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/2508
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2508/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2508/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2508/events
|
https://github.com/materialsproject/pymatgen/issues/2508
| 1,217,943,241
|
I_kwDOACgets5ImFbJ
| 2,508
|
QUAD_EFG includes units for efg mode of MPNMRSet
|
{
"login": "jacksund",
"id": 47992949,
"node_id": "MDQ6VXNlcjQ3OTkyOTQ5",
"avatar_url": "https://avatars.githubusercontent.com/u/47992949?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jacksund",
"html_url": "https://github.com/jacksund",
"followers_url": "https://api.github.com/users/jacksund/followers",
"following_url": "https://api.github.com/users/jacksund/following{/other_user}",
"gists_url": "https://api.github.com/users/jacksund/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jacksund/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jacksund/subscriptions",
"organizations_url": "https://api.github.com/users/jacksund/orgs",
"repos_url": "https://api.github.com/users/jacksund/repos",
"events_url": "https://api.github.com/users/jacksund/events{/privacy}",
"received_events_url": "https://api.github.com/users/jacksund/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-04-27T22:26:56
| 2022-04-28T15:03:10
|
2022-04-28T15:03:10Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
The MPNMRSet (with mode="efg") writes units to file for the QUAD_EFG setting. This occurs because it is using FloatWithUnit class under the hood.
**To Reproduce**
``` python
from pymatgen.core import Structure
from pymatgen.io.vasp.sets import MPNMRSet
# Random structure to test with
s = Structure(
lattice=[
[3.485437, 0.0, 2.012318],
[1.161812, 3.286101, 2.012318],
[0.0, 0.0, 4.024635],
],
species=["Na", "Cl"],
coords=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
)
MPNMRSet(s, mode="efg").incar.write_file("INCAR")
```
This produces the following INCAR:
```
ALGO = FAST
EDIFF = -1e-10
ENCUT = 520
IBRION = -1
ISIF = 3
ISMEAR = -5
ISPIN = 2
ISYM = 0
LAECHG = True
LASPH = True
LCHARG = False
LEFG = True
LORBIT = 11
LREAL = Auto
LVHAR = True
LWAVE = False
MAGMOM = 2*0.6
NELM = 100
NELMIN = 10
NSW = 0
PREC = ACCURATE
QUAD_EFG = 104.1 mbarn -81.65 mbarn # <------------ Note the bug here
SIGMA = 0.01
```
**Expected behavior**
The INCAR should instead have the following result for QUAD_EFG:
```
QUAD_EFG = 104.1 -81.65
```
**Desktop:**
- OS: Linux
- Version 2022.4.19
**Additional context**
This is a quick, one-line fix. We need to just convert from FloatWithUnit to Float here:
https://github.com/materialsproject/pymatgen/blob/1b6d1d2212dcf3a559cb2c489dd25e9754f9f788/pymatgen/io/vasp/sets.py#L1942
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2508/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2508/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2509
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2509/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2509/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2509/events
|
https://github.com/materialsproject/pymatgen/pull/2509
| 1,217,949,043
|
PR_kwDOACgets425-Gc
| 2,509
|
fix bug with nmr set writing units
|
{
"login": "jacksund",
"id": 47992949,
"node_id": "MDQ6VXNlcjQ3OTkyOTQ5",
"avatar_url": "https://avatars.githubusercontent.com/u/47992949?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jacksund",
"html_url": "https://github.com/jacksund",
"followers_url": "https://api.github.com/users/jacksund/followers",
"following_url": "https://api.github.com/users/jacksund/following{/other_user}",
"gists_url": "https://api.github.com/users/jacksund/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jacksund/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jacksund/subscriptions",
"organizations_url": "https://api.github.com/users/jacksund/orgs",
"repos_url": "https://api.github.com/users/jacksund/repos",
"events_url": "https://api.github.com/users/jacksund/events{/privacy}",
"received_events_url": "https://api.github.com/users/jacksund/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Please add a Unittest to catch this bug and prevent it from recurring. ",
"Yep, I'm working on that now :smile: ",
"\n[](https://coveralls.io/builds/48642946)\n\nCoverage decreased (-0.7%) to 83.279% when pulling **08daf1518e1c2377df7b149c866ee686a3d2ee9a on jacksund:fix-nmr-set** into **6c84eb53f00de42dc2110ce39f3ce4c083c5e0a9 on materialsproject:master**.\n",
"I was trying to add a lower-level check to all float-type INCAR settings, but am unsure the best place to do this. Maybe this would be in the `get_string` method of the `Incar` class? Might be something to consider in order to avoid issues with other vasp sets.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/6c84eb53f00de42dc2110ce39f3ce4c083c5e0a9/pymatgen/io/vasp/inputs.py#L693\r\n\r\nAnd the addition would be something like...\r\n``` python\r\nelif isinstance(self[k], float):\r\n # note the added float() which ensures FloatWithUnit conversion\r\n lines.append([k, \" \".join([str(float(i)) for i in self[k]])])\r\n# plus another check for a list of floats\r\n```\r\n\r\nEDIT: currently this PR only implements a check on the NMR set. This lower-level check would need to be a separate PR",
"@shyuep a unittest is in place and this is ready for review",
"Thanks."
] | 2022-04-27T22:35:52
| 2022-06-22T13:19:00
|
2022-04-28T15:03:11Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
resolves #2508
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2509/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2509/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2509",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2509",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2509.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2509.patch",
"merged_at": "2022-04-28T15:03:10Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2510
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2510/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2510/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2510/events
|
https://github.com/materialsproject/pymatgen/issues/2510
| 1,218,762,886
|
I_kwDOACgets5IpNiG
| 2,510
|
LAMMPS IO: update to accomodate pandas deprecation
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks. Go ahead and submit a PR to fix this.",
"@manaslkht would you be able to tackle this?",
"@rkingsbury Yes, will get this done by this weekend. "
] | 2022-04-28T13:50:28
| 2022-10-22T17:41:42
|
2022-10-22T17:41:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
Several lines in `pymatgen.io.lammps.data.py` make use of the pandas `DataFrame.append` method, which is being deprecated, causing many warnings along the lines of:
```
/Users/ryan/miniconda3/envs/md/code/pymatgen/pymatgen/io/lammps/data.py:1283:
FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version.
Use pandas.concat instead.
self.atoms = self.atoms.append(atoms_df, ignore_index=True)
/Users/ryan/miniconda3/envs/md/code/pymatgen/pymatgen/io/lammps/data.py:1307:
FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version.
Use pandas.concat instead.
self.topology[kw] = self.topology[kw].append(topo_df, ignore_index=True)
```
when creating `CombinedData` objects. These calls should be replaced with `pd.concat` as directed by the warning. Note that there may be other instances of `DataFrame.append` beyond the two lines referenced - these are just two that I encountered in my work recently.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2510/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2510/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2511
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2511/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2511/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2511/events
|
https://github.com/materialsproject/pymatgen/issues/2511
| 1,218,821,550
|
I_kwDOACgets5Ipb2u
| 2,511
|
Packmol IO: Address which deprecation
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Go ahead and submit a PR to change this.",
"Nvm I just puyshed a fix."
] | 2022-04-28T14:30:56
| 2022-04-28T15:05:49
|
2022-04-28T15:02:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The `run` method of Packmol IO makes use of `monty.io.which` to detect whether packmol is installed, and this method will be deprecated soon. This should be changed to `shutil.which` from the standard library, or (perhaps a better solution), use the `monty.dev.requires` decorator as shown [here](https://github.com/materialsproject/pymatgen/blob/95352c96d7aba865d01230d5c32a5a6704c0edba/pymatgen/io/babel.py#L39).
```
/Users/ryan/miniconda3/envs/md/code/pymatgen/pymatgen/io/packmol.py:54:
FutureWarning: which is deprecated; use which in shutil instead.
shutil.which has been available since Python 3.3. This will be removed in v2023.
if not which("packmol"):
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2511/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2511/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2512
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2512/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2512/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2512/events
|
https://github.com/materialsproject/pymatgen/pull/2512
| 1,223,245,782
|
PR_kwDOACgets43L55e
| 2,512
|
[pre-commit.ci] pre-commit autoupdate
|
{
"login": "pre-commit-ci[bot]",
"id": 66853113,
"node_id": "MDM6Qm90NjY4NTMxMTM=",
"avatar_url": "https://avatars.githubusercontent.com/in/68672?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D",
"html_url": "https://github.com/apps/pre-commit-ci",
"followers_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/48766999)\n\nCoverage decreased (-0.001%) to 84.04% when pulling **efd51159085d0fcea9452bf6d5e251266bc51812 on pre-commit-ci-update-config** into **6302e7db8c9c46d8a69b2a2888e9ca5880e43e5f on master**.\n"
] | 2022-05-02T19:12:44
| 2022-05-02T19:40:41
|
2022-05-02T19:14:29Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.31.1 → v2.32.0](https://github.com/asottile/pyupgrade/compare/v2.31.1...v2.32.0)
- [github.com/pre-commit/pre-commit-hooks: v4.1.0 → v4.2.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.1.0...v4.2.0)
- [github.com/pre-commit/mirrors-mypy: v0.942 → v0.950](https://github.com/pre-commit/mirrors-mypy/compare/v0.942...v0.950)
<!--pre-commit.ci end-->
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2512/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2512/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2512",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2512",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2512.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2512.patch",
"merged_at": "2022-05-02T19:14:29Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2513
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2513/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2513/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2513/events
|
https://github.com/materialsproject/pymatgen/issues/2513
| 1,225,156,651
|
I_kwDOACgets5JBmgr
| 2,513
|
how to convert many cif file to poscar format in vasp?
|
{
"login": "Amadeus-System",
"id": 76824867,
"node_id": "MDQ6VXNlcjc2ODI0ODY3",
"avatar_url": "https://avatars.githubusercontent.com/u/76824867?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Amadeus-System",
"html_url": "https://github.com/Amadeus-System",
"followers_url": "https://api.github.com/users/Amadeus-System/followers",
"following_url": "https://api.github.com/users/Amadeus-System/following{/other_user}",
"gists_url": "https://api.github.com/users/Amadeus-System/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Amadeus-System/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Amadeus-System/subscriptions",
"organizations_url": "https://api.github.com/users/Amadeus-System/orgs",
"repos_url": "https://api.github.com/users/Amadeus-System/repos",
"events_url": "https://api.github.com/users/Amadeus-System/events{/privacy}",
"received_events_url": "https://api.github.com/users/Amadeus-System/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Sorry, I found useful way in pymatgen tutorial. Thank you very much!",
"You might also have a look here: https://matsci.org/c/pymatgen/9\r\n\r\nThis is the discussion forum and the place where you can ask about the usage of pymatgen 🙂."
] | 2022-05-04T09:56:58
| 2022-05-04T10:13:55
|
2022-05-04T10:01:22Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi. I am a researcher in computational physics and I have been using pymatgen very well.
Recently, I have obtained hundreds (or even thousands of) of CIF files and I need to convert all CIF files to POSCAR format in vasp.
I already know how to convert single cif file to poscar format using VESTA, but I would like to know more convenient ways to process many cif files.
When I access to pymatgen homepage, example codes just show how to read information in poscar file and save it to cif format.
Do you know another ways that save structure information to poscar format in vasp?
I expect your kind explanation. Thank you!
|
{
"login": "Amadeus-System",
"id": 76824867,
"node_id": "MDQ6VXNlcjc2ODI0ODY3",
"avatar_url": "https://avatars.githubusercontent.com/u/76824867?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Amadeus-System",
"html_url": "https://github.com/Amadeus-System",
"followers_url": "https://api.github.com/users/Amadeus-System/followers",
"following_url": "https://api.github.com/users/Amadeus-System/following{/other_user}",
"gists_url": "https://api.github.com/users/Amadeus-System/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Amadeus-System/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Amadeus-System/subscriptions",
"organizations_url": "https://api.github.com/users/Amadeus-System/orgs",
"repos_url": "https://api.github.com/users/Amadeus-System/repos",
"events_url": "https://api.github.com/users/Amadeus-System/events{/privacy}",
"received_events_url": "https://api.github.com/users/Amadeus-System/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2513/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2513/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2514
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2514/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2514/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2514/events
|
https://github.com/materialsproject/pymatgen/pull/2514
| 1,226,053,650
|
PR_kwDOACgets43UrcB
| 2,514
|
Replace IALGO with ALGO in MVLNPTMDSet
|
{
"login": "qianchenqc",
"id": 92953848,
"node_id": "U_kgDOBYpc-A",
"avatar_url": "https://avatars.githubusercontent.com/u/92953848?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/qianchenqc",
"html_url": "https://github.com/qianchenqc",
"followers_url": "https://api.github.com/users/qianchenqc/followers",
"following_url": "https://api.github.com/users/qianchenqc/following{/other_user}",
"gists_url": "https://api.github.com/users/qianchenqc/gists{/gist_id}",
"starred_url": "https://api.github.com/users/qianchenqc/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/qianchenqc/subscriptions",
"organizations_url": "https://api.github.com/users/qianchenqc/orgs",
"repos_url": "https://api.github.com/users/qianchenqc/repos",
"events_url": "https://api.github.com/users/qianchenqc/events{/privacy}",
"received_events_url": "https://api.github.com/users/qianchenqc/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/48846336)\n\nCoverage decreased (-0.7%) to 83.295% when pulling **5acde0edd9ca1730583c82084c33809439b34f42 on qianchenqc:master** into **61032a3365cfbae66d1aefae6c6606b66361ca80 on materialsproject:master**.\n",
"Thanks."
] | 2022-05-04T23:12:44
| 2022-05-05T13:21:24
|
2022-05-05T13:21:17Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Replaced the IALGO tag with ALGO as recommended in the vasp documentation https://www.vasp.at/wiki/index.php/IALGO.
