| 156,064,139
|
MDExOlB1bGxSZXF1ZXN0NzA5MjY5NDQ=
| 389
|
Deformed structure transformer
|
{
"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 |
[] | 2016-05-20T22:44:05
| 2016-05-26T18:37:10
|
2016-05-26T18:37:09Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added DeformStructureTransformation
Allows deformations to be included in a transformation list.
|
{
"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/389/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/389/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/389",
"html_url": "https://github.com/materialsproject/pymatgen/pull/389",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/389.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/389.patch",
"merged_at": "2016-05-26T18:37:09Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/390
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/390/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/390/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/390/events
|
https://github.com/materialsproject/pymatgen/pull/390
| 156,218,761
|
MDExOlB1bGxSZXF1ZXN0NzEwMTc0NzQ=
| 390
|
Fixing Chemenv tests
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/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 |
[] | 2016-05-23T07:47:18
| 2016-05-23T13:18:10
|
2016-05-23T13:18:10Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
The unit tests in chemenv had some randomness which would sometimes lead to random failures of the CI. They should now be ok.
|
{
"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/390/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/390/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/390",
"html_url": "https://github.com/materialsproject/pymatgen/pull/390",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/390.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/390.patch",
"merged_at": "2016-05-23T13:18:10Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/391
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/391/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/391/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/391/events
|
https://github.com/materialsproject/pymatgen/pull/391
| 156,377,429
|
MDExOlB1bGxSZXF1ZXN0NzExMjg0MzE=
| 391
|
correct handling of disordered structures that are incorrectly parsed as ordered by CifParser
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 caused the tests to fail. See https://circleci.com/gh/materialsproject/pymatgen/4705. \n\nI am going to revert the changes until you fix all the errors.\n"
] | 2016-05-23T22:06:00
| 2016-05-23T23:50:53
|
2016-05-23T22:48:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Problem:
CifParser parses the attached cif file ([Al2CuO4_orig.cif.zip] https://github.com/materialsproject/pymatgen/files/278361/Al2CuO4_orig.cif.zip)
) as ordered, but the lines,
Al,Cutet '0.615(5)Cu + 0.385(5)Al' .8a .-43m 0.125 0.125 0.125 1 ? '?'
Cu,Aloct '0.807(3)Al + 0.193(3)Cu' .16d ..-3m 0.5 0.5 0.5 1 ? '?'
in the cif file indicate disorder on these sites.
- Proposed fix:
Parse the above lines with elements and occupancies to introduce disorder to the 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/391/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/391/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/391",
"html_url": "https://github.com/materialsproject/pymatgen/pull/391",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/391.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/391.patch",
"merged_at": "2016-05-23T22:48:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/392
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/392/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/392/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/392/events
|
https://github.com/materialsproject/pymatgen/issues/392
| 156,448,968
|
MDU6SXNzdWUxNTY0NDg5Njg=
| 392
|
Suggestion for plotter & boltztrap in pymatgen.electronic_structure
|
{
"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
}
|
[
{
"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"
},
{
"id": 5322856717,
"node_id": "LA_kwDOACgets8AAAABPURZDQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/data%20viz",
"name": "data viz",
"color": "3C19AC",
"default": false,
"description": "PRs and issues about pymatgen plotting functionality"
}
] |
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 |
[
"@shyuep @computron will someone help me to apply the Feature request label to this issue?\n",
"@specter119 - just find the \"labels\" button on the right of the page, click the gear icon, and then click \"Feature request\"\n",
"Seems like this issue has been defunct for 7 years. Closing...."
] | 2016-05-24T08:31:29
| 2023-08-08T21:17:13
|
2023-08-08T21:17:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Here is your corrected markdown:
---
## System
- Pymatgen version: 3.6.0 (pip)
- Python version: 2.7.11
- OS version: OSX 10.11.5
## Summary
- Should add `kl` to [plot_zt_mu](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/plotter.py#L1114)
- Have a choice to sort three eigenvalues of power factor, `zt` etc. (in [BoltztrapAnalyzer class](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/boltztrap.py#L664))
## Reasons
1. Add `kl` to [plot_zt_mu](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/plotter.py#L1114):
I think it is easy to add `kl` to `plot_zt_mu`, therefore this method could plot `zt` with `kl` other than default 0.2.
2. Choose to sort eigenvalues:
The plot methods like [plot_zt_mu](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/plotter.py#L1114) will get a figure in which the red line is always above the other two lines, because the eigenvalues are sorted
according to ascending order. I think it should obtain unsorted values especially when plotting.
