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/eanton... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": n... | |||
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/Zhu... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/Zhu... | {
"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": n... | |||
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/dwins... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 ... | 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 r... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/fra... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks 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_structu... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/comp... | [
{
"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":... | [] | 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...\... | 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.vas... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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": "... | |||
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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks. 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/follow... | {
"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": "... | |||
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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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": "... | |||
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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 t... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/comp... | [
{
"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":... | [] | 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
fro... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/comp... | [
{
"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":... | [] | 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 t... | 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_... | {
"login": "computron",
"id": 986759,
"node_id": "MDQ6VXNlcjk4Njc1OQ==",
"avatar_url": "https://avatars.githubusercontent.com/u/986759?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/computron",
"html_url": "https://github.com/computron",
"followers_url": "https://api.github.com/users/comp... | {
"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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Hi 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 ... | 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.input... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/gp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 vale... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is 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. %mat... | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/us... | [
{
"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,
"nod... | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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... | 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 copyi... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/hyllio... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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... | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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\... | 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/follow... | {
"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": "... | |||
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/comp... | [
{
"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... | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@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 t... | 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 pymat... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/dwins... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 chan... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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.g... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 wro... | 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
-... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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.
- Attachm... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks. 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... | 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... | {
"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/follower... | {
"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": n... | |||
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.g... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks!\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/follow... | {
"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": "... | |||
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.g... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is 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 th... | 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 -0.00000... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"It 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 tes... | 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_fi... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/xhqu1... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 direct... | 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/follow... | {
"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": "... | |||
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/hautier... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks.\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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is 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 ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@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 Ch... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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": "... | ||||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/xhqu1... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks. 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 c... | 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/follow... | {
"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": "... | |||
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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 not... | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/rtrot... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is 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 exa... | 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/follow... | {
"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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/monto... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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,... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/xhqu1... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 ... | 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 stab... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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... | 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 l... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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_util... | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/comp... | [
{
"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":... | [] | 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 sh... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 ba... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/fra... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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. ... | 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 eigen... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 ... | 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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/follower... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 warn... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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 ba... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/xhqu1... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/monto... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks. 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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.col... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 ... | 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 standa... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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",
... | 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 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/follow... | {
"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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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... | 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:... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/gp... | [] | 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/hautier... | [
{
"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.gith... | 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 retu... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Thanks.\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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This is 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.... | 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<... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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:... | 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 ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/follow... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 consider... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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/follow... | {
"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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | ||||
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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/foll... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/monto... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Can you 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 (notificat... | 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... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/monto... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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, an... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/fo... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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.g... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/follow... | {
"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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"This 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.... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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... | [
{
"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,
"nod... | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"@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 th... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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
- A... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [] | 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/sa... | {
"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": n... | |||
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/sa... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"Sorry, 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 ... | {
"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/sa... | {
"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": n... | |||
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/comp... | [
{
"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":... | [] | 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 ... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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/costr... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"I think the 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/costr... | {
"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/comp... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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"... | 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
##... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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": "... | |||
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... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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)
... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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.gith... | [] | closed | false | {
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url":... | [] | null | [
"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 PointGroupAna... | {
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/follow... | {
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/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.