* Removed IALGO tag to enable Davidson first and then switch to the RMM-DIIS with ALGO=Fast.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2514/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2514/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2514",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2514",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2514.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2514.patch",
"merged_at": "2022-05-05T13:21:17Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2515
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2515/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2515/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2515/events
|
https://github.com/materialsproject/pymatgen/pull/2515
| 1,227,472,192
|
PR_kwDOACgets43ZSxD
| 2,515
|
Clean up Trajectory
|
{
"login": "mjwen",
"id": 10203513,
"node_id": "MDQ6VXNlcjEwMjAzNTEz",
"avatar_url": "https://avatars.githubusercontent.com/u/10203513?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mjwen",
"html_url": "https://github.com/mjwen",
"followers_url": "https://api.github.com/users/mjwen/followers",
"following_url": "https://api.github.com/users/mjwen/following{/other_user}",
"gists_url": "https://api.github.com/users/mjwen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mjwen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mjwen/subscriptions",
"organizations_url": "https://api.github.com/users/mjwen/orgs",
"repos_url": "https://api.github.com/users/mjwen/repos",
"events_url": "https://api.github.com/users/mjwen/events{/privacy}",
"received_events_url": "https://api.github.com/users/mjwen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51100719)\n\nCoverage decreased (-20.5%) to 63.575% when pulling **9d8a0cfc1b4e8fcc5e037a9aadf30c8a474a572a on mjwen:master** into **2b75957884934470962b56c644588eba1454dbaa on materialsproject:master**.\n",
"The changes look good so far. They make things more clear/transparent about what's happening. \r\n\r\n While this isn't being used much in our group at the moment, It's unclear to me how many people are using it by external users of pymatgen. What did you have in mind for changes to to_positions() and to_displacements()? I'd be a bit cautious to make changes that change the fundamental operation of the class.\r\n \r\n P.S. On line 167, regarding your comment about figuring out what that code is doing:\r\n It's correcting the displacements to account for periodic boundary conditions (in a wrapped simulation). For example - If in one frame an atom has fractional coordinates of [0, 0, 0.98] and in the next its coordinates are [0, 0, 0.01], this atom will have moved 0.03*c, but if we only subtract the positions, we would get a displacement vector of [0, 0, -0.97]. Therefore, we can correct for this by adding or subtracting 1 from the value. To do this in a more simple way, we can just round that displacement vector (to [0, 0, -1]) and subtract it from the original displacement vector, giving us the correct displacement vector of [0, 0, 0.03].",
"Thanks @sivonxay ! \r\n\r\nYes, I hear you. We'd better keep backward compatibility as much as possible.\r\n\r\nI guess the biggest issue for me is why keeping possibilities to use either frac_coords and displacement. Currently methods like `__getitem__` are heavily overloaded. The returns depend heavily on the input type, and which mode (frac_coods or displacement) this class is in. I am imagining using only one of them, and then possibly a separate utility function to convert between the two. Hopefully this will significantly simplify the code. I guess I did not know the use cases, and keeping both of them might be easier in some cases. But for backward compatibility stuff, I think we'd better stick to what it is now. \r\n\r\n\r\n \r\n\r\n\r\n\r\n",
"@mkhorton @sivonxay I've finally got this cleaned up. I've introduced one backward incompatibility (see top). \r\n\r\nIn addition, I have two TODOs to remove some code to further simplify it, and would love your feedback. \r\n- Remove the .copy() function. We can use `copy.copy()`. \r\n- Remove the mode to return frac_coords in `__getitem__`, simplifying it to avoid overloading \r\n\r\nAfter we get these two fixed, it'll be good for you to review. ",
"Thanks @mjwen, I'll take a look -- I think the change to `frame_properties` is very sensible.",
"Let me know when this is ready to merge @mjwen when the last action items are handled, otherwise looks good",
"I hoped to get some feedback on whether we want to do the two action items, and was waiting for it. But looking at my comments above, it is very badly communicated. 😞Thanks for checking back @mkhorton ! \r\n\r\n I am leaning towards performing the two items, and if you also think so, I'll make the changes.",
"No problem, I mis-read too -- as long as `copy.copy()` works as expected, I would remove it. I'm also in favor of simplifying `__getitems__`, although which mode should be the default I'm less sure about.",
"@mkhorton I handled the two items, and this is ready for merging. ",
"These changes look good. Thanks for cleaning up this class, @mjwen!",
"Thanks both, will get this merged. Adding a note to myself to include a mention of this change on our [compatibility](https://pymatgen.org/compatibility.html#recent-breaking-changes) page.",
"Sorry I let this sit before merging, and now we have some merge conflicts. Would it be ok to ask to resolve? It's a bit confusing because both branch names are named `master` or I would have resolved quickly myself, but just want to make sure.",
"@mkhorton conflicts resolved. Should be good now. ",
"Thanks @mjwen!",
"I saw this GH action error, which may require a hot fix? \r\n```\r\n7s\r\n[1](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:1)\r\nRun pytest pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line --cov=pymatgen\r\n[9](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:10)\r\n\r\n[10](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:11)\r\n==================================== ERRORS ====================================\r\n[11](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:12)\r\n___________ ERROR collecting pymatgen/core/tests/test_trajectory.py ____________\r\n[12](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:13)\r\npymatgen/core/tests/test_trajectory.py:8: in <module>\r\n[13](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:14)\r\n from pymatgen.core.trajectory import Trajectory\r\n[14](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:15)\r\npymatgen/core/trajectory.py:35: in <module>\r\n[15](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:16)\r\n Vector3D = tuple[float, float, float]\r\n[16](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:17)\r\nE TypeError: 'type' object is not subscriptable\r\n[17](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:18)\r\n!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n[18](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:19)\r\n1 error in 6.55s\r\n[19](https://github.com/materialsproject/pymatgen/runs/8083026804?check_suite_focus=true#step:4:20)\r\nError: Process completed with exit code 1.\r\n```"
] | 2022-05-06T06:30:51
| 2022-08-30T01:40:01
|
2022-08-30T01:29:50Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR cleans up the Trajectory class:
- add type annotation
- make doc string consistent with what the code is actually doing
- remove unused code pieces and slightly reorganize some parts
This breaks backward compatibility in one place. Previous `frame_properties` accepts a dict as input and properties of different frames are gathered in a sequence. Now, it has a similar signature as `site_properties`, that is, it accepts a list of dict, one for each frame. By doing this, the `frame_properties` can accommodate more use cases, e.g. accepting nested dict as frame properties, also, this makes extending and slicing easier.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2515/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2515/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2515",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2515",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2515.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2515.patch",
"merged_at": "2022-08-30T01:29:50Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2516
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2516/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2516/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2516/events
|
https://github.com/materialsproject/pymatgen/issues/2516
| 1,228,408,102
|
I_kwDOACgets5JOAUm
| 2,516
|
unclear how to retrieve bandstructures
|
{
"login": "rkurchin",
"id": 11233777,
"node_id": "MDQ6VXNlcjExMjMzNzc3",
"avatar_url": "https://avatars.githubusercontent.com/u/11233777?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkurchin",
"html_url": "https://github.com/rkurchin",
"followers_url": "https://api.github.com/users/rkurchin/followers",
"following_url": "https://api.github.com/users/rkurchin/following{/other_user}",
"gists_url": "https://api.github.com/users/rkurchin/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkurchin/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkurchin/subscriptions",
"organizations_url": "https://api.github.com/users/rkurchin/orgs",
"repos_url": "https://api.github.com/users/rkurchin/repos",
"events_url": "https://api.github.com/users/rkurchin/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkurchin/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hi @rkurchin, thanks for sharing this experience, this kind of feedback is useful!\r\n\r\nOne factor here is that you've caught us during a transition period where we're deploying a new API (first major change in 10+ years), which is going to cause some additional confusion since it changes some things, see https://next-gen.materialsproject.org/api for a comparison table between the two -- in particular, be aware that the new API is the one receiving new database updates, and the legacy API is frozen to an older database version, so there may be disagreements between the two.\r\n\r\nSome general comments:\r\n\r\n* For now, we are still recommending people use the API you're using, but I did want to highlight the new API since this advice may change in the near future. One of the reasons we're developing the new API is to have an opportunity to clear up some points of confusion like this, although the fundamental issue of the difference between `task_id` and `material_id` will remain since this is baked into the database design.\r\n\r\n* In the new MPRester, `mpr.get_bandstructure_by_material_id()` should return the bandstructure for either the `material_id` or the `task_id`. For the latter, it will print a warning and the corresponding `material_id`.\r\n\r\n* I tried to think what this query would look like in the new API and came up with this:\r\n\r\n```\r\nfrom mp_api import MPRester\r\nfrom emmet.core.summary import HasProps # non-obvious import\r\n\r\nmpr = MPRester()\r\n\r\ndocs = mpr.summary.search_summary_docs(\r\n energy_above_hull=0,\r\n has_props=[HasProps.bandstructure],\r\n fields=[\"material_id\"]\r\n) # returns 64,115 entries, i.e. only those with bandstructure objects\r\n\r\n\r\nbs = mpr.get_bandstructure_by_material_id(docs[0].material_id) # retrieve a sample band structure\r\n```\r\n\r\n* Based on this example, I would think something that might still confuse new users is the `HasProps` import, so perhaps something for us to think about.\r\n\r\nTagging @munrojm, who's been leading the new API development, in case he wants to comment further or correct me if I've mis-stated anything.\r\n\r\n@munrojm, I also noticed another user experience issues which is that querying for a valid `material_id`, but for which a bandstructure object is _not_ available, the error message is perhaps not helpful.\r\n\r\nSome more examples from the new API are here: https://next-gen-docs.materialsproject.org/downloading-data/using-the-api/examples\r\n\r\nSince this is being developed in a separate repo, if there are follow-up issues related to the new API, they can be posted at https://github.com/materialsproject/api\r\n",
"Another place to post generate usage questions or feedback about the API is https://matsci.org/materials-project too, which is the more general Materials Project discussion forum.",
"Thanks for the detailed reply; this is all useful context and very helpful! I'll poke around with the new API too, looks like there are some exciting and useful improvements!\r\n\r\nAlso, so noted about the forum as well – I had already debated if this or mapidoc was the right place to file this issue, but seems like that might have been a better option all-around. 😄 ",
"Yes, apologies, there are in some ways too many places to ask questions, and not obvious where the best place might be (and not everyone monitors every venue), so it's really ok to ask questions wherever, and I do my best to route them to the right people when I can!",
"I realize I gave an error in my example above too; querying for a zero energy above hull would look like this:\r\n\r\n```\r\ndocs = mpr.summary.search_summary_docs(\r\n energy_above_hull=[0, 0], # this is a range, for a min/max of 0\r\n has_props=[HasProps.bandstructure],\r\n fields=[\"material_id\"]\r\n) # now returns 21,291 entries, i.e. only those with bandstructure objects\r\n```\r\n\r\nCorrecting for the record."
] | 2022-05-06T21:43:04
| 2022-05-10T03:08:09
|
2022-05-10T03:08:09Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
This is not _exactly_ a bug, so much as something I thought was a bug but was actually unclear documentation.
Basically, I wanted to download entries corresponding to stable materials with nonzero bandgap that have computed bandstructures. I'll describe what I did below...
**To Reproduce**
Steps to reproduce the behavior:
I want to download entries corresponding to stable materials with nonzero bandgap that have bandstructures computed.
With the following setup:
```python
from pymatgen.ext.matproj import MPRester
m = MPRester(api_key=api_key)
```
First, I tried:
```python
data = m.query(criteria={"e_above_hull":0, "has_bandstructure":True, "band_gap":{"$gt":0}},
properties=["full_formula","material_id", #"cif",
"elements","band_structure", "band_gap"])
```
This gave me a list of 11700 entries, but most of them seem not to actually have bandstructures, e.g. here's `data[1]`:
```python
{'full_formula': 'Hf2S1N2',
'material_id': 'mp-1017567',
'elements': ['Hf', 'N', 'S'],
'band_structure': None,
'band_gap': 1.0769000000000002}
```
(spoiler: this turns out to be the correct approach, but in a non-obvious way that I think should be clarified somehow)
So I next changed my query from `"has_bandstructure":True` to instead include `"band_structure":{"$ne":None}`. This gave a much shorter list of 180 entries, and `data[1]` looks like
```python
{'full_formula': 'Mg2U4P4H40O44',
'material_id': 'mp-1211200',
'elements': ['H', 'Mg', 'O', 'P', 'U'],
'band_structure': {'GGA': {'task_id': 'mp-1628661'}},
'band_gap': 2.4764999999999997}
```
I understood from [the API documentation](https://github.com/materialsproject/mapidoc) that a query for bandstructure wouldn't actually return the bandstructure, but rather a reference to it, which I assume is what that other `mp-XXX` ID is.
So now I try `bs = m.get_bandstructure_by_material_id('mp-1628661')` but I get an `IndexError`. Hmm. Next, I try the `material_id` field and do `bs = m.get_bandstructure_by_material_id('mp-1211200')` but that just returns a `NoneType`.
Initially, I came here to file a "traditional" bug report that this wasn't working, but then I (honestly kind of by accident) tried the `material_id` from `data[1]` in my first query from the longer list, and lo and behold, I got a bandstructure object! Problem solved.
**Expected behavior**
I expected more intuitive names of things and/or documentation of what the names mean. As I said, I did eventually figure out the "correct" way to do what I was trying to do, but it took awhile. While I can understand how `material_id` and `task_id` would be different and thus my first attempt was perhaps nonsensical, I maintain that the inequivalence of the two queries `"has_bandstructure":True` and `"band_structure":{"$ne":None}` can lead to confusion...if lead devs agree, I'm certainly happy to help brainstorm and/or contribute to solutions to this.
**Desktop (please complete the following information):**
- OS: macOS Monterey
- Version 2022.4.26
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2516/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2516/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2517
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2517/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2517/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2517/events
|
https://github.com/materialsproject/pymatgen/pull/2517
| 1,231,165,769
|
PR_kwDOACgets43k8Iy
| 2,517
|
Fixed MSONable + InputSet's str(object)
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/48988239)\n\nCoverage decreased (-0.7%) to 83.319% when pulling **79e1a8770942671ec2b51dce7c0f6dccdca34f88 on davidwaroquiers:input_sets_strcast** into **2b75957884934470962b56c644588eba1454dbaa on materialsproject:master**.\n",
"Thanks."
] | 2022-05-10T13:29:34
| 2022-05-10T17:26:50
|
2022-05-10T17:26:50Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Added functionality to write the __str__ contents of an object in the contents of one of the InputSet's files, if this object is not an instance (subclass) of InputFile.
* Added unit tests for InputFile and InputSet.
* Fixed MSONable for InputSet when kwargs are given.
## 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/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2517/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2517/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2517",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2517",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2517.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2517.patch",
"merged_at": "2022-05-10T17:26:50Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2518
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2518/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2518/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2518/events
|
https://github.com/materialsproject/pymatgen/pull/2518
| 1,232,801,163
|
PR_kwDOACgets43qO80
| 2,518
|
Fix reading of orbitalwise ICOHPLIST.lobster
|
{
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/followers",
"following_url": "https://api.github.com/users/JaGeo/following{/other_user}",
"gists_url": "https://api.github.com/users/JaGeo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JaGeo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JaGeo/subscriptions",
"organizations_url": "https://api.github.com/users/JaGeo/orgs",
"repos_url": "https://api.github.com/users/JaGeo/repos",
"events_url": "https://api.github.com/users/JaGeo/events{/privacy}",
"received_events_url": "https://api.github.com/users/JaGeo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49030586)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **066299048cfb779c8edabc8792ff60e31aafdca1 on JaGeo:master** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"From my side, this would be ready. Let me know if I can do anything else.",
"Thanks. "
] | 2022-05-11T15:03:51
| 2022-05-17T14:59:14
|
2022-05-17T14:59:08Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
By accident, the wrong line in ICOHPLIST.lobster was read to assess whether orbitalwise interactions are included in these files. This lead to erros in case the first atom only has one relevant valence orbital. I fixed the problem. And, I included a test to fix this for the future.
JG
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2518/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2518/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2518",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2518",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2518.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2518.patch",
"merged_at": "2022-05-17T14:59:08Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2519
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2519/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2519/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2519/events
|
https://github.com/materialsproject/pymatgen/issues/2519
| 1,233,100,521
|
I_kwDOACgets5Jf57p
| 2,519
|
`Atoms` --> `Structure` conversion fails for linear molecules
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Never mind. This was a user error. I called `.get_structure()` on a non-PBC object. It should have been `.get_molecule()`. It could be worth adding a check for this."
] | 2022-05-11T19:36:50
| 2022-06-06T23:49:53
|
2022-05-11T19:44:30Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
For linear structures, the ASE `Atoms` to Pymatgen `Structure` conversion fails due to a singular matrix.
```python
from ase.build import molecule
from pymatgen.io.ase import AseAtomsAdaptor
atoms = molecule('CO2')
AseAtomsAdaptor.get_structure(atoms)
```
```python
--------------------------------------------------------------------------
LinAlgError Traceback (most recent call last)
Input In [8], in <module>
----> 1 p = AseAtomsAdaptor.get_structure(a)
File c:\users\asros\github\pymatgen\pymatgen\io\ase.py:200, in AseAtomsAdaptor.get_structure(atoms, cls, **cls_kwargs)
198 structure = cls(symbols, positions, **cls_kwargs)
199 else:
--> 200 structure = cls(lattice, symbols, positions, coords_are_cartesian=True, **cls_kwargs)
202 # Set the site magmoms in the Pymatgen structure object
203 # Note: ASE distinguishes between initial and converged
204 # magnetic moment site properties, whereas pymatgen does not. Therefore, we
(...)
209 # ASE initial charge <--> Pymatgen "charge"
210 # ASE final charge <--> Pymatgen "final_charge"
211 if magmoms is not None:
File c:\users\asros\github\pymatgen\pymatgen\core\structure.py:3207, in Structure.__init__(self, lattice, species, coords, charge, validate_proximity, to_unit_cell, coords_are_cartesian, site_properties)
3162 def __init__(
3163 self,
3164 lattice: ArrayLike | Lattice,
(...)
3171 site_properties: dict = None,
3172 ):
3173 """
3174 Create a periodic structure.
3175
(...)
3205 fractional_coords. Defaults to None for no properties.
3206 """
-> 3207 super().__init__(
3208 lattice,
3209 species,
3210 coords,
3211 charge=charge,
3212 validate_proximity=validate_proximity,
3213 to_unit_cell=to_unit_cell,
3214 coords_are_cartesian=coords_are_cartesian,
3215 site_properties=site_properties,
3216 )
3218 self._sites: list[PeriodicSite] = list(self._sites)
File c:\users\asros\github\pymatgen\pymatgen\core\structure.py:705, in IStructure.__init__(self, lattice, species, coords, charge, validate_proximity, to_unit_cell, coords_are_cartesian, site_properties)
701 if site_properties:
702 prop = {k: v[i] for k, v in site_properties.items()}
704 sites.append(
--> 705 PeriodicSite(
706 sp,
707 coords[i],
708 self._lattice,
709 to_unit_cell,
710 coords_are_cartesian=coords_are_cartesian,
711 properties=prop,
712 )
713 )
714 self._sites: tuple[PeriodicSite, ...] = tuple(sites)
715 if validate_proximity and not self.is_valid():
File c:\users\asros\github\pymatgen\pymatgen\core\sites.py:333, in PeriodicSite.__init__(self, species, coords, lattice, to_unit_cell, coords_are_cartesian, properties, skip_checks)
307 """
308 Create a periodic site.
309
(...)
329 controlled manner and speed is desired.
330 """
332 if coords_are_cartesian:
--> 333 frac_coords = lattice.get_fractional_coords(coords)
334 else:
335 frac_coords = coords # type: ignore
File c:\users\asros\github\pymatgen\pymatgen\core\lattice.py:171, in Lattice.get_fractional_coords(self, cart_coords)
161 def get_fractional_coords(self, cart_coords: ArrayLike) -> np.ndarray:
162 """
163 Returns the fractional coordinates given Cartesian coordinates.
164
(...)
169 Fractional coordinates.
170 """
--> 171 return dot(cart_coords, self.inv_matrix)
File c:\users\asros\github\pymatgen\pymatgen\core\lattice.py:138, in Lattice.inv_matrix(self)
134 """
135 Inverse of lattice matrix.
136 """
137 if self._inv_matrix is None:
--> 138 self._inv_matrix = inv(self._matrix)
139 self._inv_matrix.setflags(write=False)
140 return self._inv_matrix
File <__array_function__ internals>:5, in inv(*args, **kwargs)
File ~\miniconda3\envs\cms\lib\site-packages\numpy\linalg\linalg.py:545, in inv(a)
543 signature = 'D->D' if isComplexType(t) else 'd->d'
544 extobj = get_linalg_error_extobj(_raise_linalgerror_singular)
--> 545 ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
546 return wrap(ainv.astype(result_t, copy=False))
File ~\miniconda3\envs\cms\lib\site-packages\numpy\linalg\linalg.py:88, in _raise_linalgerror_singular(err, flag)
87 def _raise_linalgerror_singular(err, flag):
---> 88 raise LinAlgError("Singular matrix")
LinAlgError: Singular matrix
```
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2519/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2519/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2520
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2520/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2520/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2520/events
|
https://github.com/materialsproject/pymatgen/pull/2520
| 1,233,243,098
|
PR_kwDOACgets43rr6p
| 2,520
|
Add rotational symmetry number property to `PointGroupAnalyzer`
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49048738)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **05cbb1febd9b4e259d27ce381267f222694239fd on arosen93:rosen-symm** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"Thanks."
] | 2022-05-11T22:28:02
| 2022-05-17T14:58:46
|
2022-05-17T14:58:41Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This PR adds a new property to the `PointGroupAnalyzer`: the rotational symmetry number.
Example:
```python
from pymatgen.core import Molecule
from pymatgen.symmetry.analyzer import PointGroupAnalyzer
CH4 = Molecule.from_file('methane.xyz')
pga = PointGroupAnalyzer(CH4)
print(pga.get_rotational_symmetry_number()) # outputs 12
```
This is often needed for thermochemical analyses.
Edit: Thanks for the help, @munrojm!
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2520/reactions",
"total_count": 3,
"+1": 1,
"-1": 0,
"laugh": 1,
"hooray": 0,
"confused": 0,
"heart": 1,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2520/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2520",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2520",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2520.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2520.patch",
"merged_at": "2022-05-17T14:58:41Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2521
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2521/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2521/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2521/events
|
https://github.com/materialsproject/pymatgen/pull/2521
| 1,234,399,551
|
PR_kwDOACgets43vfpq
| 2,521
|
Q-Chem updates to NBO and new geometry optimizer
|
{
"login": "samblau",
"id": 7431223,
"node_id": "MDQ6VXNlcjc0MzEyMjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/7431223?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/samblau",
"html_url": "https://github.com/samblau",
"followers_url": "https://api.github.com/users/samblau/followers",
"following_url": "https://api.github.com/users/samblau/following{/other_user}",
"gists_url": "https://api.github.com/users/samblau/gists{/gist_id}",
"starred_url": "https://api.github.com/users/samblau/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/samblau/subscriptions",
"organizations_url": "https://api.github.com/users/samblau/orgs",
"repos_url": "https://api.github.com/users/samblau/repos",
"events_url": "https://api.github.com/users/samblau/events{/privacy}",
"received_events_url": "https://api.github.com/users/samblau/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49386982)\n\nCoverage decreased (-0.8%) to 83.285% when pulling **0bf3c4c4f3552db52da5465339332cdc6f4d64b0 on samblau:qchem** into **30e36f658aa121ee58caf962e230014e0e3fbbf9 on materialsproject:master**.\n",
"@mkhorton This should be ready for review and to be merged. Thanks!"
] | 2022-05-12T19:30:59
| 2022-05-24T14:06:13
|
2022-05-24T14:06:13Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Tweaks to Q-Chem - NBO functionality given latest Q-Chem release
* IO for new geometry optimizer that is hidden but present in latest Q-Chem release
* Parsing various new errors
Ready to merge!
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2521/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2521/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2521",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2521",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2521.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2521.patch",
"merged_at": "2022-05-24T14:06:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2522
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2522/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2522/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2522/events
|
https://github.com/materialsproject/pymatgen/pull/2522
| 1,235,788,492
|
PR_kwDOACgets430CEP
| 2,522
|
fixed deserialization of phase diagrams
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49117949)\n\nCoverage decreased (-0.7%) to 83.324% when pulling **bb87db4c4fa73d731a21fae0433ba5c7db9e332c on jmmshn:pd_fix** into **8a78794a8965586802ae350d11af7ec8d51b9671 on materialsproject:master**.\n",
"Thanks @jmmshn!"