## Suggested solution (if any)
- Adding `kl` is very straightforward, and I've done it locally:
In [line 1115 of plotter.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/plotter.py#L1114)
```python
def plot_zt_mu(self, temp=600, output='eig', relaxation_time=1e-14,
kl=0.2, xlim=None):
```
In [line 1129 of plotter.py](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/plotter.py#L1129)
```python
zt = self._bz.get_zt(relaxation_time=relaxation_time, output=output,
kl=kl, doping_levels=False)[temp]
```
- I've tried to remove `sorted()` from [_format_to_output](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/electronic_structure/boltztrap.py#L1351), but nothing happened.
|
{
"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/392/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/392/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/393
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/393/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/393/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/393/events
|
https://github.com/materialsproject/pymatgen/pull/393
| 156,568,429
|
MDExOlB1bGxSZXF1ZXN0NzEyNjMzMDg=
| 393
|
Boltztrap
|
{
"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 |
[] | 2016-05-24T17:47:26
| 2016-05-24T18:19:29
|
2016-05-24T18:19:28Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Cleanups to BoltztrapRunner and BoltztrapAnalyzer
- Mostly retain the current functionality, but rewrite code to be much easier to understand and debug for an outsider. Integrated some methods, reorganized methods, rewrote code, etc.
- Change a few defaults, e.g. k_l for zT, warnings as str, tgrid to 50
- Add get_extreme() method that makes it easy to find things like maximum zT, maximum power factor, lowest kappa, etc. as a function of imposed doping and temperature limits
- Allow recreating a BoltztrapAnalyzer from incomplete data, allowing you to call useful functions even if you don't store the entire massive BTAnalyzer.as_dict().
- Speed up BoltztrapTests ~10X by not redundantly calling setUp before each test
- minor improvements, e.g. using lstrip() to better detect comment lines in output files
## Additional dependencies introduced (if any)
none
## TODO (if any)
There is still plenty more that can be done for this module, but at this point I will stop until I need to extend it more and concentrate on integrating the Boltztrap code into workflows. The merge is fully functional already and reasonable from an end user perspective. There are a few scattered "#TODO" in the code.
|
{
"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/393/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/393/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/393",
"html_url": "https://github.com/materialsproject/pymatgen/pull/393",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/393.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/393.patch",
"merged_at": "2016-05-24T18:19:28Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/394
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/394/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/394/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/394/events
|
https://github.com/materialsproject/pymatgen/pull/394
| 156,634,778
|
MDExOlB1bGxSZXF1ZXN0NzEzMTE0NDI=
| 394
|
Revert "correct handling of disordered structures that are incorrectly parsed as ordered by CifParser"
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[] | 2016-05-24T23:52:47
| 2016-05-24T23:53:08
|
2016-05-24T23:53:08Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Reverts materialsproject/pymatgen#391
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/394/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/394/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/394",
"html_url": "https://github.com/materialsproject/pymatgen/pull/394",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/394.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/394.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/395
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/395/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/395/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/395/events
|
https://github.com/materialsproject/pymatgen/pull/395
| 156,638,864
|
MDExOlB1bGxSZXF1ZXN0NzEzMTQzMzA=
| 395
|
correct handling of disordered structures that are incorrectly parsed as ordered by CifParser
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/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 |
[
"Sorry, let me work on this\n"
] | 2016-05-25T00:30:46
| 2016-05-25T01:32:55
|
2016-05-25T01:32:55Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Problem
CifParser parses the attached cif file ([Al2CuO4_orig.cif.zip] https://github.com/materialsproject/pymatgen/files/278361/Al2CuO4_orig.cif.zip)
) as ordered, but the lines,
Al,Cutet '0.615(5)Cu + 0.385(5)Al' .8a .-43m 0.125 0.125 0.125 1 ? '?'
Cu,Aloct '0.807(3)Al + 0.193(3)Cu' .16d ..-3m 0.5 0.5 0.5 1 ? '?'
in the cif file indicate disorder on these sites.