] | 2022-05-13T23:23:09
| 2022-05-14T00:57:24
|
2022-05-14T00:57:24Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
JSON reconstruction bug:
The problem is: Because MSONables from_dict was replaced, there is no recursive reconstruction of the objects when you hit `el_ref` . When you do `as_dict` -> `from_dict` in python everything looks fine.
but the object was never completely serialized.
If you completely serialized it like putting it into as json file or database then you cannot reconstruct the phase diagram.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2522/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2522/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2522",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2522",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2522.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2522.patch",
"merged_at": "2022-05-14T00:57:24Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2525
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2525/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2525/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2525/events
|
https://github.com/materialsproject/pymatgen/pull/2525
| 1,242,120,971
|
PR_kwDOACgets44I29A
| 2,525
|
volumetric list -> array
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49285272)\n\nCoverage decreased (-0.7%) to 83.323% when pulling **c034c3024d6259b1bea055576e53683e276d0cab on jmmshn:main** into **1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1 on materialsproject:master**.\n"
] | 2022-05-19T17:54:48
| 2022-05-20T20:47:43
|
2022-05-20T20:47:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Allow lists to be used to construct the `data` field of `VolumetricData`
Depending on how the object was `jsantize` and store one might be reconstructing the `VolumetricData` object from a `list` rather than an `np.array`.
This small tweak just ensures that the reconstructive data is always an `np.array`
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2525/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2525/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2525",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2525",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2525.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2525.patch",
"merged_at": "2022-05-20T20:47:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2526
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2526/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2526/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2526/events
|
https://github.com/materialsproject/pymatgen/issues/2526
| 1,243,181,852
|
I_kwDOACgets5KGXMc
| 2,526
|
XRD as a function of q
|
{
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/followers",
"following_url": "https://api.github.com/users/JaGeo/following{/other_user}",
"gists_url": "https://api.github.com/users/JaGeo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JaGeo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JaGeo/subscriptions",
"organizations_url": "https://api.github.com/users/JaGeo/orgs",
"repos_url": "https://api.github.com/users/JaGeo/repos",
"events_url": "https://api.github.com/users/JaGeo/events{/privacy}",
"received_events_url": "https://api.github.com/users/JaGeo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Sure. By all means propose an implementation.",
"We will propose one via pull request once it is ready. Thanks!"
] | 2022-05-20T13:53:32
| 2022-05-20T14:04:44
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
It concerns `pymatgen.analysis.diffraction.xrd`
Would there be interest to also offer XRD patterns as a function of q (1/Angstrom) instead of 2 Theta? It would be interesting to have this data for comparison with SAXS data. As the class currently starts from a wavelengths, some changes would be necessary.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2526/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2526/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2527
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2527/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2527/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2527/events
|
https://github.com/materialsproject/pymatgen/issues/2527
| 1,244,125,842
|
I_kwDOACgets5KJ9qS
| 2,527
|
Is there a way that I can get a layered pdos for the selected different atoms like that in p4vasp?
|
{
"login": "SJTU-H",
"id": 75257242,
"node_id": "MDQ6VXNlcjc1MjU3MjQy",
"avatar_url": "https://avatars.githubusercontent.com/u/75257242?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/SJTU-H",
"html_url": "https://github.com/SJTU-H",
"followers_url": "https://api.github.com/users/SJTU-H/followers",
"following_url": "https://api.github.com/users/SJTU-H/following{/other_user}",
"gists_url": "https://api.github.com/users/SJTU-H/gists{/gist_id}",
"starred_url": "https://api.github.com/users/SJTU-H/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/SJTU-H/subscriptions",
"organizations_url": "https://api.github.com/users/SJTU-H/orgs",
"repos_url": "https://api.github.com/users/SJTU-H/repos",
"events_url": "https://api.github.com/users/SJTU-H/events{/privacy}",
"received_events_url": "https://api.github.com/users/SJTU-H/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-05-22T02:06:12
| 2022-05-27T14:23:05
|
2022-05-27T14:22:52Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "SJTU-H",
"id": 75257242,
"node_id": "MDQ6VXNlcjc1MjU3MjQy",
"avatar_url": "https://avatars.githubusercontent.com/u/75257242?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/SJTU-H",
"html_url": "https://github.com/SJTU-H",
"followers_url": "https://api.github.com/users/SJTU-H/followers",
"following_url": "https://api.github.com/users/SJTU-H/following{/other_user}",
"gists_url": "https://api.github.com/users/SJTU-H/gists{/gist_id}",
"starred_url": "https://api.github.com/users/SJTU-H/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/SJTU-H/subscriptions",
"organizations_url": "https://api.github.com/users/SJTU-H/orgs",
"repos_url": "https://api.github.com/users/SJTU-H/repos",
"events_url": "https://api.github.com/users/SJTU-H/events{/privacy}",
"received_events_url": "https://api.github.com/users/SJTU-H/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2527/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2527/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2528
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2528/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2528/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2528/events
|
https://github.com/materialsproject/pymatgen/issues/2528
| 1,245,312,529
|
I_kwDOACgets5KOfYR
| 2,528
|
LAMMPS IO: update parse_lammps_log for thermo_style yaml
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-05-23T15:04:22
| 2022-05-24T20:50:20
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
The format of data output by LAMMPS is completely dependent on what a user specifies in the input file, making it difficult to parse the output text files in a robust way.
**Describe the solution you'd like**
LAMMPS has recently introduced `thermo_style yaml` to enable outputting formatted thermodynamic data (see [discussion post](https://matsci.org/t/topic-of-the-month-yaml-support-in-lammps/42005) and [documentation page](https://docs.lammps.org/Howto_structured_data.html)). It would be great to update the associated pymatgen output parsers to take advantage of this. Specifically, `parse_lammps_log`.
The high throughput MD development team (myself, @manaslkht, @orioncohen, others) will put this on our roadmap as a future enhancement
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2528/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2528/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2529
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2529/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2529/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2529/events
|
https://github.com/materialsproject/pymatgen/issues/2529
| 1,245,861,520
|
I_kwDOACgets5KQlaQ
| 2,529
|
Magic Number of "max_sites=-20" in MP2020Compatibility Leads to Hidden Error
|
{
"login": "JiQi535",
"id": 54908836,
"node_id": "MDQ6VXNlcjU0OTA4ODM2",
"avatar_url": "https://avatars.githubusercontent.com/u/54908836?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JiQi535",
"html_url": "https://github.com/JiQi535",
"followers_url": "https://api.github.com/users/JiQi535/followers",
"following_url": "https://api.github.com/users/JiQi535/following{/other_user}",
"gists_url": "https://api.github.com/users/JiQi535/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JiQi535/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JiQi535/subscriptions",
"organizations_url": "https://api.github.com/users/JiQi535/orgs",
"repos_url": "https://api.github.com/users/JiQi535/repos",
"events_url": "https://api.github.com/users/JiQi535/events{/privacy}",
"received_events_url": "https://api.github.com/users/JiQi535/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@JiQi535 thanks for posting. Your understanding of what's happening is 100% correct, and I hadn't realized that this wasn't documented (my apologies for that). The oxidation state guessing was a feature that we added somewhat at the last minute and the documentation must have slipped through the cracks. That said, you should be seeing a warning along the lines of \"Failed to guess oxidation states...\" as per [ this line](https://github.com/materialsproject/pymatgen/blob/1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1/pymatgen/entries/compatibility.py#L1056). Were you not seeing that in your work?\r\n\r\nI remember we did try a default value of `max_sites=-1` but that led to unacceptable performance hangs with modestly large structures. My concern with setting to `-1` is that a user might find `process_entries` hanging and not be able to figure out why. \r\nNote that any materials you obtain from `MPRester()` will have oxidation states already populated, and hence the corrections will be applied correctly even for larger structures.\r\n\r\nI would suggest a few things:\r\n1. make `max_sites` a kwarg in the `__init__` , keeping the default value at -20\r\n2. Add documentation explaining what the kwarg does and that a value of -1 will try regardless of the no. of sites\r\n3. If the warning is not working as intended and notifying users when oxidation state guessing is being skipped, we need to fix that. There is a unit test [here ](https://github.com/materialsproject/pymatgen/blob/1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1/pymatgen/entries/tests/test_compatibility.py#L808)that perhaps needs to be expanded?\r\n\r\nLet me know what you think about the above. If this sounds good to you I'd be happy to review a PR with the changes. Also flagging @mkhorton for comments.\r\n\r\n"
] | 2022-05-24T01:25:34
| 2022-05-24T20:34:38
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
Yes. The current get_adjustments() function in MP2020Compatibility fails to get the correct energy adjustments for compositions with over 20 atoms and specific mixed anions, e.g. Li20O9Cl2. For Li20O9Cl2, it can only get the energy correction for O2-, while correction for Cl- is missed.
https://github.com/materialsproject/pymatgen/blob/1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1/pymatgen/entries/compatibility.py#L1041-L1047
It is because of using a magic number of "max_sites=-20" to set 20 as the cutoff for the maximum number of sites in a reduced formula whose oxidation states will be guessed. Together with the below codes, energy corrections for anions that are not the most electronegative are missed. https://github.com/materialsproject/pymatgen/blob/1f1056cab8b9358f4d1ac2012f2a5732cd29bcf1/pymatgen/entries/compatibility.py#L1061-L1071
Without documentation, this current setting can lead to hidden error when analysing the Ehull of materials with over 20 atoms and mixed anions, like missing Cl- in Li20O9Cl2 and missing N3- in Li20Cl17N.
**Describe the solution you'd like**
We can set "max_sites=-1" so that this error no longer exist, while reduced formula will be tried to find so that composition will be as small as possible to keep performance. I believe that being correct is more important than having good speed, and some compromise in performance should be acceptable.
@rkingsbury Hey Ryan, I saw your helpful post about MP2020Compatibility before, so I'm quoting you here. Thanks in advance! 😁
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2529/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2529/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2530
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2530/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2530/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2530/events
|
https://github.com/materialsproject/pymatgen/issues/2530
| 1,246,431,746
|
I_kwDOACgets5KSwoC
| 2,530
|
How to parse a complete dos object from DOSCAR but not from vasprun.xml by pymatgen
|
{
"login": "OldrayHex",
"id": 57491512,
"node_id": "MDQ6VXNlcjU3NDkxNTEy",
"avatar_url": "https://avatars.githubusercontent.com/u/57491512?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/OldrayHex",
"html_url": "https://github.com/OldrayHex",
"followers_url": "https://api.github.com/users/OldrayHex/followers",
"following_url": "https://api.github.com/users/OldrayHex/following{/other_user}",
"gists_url": "https://api.github.com/users/OldrayHex/gists{/gist_id}",
"starred_url": "https://api.github.com/users/OldrayHex/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/OldrayHex/subscriptions",
"organizations_url": "https://api.github.com/users/OldrayHex/orgs",
"repos_url": "https://api.github.com/users/OldrayHex/repos",
"events_url": "https://api.github.com/users/OldrayHex/events{/privacy}",
"received_events_url": "https://api.github.com/users/OldrayHex/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There is only a class to parse the Doscar from LOBSTER calculations. I am not sure why there is a need to do it from the DOSCAR since the vasprun.xml contains the same information as far as I can tell. To my knowledge, parsing the GW DOS from vasprun.xml should be the same as that from regular PBE. You should make some attempt to do this yourself and if it doesn't work, then you report an Issue. ",
"Thanks very much for your reply. I have tried to use LOBSTER to parse the DOS but it still failed because LOBSTER can not succeed on the results of GW electronic calculations. I am sure my GW calculations were conducted correctly. My problem is just that pymatgen can not parse the vasprun.xml from GW. So I hope someone can write a certain class for GW calculations to parse DOS files either by using vasprun.xml or DOSCAR. Thanks.\r\n",
"You will have to provide a GW vasprun.xml and show how it fails. ",
"Thank you so much dear shyuep. I will send you my GW vasprun.xml and PBE vasprun.xml right now by email.",
"> You will have to provide a GW vasprun.xml and show how it fails.\r\n\r\nHi, I found I couldn't send you my vasprun.xml files by this dialog. Thus I have sent them to your email address: notifications@github.com. Thank you.",
"Okay, thank you so much. I will send the files tomorrow.\n\n发自我的iPhone\n\n> 在 2022年5月24日，23:32，Shyue Ping Ong ***@***.***> 写道：\n> \n> \n> You will have to provide a GW vasprun.xml and show how it fails.\n> \n> —\n> Reply to this email directly, view it on GitHub, or unsubscribe.\n> You are receiving this because you authored the thread.\n"
] | 2022-05-24T11:54:42
| 2022-10-11T08:32:55
|
2022-05-24T13:52:20Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello dear,
I have some trouble when I parse a DOS object with vasprun.xml obtained from GW calculation. The error is as follows:
“NotImplementedError: This vasprun.xml has >2 unlabelled dielectric functions”
So I want to parse it by using DOSCAR instead of the vasprun.xml. But I have not found a class that can do this in pymatgen. If anyone can help me write a new class or some advice in pymatgen, I will be super grateful to you. Thanks.
My goal is to calculate fermi levels at the given temperatures with defect formation energies, so I need to parse the total DOS via the electronic structure calculations obtained from VASP GW calculations to estimate band edges accurately. If anyone can help me to add some functionalities of parsing DOS for GW calculations either using vasprun.xml or DOSCAR obtained from GW calculations, I will be very grateful.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2530/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2530/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2531
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2531/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2531/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2531/events
|
https://github.com/materialsproject/pymatgen/pull/2531
| 1,246,577,911
|
PR_kwDOACgets44XX5V
| 2,531
|
Fix `MPRester.__init__` raising `TypeError: NoneType not iterable` on empty `.pmgrc.yaml`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49406524)\n\nCoverage decreased (-0.7%) to 83.322% when pulling **a687dab12d754cefe44954ff0852d5218c7c02ba on janosh:fix-mprester-typeerror-on-empty-pmgrc** into **30e36f658aa121ee58caf962e230014e0e3fbbf9 on materialsproject:master**.\n"
] | 2022-05-24T13:42:45
| 2022-05-24T14:15:12
|
2022-05-24T14:05:58Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
`MPRester.__init__()` raises
```py
TypeError: 'NoneType' object is not iterable
```
if `.pmgrc.yaml` exists but is empty.
Plus add some more type hints for frequently used functions.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2531/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2531/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2531",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2531",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2531.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2531.patch",
"merged_at": "2022-05-24T14:05:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2532
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2532/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2532/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2532/events
|
https://github.com/materialsproject/pymatgen/issues/2532
| 1,247,516,541
|
I_kwDOACgets5KW5d9
| 2,532
|
Get symmops in cartesian coordinates with the get_recp_symmetry_operation method of the Lattice class in pymatgen.core.lattice
|
{
"login": "RyanNKHall",
"id": 31651110,
"node_id": "MDQ6VXNlcjMxNjUxMTEw",
"avatar_url": "https://avatars.githubusercontent.com/u/31651110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/RyanNKHall",
"html_url": "https://github.com/RyanNKHall",
"followers_url": "https://api.github.com/users/RyanNKHall/followers",
"following_url": "https://api.github.com/users/RyanNKHall/following{/other_user}",
"gists_url": "https://api.github.com/users/RyanNKHall/gists{/gist_id}",
"starred_url": "https://api.github.com/users/RyanNKHall/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/RyanNKHall/subscriptions",
"organizations_url": "https://api.github.com/users/RyanNKHall/orgs",
"repos_url": "https://api.github.com/users/RyanNKHall/repos",
"events_url": "https://api.github.com/users/RyanNKHall/events{/privacy}",
"received_events_url": "https://api.github.com/users/RyanNKHall/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-05-25T05:46:52
| 2022-05-25T06:08:26
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
I have a module that takes a [`BandStructureSymmLine`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/electronic_structure/bandstructure.py#:~:text=class%20BandStructureSymmLine(BandStructure%2C%20MSONable)%3A) object obtained from the materials project database and applies the symmetry operations corresponding to the Brillouin Zone in order to build up the dataset for the whole BZ (and then permitting interpolation in k-space). I currently use the [`SpacegroupAnalyzer`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/symmetry/analyzer.py#:~:text=class%20SpacegroupAnalyzer%3A) from from `pymatgen.symmetry.analyzer` to get the symmetry operations, taking the [`lattice_rec`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/electronic_structure/bandstructure.py#:~:text=self.lattice_rec%20%3D%20lattice) class of the [`BandStructureSymmLine`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/electronic_structure/bandstructure.py#:~:text=class%20BandStructureSymmLine(BandStructure%2C%20MSONable)%3A) object as input. I can't help but notice that the [`get_recp_symmetry_operation`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/core/lattice.py#:~:text=def%20get_recp_symmetry_operation(self%2C%20symprec%3A%20float%20%3D%200.01)%20%2D%3E%20list%3A) method of the [`Lattice`](https://github.com/materialsproject/pymatgen/blob/v2022.5.19/pymatgen/core/lattice.py#:~:text=class%20Lattice(MSONable)%3A) class in `pymatgen.core.lattice` almost does this exact thing but there are several factors that make using this method less straightforward.
1) The `BandStructureSymmLine` object contains the reciprocal lattice, not the real lattice and hence the `get_recp_symmetry_operation` would return the symmetry operations of the real lattice (reciprocal of the reciprocal). I know the real lattice can be obtained from the `reciprocal_lattice_crystallographic` parameter but this is hindered by point 2
2) The reciprocal lattice (lattice_rec) parameter of the `BandStructureSymmLine` object contains the lattice constants of the reciprocal lattice with a factor of 2 * pi i.e. not in "crystallographic" format. Thus the `reciprocal_lattice_crystallographic` parameter of `lattice_rec` is also out by 2*pi from what is needed as input to the `get_recp_symmetry_operation method`
3) Lastly the `get_recp_symmetry_operation` method calls the `get_symmetry_operations` method on the `SpacegroupAnalyzer` class to get a list of `symmop` objects with fractional coordinates as the default. This means cartesian points in reciprocal space need to first be converted to fractional points before `symmop.operate` or `operate_multi` can be called
**Describe the solution you'd like**
It would be nice to be able to have the cartesian boolean used in `SpacegroupAnalyzer.get_symmetry_operations()` accessible as an input to the `get_recp_symmetry_operation` method, perhaps with cartesian=False as default so existing behaviour is conserved.
**Describe alternatives you've considered**
Additionally, as either a more generalised function or as a replacement to `get_recp_symmetry_operation`, a `get_symmetry_operation` method for the lattice class would be useful as then the method can be called directly on the `lattice_rec` object in the `BandStructureSymmLine object`. This would look almost identical to the existing `get_recp_symmetry_operation` method, but take a `Lattice` object as an argument to pass onto the `SpacegroupAnalyzer`.
If the `get_recp_symmetry_operation` method was retained, the latter could call this new `get_symmetry_operation` with the reciprocal lattice as the input argument, thus preserving existing functionality/behaviour
**Additional context**
It is entirely possible that the application I have in mind has been addressed elsewhere in this extensive set of libraries which might make my feature request redundant, but thank you anyways for your consideration.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2532/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2532/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2533
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2533/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2533/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2533/events
|
https://github.com/materialsproject/pymatgen/pull/2533
| 1,250,084,881
|
PR_kwDOACgets44jE8I
| 2,533
|
Fix function to produce continuous line-mode band structures
|
{
"login": "munrojm",
"id": 6877334,
"node_id": "MDQ6VXNlcjY4NzczMzQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/6877334?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/munrojm",
"html_url": "https://github.com/munrojm",
"followers_url": "https://api.github.com/users/munrojm/followers",
"following_url": "https://api.github.com/users/munrojm/following{/other_user}",
"gists_url": "https://api.github.com/users/munrojm/gists{/gist_id}",
"starred_url": "https://api.github.com/users/munrojm/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/munrojm/subscriptions",
"organizations_url": "https://api.github.com/users/munrojm/orgs",
"repos_url": "https://api.github.com/users/munrojm/repos",
"events_url": "https://api.github.com/users/munrojm/events{/privacy}",
"received_events_url": "https://api.github.com/users/munrojm/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49611807)\n\nCoverage decreased (-0.7%) to 83.29% when pulling **a586eff982d3ee4f45aa2c286738560714b7a445 on munrojm:continuous_bs_fix** into **aa0e9cf43bdae3df4a87fd77d5bbfd6dc1603eec on materialsproject:master**.\n"
] | 2022-05-26T21:04:19
| 2022-06-06T19:10:10
|
2022-06-06T19:10:10Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR fixes a bug in the `get_continuous_path` method of `HighSymmKpath` which formats line-mode band structure to ensure the k-path is continuous. Previously, the last segment of the path was not correctly being added to the new one in all cases. This fix ensures the final k-point is always the same as the starting one.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2533/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2533/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2533",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2533",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2533.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2533.patch",
"merged_at": "2022-06-06T19:10:10Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2534
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2534/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2534/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2534/events
|
https://github.com/materialsproject/pymatgen/issues/2534
| 1,251,428,459
|
I_kwDOACgets5Kl0hr
| 2,534
|
Need to add `enthalpy is TOTEN` to `pymatgen.io.vasp.outputs` module?
|
{
"login": "chunweizhu",
"id": 47244527,
"node_id": "MDQ6VXNlcjQ3MjQ0NTI3",
"avatar_url": "https://avatars.githubusercontent.com/u/47244527?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chunweizhu",
"html_url": "https://github.com/chunweizhu",
"followers_url": "https://api.github.com/users/chunweizhu/followers",
"following_url": "https://api.github.com/users/chunweizhu/following{/other_user}",
"gists_url": "https://api.github.com/users/chunweizhu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chunweizhu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chunweizhu/subscriptions",
"organizations_url": "https://api.github.com/users/chunweizhu/orgs",
"repos_url": "https://api.github.com/users/chunweizhu/repos",
"events_url": "https://api.github.com/users/chunweizhu/events{/privacy}",
"received_events_url": "https://api.github.com/users/chunweizhu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-05-28T02:38:53
| 2022-05-28T02:40:16
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
When the calculation of VASP is performed under pressure conditions, the `PSTRESS` parameter needs to be added to `INCAR`, and the `enthalpy is TOTEN` item will be obtained in OUTCAR. Sometimes we need to extract the value of this item, so I wonder if we need to implement this operation to `pymatgen.io.vasp.outputs` module?
I can submit a PR if needed. thanks！
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2534/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2534/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2536
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2536/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2536/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2536/events
|
https://github.com/materialsproject/pymatgen/pull/2536
| 1,252,006,361
|
PR_kwDOACgets44pUnG
| 2,536
|
Pandas fix and Black version update in pre-commit YAML file
|
{
"login": "manaslkht",
"id": 33138283,
"node_id": "MDQ6VXNlcjMzMTM4Mjgz",
"avatar_url": "https://avatars.githubusercontent.com/u/33138283?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/manaslkht",
"html_url": "https://github.com/manaslkht",
"followers_url": "https://api.github.com/users/manaslkht/followers",
"following_url": "https://api.github.com/users/manaslkht/following{/other_user}",
"gists_url": "https://api.github.com/users/manaslkht/gists{/gist_id}",
"starred_url": "https://api.github.com/users/manaslkht/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/manaslkht/subscriptions",
"organizations_url": "https://api.github.com/users/manaslkht/orgs",
"repos_url": "https://api.github.com/users/manaslkht/repos",
"events_url": "https://api.github.com/users/manaslkht/events{/privacy}",
"received_events_url": "https://api.github.com/users/manaslkht/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Closing as I can't push to this fork to fix CI:\r\n\r\n> remote: Permission to manaslkht/pymatgen.git denied to janosh.\r\nfatal: unable to access 'https://github.com/manaslkht/pymatgen.git/': The requested URL returned error: 403"
] | 2022-05-29T22:20:04
| 2022-10-22T17:14:27
|
2022-10-22T17:14:26Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #2510. Update the deprecated `Dataframe.append` method to `Dataframe.concat` in `pymatgen/io/lammps/data.py`.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2536/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2536/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2536",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2536",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2536.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2536.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2537
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2537/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2537/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2537/events
|
https://github.com/materialsproject/pymatgen/issues/2537
| 1,252,213,546
|
I_kwDOACgets5Ko0Mq
| 2,537
|
Voronoi charges in `pymatgen.command_line.bader_caller`
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Closing this because I thought `bader` output the voronoi deformation density, but the voronoi analysis is simpler here."
] | 2022-05-30T05:31:46
| 2022-06-01T07:13:27
|
2022-06-01T07:13:27Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The `bader` code by the Henkelman group, which is currently used in `pymatgen.command_line.bader_caller`, can also compute Voronoi charges for basically free simply by adding the `-c voronoi` command-line argument. It would be ideal to add support for this to the `bader_caller` and to have it store the Voronoi charges (which are printed to `stdout`) in a dictionary for easy querying.
I will likely get to this one of these days, but it may take a little while.
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2537/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2537/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2538
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2538/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2538/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2538/events
|
https://github.com/materialsproject/pymatgen/pull/2538
| 1,252,871,916
|
PR_kwDOACgets44sMR5
| 2,538
|
Allow compressed lammps and xyz files in io.lammps.data
|
{
"login": "ab5424",
"id": 57258530,
"node_id": "MDQ6VXNlcjU3MjU4NTMw",
"avatar_url": "https://avatars.githubusercontent.com/u/57258530?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ab5424",
"html_url": "https://github.com/ab5424",
"followers_url": "https://api.github.com/users/ab5424/followers",
"following_url": "https://api.github.com/users/ab5424/following{/other_user}",
"gists_url": "https://api.github.com/users/ab5424/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ab5424/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ab5424/subscriptions",
"organizations_url": "https://api.github.com/users/ab5424/orgs",
"repos_url": "https://api.github.com/users/ab5424/repos",
"events_url": "https://api.github.com/users/ab5424/events{/privacy}",
"received_events_url": "https://api.github.com/users/ab5424/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks.",
"\n[](https://coveralls.io/builds/49568292)\n\nCoverage decreased (-0.7%) to 83.293% when pulling **fe1eb5d15c149a2196081105d50a665b29d6feaf on ab5424:lammps-zopen** into **aa0e9cf43bdae3df4a87fd77d5bbfd6dc1603eec on materialsproject:master**.\n"
] | 2022-05-30T15:14:32
| 2022-05-30T15:59:31
|
2022-05-30T15:30:55Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Add `zopen()` to `LammpsData`
* Spelling & updated links
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2538/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2538/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2538",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2538",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2538.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2538.patch",
"merged_at": "2022-05-30T15:30:55Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2539
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2539/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2539/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2539/events
|
https://github.com/materialsproject/pymatgen/pull/2539
| 1,256,669,436
|
PR_kwDOACgets445PD_
| 2,539
|
small bug in gruneisen.py
|
{
"login": "antonf-ekb",
"id": 10402828,
"node_id": "MDQ6VXNlcjEwNDAyODI4",
"avatar_url": "https://avatars.githubusercontent.com/u/10402828?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/antonf-ekb",
"html_url": "https://github.com/antonf-ekb",
"followers_url": "https://api.github.com/users/antonf-ekb/followers",
"following_url": "https://api.github.com/users/antonf-ekb/following{/other_user}",
"gists_url": "https://api.github.com/users/antonf-ekb/gists{/gist_id}",
"starred_url": "https://api.github.com/users/antonf-ekb/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/antonf-ekb/subscriptions",
"organizations_url": "https://api.github.com/users/antonf-ekb/orgs",
"repos_url": "https://api.github.com/users/antonf-ekb/repos",
"events_url": "https://api.github.com/users/antonf-ekb/events{/privacy}",
"received_events_url": "https://api.github.com/users/antonf-ekb/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49647815)\n\nCoverage decreased (-0.7%) to 83.294% when pulling **4c13d29b13644a122b1b7921fb163d4a7d374a21 on antonf-ekb:master** into **2c62d53588e70b22e8e0f6352a7d1974f3cfcb16 on materialsproject:master**.\n",
"Thank you for finding the bug. I think you are correct. We had developed/adapted this module within a Master thesis and hadn't used this option for further studies.\r\n\r\nWould you be able to add a short test to avoid this bug in the future? Otherwise, @ab5424 or I would try to get back to it in one of the next weeks.",
"> Thank you for finding the bug. I think you are correct. We had developed/adapted this module within a Master thesis and hadn't used this option for further studies.\r\n> \r\n> Would you be able to add a short test to avoid this bug in the future? Otherwise, @ab5424 or I would try to get back to it in one of the next weeks.\r\n\r\nHi, I'm sorry, but I don't quite understand what test do you mean.",
"I was referring to the unit tests in pymatgen/phonon/tests/test_gruneisen.py that do automatic testing of the code. It would be great to add a test where we test this part of the code. If you have never done this, we can also offer to do this, as we should have added a test in the first place. ",
"Thank you very much again @antonf-ekb . As we have fixed the issue in another pull-request, this could be closed now, I think."
] | 2022-06-01T18:03:10
| 2022-08-04T18:11:39
|
2022-08-04T18:11:39Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
At converting adt from K to Hz we get numbers of the order 10^12 (TeraHz) but since w are not yet multiplied by 10^12, the value adt * const.value ("Boltzmann constant in Hz/K") should be divided by the const.tera. The error lead to that all values of w satisfy the condition while this should not be the case.
## Summary
Include a summary of major changes in bullet points:
* Feature 1
* Feature 2
* Fix 1
* Fix 2
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.
## TODO (if any)
If this is a work-in-progress, write something about what else needs
to be done
* Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "antonf-ekb",
"id": 10402828,
"node_id": "MDQ6VXNlcjEwNDAyODI4",
"avatar_url": "https://avatars.githubusercontent.com/u/10402828?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/antonf-ekb",
"html_url": "https://github.com/antonf-ekb",
"followers_url": "https://api.github.com/users/antonf-ekb/followers",
"following_url": "https://api.github.com/users/antonf-ekb/following{/other_user}",
"gists_url": "https://api.github.com/users/antonf-ekb/gists{/gist_id}",
"starred_url": "https://api.github.com/users/antonf-ekb/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/antonf-ekb/subscriptions",
"organizations_url": "https://api.github.com/users/antonf-ekb/orgs",
"repos_url": "https://api.github.com/users/antonf-ekb/repos",
"events_url": "https://api.github.com/users/antonf-ekb/events{/privacy}",
"received_events_url": "https://api.github.com/users/antonf-ekb/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2539/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2539/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2539",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2539",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2539.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2539.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2540
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2540/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2540/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2540/events
|
https://github.com/materialsproject/pymatgen/issues/2540
| 1,258,692,925
|
I_kwDOACgets5LBiE9
| 2,540
|
Feature Suggestion: Add ZVAL to POTCAR metadata
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Sorry, I see this is under `nelectrons`. It just doesn't make its way into the POTCAR spec.",
"I have no objection to adding a ZVAL as a alternative name or in the spec.",
"Thanks! I might consider adding it to the spec. But I also think it's mostly a non-issue if the data is present elsewhere already."
] | 2022-06-02T20:42:40
| 2022-06-02T20:46:36
|
2022-06-02T20:43:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Currently, the `Potcar()` object in pymatgen does not store the `ZVAL` as a property. However, when carrying out partial charge calculations (e.g. a Bader analysis), having information about the `ZVAL` is crucial. Since the `ZVAL` isn't stored anywhere other than the POTCAR file or OUTCAR file itself, this means that downstream codes like Atomate/Atomate2 don't have the `ZVAL` stored anywhere in the tabulated data and it can be annoying to access.
In short, we should add the `ZVAL` as a property to the `Potcar()` object. Up for debate, but perhaps it should also be added to the `spec` property.
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2540/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2540/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2541
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2541/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2541/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2541/events
|
https://github.com/materialsproject/pymatgen/issues/2541
| 1,260,870,290
|
I_kwDOACgets5LJ1qS
| 2,541
|
[FEATURE REQUEST] Python 3.7 support
|
{
"login": "sgbaird",
"id": 45469701,
"node_id": "MDQ6VXNlcjQ1NDY5NzAx",
"avatar_url": "https://avatars.githubusercontent.com/u/45469701?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sgbaird",
"html_url": "https://github.com/sgbaird",
"followers_url": "https://api.github.com/users/sgbaird/followers",
"following_url": "https://api.github.com/users/sgbaird/following{/other_user}",
"gists_url": "https://api.github.com/users/sgbaird/gists{/gist_id}",
"starred_url": "https://api.github.com/users/sgbaird/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/sgbaird/subscriptions",
"organizations_url": "https://api.github.com/users/sgbaird/orgs",
"repos_url": "https://api.github.com/users/sgbaird/repos",
"events_url": "https://api.github.com/users/sgbaird/events{/privacy}",
"received_events_url": "https://api.github.com/users/sgbaird/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Well, any version of pymatgen pre 2022.X would support python 3.7. Unless you are planning to demo some cutting feature, you can just install one of those? I would say 99% of users do not need the latest version of pymatgen. ",
"@shyuep thanks for the quick response. An alternative is for me to switch back to the legacy MPRester API which doesn't [depend on a `2022.X` version](https://github.com/materialsproject/api/blob/250f51cade1aead4be6016d1a61329ff1c2ce99b/setup.py#L27). @rkingsbury [suggested I try out the new API](https://matsci.org/t/how-do-i-do-a-time-split-of-materials-project-entries-e-g-pre-2018-vs-post-2018/42584/2?u=sgbaird), which has been cool to see. However, as expected and clearly advertised, the new API is kind of fluid right now with breaking changes flowing (e.g. removal of `query` method, change of kwarg names in `search`), and I'm not sure it will make sense to keep my code compatible with `v0.18.0` (Python 3.7 compatible).\r\n\r\nAfter some trial-and-error with getting `mp_api==0.24.0` installed on Colab, making `mp-api` an optional dependency for [`mp-time-split`](https://github.com/sparks-baird/mp-time-split) (WIP) seems like one of the better options: `pip install mp-time-split[api]` or similar with Python 3.8+ to use the data fetching capabilities rather than simply loading a snapshot from figshare. Seems like a good compromise for my use-case.",
"> Made a [](https://colab.research.google.com/github/sparks-baird/mp-time-split/blob/main/notebooks/other/mp-api-colab-py38.ipynb) example of running `mp-api`, it takes ~20 minutes, requires kernel restarts, and browser refreshing to get to the first `MPRester` statement and supposedly has to be a copy of that exact notebook due to internal metadata (i.e. can't copy-paste the code to another notebook and have it run) 😅\r\n> \r\n> The first few statements can be condensed to a single cell of course.\r\n\r\n_Originally posted by @sgbaird in https://github.com/materialsproject/api/issues/600#issuecomment-1146678005_",
"I see. Honestly, I was not aware that there is a separate client for the new API or why it actually needed to be in a separate repository/package. It would have been much easier if that was developed within the existing pymatgen.ext.matproj package and certainly would have far more input from other users/developers (@rkingsbury @mkhorton). Given that mp-api is a separate package in and of itself, I don't have input as to whether it is supposed to support Python 3.7 or not. What I can tell you is that the existing MPRester in pymatgen has seen relatively few changes in recent months and the pre-2022 versions would basically support Py3.7 with no loss in functionality.",
"@shyuep please see correspondence dated 01/2022 (\"Home of MP API client\"). In brief, developing in a separate repo is likely advantageous, but we can certainly re-integrate into pymatgen as an add-on. The main barrier to inclusion is that it would necessitate adding new dependencies to pymatgen, notably `pydantic`, but also potentially others, due to the stricter validation applied in the new API.\r\n\r\n@sgbaird we're ultimately following pymatgen version requirements, and from that following the latest numpy version requirements. Ultimately, I would place this on Colab to support newer Python versions; 3.11 is imminent now and is impressively faster, and there have been many quality of life improvements in the intervening versions that would be unfortunate to lose. I think my advice would be two-fold:\r\n\r\n1. If there are any problems or bugs with the new MPRester, please continue to post issues in the `api` repo and we will try to get them addressed.\r\n2. If you really need 3.7 support, the API itself is OpenAPI-compliant and has a spec available at https://api.materialsproject.org -- you can continue to make queries directly via `requests` or otherwise.",
"@mkhorton I am aware that there is a new API under development. What I meant is that I am unclear why it needs to be in a separate package. pydantic is already part of monty since some time ago.",
"> Ultimately, I would place this on Colab to support newer Python versions!\r\n\r\nThis! Don't understand why it's taking Google so long. py38+ support on Colab has been requested [many times for 2 years now](https://github.com/googlecolab/colabtools/issues/1422)."