- Proposed fix
Parse the above lines with elements and occupancies to introduce disorder to the site.
|
{
"login": "saurabh02",
"id": 8379761,
"node_id": "MDQ6VXNlcjgzNzk3NjE=",
"avatar_url": "https://avatars.githubusercontent.com/u/8379761?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/saurabh02",
"html_url": "https://github.com/saurabh02",
"followers_url": "https://api.github.com/users/saurabh02/followers",
"following_url": "https://api.github.com/users/saurabh02/following{/other_user}",
"gists_url": "https://api.github.com/users/saurabh02/gists{/gist_id}",
"starred_url": "https://api.github.com/users/saurabh02/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/saurabh02/subscriptions",
"organizations_url": "https://api.github.com/users/saurabh02/orgs",
"repos_url": "https://api.github.com/users/saurabh02/repos",
"events_url": "https://api.github.com/users/saurabh02/events{/privacy}",
"received_events_url": "https://api.github.com/users/saurabh02/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/395/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/395/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/395",
"html_url": "https://github.com/materialsproject/pymatgen/pull/395",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/395.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/395.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/396
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/396/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/396/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/396/events
|
https://github.com/materialsproject/pymatgen/issues/396
| 157,045,321
|
MDU6SXNzdWUxNTcwNDUzMjE=
| 396
|
Inputset YAML format should allow setting **kwargs
|
{
"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 |
[
"Can you see if the new BuiltInConfig set does what you want?\n",
"Also done for DictSEt.\n"
] | 2016-05-26T18:12:45
| 2016-05-26T22:28:16
|
2016-05-26T22:28:16Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The DictVaspInputSet allows setting two types of properties
1. config_dict - i.e., INCAR, KPOINTS, etc. params
2. kwargs - e.g., force_gamma, ediff_per_atom, etc.
Currently, it seems that the YAML format of DictVaspInputSet only supports the config_dict parameters. However, I would like to do things like specify in a YAML that a particular input set should be able to do something like (i) force gamma or (ii) make sure ediff_per_atom is set False, i.e. for dielectric runs. Currently, those "type 2" modifications cannot be put in the YAML file.
I would like to have the "type 2" mods also be part of the YAML file. An easy way is to just have a key called kwargs in the YAML file that gets shipped as **kwargs to the DictVaspInputSet
|
{
"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/396/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/396/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/397
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/397/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/397/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/397/events
|
https://github.com/materialsproject/pymatgen/issues/397
| 157,074,857
|
MDU6SXNzdWUxNTcwNzQ4NTc=
| 397
|
Strain Transformation
|
{
"login": "costrouc",
"id": 1740337,
"node_id": "MDQ6VXNlcjE3NDAzMzc=",
"avatar_url": "https://avatars.githubusercontent.com/u/1740337?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/costrouc",
"html_url": "https://github.com/costrouc",
"followers_url": "https://api.github.com/users/costrouc/followers",
"following_url": "https://api.github.com/users/costrouc/following{/other_user}",
"gists_url": "https://api.github.com/users/costrouc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/costrouc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/costrouc/subscriptions",
"organizations_url": "https://api.github.com/users/costrouc/orgs",
"repos_url": "https://api.github.com/users/costrouc/repos",
"events_url": "https://api.github.com/users/costrouc/events{/privacy}",
"received_events_url": "https://api.github.com/users/costrouc/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 the most recent code has a DeformationTransformation. That was just added two days ago.\n",
"Found it `pymatgen.transformations.standard_transformations.DeformStructureTransformation`\n\nThanks\n"
] | 2016-05-26T20:43:52
| 2016-05-26T20:56:21
|
2016-05-26T20:56:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
[Feature Request]
I would like to contribute to the pymatgen project and I found a feature that I do not believe is available for Transformations.
Is there a `StrainTransformation` like object that I am missing in the transformation module?
Best,
Chris
|
{
"login": "costrouc",
"id": 1740337,
"node_id": "MDQ6VXNlcjE3NDAzMzc=",
"avatar_url": "https://avatars.githubusercontent.com/u/1740337?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/costrouc",
"html_url": "https://github.com/costrouc",
"followers_url": "https://api.github.com/users/costrouc/followers",
"following_url": "https://api.github.com/users/costrouc/following{/other_user}",
"gists_url": "https://api.github.com/users/costrouc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/costrouc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/costrouc/subscriptions",
"organizations_url": "https://api.github.com/users/costrouc/orgs",
"repos_url": "https://api.github.com/users/costrouc/repos",
"events_url": "https://api.github.com/users/costrouc/events{/privacy}",
"received_events_url": "https://api.github.com/users/costrouc/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/397/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/397/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/398
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/398/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/398/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/398/events
|
https://github.com/materialsproject/pymatgen/pull/398
| 157,082,834
|
MDExOlB1bGxSZXF1ZXN0NzE2MjcxOTU=
| 398
|
Derived hse
|
{
"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 |
[
"Also, \n- changed the \"grid density\" kpoints to \"reciprocal_density\"\n- parse dos and eigen by default (every method calling the function sets those parameters true)\n",
"@shyuep This looks like a pretty bad merge since there was significant changes to sets.py in your refactor. I am going to try to fix...\n",
"Ok this should now be ready for merge - best to give it a once-over though, especially since you are deprecating some sets.\n"
] | 2016-05-26T21:25:33
| 2016-05-26T22:28:24
|
2016-05-26T22:28:24Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Updates and additions for running HSE band structures and gap estimates
- Rename of existing MPBSHSEVaspInputSet (now MPHSEBSVaspInputSet)
- Cleanup / restructuring and minor bug fixes to the code above
- add MPHSEBSSet, a new-style set that for HSE BS
## Additional dependencies introduced (if any)
None
## TODO (if any)
No known todos - should be working and complete.