] | 2022-06-04T19:06:03
| 2022-06-17T10:27:39
|
2022-06-04T19:52:24Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
It would be nice to have Python 3.7 support for exposing code examples that depend on `mp_api` on Google Colab. See https://github.com/materialsproject/api/issues/600
**Describe the solution you'd like**
Support for Python 3.7 until Colab starts supporting Python 3.8 directly. https://github.com/googlecolab/colabtools/issues/2165
On Feb 25, 2021, Colab bumped to Python 3.7 despite Python 3.8 available since 2018 https://twitter.com/googlecolab/status/1365062244225060865
**Describe alternatives you've considered**
- [Roundabout hacks to get Python 3.8 installed on Colab](https://stackoverflow.com/a/63797862/13697228)
- Drop Colab as a way to expose top-level code examples when depending on pymatgen
I understand if this isn't in the scope/vision of `pymatgen`, but figured it was worth probing and getting an issue up for added visibility if someone goes looking.
|
{
"login": "sgbaird",
"id": 45469701,
"node_id": "MDQ6VXNlcjQ1NDY5NzAx",
"avatar_url": "https://avatars.githubusercontent.com/u/45469701?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sgbaird",
"html_url": "https://github.com/sgbaird",
"followers_url": "https://api.github.com/users/sgbaird/followers",
"following_url": "https://api.github.com/users/sgbaird/following{/other_user}",
"gists_url": "https://api.github.com/users/sgbaird/gists{/gist_id}",
"starred_url": "https://api.github.com/users/sgbaird/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/sgbaird/subscriptions",
"organizations_url": "https://api.github.com/users/sgbaird/orgs",
"repos_url": "https://api.github.com/users/sgbaird/repos",
"events_url": "https://api.github.com/users/sgbaird/events{/privacy}",
"received_events_url": "https://api.github.com/users/sgbaird/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2541/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2541/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2542
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2542/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2542/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2542/events
|
https://github.com/materialsproject/pymatgen/issues/2542
| 1,260,960,742
|
I_kwDOACgets5LKLvm
| 2,542
|
'diff' parameter not working in StructureGraph.draw_graph_to_file
|
{
"login": "Anny-tech",
"id": 45486431,
"node_id": "MDQ6VXNlcjQ1NDg2NDMx",
"avatar_url": "https://avatars.githubusercontent.com/u/45486431?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Anny-tech",
"html_url": "https://github.com/Anny-tech",
"followers_url": "https://api.github.com/users/Anny-tech/followers",
"following_url": "https://api.github.com/users/Anny-tech/following{/other_user}",
"gists_url": "https://api.github.com/users/Anny-tech/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Anny-tech/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Anny-tech/subscriptions",
"organizations_url": "https://api.github.com/users/Anny-tech/orgs",
"repos_url": "https://api.github.com/users/Anny-tech/repos",
"events_url": "https://api.github.com/users/Anny-tech/events{/privacy}",
"received_events_url": "https://api.github.com/users/Anny-tech/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hi @Anny-tech, thanks for the report. To be able to reproduce, could you supply the input structure too?\r\n\r\nMy suggestions are:\r\n\r\n1. Try `st1_1.diff(st2_1)` first. This calls the `.diff()` method which needs to work for the drawing method to work, and if this gives an error it may be more helpful.\r\n2. Bear in mind that the intent for this method is to compare different bonding strategies for the _same_ structure. Trying to do a comparison between different structures will not be meaningful, since the nodes of the graph (atomic sites) are also different, not just the edges (bonds).",
"Hi @mkhorton , thanks for the reply. \r\n1. I tried this already. It works. As in gives a Valu\r\n[st1.cif.txt](https://github.com/materialsproject/pymatgen/files/8846305/st1.cif.txt)\r\n[st2.cif.txt](https://github.com/materialsproject/pymatgen/files/8846306/st2.cif.txt)\r\neError, with the same statement you mentioned in point 2 above. \r\n2. That is exactly our aim. I derived the structures from another code. Wanted to check using pymatgen whether the structures are indeed different or not!\r\nI am attaching the input structures here.",
"Ok, for this application maybe [`StructureMatcher`](https://pymatgen.org/pymatgen.analysis.structure_matcher.html?highlight=structurematcher#pymatgen.analysis.structure_matcher.StructureMatcher) maybe more appropriate. This can compare structures based on atomic co-ordinates and tell you if they are the same structure or not. The `StructureGraph.diff` methods are more for differences in number of bonds; it's possible for two different polymorphs (with different symmetries) to have the same bonds/graphs if their respective atoms are in the same co-ordination environments. "
] | 2022-06-05T04:54:39
| 2022-06-06T18:40:32
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
'diff' parameter not working in 'draw_graph_to_file' from StructureGraph class of the pymatgen.analysis.graphs module
**To Reproduce**
Steps to reproduce the behavior:
1. Generated structure using *.cif file
2. Generated structuregraph using 'with_local_env_strategy', with strategy=CrystalNN() in the StructureGraph class.
3. Tried to generate graph image using st1_1.draw_graph_to_file(filename='graph.png',diff=st2_1), where st1_1= structuregraph1 and st2_1=structuregraph2.
4. Error: [TypeError: 'ValueError' object is not subscriptable]
**Screenshots**
**Desktop (please complete the following information):**
- OS: [Linux]
- Version [Ubuntu 20.04.4 LTS]
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2542/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2542/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2543
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2543/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2543/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2543/events
|
https://github.com/materialsproject/pymatgen/pull/2543
| 1,261,897,438
|
PR_kwDOACgets45K37l
| 2,543
|
Fix bug in Grüneisen parameter calculation
|
{
"login": "ab5424",
"id": 57258530,
"node_id": "MDQ6VXNlcjU3MjU4NTMw",
"avatar_url": "https://avatars.githubusercontent.com/u/57258530?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ab5424",
"html_url": "https://github.com/ab5424",
"followers_url": "https://api.github.com/users/ab5424/followers",
"following_url": "https://api.github.com/users/ab5424/following{/other_user}",
"gists_url": "https://api.github.com/users/ab5424/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ab5424/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ab5424/subscriptions",
"organizations_url": "https://api.github.com/users/ab5424/orgs",
"repos_url": "https://api.github.com/users/ab5424/repos",
"events_url": "https://api.github.com/users/ab5424/events{/privacy}",
"received_events_url": "https://api.github.com/users/ab5424/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@mkhorton Tests are passing now. :)",
"\n[](https://coveralls.io/builds/49983249)\n\nCoverage decreased (-0.7%) to 83.285% when pulling **09b7c308fc86dcb83fe5cafa7186e087ba6bd029 on ab5424:gruneisen-bug** into **9c0fe8ed4a1719f59bef901726c746c2a4a83230 on materialsproject:master**.\n",
"Thanks both!"
] | 2022-06-06T14:07:31
| 2022-06-14T20:04:08
|
2022-06-14T18:01:50Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Fix bug in `average_gruneisen` with a wrong unit @JaGeo #2539
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply ` #cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2543/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2543/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2543",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2543",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2543.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2543.patch",
"merged_at": "2022-06-14T18:01:50Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2544
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2544/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2544/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2544/events
|
https://github.com/materialsproject/pymatgen/pull/2544
| 1,262,252,338
|
PR_kwDOACgets45MEuS
| 2,544
|
[pre-commit.ci] pre-commit autoupdate
|
{
"login": "pre-commit-ci[bot]",
"id": 66853113,
"node_id": "MDM6Qm90NjY4NTMxMTM=",
"avatar_url": "https://avatars.githubusercontent.com/in/68672?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D",
"html_url": "https://github.com/apps/pre-commit-ci",
"followers_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-06-06T19:05:22
| 2022-06-06T19:08:02
|
2022-06-06T19:08:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.32.0 → v2.32.1](https://github.com/asottile/pyupgrade/compare/v2.32.0...v2.32.1)
- [github.com/pre-commit/mirrors-mypy: v0.950 → v0.960](https://github.com/pre-commit/mirrors-mypy/compare/v0.950...v0.960)
<!--pre-commit.ci end-->
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2544/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2544/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2544",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2544",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2544.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2544.patch",
"merged_at": "2022-06-06T19:08:01Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2545
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2545/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2545/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2545/events
|
https://github.com/materialsproject/pymatgen/pull/2545
| 1,262,564,509
|
PR_kwDOACgets45NKLW
| 2,545
|
Fixes duplicates site properties for initial magnetic moments when using `AseAtomsAdaptor`
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-06-07T00:10:32
| 2022-06-09T22:45:28
|
2022-06-07T15:37:13Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Currently, the `AseAtomsAdaptor()` conversion of an `Atoms` object to a Pymatgen `structure` object includes duplicate site properties for initial magnetic moments. This PR resolves the duplication -- the docs indicate that the initial magmoms should only be stored under `magmom` and that `initial_magmoms` should not exist as a site property.
```python
from pymatgen.io.ase import AseAtomsAdaptor
from ase.io import read
atoms = read('Ac.cif')
atoms.set_initial_magnetic_moments([1.0]*len(atoms))
struct = AseAtomsAdaptor.get_structure(atoms)
print(struct[0].properties)
```
This currently outputs
```python
{'magmom': 1.0, 'spacegroup_kinds': 0, 'initial_magmoms': 1.0}
```
The last entry should not be present.
[Ac.cif.txt](https://github.com/materialsproject/pymatgen/files/8849023/Ac.cif.txt)
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2545/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2545/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2545",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2545",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2545.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2545.patch",
"merged_at": "2022-06-07T15:37:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2546
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2546/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2546/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2546/events
|
https://github.com/materialsproject/pymatgen/issues/2546
| 1,265,189,841
|
I_kwDOACgets5LaUPR
| 2,546
|
Qhull algorithm used to create the VoronoiNN class does not take care of the periodic boundary conditions.
|
{
"login": "Anny-tech",
"id": 45486431,
"node_id": "MDQ6VXNlcjQ1NDg2NDMx",
"avatar_url": "https://avatars.githubusercontent.com/u/45486431?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Anny-tech",
"html_url": "https://github.com/Anny-tech",
"followers_url": "https://api.github.com/users/Anny-tech/followers",
"following_url": "https://api.github.com/users/Anny-tech/following{/other_user}",
"gists_url": "https://api.github.com/users/Anny-tech/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Anny-tech/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Anny-tech/subscriptions",
"organizations_url": "https://api.github.com/users/Anny-tech/orgs",
"repos_url": "https://api.github.com/users/Anny-tech/repos",
"events_url": "https://api.github.com/users/Anny-tech/events{/privacy}",
"received_events_url": "https://api.github.com/users/Anny-tech/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"You can handle periodic systems by taking a supercell, applying qhull to the super cell and then folding the images back into the unit cell. This is the approach used in pymatgen."
] | 2022-06-08T19:21:34
| 2022-06-17T21:23:18
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi
I had been trying to use the VoronoiNN class to find nearest neighbors w.r.t a particular site within the structures I am studying. However, I found from literature, that the quickhull algorithm used to create VoronoiNN does not take care of periodic boundary conditions. In that case, how can I be sure whether the nearest neighbors analysis I am doing using the VoronoiNN class is good enough?
Does the 'allow_pathological' parameter help?
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2546/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2546/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2547
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2547/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2547/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2547/events
|
https://github.com/materialsproject/pymatgen/pull/2547
| 1,268,114,721
|
PR_kwDOACgets45fyo3
| 2,547
|
chore: Set permissions for GitHub actions
|
{
"login": "naveensrinivasan",
"id": 172697,
"node_id": "MDQ6VXNlcjE3MjY5Nw==",
"avatar_url": "https://avatars.githubusercontent.com/u/172697?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/naveensrinivasan",
"html_url": "https://github.com/naveensrinivasan",
"followers_url": "https://api.github.com/users/naveensrinivasan/followers",
"following_url": "https://api.github.com/users/naveensrinivasan/following{/other_user}",
"gists_url": "https://api.github.com/users/naveensrinivasan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/naveensrinivasan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/naveensrinivasan/subscriptions",
"organizations_url": "https://api.github.com/users/naveensrinivasan/orgs",
"repos_url": "https://api.github.com/users/naveensrinivasan/repos",
"events_url": "https://api.github.com/users/naveensrinivasan/events{/privacy}",
"received_events_url": "https://api.github.com/users/naveensrinivasan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks.",
"\n[](https://coveralls.io/builds/49940384)\n\nCoverage decreased (-0.7%) to 83.288% when pulling **643f34f0c61f2c6c926e6796d97df20df4ed4e32 on turrisxyz:Pinned-Dependencies-GitHub** into **f61869ed20f942c00e7ba592d44ca5338ffbbb2f on materialsproject:master**.\n"
] | 2022-06-11T00:32:13
| 2022-06-11T03:05:25
|
2022-06-11T02:43:58Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Restrict the GitHub token permissions only to the required ones; this way, even if the attackers will succeed in compromising your workflow, they won’t be able to do much.
- Included permissions for the action. https://github.com/ossf/scorecard/blob/main/docs/checks.md#token-permissions
https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#permissions
https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
[Keeping your GitHub Actions and workflows secure Part 1: Preventing pwn requests](https://securitylab.github.com/research/github-actions-preventing-pwn-requests/)
Signed-off-by: naveen <172697+naveensrinivasan@users.noreply.github.com>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2547/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2547/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2547",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2547",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2547.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2547.patch",
"merged_at": "2022-06-11T02:43:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2548
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2548/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2548/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2548/events
|
https://github.com/materialsproject/pymatgen/pull/2548
| 1,268,415,246
|
PR_kwDOACgets45gryh
| 2,548
|
chore: Included githubactions in the dependabot config
|
{
"login": "naveensrinivasan",
"id": 172697,
"node_id": "MDQ6VXNlcjE3MjY5Nw==",
"avatar_url": "https://avatars.githubusercontent.com/u/172697?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/naveensrinivasan",
"html_url": "https://github.com/naveensrinivasan",
"followers_url": "https://api.github.com/users/naveensrinivasan/followers",
"following_url": "https://api.github.com/users/naveensrinivasan/following{/other_user}",
"gists_url": "https://api.github.com/users/naveensrinivasan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/naveensrinivasan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/naveensrinivasan/subscriptions",
"organizations_url": "https://api.github.com/users/naveensrinivasan/orgs",
"repos_url": "https://api.github.com/users/naveensrinivasan/repos",
"events_url": "https://api.github.com/users/naveensrinivasan/events{/privacy}",
"received_events_url": "https://api.github.com/users/naveensrinivasan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49945687)\n\nCoverage decreased (-0.7%) to 83.286% when pulling **e1289b3408f9953f872f95b70082b0c7266c14fe on turrisxyz:Dependabot-GitHub-Actions** into **9c0fe8ed4a1719f59bef901726c746c2a4a83230 on materialsproject:master**.\n"
] | 2022-06-12T01:36:31
| 2022-06-22T17:01:36
|
2022-06-22T17:01:35Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This should help with keeping the GitHub actions updated on new releases. This will also help with keeping it secure.
Dependabot helps in keeping the supply chain secure https://docs.github.com/en/code-security/dependabot
GitHub actions up to date https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
https://github.com/ossf/scorecard/blob/main/docs/checks.md#dependency-update-tool
Signed-off-by: naveen <172697+naveensrinivasan@users.noreply.github.com>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2548/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2548/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2548",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2548",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2548.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2548.patch",
"merged_at": "2022-06-22T17:01:35Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2549
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2549/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2549/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2549/events
|
https://github.com/materialsproject/pymatgen/pull/2549
| 1,270,094,815
|
PR_kwDOACgets45mL8C
| 2,549
|
allow a comment on KPOINTS line 4
|
{
"login": "xivh",
"id": 37019938,
"node_id": "MDQ6VXNlcjM3MDE5OTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/37019938?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xivh",
"html_url": "https://github.com/xivh",
"followers_url": "https://api.github.com/users/xivh/followers",
"following_url": "https://api.github.com/users/xivh/following{/other_user}",
"gists_url": "https://api.github.com/users/xivh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xivh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xivh/subscriptions",
"organizations_url": "https://api.github.com/users/xivh/orgs",
"repos_url": "https://api.github.com/users/xivh/repos",
"events_url": "https://api.github.com/users/xivh/events{/privacy}",
"received_events_url": "https://api.github.com/users/xivh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/49990245)\n\nCoverage decreased (-0.7%) to 83.288% when pulling **d2ec302523544ee35606f6fef5e542384eff572d on xivh:fix-kpoints-from-string** into **9c0fe8ed4a1719f59bef901726c746c2a4a83230 on materialsproject:master**.\n",
"Thanks."
] | 2022-06-14T00:13:38
| 2022-08-26T19:56:58
|
2022-06-22T14:21:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Include a summary of major changes in bullet points:
* Ignore the comment on the last line of a KPOINTS file.
## Additional dependencies introduced (if any)
## TODO (if any)
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2549/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2549/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2549",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2549",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2549.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2549.patch",
"merged_at": "2022-06-22T14:21:01Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2550
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2550/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2550/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2550/events
|
https://github.com/materialsproject/pymatgen/issues/2550
| 1,270,095,186
|
I_kwDOACgets5LtB1S
| 2,550
|
A comment on the last line of KPOINTS cannot be parsed.
|
{
"login": "xivh",
"id": 37019938,
"node_id": "MDQ6VXNlcjM3MDE5OTM4",
"avatar_url": "https://avatars.githubusercontent.com/u/37019938?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xivh",
"html_url": "https://github.com/xivh",
"followers_url": "https://api.github.com/users/xivh/followers",
"following_url": "https://api.github.com/users/xivh/following{/other_user}",
"gists_url": "https://api.github.com/users/xivh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xivh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xivh/subscriptions",
"organizations_url": "https://api.github.com/users/xivh/orgs",
"repos_url": "https://api.github.com/users/xivh/repos",
"events_url": "https://api.github.com/users/xivh/events{/privacy}",
"received_events_url": "https://api.github.com/users/xivh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-06-14T00:14:18
| 2022-06-22T15:29:55
|
2022-06-22T15:29:55Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
A KPOINTS file with a comment on the last line cannot be parsed by Kpoints.from_string().
**To Reproduce**
Example KPOINTS file that fails:
> Automatic mesh
0 ! number of k-points = 0 -> automatic generation scheme
Auto ! fully automatic
40 ! length (R_k parameter)
Error:
> ValueError: invalid literal for int() with base 10: '40\t\t! length (R_k parameter)'
**Expected behavior**
The comment should be ignored.
**Screenshots**
**Desktop (please complete the following information):**
- OS: Linux
- Version: CentOS 6.9
**Additional context**
I did not check to see if the last line is used by any other functions.
Pull request: #2549
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2550/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2550/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2551
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2551/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2551/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2551/events
|
https://github.com/materialsproject/pymatgen/pull/2551
| 1,270,552,752
|
PR_kwDOACgets45ns6l
| 2,551
|
Add `flake8` plugin `bugbear` as pre-commit hook
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Something keeps shaving off the last line from `requirements.txt` and then pre-commit.ci adds it back. @shyuep What's that 1st thing doing the shaving?",
"No idea....",
"Didn't realize this would turn into such a hornets' nest of `mypy` errors... 😅 ",
"\n[](https://coveralls.io/builds/50966524)\n\nCoverage increased (+0.005%) to 63.642% when pulling **8a017e0be537ba92fe8a5454d4734c9b05e85020 on janosh:flake8-bugbear** into **c872789fcddf905862ffddc95884332cc996b1b8 on materialsproject:master**.\n",
"@shyuep pre-commit.ci complains about `CHANGES.rst` which I didn't touch so I think this is ready for review.",
"Thanks! Looks like this caught some important things "
] | 2022-06-14T09:55:18
| 2022-07-21T17:21:48
|
2022-07-21T17:08:55Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Just discovered [`flake8-bugbear`](https://github.com/PyCQA/flake8-bugbear) and tried it out on pymatgen. I think it makes sense to add it to `pre-commit`. it points out a lot of mutable function default values, unused loop control variables (stuff like `for i, val in enumerate(values): print(value)` where `i` is never used) and other code quality issues ([full list of warnings](https://github.com/PyCQA/flake8-bugbear#list-of-warnings)). Started fixing some of them in this PR but having it as a commit hook means we avoid adding new ones in the future.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2551/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2551/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2551",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2551",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2551.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2551.patch",
"merged_at": "2022-07-21T17:08:55Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2552
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2552/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2552/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2552/events
|
https://github.com/materialsproject/pymatgen/pull/2552
| 1,275,587,379
|
PR_kwDOACgets454hJ3
| 2,552
|
Remove vertical lines from VoltageProfilePlotter.get_plotly_figure()
|
{
"login": "acrutt",
"id": 42151899,
"node_id": "MDQ6VXNlcjQyMTUxODk5",
"avatar_url": "https://avatars.githubusercontent.com/u/42151899?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/acrutt",
"html_url": "https://github.com/acrutt",
"followers_url": "https://api.github.com/users/acrutt/followers",
"following_url": "https://api.github.com/users/acrutt/following{/other_user}",
"gists_url": "https://api.github.com/users/acrutt/gists{/gist_id}",
"starred_url": "https://api.github.com/users/acrutt/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/acrutt/subscriptions",
"organizations_url": "https://api.github.com/users/acrutt/orgs",
"repos_url": "https://api.github.com/users/acrutt/repos",
"events_url": "https://api.github.com/users/acrutt/events{/privacy}",
"received_events_url": "https://api.github.com/users/acrutt/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50146362)\n\nCoverage decreased (-0.8%) to 83.285% when pulling **cd860eb890ff026c2977cd3f61c62a20ef6d41e6 on acrutt:voltage_profile** into **e0c1ee845e7131213055c5b4fc6df2cb12fcc667 on materialsproject:master**.\n",
"Thanks."
] | 2022-06-17T23:37:30
| 2022-06-22T13:25:27
|
2022-06-22T13:25:22Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Change VoltageProfilePlotter.get_plotly_figure() so connecting vertical lines are not drawn in voltage profile. These vertical lines are misleading for interpreting voltage profile plots.
@mkhorton this change was discussed with Kristin at the Jun 13 meeting on the current state of the battery code infrastructure. Please let me know if any revisions are needed but otherwise I think this PR is ready to merge.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2552/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2552/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2552",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2552",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2552.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2552.patch",
"merged_at": "2022-06-22T13:25:22Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2553
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2553/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2553/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2553/events
|
https://github.com/materialsproject/pymatgen/issues/2553
| 1,279,378,105
|
I_kwDOACgets5MQcK5
| 2,553
|
`Composition.replace` incorrect with complex mappings
|
{
"login": "jacksund",
"id": 47992949,
"node_id": "MDQ6VXNlcjQ3OTkyOTQ5",
"avatar_url": "https://avatars.githubusercontent.com/u/47992949?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jacksund",
"html_url": "https://github.com/jacksund",
"followers_url": "https://api.github.com/users/jacksund/followers",
"following_url": "https://api.github.com/users/jacksund/following{/other_user}",
"gists_url": "https://api.github.com/users/jacksund/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jacksund/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jacksund/subscriptions",
"organizations_url": "https://api.github.com/users/jacksund/orgs",
"repos_url": "https://api.github.com/users/jacksund/repos",
"events_url": "https://api.github.com/users/jacksund/events{/privacy}",
"received_events_url": "https://api.github.com/users/jacksund/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"fyi -- I don't have a dev env for pymatgen set up at the moment, and it's late here -- so I'll open the PR and add unittests for this tomorrow. ",
"I think there are two issues - one which I think I can fix, but the other one is a logic problem. \r\nThe problem with a substitution like `{\"Ca\": \"Sr\", \"N\": \"F\", \"F\": \"Cl\"}` is that it is fundamentally uninterpretable. A dict is unordered. How does the code know whether the user intend to substitute F with Cl first, followed by N with F (giving Sr2FCl) or substitute N with F followed by F with Cl (giving Sr2Cl2)? There is no reason to choose one interpretation over another.\r\n\r\nA substitution like `{\"Ca\": \"Sr\", \"N\": \"O\", \"F\": \"O\"}` should indeed be allowed. I will do the fix for this case.",
"> The problem with a substitution like {\"Ca\": \"Sr\", \"N\": \"F\", \"F\": \"Cl\"} is that it is fundamentally uninterpretable. A dict is unordered. How does the code know whether the user intend to substitute F with Cl first, followed by N with F (giving Sr2FCl) or substitute N with F followed by F with Cl (giving Sr2Cl2)? There is no reason to choose one interpretation over another.\r\n\r\nI might be misunderstanding, but as-is, I believe I disagree. For the element mapping, the key should always be the *original* element while the value is always the *new* element -- so the scenario of \"substitute N with F followed by F with Cl\" shouldn't be a thing. If you wanted the behavior of \"substitute N with F followed by F with Cl\", your element mapping should instead be `{\"Ca\": \"Sr\", \"N\": \"Cl\", \"F\": \"Cl\"}` (NOT `{\"Ca\": \"Sr\", \"N\": \"F\", \"F\": \"Cl\"}`)\r\n",
"We do allow substitutions where the key is not present in the original composition (because sometimes you want to mass process compositions). The code will just throw a warning. ",
"okay, gotcha.\r\n\r\nI was also making a PR while you made your comment -- sorry about the overlap. If you prefer to close my PR in favor of your changes, go ahead 😄 ",
"No problem. Please double check that the code I pushed works in all cases. The uninterpretable case should now throw a valueError.",
"Looks like it works as intended! Thanks. \r\n\r\nAlso, I still think it's interpretable to have an element in both keys and values -- substitutions from the `Substitutor` class even request this sometimes (that's how I stumbled onto this bug). But I'll write a workaround for this in my code.",
"@jacksund Anyway, I changed the code to allow it but throw a warning. This should now work.",
"I would argue that it is ambiguous though.... :-)",
"Thank you, and sorry about the disagreement :sweat_smile:. I really appreciate you adding the fix! It makes things a lot easier on my end. ",
"No worries. Disagreements are no problem at all! I wish there are more of them!",
"@shyuep sorry to reopen this issue, but it looks like the revised version added a new bug. `replace` can't handle oxidation states anymore. It tries to call something like `Composition(\"Ca2+\")` which fails. This breaks some functionality in the `Substitutor` class which requires inputs to be oxidation-state decorated. Here's an example of the bug...\r\n\r\n``` python\r\nfrom pymatgen.core import Composition\r\nelem_map = {'Ca2+': 'Mg2+', 'N3-': 'O2-', 'F-': 'O2-'}\r\nc = Composition(\"Ca2NF\").add_charges_from_oxi_state_guesses()\r\nc.replace(elem_map)\r\n```\r\n\r\nI've reopened my pull request #2555 to fix this and added a unittest. It's more lines of code than your solution, but hopefully that's alright. Time testing shows that both are about the same speed:\r\n``` python\r\n# from PR 2555\r\n62.7 µs ± 147 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)\r\n\r\n# from commit c676b6f (currently in main)\r\n66.1 µs ± 112 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)\r\n```",
"No problem. Thanks for fixing."
] | 2022-06-22T02:21:00
| 2022-06-23T01:41:51
|
2022-06-22T14:00:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
If an element is present in multiple places of the `elem_map`, the `Composition.replace` will return an incorrect result.
**To Reproduce**
``` python
from pymatgen.core import Composition
c = Composition("Ca2NF")
example_sub_1 = {"Ca": "Sr", "N": "O", "F": "O"}
c_new_1 = c.replace(example_sub_1)
assert c_new_1 == Composition("Sr2O2") # FAILS -- instead c_new_1 is Sr2O1
example_sub_2 = {"Ca": "Sr", "N": "F", "F": "Cl"}
c_new_2 = c.replace(example_sub_2)
assert c_new_2 == Composition("Sr2ClF") # FAILS -- instead c_new_2 is Sr2Cl
example_sub_3 = {"Ca": "Sr", "N": "F", "F": "N"} # swaps F and N sites
c_new_3 = c.replace(example_sub_3)
assert c_new_3 == Composition("Sr2NF") # FAILS -- instead c_new_3 is Sr2N
```
**Expected behavior**
``` python
import warnings
from pymatgen.core import Composition
def replace_new(comp, elem_map):
""" This is an updated version of the replace method, and I'll open a PR with this update """
# drop inapplicable substitutions
invalid_elems = [key for key in elem_map if key not in comp]
if invalid_elems:
warnings.warn(
"Some elements to be substituted are not present in composition. Please check your input. "
f"Problematic element = {invalid_elems}; {comp}"
)
for elem in invalid_elems:
elem_map.pop(elem)
# start with elements not in elem_map and remain unchanged
new_comp = {
elem: amount for elem, amount in comp.as_dict().items() if elem not in elem_map
}
for old_elem, new_elem in elem_map.items():
amount = comp[old_elem]
subs = {}
if isinstance(new_elem, dict):
for el, factor in new_elem.items():
subs[el] = factor * amount
else:
subs = {new_elem: amount}
for el, amt in subs.items():
if el in new_comp:
new_comp[el] += amt
else:
new_comp[el] = amt
return Composition(new_comp)
c = Composition("Ca2NF")
example_sub_1 = {"Ca": "Sr", "N": "O", "F": "O"}
c_new_1 = replace_new(c, example_sub_1)
assert c_new_1 == Composition("Sr2O2")
example_sub_2 = {"Ca": "Sr", "N": "F", "F": "Cl"}
c_new_2 = replace_new(c, example_sub_2)
assert c_new_2 == Composition("Sr2ClF")
example_sub_3 = {"Ca": "Sr", "N": "F", "F": "N"}
c_new_3 = replace_new(c, example_sub_3)
assert c_new_3 == Composition("Sr2NF")
# Confirming old functionality
assert replace_new(
Composition("Fe2O3"), {"Fe": {"Mg": 0.5, "Cu": 0.5}}
) == Composition("MgCuO3")
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2553/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2553/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2555
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2555/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2555/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2555/events
|
https://github.com/materialsproject/pymatgen/pull/2555
| 1,280,193,133
|
PR_kwDOACgets46H5PL
| 2,555
|
fix replace method for complex mappings
|
{
"login": "jacksund",
"id": 47992949,
"node_id": "MDQ6VXNlcjQ3OTkyOTQ5",
"avatar_url": "https://avatars.githubusercontent.com/u/47992949?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jacksund",
"html_url": "https://github.com/jacksund",
"followers_url": "https://api.github.com/users/jacksund/followers",
"following_url": "https://api.github.com/users/jacksund/following{/other_user}",
"gists_url": "https://api.github.com/users/jacksund/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jacksund/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jacksund/subscriptions",
"organizations_url": "https://api.github.com/users/jacksund/orgs",
"repos_url": "https://api.github.com/users/jacksund/repos",
"events_url": "https://api.github.com/users/jacksund/events{/privacy}",
"received_events_url": "https://api.github.com/users/jacksund/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"closed in favor of https://github.com/materialsproject/pymatgen/commit/c676b6f115d2e9e696ffb6ebc0335cba5c564152",
"\n[](https://coveralls.io/builds/50279121)\n\nCoverage increased (+0.003%) to 63.534% when pulling **43b039723c8709964066e22db7ba255cca9b4056 on jacksund:fix-2553** into **5dbb04a4338f58064e8b060da6badc09f4fe46a3 on materialsproject:master**.\n"
] | 2022-06-22T13:59:03
| 2022-06-23T02:32:00
|
2022-06-23T01:41:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
- resolves #2553
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2555/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2555/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2555",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2555",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2555.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2555.patch",
"merged_at": "2022-06-23T01:41:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2556
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2556/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2556/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2556/events
|
https://github.com/materialsproject/pymatgen/pull/2556
| 1,280,556,773
|
PR_kwDOACgets46JI07
| 2,556
|
Bump actions/download-artifact from 1 to 3
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50264654)\n\nCoverage decreased (-19.8%) to 63.526% when pulling **f17ebefa7fcbc6434203b459cb1701899a46a75c on dependabot/github_actions/actions/download-artifact-3** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on master**.\n"
] | 2022-06-22T17:02:05
| 2022-06-22T17:26:52
|
2022-06-22T17:02:22Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 1 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p>
<blockquote>
<h2>v3.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update default runtime to node16 (<a href="https://github-redirect.dependabot.com/actions/download-artifact/pull/134">actions/download-artifact#134</a>)</li>
<li>Update package-lock.json file version to 2 (<a href="https://github-redirect.dependabot.com/actions/download-artifact/pull/136">actions/download-artifact#136</a>)</li>
</ul>
<h3>Breaking Changes</h3>
<p>With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.</p>
<h2>v2.1.0 Download Artifact</h2>
<ul>
<li>Improved output & logging</li>
<li>Fixed issue where downloading all artifacts could cause display percentages to be over 100%</li>
<li>Various small bug fixes & improvements</li>
</ul>
<h2>v2.0.10</h2>
<ul>
<li>Retry on HTTP 500 responses from the service</li>
</ul>
<h2>v2.0.9</h2>
<ul>
<li>Fixes to proxy related issues</li>
</ul>
<h2>v2.0.8</h2>
<ul>
<li>Improvements to retryability if an error is encountered during artifact download</li>
</ul>
<h2>v2.0.7 download-artifact</h2>
<ul>
<li>Improved download retry-ability if a partial download is encountered</li>
</ul>
<h2>v2.0.6</h2>
<p>Update actions/core NPM package that is used internally</p>
<h2>v2.0.5</h2>
<ul>
<li>Add Third Party License Information</li>
</ul>
<h2>v2.0.4</h2>
<ul>
<li>Use the latest version of the <code>@actions/artifact</code> NPM package</li>
</ul>
<h2>v2.0.3</h2>
<ul>
<li>Misc improvements</li>
</ul>
<h2>v2.0.2</h2>
<ul>
<li>Support for tilde expansion</li>
</ul>
<h2>v2.0.1</h2>
<ul>
<li>Download path output</li>
<li>Improved logging</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/actions/download-artifact/commit/fb598a63ae348fa914e94cd0ff38f362e927b741"><code>fb598a6</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/download-artifact/issues/136">#136</a> from actions/jtamsut/update-lockfile-version</li>
<li><a href="https://github.com/actions/download-artifact/commit/a4a09c5d7eb5932e0e6c4e77a434738189a24f1b"><code>a4a09c5</code></a> regenerate index.js</li>
<li><a href="https://github.com/actions/download-artifact/commit/9acf51df7946118a04918663acc5d955f49de177"><code>9acf51d</code></a> regenerate package lock</li>
<li><a href="https://github.com/actions/download-artifact/commit/882107232564f8bc8c5083706e009246f11aa871"><code>8821072</code></a> upgrade artifact version</li>
<li><a href="https://github.com/actions/download-artifact/commit/b8bbd3b64f298f12cfabf7d85ee4e716714eae3b"><code>b8bbd3b</code></a> regenerate lockfile</li>
<li><a href="https://github.com/actions/download-artifact/commit/6ee3d963e5a7ed7dac02925e126c37e459c36aa6"><code>6ee3d96</code></a> revert artifact version</li>
<li><a href="https://github.com/actions/download-artifact/commit/d4793f4e27ec52069836c96d310f815ffa48176c"><code>d4793f4</code></a> update docs for v3</li>
<li><a href="https://github.com/actions/download-artifact/commit/2d338d2145c33c497f1f4f574ca1eb88e1061a8e"><code>2d338d2</code></a> upgrade package to v3</li>
<li><a href="https://github.com/actions/download-artifact/commit/360d0830b5796c983178d8073e39063e8d32bc46"><code>360d083</code></a> update dependency on artifact lib</li>
<li><a href="https://github.com/actions/download-artifact/commit/d9b73cccacd09ac21cc34b82578e6cbb1b4e2539"><code>d9b73cc</code></a> update lock file</li>
<li>Additional commits viewable in <a href="https://github.com/actions/download-artifact/compare/v1...v3">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2556/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2556/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2556",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2556",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2556.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2556.patch",
"merged_at": "2022-06-22T17:02:21Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2557
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2557/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2557/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2557/events
|
https://github.com/materialsproject/pymatgen/pull/2557
| 1,280,556,815
|
PR_kwDOACgets46JI1e
| 2,557
|
Bump actions/upload-artifact from 1 to 3
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50264584)\n\nCoverage decreased (-0.002%) to 83.287% when pulling **97ec22645ec549b12b0cad374b5c8050dcba5fc1 on dependabot/github_actions/actions/upload-artifact-3** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on master**.\n"
] | 2022-06-22T17:02:07
| 2022-06-22T17:25:48
|
2022-06-22T17:02:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 1 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's releases</a>.</em></p>
<blockquote>
<h2>v3.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update default runtime to node16 (<a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/293">#293</a>)</li>
<li>Update package-lock.json file version to 2 (<a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/302">#302</a>)</li>
</ul>
<h3>Breaking Changes</h3>
<p>With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.</p>
<h2>v2.3.1</h2>
<p>Fix for empty fails on Windows failing on upload <a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/281">#281</a></p>
<h2>v2.3.0 Upload Artifact</h2>
<ul>
<li>Optimizations for faster uploads of larger files that are already compressed</li>
<li>Significantly improved logging when there are chunked uploads</li>
<li>Clarifications in logs around the upload size and prohibited characters that aren't allowed in the artifact name or any uploaded files</li>
<li>Various other small bugfixes & optimizations</li>
</ul>
<h2>v2.2.4</h2>
<ul>
<li>Retry on HTTP 500 responses from the service</li>
</ul>
<h2>v2.2.3</h2>
<ul>
<li>Fixes for proxy related issues</li>
</ul>
<h2>v2.2.2</h2>
<ul>
<li>Improved retryability and error handling</li>
</ul>
<h2>v2.2.1</h2>
<ul>
<li>Update used actions/core package to the latest version</li>
</ul>
<h2>v2.2.0</h2>
<ul>
<li>Support for artifact retention</li>
</ul>
<h2>v2.1.4</h2>
<ul>
<li>Add Third Party License Information</li>
</ul>
<h2>v2.1.3</h2>
<ul>
<li>Use updated version of the <code>@action/artifact</code> NPM package</li>
</ul>
<h2>v2.1.2</h2>
<ul>
<li>Increase upload chunk size from 4MB to 8MB</li>
<li>Detect case insensitive file uploads</li>
</ul>
<h2>v2.1.1</h2>
<ul>
<li>Fix for certain symlinks not correctly being identified as directories before starting uploads</li>
</ul>
<h2>v2.1.0</h2>
<ul>
<li>Support for uploading artifacts with multiple paths</li>
<li>Support for using exclude paths</li>
<li>Updates to dependencies</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/actions/upload-artifact/commit/3cea5372237819ed00197afe530f5a7ea3e805c8"><code>3cea537</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/327">#327</a> from actions/robherley/artifact-1.1.0</li>
<li><a href="https://github.com/actions/upload-artifact/commit/849aa7758a428ee22be38de371b49c8bd57c4b9d"><code>849aa77</code></a> nvm use 12 & npm run release</li>
<li><a href="https://github.com/actions/upload-artifact/commit/4d3986961d0423ba9a593efb490a2960eb65f43b"><code>4d39869</code></a> recompile with correct ncc version</li>
<li><a href="https://github.com/actions/upload-artifact/commit/2e0d362ec5cf81e334dda822c49c96dcd4b7df2c"><code>2e0d362</code></a> bump <code>@actions/artifact</code> to 1.1.0</li>
<li><a href="https://github.com/actions/upload-artifact/commit/09a5d6a283da3e7c9f3253a5d4cdab2347712a66"><code>09a5d6a</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/320">#320</a> from actions/dependabot/npm_and_yarn/ansi-regex-4.1.1</li>
<li><a href="https://github.com/actions/upload-artifact/commit/189315d9106f43a2a8eb60836608bb96b1f69d77"><code>189315d</code></a> Bump ansi-regex from 4.1.0 to 4.1.1</li>
<li><a href="https://github.com/actions/upload-artifact/commit/d159c2d80bf32e77611286e4d71bfe6d15208d88"><code>d159c2d</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/297">#297</a> from actions/dependabot/npm_and_yarn/ajv-6.12.6</li>
<li><a href="https://github.com/actions/upload-artifact/commit/c26a7ba4b5dbaecea906fec3b7d2c0c86f1ccaba"><code>c26a7ba</code></a> Bump ajv from 6.11.0 to 6.12.6</li>
<li><a href="https://github.com/actions/upload-artifact/commit/6ed6c729229a623bcb1fdd75903dc6e436b3d0a7"><code>6ed6c72</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/303">#303</a> from actions/dependabot/npm_and_yarn/yargs-parser-13.1.2</li>
<li><a href="https://github.com/actions/upload-artifact/commit/2aeee267b2cb1f938c861a763b9770ee6e921dc3"><code>2aeee26</code></a> Bump yargs-parser from 13.1.1 to 13.1.2</li>
<li>Additional commits viewable in <a href="https://github.com/actions/upload-artifact/compare/v1...v3">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2557/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2557/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2557",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2557",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2557.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2557.patch",
"merged_at": "2022-06-22T17:02:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2558