|
{
"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/398/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/398/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/398",
"html_url": "https://github.com/materialsproject/pymatgen/pull/398",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/398.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/398.patch",
"merged_at": "2016-05-26T22:28:24Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/399
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/399/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/399/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/399/events
|
https://github.com/materialsproject/pymatgen/issues/399
| 157,423,111
|
MDU6SXNzdWUxNTc0MjMxMTE=
| 399
|
Seg fault from SpacegroupAnalyzer on cif file
|
{
"login": "leeaburton",
"id": 3264334,
"node_id": "MDQ6VXNlcjMyNjQzMzQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/3264334?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/leeaburton",
"html_url": "https://github.com/leeaburton",
"followers_url": "https://api.github.com/users/leeaburton/followers",
"following_url": "https://api.github.com/users/leeaburton/following{/other_user}",
"gists_url": "https://api.github.com/users/leeaburton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/leeaburton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/leeaburton/subscriptions",
"organizations_url": "https://api.github.com/users/leeaburton/orgs",
"repos_url": "https://api.github.com/users/leeaburton/repos",
"events_url": "https://api.github.com/users/leeaburton/events{/privacy}",
"received_events_url": "https://api.github.com/users/leeaburton/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 |
[
"For this problem, just add a structure.merge_sites() before determiing symmetry.\n",
"The reason why we don't do it by default is that it is a very expensive operatino to check validity of structures. The user should be responsible for checking structure validity when working with such files.\n"
] | 2016-05-30T02:54:29
| 2016-06-11T03:20:25
|
2016-06-11T03:20:25Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## System
- Pymatgen version: pymatgen-3.6.1
- Python version: Python 2.7.11
- OS version: OSX El Capitan 10.11.5
## Summary
segmentation fault when using SpacegroupAnalyzer on some cif files
## Example code
for filename in glob.glob('*.cif'):
try:
s = Structure.from_file(filename)
a = SpacegroupAnalyzer(s)
except:
pass
## Error message
"python quit unexpectedly" or "Segmentation fault: 11"
## Suggested solution (if any)
previous version of pymatgen exited with helpful message/warning such as 'site occupation > 1' etc.. but current version kills job mid run and gives no indication. Unfortunately not been able to identify the problem
## Files (if any)
Just one of several identified culprit cif files:
```
data_245140-ICSD
#c2014 by Fachinformationszentrum Karlsruhe, and the U.S. Secretary of
#Commerce on behalf of the United States. All rights reserved.
_database_code_ICSD 245140
_audit_creation_date 2007/08/01
_chemical_name_systematic
;
Chromium Selenide Telluride (5.08/2/6)
;
_chemical_formula_structural 'Cr5.08 Se2 Te6'
_chemical_formula_sum 'Cr5.08 Se2 Te6'
_publ_section_title
;
Anion substitution effects on structure and magnetism of the chromium
chalcogenide Cr5 Te8 - Part II: Cluster-glass and spin-glass behavior
in trigonal Cr(1+x) Q2 with basic cells and trigonal Cr(5+x) Q8 with
superstructures (Q = Te, Se; Te:Se = 6:2)
;
loop_
_citation_id
_citation_journal_abbrev
_citation_year
_citation_journal_volume
_citation_journal_issue
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Journal of Solid State Chemistry' 2006 179 7 2067 2078 JSSCBI
_publ_author_name
;
Huang Zhongle;Bensch, W.;Mankovsky, S.;Polesya, S.;Ebert, H.;Kremer,
R.K.