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2558/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2558/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2558/events
|
https://github.com/materialsproject/pymatgen/pull/2558
| 1,280,556,980
|
PR_kwDOACgets46JI37
| 2,558
|
Bump actions/setup-python from 3 to 4
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50264901)\n\nCoverage remained the same at 83.289% when pulling **d0cb3b1481e19dfa224b3d66732508761b4aaade on dependabot/github_actions/actions/setup-python-4** into **c6e6ed689e1e6df54845f968ea9a8c66ba2cf9ca on master**.\n"
] | 2022-06-22T17:02:12
| 2022-06-22T17:32:15
|
2022-06-22T17:02:45Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 4.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/setup-python/releases">actions/setup-python's releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h3>What's Changed</h3>
<ul>
<li>Support for <code>python-version-file</code> input: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/336">#336</a></li>
</ul>
<p>Example of usage:</p>
<pre lang="yaml"><code>- uses: actions/setup-python@v4
with:
python-version-file: '.python-version' # Read python version from a file
- run: python my_script.py
</code></pre>
<p>There is no default python version for this <code>setup-python</code> major version, the action requires to specify either <code>python-version</code> input or <code>python-version-file</code> input. If the <code>python-version</code> input is not specified the action will try to read required version from file from <code>python-version-file</code> input.</p>
<ul>
<li>Use pypyX.Y for PyPy <code>python-version</code> input: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/349">#349</a></li>
</ul>
<p>Example of usage:</p>
<pre lang="yaml"><code>- uses: actions/setup-python@v4
with:
python-version: 'pypy3.9' # pypy-X.Y kept for backward compatibility
- run: python my_script.py
</code></pre>
<ul>
<li>
<p><code>RUNNER_TOOL_CACHE</code> environment variable is equal <code>AGENT_TOOLSDIRECTORY</code>: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/338">#338</a></p>
</li>
<li>
<p>Bugfix: create missing <code>pypyX.Y</code> symlinks: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/347">#347</a></p>
</li>
<li>
<p><code>PKG_CONFIG_PATH</code> environment variable: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/400">#400</a></p>
</li>
<li>
<p>Added <code>python-path</code> output: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/405">#405</a>
<code>python-path</code> output contains Python executable path.</p>
</li>
<li>
<p>Updated <code>zeit/ncc</code> to <code>vercel/ncc</code> package: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/393">#393</a></p>
</li>
<li>
<p>Bugfix: fixed output for prerelease version of poetry: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/409">#409</a></p>
</li>
<li>
<p>Made <code>pythonLocation</code> environment variable consistent for Python and PyPy: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/418">#418</a></p>
</li>
<li>
<p>Bugfix for <code>3.x-dev</code> syntax: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/417">#417</a></p>
</li>
<li>
<p>Other improvements: <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/318">#318</a> <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/396">#396</a> <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/384">#384</a> <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/387">#387</a> <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/388">#388</a></p>
</li>
</ul>
<h2>Update actions/cache version to 2.0.2</h2>
<p>In scope of this release we updated <code>actions/cache</code> package as the new version contains fixes related to GHES 3.5 (<a href="https://github-redirect.dependabot.com/actions/setup-python/pull/382">actions/setup-python#382</a>)</p>
<h2>Add "cache-hit" output and fix "python-version" output for PyPy</h2>
<p>This release introduces new output cache-hit (<a href="https://github-redirect.dependabot.com/actions/setup-python/pull/373">actions/setup-python#373</a>) and fix python-version output for PyPy (<a href="https://github-redirect.dependabot.com/actions/setup-python/pull/365">actions/setup-python#365</a>)</p>
<p>The cache-hit output contains boolean value indicating that an exact match was found for the key. It shows that the action uses already existing cache or not. The output is available only if cache is enabled.</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/actions/setup-python/commit/d09bd5e6005b175076f227b13d9730d56e9dcfcb"><code>d09bd5e</code></a> fix: 3.x-dev can install a 3.y version (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/417">#417</a>)</li>
<li><a href="https://github.com/actions/setup-python/commit/f72db171abf897c3f4cea0427d5af95fa57fb1bc"><code>f72db17</code></a> Made env.var pythonLocation consistent for Python and PyPy (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/418">#418</a>)</li>
<li><a href="https://github.com/actions/setup-python/commit/53e15292cd6a522cb460037b6f031eadbd6f6920"><code>53e1529</code></a> add support for python-version-file (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/336">#336</a>)</li>
<li><a href="https://github.com/actions/setup-python/commit/3f82819745be54edd3bd8a83639605e58826bfe9"><code>3f82819</code></a> Fix output for prerelease version of poetry (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/409">#409</a>)</li>
<li><a href="https://github.com/actions/setup-python/commit/397252c5825684a4ffed92b79e0d840c618c0a93"><code>397252c</code></a> Update zeit/ncc to vercel/ncc (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/393">#393</a>)</li>
<li><a href="https://github.com/actions/setup-python/commit/de977ad1321ff211fd43f0f232a4d8851726d4bb"><code>de977ad</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/412">#412</a> from vsafonkin/v-vsafonkin/fix-poetry-cache-test</li>
<li><a href="https://github.com/actions/setup-python/commit/22c6af91ce03997c5925db1f6e9f0b9b2364adcc"><code>22c6af9</code></a> Change PyPy version to rebuild cache</li>
<li><a href="https://github.com/actions/setup-python/commit/081a3cf1a51ab5fff2ae9d70f0cfacf0686293ea"><code>081a3cf</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/actions/setup-python/issues/405">#405</a> from mayeut/interpreter-path</li>
<li><a href="https://github.com/actions/setup-python/commit/ff706563d754e642609a7008f4568a5386f3e94c"><code>ff70656</code></a> feature: add a <code>python-path</code> output</li>
<li><a href="https://github.com/actions/setup-python/commit/fff15a21cc8b16191cb1249f621fa3a55b9005b8"><code>fff15a2</code></a> Use pypyX.Y for PyPy python-version input (<a href="https://github-redirect.dependabot.com/actions/setup-python/issues/349">#349</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/actions/setup-python/compare/v3...v4">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2558/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2558/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2558",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2558",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2558.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2558.patch",
"merged_at": "2022-06-22T17:02:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2559
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2559/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2559/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2559/events
|
https://github.com/materialsproject/pymatgen/pull/2559
| 1,284,214,163
|
PR_kwDOACgets46VnlO
| 2,559
|
Minor changes
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50350919)\n\nCoverage decreased (-0.002%) to 63.532% when pulling **0abcd1c818204caa7b3c7586ce1cc7ea49c78ddb on jmmshn:main** into **96aa3c028b29bf656640a14579ad0e24a2003105 on materialsproject:master**.\n"
] | 2022-06-24T21:38:54
| 2022-06-24T22:40:24
|
2022-06-24T22:40:24Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
1. Change the background color on the chemical potential plots (for dark backgrounds)
2. Added warning that the `pymatgen.analysis.defects` module will be replaced with a namespace package.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2559/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2559/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2559",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2559",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2559.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2559.patch",
"merged_at": "2022-06-24T22:40:24Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2560
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2560/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2560/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2560/events
|
https://github.com/materialsproject/pymatgen/issues/2560
| 1,284,670,129
|
I_kwDOACgets5MkoKx
| 2,560
|
Parsing AIRSS results into structures
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Closed in #2625, thanks @ScottNotFound.\r\n\r\nI think [`matador`](https://github.com/ml-evs/matador) by @ml-evs deserves an honorable mention here since its [`matador.scrapers.res2dict`](https://docs.matador.science/en/latest/matador.scrapers.html#matador.scrapers.res2dict) also offers `.res` file parsing."
] | 2022-06-25T17:44:46
| 2022-09-01T19:39:34
|
2022-09-01T19:39:26Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
[Ab initio random structure searching (AIRSS)](https://airss-docs.github.io) run creates a directory of `.res` result files describing final structures and some high-level properties like Pressure, Volume, Enthalpy, Symmetry for each randomly sampled crystal relaxation.
I saw https://github.com/materialsproject/pymatgen/pull/2048 by @mkhorton to add Castep IO. The ability to parse `.res` files into Pymatgen structures would go well with that. How about we add support for
```py
Structure.from_file('airss-run-1234.res')
```
which could be used to leverage pymatgen functionality like structure matching/grouping to analyze AIRSS results with pymatgen.
```py
from glob import glob
from pymatgen.core import Structure
structures = []
for res_file in glob("good_castep/airss-run-*.res"):
struct = Structure.from_file(res_file)
structures.append(struct)
# start analysis
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2560/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2560/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2561
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2561/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2561/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2561/events
|
https://github.com/materialsproject/pymatgen/pull/2561
| 1,284,758,470
|
PR_kwDOACgets46XQty
| 2,561
|
Fix typos in pymatgen.symmetry.analyzer docstrings
|
{
"login": "dgaines2",
"id": 38781226,
"node_id": "MDQ6VXNlcjM4NzgxMjI2",
"avatar_url": "https://avatars.githubusercontent.com/u/38781226?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dgaines2",
"html_url": "https://github.com/dgaines2",
"followers_url": "https://api.github.com/users/dgaines2/followers",
"following_url": "https://api.github.com/users/dgaines2/following{/other_user}",
"gists_url": "https://api.github.com/users/dgaines2/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dgaines2/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dgaines2/subscriptions",
"organizations_url": "https://api.github.com/users/dgaines2/orgs",
"repos_url": "https://api.github.com/users/dgaines2/repos",
"events_url": "https://api.github.com/users/dgaines2/events{/privacy}",
"received_events_url": "https://api.github.com/users/dgaines2/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50360788)\n\nCoverage decreased (-0.002%) to 63.535% when pulling **bef64d16fe2543f2f4f695cd336431499dd2b222 on dgaines2:master** into **d2042532624b363d5ace8c4199d22d4503e853dd on materialsproject:master**.\n"
] | 2022-06-26T00:44:34
| 2022-06-26T03:46:40
|
2022-06-26T03:26:11Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Just a small fix for some recently added docstrings.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2561/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2561/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2561",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2561",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2561.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2561.patch",
"merged_at": "2022-06-26T03:26:11Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2562
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2562/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2562/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2562/events
|
https://github.com/materialsproject/pymatgen/pull/2562
| 1,288,056,123
|
PR_kwDOACgets46iGNt
| 2,562
|
Parsing the Fock matrix and eigenvalues from the QChem output file
|
{
"login": "sudarshanv01",
"id": 47235474,
"node_id": "MDQ6VXNlcjQ3MjM1NDc0",
"avatar_url": "https://avatars.githubusercontent.com/u/47235474?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sudarshanv01",
"html_url": "https://github.com/sudarshanv01",
"followers_url": "https://api.github.com/users/sudarshanv01/followers",
"following_url": "https://api.github.com/users/sudarshanv01/following{/other_user}",
"gists_url": "https://api.github.com/users/sudarshanv01/gists{/gist_id}",
"starred_url": "https://api.github.com/users/sudarshanv01/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/sudarshanv01/subscriptions",
"organizations_url": "https://api.github.com/users/sudarshanv01/orgs",
"repos_url": "https://api.github.com/users/sudarshanv01/repos",
"events_url": "https://api.github.com/users/sudarshanv01/events{/privacy}",
"received_events_url": "https://api.github.com/users/sudarshanv01/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks Sudarshan! Flagging @samblau for comment. I don't use these features so don't have much to say other than I think it's great when our IO classes support as many features of the underlying code as possible.",
"\n[](https://coveralls.io/builds/53778237)\n\nCoverage remained the same at 0.0% when pulling **15807dbaa49edeba884e4a02851cfaec005acc16 on sudarshanv01:qchem_io_eigenvals** into **c1f1e95d93a1fab758610aeb9a68d5711e1fce82 on materialsproject:master**.\n",
"Hi @samblau ! I have added tests for parsing the Fock matrix and eigenvalues through the latest commit. These tests have been added to `test_outputs.py` and `test_sets.py`. Pylint requested changes in parts of the code that I have not changed are highlighted through comments. \r\n\r\nNote that this commit is needed to complete [this](https://github.com/hackingmaterials/atomate/pull/759) PR on atomate (which fails tests because it doesn't have the right keys for a dict implemented through this PR).",
"Thanks @janosh for taking a look at this! It appears that all checks pass now. ",
"Looks good to me, let's get this PR merged @mkhorton @shyuep ",
"Done :) thanks @sudarshanv01!"
] | 2022-06-29T01:09:22
| 2022-11-01T16:47:12
|
2022-11-01T16:47:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
I am not sure if this typically required output to be parsed from a QChem file, so please feel free to let me know if this is not of interest.
This PR includes changes to `qchem/outputs.py` and `qchem/utils.py` files. In case the Fock-matrix and eigenvalues are requested by the user (though the flags `scf_final_print` or `scf_print`), the modifications to `outputs.py` allows for parsing both these quantities.
## Additional dependencies introduced (if any)
No additional dependencies.
## TODO (if any)
If this parsing is of interest, other matrix quantities such as the coefficients of the MO can be parsed by the same function in `qchem/utils.py`. Tests need to be added as well.
## Checklist
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2562/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2562/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2562",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2562",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2562.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2562.patch",
"merged_at": "2022-11-01T16:47:01Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2563
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2563/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2563/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2563/events
|
https://github.com/materialsproject/pymatgen/pull/2563
| 1,289,616,042
|
PR_kwDOACgets46nUTR
| 2,563
|
Molecule: warn when writing charged mol to xyz
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Again, I have to question whether this is necessary at all. Surely a user would know the XYZ format doesn't store charge and use something else if he wants the charge?",
"> Again, I have to question whether this is necessary at all. Surely a user would know the XYZ format doesn't store charge and use something else if he wants the charge?\r\n\r\nI've been using .xyz format for a while and only just learned this. Considering that outreach and making computational tools accessible to non-expert users is part of MP's mission, I absolutely do not think we should expect users to know these kinds of nuanced details. Someone might become a fluent user of pymatgen's `Molecule` class without knowing much of anything about the different file formats. If a warning, which is only raised in an edge case like this, can teach a user something or prevent them from wasting time, I think it adds value and makes our code more user friendly.",
"Because I think in general, the expectation throughout pymatgen is that you can use `to_file` / `from_file` methods to reversibly write out and reconstruct pymatgen objects. This is a particular case where that will not work, which is why I think it warrants an extra warning.",
"I don't actually think that statement is true. For example, you can specify all kinds of site properties for Structures. Except for the json format, most of the other formats do not preserve all that information. \r\n\r\nI get that you can add warnings all over the place. But it does contribute to noise when using the code. I think many of us have been irritated by this in the past both in pymatgen and other codes. E.g., when Excel tells you that saving in csv loses information as opposed to saving in xlsx. I have probably seen that warning more than a hundred times in my lifetime and it still bugs me today when I see it. \r\n\r\nIn the end, the Python representations in pymatgen are by definition a superset of the features of specific output formats (ideally speaking). Other than the pickled/json serialized forms where we are explicit in supporting full reconstruction, all bets are off when you output to another format since support depends on the specifications of that format. Moreover, if you didn't realize XYZ doesn't support charge, you probably didn't need the charge until the day you actually found that out. ",
"The `XYZ` class does have a [docstring note](https://github.com/materialsproject/pymatgen/blob/c30082466191abcb9ca714a2d871a0dd8e92b13b/pymatgen/io/xyz.py#L23-L26) about losing periodicity, so perhaps reasonable to add an additional note here (and in the `.to` docstring) about charge, as an alternative?",
"I have no problems with a docstring comment. It is more warnings that I think we should make judicious use of. If anything, I am all for using Python logging to log some of these messages and people can set a logging.basicConfig(BEGINNERMODE) if they want all the noise. BTW, non-beginner people have been complaining about such noise from pymatgen and other codes. ",
"Closing this. If docstring is desired, pls go ahead and implement and submit a new PR. Thanks."
] | 2022-06-30T05:44:34
| 2024-10-10T01:54:46
|
2022-07-06T23:59:49Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
`Molecule.to()` supports many formats including .xyz; however .xyz format does not store charge information; only atomic positions. For users not intimately familiar with details of the .xyz format, this can lead to unexpected behavior when working with charged `Molecule`, e.g.
```
>>> m = Molecule([Element("K")], [[0,0,0]], charge =1)
>>> m.charge
1
>>> m.to(filename='test.xyz')
>>> m2=Molecule.from_file('test.xyz')
>>> m2.charge
0
```
This PR simply adds a warning to alert the user that they will lose information when writing to .xyz. The warning is only raised when 1) the `Molecule` has a charge and 2) the user tries to write to .xyz format.
```
>>> m.to(fmt='test.xyz')
UserWarning: Your molecule has a charge of 1, but the XYZ format only stores atomic positions, not charge.
Using Molecule.from_file() with this file will result in an uncharged Molecule.