;
_cell_length_a 3.8226(1)
_cell_length_b 3.8226(1)
_cell_length_c 5.9793(2)
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 75.67
_cell_formula_units_Z 2
_symmetry_space_group_name_H-M 'P -3 m 1'
_symmetry_Int_Tables_number 164
_refine_ls_R_factor_all 0.0467
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x-y, -y, -z'
2 '-x, -x+y, -z'
3 'y, x, -z'
4 'x-y, x, -z'
5 'y, -x+y, -z'
6 '-x, -y, -z'
7 '-x+y, y, z'
8 'x, x-y, z'
9 '-y, -x, z'
10 '-x+y, -x, z'
11 '-y, x-y, z'
12 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cr0+ 0
Se0+ 0
Te0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_attached_hydrogens
_atom_site_B_iso_or_equiv
Cr1 Cr0+ 1 b 0 0 0.5 0.576(12) 0 4.79(5)
Cr2 Cr0+ 6 i 0.5022(6) 0.4978(6) 0.2515(13) 1. 0 4.79(5)
Cr3 Cr0+ 2 c 0 0 0.2480(16) 1. 0 4.79(5)
Cr4 Cr0+ 3 e 0 0.5 0 0.528(12) 0 4.79(5)
Te1 Te0+ 2 d 0.3333 0.6667 0.3902(7) 0.75 0 3.56(2)
Te2 Te0+ 2 d 0.3333 0.6667 0.1254(7) 0.75 0 3.56(2)
Te3 Te0+ 6 i 0.1617(4) 0.8383(4) 0.1208(5) 0.75 0 3.56(2)
Te4 Te0+ 6 i 0.8315(4) 0.1685(4) 0.3695(5) 0.75 0 3.56(2)
Se1 Se0+ 2 d 0.3333 0.6667 0.3903(7) 0.25 0 3.56(2)
Se2 Se0+ 2 d 0.3333 0.6667 0.1254(7) 0.25 0 3.56(2)
Se3 Se0+ 6 i 0.1617(4) 0.8382(4) 0.1208(6) 0.25 0 3.56(2)
Se4 Se0+ 6 i 0.8315(4) 0.1685(4) 0.3695(5) 0.25 0 3.56(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/399/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/399/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/400
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/400/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/400/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/400/events
|
https://github.com/materialsproject/pymatgen/issues/400
| 158,243,276
|
MDU6SXNzdWUxNTgyNDMyNzY=
| 400
|
For high symmetry molecules like Carborane PointGroupAnalyzer gives value error: max() arg is an empty sequence
|
{
"login": "navnidhirajput",
"id": 4096364,
"node_id": "MDQ6VXNlcjQwOTYzNjQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/4096364?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/navnidhirajput",
"html_url": "https://github.com/navnidhirajput",
"followers_url": "https://api.github.com/users/navnidhirajput/followers",
"following_url": "https://api.github.com/users/navnidhirajput/following{/other_user}",
"gists_url": "https://api.github.com/users/navnidhirajput/gists{/gist_id}",
"starred_url": "https://api.github.com/users/navnidhirajput/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/navnidhirajput/subscriptions",
"organizations_url": "https://api.github.com/users/navnidhirajput/orgs",
"repos_url": "https://api.github.com/users/navnidhirajput/repos",
"events_url": "https://api.github.com/users/navnidhirajput/events{/privacy}",
"received_events_url": "https://api.github.com/users/navnidhirajput/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 you try to implement a fix with a unittest? This should be relatively easy?\n"
] | 2016-06-02T21:24:35
| 2016-06-03T12:27:18
|
2016-06-03T12:27:18Z
|
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: pymatgen-3.6.1
Python version: Python 2.7.9
OS version: OSX El Capitan 10.11.3
## Summary
For high symmetry molecules like Carborane PointGroupAnalyzer gives value error: max() arg is an empty sequence. It works fine for smaller anions such as TFSI.
## Example code
from monty.os.path import zpath
from pymatgen import Molecule
from pymatgen.io.qchem import QcOutput
from pymatgen.symmetry.analyzer import PointGroupAnalyzer
qcout = QcOutput(zpath("mol.qcout.gz"))
data = qcout.data
mol = data[0]["molecules"][-1]
pga = PointGroupAnalyzer(mol)
## Error message
File "/global/u1/n/nrajput/nr_test/codes/pymatgen/pymatgen/symmetry/analyzer.py", line 743, in **init**
```
self._analyze()
```
File "/global/u1/n/nrajput/nr_test/codes/pymatgen/pymatgen/symmetry/analyzer.py", line 784, in _analyze
```
self._proc_sph_top()
```
File "/global/u1/n/nrajput/nr_test/codes/pymatgen/pymatgen/symmetry/analyzer.py", line 996, in _proc_sph_top
```
main_axis, rot = max(self.rot_sym, key=lambda v: v[1])
```
ValueError: max() arg is an empty sequence
## Files (if any)
Dropbox link: https://www.dropbox.com/s/k2e1g1sif8tin8z/mol.qcout?dl=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/400/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/400/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.