'1\nK1\nK 0.000000 0.000000 0.000000'
```
Other minor changes to `test_structure.py` were made to satisfy the `pylint` pre-commit hooks
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2563/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2563/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2563",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2563",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2563.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2563.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2564
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2564/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2564/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2564/events
|
https://github.com/materialsproject/pymatgen/issues/2564
| 1,289,648,027
|
I_kwDOACgets5M3neb
| 2,564
|
InterstitialGenerator Wrongly Counts Interstitial Sites Due to Overlapped Interstitials
|
{
"login": "JiQi535",
"id": 54908836,
"node_id": "MDQ6VXNlcjU0OTA4ODM2",
"avatar_url": "https://avatars.githubusercontent.com/u/54908836?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JiQi535",
"html_url": "https://github.com/JiQi535",
"followers_url": "https://api.github.com/users/JiQi535/followers",
"following_url": "https://api.github.com/users/JiQi535/following{/other_user}",
"gists_url": "https://api.github.com/users/JiQi535/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JiQi535/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JiQi535/subscriptions",
"organizations_url": "https://api.github.com/users/JiQi535/orgs",
"repos_url": "https://api.github.com/users/JiQi535/repos",
"events_url": "https://api.github.com/users/JiQi535/events{/privacy}",
"received_events_url": "https://api.github.com/users/JiQi535/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The likely reason is the tolerance in symmetry finding. This can easily be solved with using Structure.merge_sites after you generate the interstitials. Or maybe refining the structure before you run the defect analysis."
] | 2022-06-30T06:13:43
| 2022-06-30T06:25:35
|
2022-06-30T06:25:35Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
The InterstitialGenerator can identify octahedral and tetrahedral interstitials, however, it overestimates the number of interstitial sites due to overlapping interstitials. _**More than that, the method of create_saturated_interstitial_structure creates structures with overlapped interstitial sites.**_ The visualized saturated structure of BCC Ti with interstitial H atoms are shown below. The bug likely from the StructureMotifInterstitial class. While I haven't found the exact source of error from the complex codes, you can reproduce the problem by my example code below.
**To Reproduce**
The error can be reproduced with the below codes:
```
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.defects.generators import InterstitialGenerator
from pymatgen.analysis.defects.core import create_saturated_interstitial_structure
mpr = MPRester()
Ti_mp73_Im3m_BCC = mpr.get_structure_by_material_id("mp-73")
IG = InterstitialGenerator(Ti_mp73_Im3m_BCC, "H")
Ti_mp73_Im3m_BCC_interH_saturated = create_saturated_interstitial_structure(IG.unique_defect_seq[0])
print("Found {} interstitals in {} with SG of {}".format(IG.unique_defect_seq[0].get_multiplicity(),Ti_mp73_Im3m_BCC.formula, Ti_mp73_Im3m_BCC.get_space_group_info()))
```
**Expected behavior**
No overlapped interstitial sites.
**Snapshot**
**Desktop (please complete the following information):**
- OS: [Mac]
@mkhorton @janosh I'm not sure who should I quote here, so I'm asking Matthew and Janosh here to help to link to the right person. Thank you!
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2564/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2564/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2565
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2565/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2565/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2565/events
|
https://github.com/materialsproject/pymatgen/pull/2565
| 1,289,654,453
|
PR_kwDOACgets46ncuH
| 2,565
|
Molecule: warn user about non-triplet O2
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"No harm in a warning. Seems good to me. ",
"No issue from me. Let's consider it a reprimanding instead of a warning though. 😉 ",
"Sorry to take an alternative position, but I am not sure this is necessary at all. It is strange to do this specially for O2. What if someone sets H2 to be in a triplet state? The code doesn't seem to warn against that? There are a potential infinite list of bad configurations and you cannot catch them all. O2 seems highly important to some people but is not even a consideration for others. \r\n\r\nFurther, note that it is not wrong to do singlet O2. That is a valid excited state.\r\n\r\nI would point out that even quantum chemistry codes do not give a warning when you run singlet O2. At least I do not see such warnings when I deigned to run my own nwchem or Gaussian a long time ago. :-)\r\n\r\nIn the end, there is some level of \"users should know what they are doing\" when using these codes. We don't need to babysit them. :-)",
"I concur. I do see value in this sort of logic somewhere; for example, in the Materials Project builders we have logic to check that a calculation is physically plausible (eg, magnetic moments are not abnormally large). I can imagine a class that can do this sort of checking with multiple rules defined, and this might be helpful for automated checking, but I do agree with @shyuep that putting it in the Molecule initializer seems heavy-handed (where does it stop if so? the initializer could get very large and cumbersome as new rules are added)."
] | 2022-06-30T06:21:48
| 2024-10-10T01:54:47
|
2022-06-30T16:53:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
When a user creates a `Molecule` to represent O2 with default keyword arguments, the spin_multiplicity will be set to 1. However, the ground state of the O2 molecule is triplet (unlike most molecules with a single covalent bond).
```
>>> mol = Molecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]])
>>> m.spin_multiplicity
1
````
This PR adds a warning to remind users of this fact. The warning is only invoked when 1) the `Molecule` is O2 (not O4, or O8, etc.), 2) the charge is zero, and 3) the spin_multiplicity is not equal to 3. It does not change the internal spin multiplicity setting either; it merely alerts the user that they may have made a mistake.
```
>>> mol = Molecule(["O"] * 2, [[0, 0, 0], [0, 0, 1.2]])
UserWarning: You have specified a spin multiplicity of 1 for an O2 molecule; however the ground state of
molecular O2 has a spin multiplicity of 3. If this was intentional, you can safely ignore this message.
>>> m.spin_multiplicity
1
````
This may be controversial; I recognize that we have to expect users to know what they are doing and can't anticipate every mistake or non-obvious behavior. That said, given how common O2 is to many different types of simulation work and that I'm sure the vast majority of users want the ground state when they make an O2 Molecule, I think it's valuable to include this warning to 1) help users catch their own mistakes (preventing wasted time and having to re-do calculations) and 2) educate less savvy users that this is something they need to think about.
Other minor changes to `test_structure.py` were made to satisfy the` pylint` pre-commit hooks
Flagging @samblau and @mkhorton and @arosen93 for any additional thoughts
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2565/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2565/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2565",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2565",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2565.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2565.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2566
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2566/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2566/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2566/events
|
https://github.com/materialsproject/pymatgen/pull/2566
| 1,289,666,911
|
PR_kwDOACgets46nfXx
| 2,566
|
Ion: pass charge to oxi_state_guesses
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This is a great edit @rkingsbury, thanks!"
] | 2022-06-30T06:36:20
| 2022-07-26T21:04:13
|
2022-06-30T19:00:47Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
`Ion.oxi_state_guesses()` currently inherits from `Composition`, and generally fails to provide useful information unless the user specifies the `target_charge` (which is an optional kwarg):
```
>>> i=Ion.from_formula('SO4-2')
>>> i.oxi_state_guesses()
[]
```
This PR overloads the parent method such that `target_charge` is always set equal to the net charge on the `Ion` object. All other kwargs are passed to the parent method.
```
>>> i=Ion.from_formula('SO4-2')
>>> i.oxi_state_guesses()
({'S': 6.0, 'O': -2.0},)
```
Other minor changes to `test_ion.py` were made to satisfy the `pylint` pre-commit hooks
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2566/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2566/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2566",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2566",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2566.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2566.patch",
"merged_at": "2022-06-30T19:00:47Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2567
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2567/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2567/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2567/events
|
https://github.com/materialsproject/pymatgen/pull/2567
| 1,289,684,041
|
PR_kwDOACgets46njAF
| 2,567
|
Element: add from_name()
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-06-30T06:55:52
| 2022-06-30T18:15:20
|
2022-06-30T16:55:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Adds an `Element.from_name` convenience function to make it possible to init an `Element` from its long name, in addition to existing methods based on symbol (default), atomic number (`Element.from_Z`), or row and group (`Element.from_row_and_group``)
```
>>> Element.from_name('Sodium')
Element Na
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2567/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2567/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2567",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2567",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2567.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2567.patch",
"merged_at": "2022-06-30T16:55:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2568
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2568/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2568/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2568/events
|
https://github.com/materialsproject/pymatgen/pull/2568
| 1,290,437,325
|
PR_kwDOACgets46qE78
| 2,568
|
allow to change voronoi_distance_cutoff in ChemEnv
|
{
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/followers",
"following_url": "https://api.github.com/users/JaGeo/following{/other_user}",
"gists_url": "https://api.github.com/users/JaGeo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JaGeo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JaGeo/subscriptions",
"organizations_url": "https://api.github.com/users/JaGeo/orgs",
"repos_url": "https://api.github.com/users/JaGeo/repos",
"events_url": "https://api.github.com/users/JaGeo/events{/privacy}",
"received_events_url": "https://api.github.com/users/JaGeo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50501842)\n\nCoverage decreased (-0.003%) to 63.532% when pulling **87bec49eee0fe3f5f3c711966fa5cde77fb3adc3 on JaGeo:fix_voronoi** into **57075245189b05f6eaba356dffc39e1ec58812a7 on materialsproject:master**.\n",
"Thanks @JaGeo and thanks @rlaplaza for finding this issue."
] | 2022-06-30T17:23:20
| 2022-06-30T20:43:46
|
2022-06-30T18:57:28Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull-request allows to change the voronoi_distance cutoff in ChemEnv. Otherwise, molecules in too large boxes cannot be investigated. I have added a test and a warning for users in case the cutoff is too small. (Issue found by @rlaplaza)
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2568/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2568/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2568",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2568",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2568.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2568.patch",
"merged_at": "2022-06-30T18:57:27Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2570
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2570/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2570/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2570/events
|
https://github.com/materialsproject/pymatgen/pull/2570
| 1,291,603,036
|
PR_kwDOACgets46uAMp
| 2,570
|
small documentation addition
|
{
"login": "orionarcher",
"id": 27712051,
"node_id": "MDQ6VXNlcjI3NzEyMDUx",
"avatar_url": "https://avatars.githubusercontent.com/u/27712051?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/orionarcher",
"html_url": "https://github.com/orionarcher",
"followers_url": "https://api.github.com/users/orionarcher/followers",
"following_url": "https://api.github.com/users/orionarcher/following{/other_user}",
"gists_url": "https://api.github.com/users/orionarcher/gists{/gist_id}",
"starred_url": "https://api.github.com/users/orionarcher/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/orionarcher/subscriptions",
"organizations_url": "https://api.github.com/users/orionarcher/orgs",
"repos_url": "https://api.github.com/users/orionarcher/repos",
"events_url": "https://api.github.com/users/orionarcher/events{/privacy}",
"received_events_url": "https://api.github.com/users/orionarcher/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50532847)\n\nCoverage decreased (-0.002%) to 63.534% when pulling **90d1b5afc573232509b39245dc774634ddd0c4d2 on orioncohen:small_docs_fix** into **99a65ac4a49a7a9c20aa7969f5b7f1db773143eb on materialsproject:master**.\n",
"Thanks,"
] | 2022-07-01T16:25:01
| 2022-07-01T17:12:53
|
2022-07-01T17:12:44Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Tiny addition to documentation. This was a gotcha for me.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2570/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2570/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2570",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2570",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2570.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2570.patch",
"merged_at": "2022-07-01T17:12:44Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2571
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2571/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2571/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2571/events
|
https://github.com/materialsproject/pymatgen/pull/2571
| 1,291,835,991
|
PR_kwDOACgets46uzEX
| 2,571
|
Remove not converted warning for MD run
|
{
"login": "mjwen",
"id": 10203513,
"node_id": "MDQ6VXNlcjEwMjAzNTEz",
"avatar_url": "https://avatars.githubusercontent.com/u/10203513?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mjwen",
"html_url": "https://github.com/mjwen",
"followers_url": "https://api.github.com/users/mjwen/followers",
"following_url": "https://api.github.com/users/mjwen/following{/other_user}",
"gists_url": "https://api.github.com/users/mjwen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mjwen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mjwen/subscriptions",
"organizations_url": "https://api.github.com/users/mjwen/orgs",
"repos_url": "https://api.github.com/users/mjwen/repos",
"events_url": "https://api.github.com/users/mjwen/events{/privacy}",
"received_events_url": "https://api.github.com/users/mjwen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks,",
"\n[](https://coveralls.io/builds/50656255)\n\nCoverage increased (+0.002%) to 63.539% when pulling **3da0e594551dd4a429e9f8503344559854290214 on mjwen:hotfix** into **38666c384fa3a0ae78d55a3e002f20c140f72fc5 on materialsproject:master**.\n"
] | 2022-07-01T21:14:28
| 2022-07-07T00:20:12
|
2022-07-06T23:58:02Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
- Do not report not converted warnings on MD runs.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2571/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2571/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2571",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2571",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2571.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2571.patch",
"merged_at": "2022-07-06T23:58:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2572
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2572/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2572/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2572/events
|
https://github.com/materialsproject/pymatgen/pull/2572
| 1,292,719,543
|
PR_kwDOACgets46xlHB
| 2,572
|
Improve messages and warnings
|
{
"login": "cajfisher",
"id": 66772456,
"node_id": "MDQ6VXNlcjY2NzcyNDU2",
"avatar_url": "https://avatars.githubusercontent.com/u/66772456?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/cajfisher",
"html_url": "https://github.com/cajfisher",
"followers_url": "https://api.github.com/users/cajfisher/followers",
"following_url": "https://api.github.com/users/cajfisher/following{/other_user}",
"gists_url": "https://api.github.com/users/cajfisher/gists{/gist_id}",
"starred_url": "https://api.github.com/users/cajfisher/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/cajfisher/subscriptions",
"organizations_url": "https://api.github.com/users/cajfisher/orgs",
"repos_url": "https://api.github.com/users/cajfisher/repos",
"events_url": "https://api.github.com/users/cajfisher/events{/privacy}",
"received_events_url": "https://api.github.com/users/cajfisher/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-07-04T07:01:51
| 2022-07-04T12:26:14
|
2022-07-04T12:26:14Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Tidies up and makes messages/warnings/errors/descriptions clearer and more consistent
## Summary
Incorrect use of "respectively" fixed
Made terminology and formatting consistent (e.g., k-path vs kpath)
It's conventional (ha-ha!) to abbreviate "Latimer and Munro convention" to "Latimer-Munro convention", and so on
Meaning of "author-intended" unclear, so details added
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2572/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2572/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2572",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2572",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2572.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2572.patch",
"merged_at": "2022-07-04T12:26:14Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2573
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2573/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2573/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2573/events
|
https://github.com/materialsproject/pymatgen/pull/2573
| 1,292,730,715
|
PR_kwDOACgets46xnf9
| 2,573
|
Fix English errors in messages, descriptions, etc.
|
{
"login": "cajfisher",
"id": 66772456,
"node_id": "MDQ6VXNlcjY2NzcyNDU2",
"avatar_url": "https://avatars.githubusercontent.com/u/66772456?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/cajfisher",
"html_url": "https://github.com/cajfisher",
"followers_url": "https://api.github.com/users/cajfisher/followers",
"following_url": "https://api.github.com/users/cajfisher/following{/other_user}",
"gists_url": "https://api.github.com/users/cajfisher/gists{/gist_id}",
"starred_url": "https://api.github.com/users/cajfisher/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/cajfisher/subscriptions",
"organizations_url": "https://api.github.com/users/cajfisher/orgs",
"repos_url": "https://api.github.com/users/cajfisher/repos",
"events_url": "https://api.github.com/users/cajfisher/events{/privacy}",
"received_events_url": "https://api.github.com/users/cajfisher/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50562835)\n\nCoverage decreased (-0.002%) to 63.581% when pulling **e2b1aea7f131969b82bc96442f9b85053e82fa61 on cajfisher:patch-5** into **85796d24190aca51a2674a7895430eb7c561b0a9 on materialsproject:master**.\n"
] | 2022-07-04T07:12:51
| 2022-07-04T12:31:33
|
2022-07-04T12:31:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Minor English corrections and improved descriptions/reduced ambiguity
## Summary
"can be incorrect" should be "may be incorrect"
The "lattice" is infinite in all dimensions and remains unchanged; only the "cell" or "lattice vectors" are reduced
Other minor improvements for clarity/ease-of-reading
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2573/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2573/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2573",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2573",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2573.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2573.patch",
"merged_at": "2022-07-04T12:31:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2574
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2574/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2574/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2574/events
|
https://github.com/materialsproject/pymatgen/pull/2574
| 1,293,537,929
|
PR_kwDOACgets460UKD
| 2,574
|
[pre-commit.ci] pre-commit autoupdate
|
{
"login": "pre-commit-ci[bot]",
"id": 66853113,
"node_id": "MDM6Qm90NjY4NTMxMTM=",
"avatar_url": "https://avatars.githubusercontent.com/in/68672?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D",
"html_url": "https://github.com/apps/pre-commit-ci",
"followers_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50582833)\n\nCoverage decreased (-0.002%) to 63.581% when pulling **75ddae179369742d1fd07c86be839be526d7e312 on pre-commit-ci-update-config** into **723260b181734337cbd75fc4ec8f55382b91dc90 on master**.\n"
] | 2022-07-04T20:13:16
| 2022-07-06T23:57:21
|
2022-07-06T23:57:21Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.32.1 → v2.34.0](https://github.com/asottile/pyupgrade/compare/v2.32.1...v2.34.0)
- [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.2.0...v4.3.0)
- [github.com/psf/black: 22.3.0 → 22.6.0](https://github.com/psf/black/compare/22.3.0...22.6.0)
- [github.com/pre-commit/mirrors-mypy: v0.960 → v0.961](https://github.com/pre-commit/mirrors-mypy/compare/v0.960...v0.961)
<!--pre-commit.ci end-->
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2574/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2574/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2574",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2574",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2574.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2574.patch",
"merged_at": "2022-07-06T23:57:21Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2575
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2575/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2575/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2575/events
|
https://github.com/materialsproject/pymatgen/pull/2575
| 1,296,272,543
|
PR_kwDOACgets469d3q
| 2,575
|
InputSet: implement equality method and fix __iter__
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50648810)\n\nCoverage increased (+0.007%) to 63.591% when pulling **ab9d4e51a5a15b3a942b882539729f9885b37bec on rkingsbury:inputset_eq** into **723260b181734337cbd75fc4ec8f55382b91dc90 on materialsproject:master**.\n",
"Thanks @rkingsbury, and thanks @orionarcher for reporting.\r\n\r\nI'm going to merge this because both changes seem sensible, but if there's an issue please alert me and we can resolve.",
"> Thanks @rkingsbury, and thanks @orionarcher for reporting.\r\n> \r\n> I'm going to merge this because both changes seem sensible, but if there's an issue please alert me and we can resolve.\r\n\r\nThanks @mkhorton . The only potential issue is that the change in behavior of `__iter__` might break existing code. However I don't think this new style `InputSet` has seen wide use yet (certainly not within pymatgen - it's only the packmol and `TemplateInputGen' afaik), and those tests all pass without modification. If others have developed `InputSet` outside of pymatgen and they happen to be iterating over the object, they would be affected. But other than @utf in atomate2 and @orionarcher in his OpenMM addon, I don't believe anyone has."
] | 2022-07-06T19:22:28
| 2022-07-06T22:50:16
|
2022-07-06T21:03:58Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request fixes two items in `InputSet`:
1. `__iter__` was previously iterating an iterator over `self.inputs.items()` rather than `self.inputs`. This was not a correct implementation (see example for implementing a `dict`-like class from `MutableMapping` [here](https://stackoverflow.com/questions/21361106/how-would-i-implement-a-dict-with-abstract-base-classes-in-python)) and prevented `__eq__` from working properly
2. After fixing item 1), I realized that the built-in `__eq__` method was only comparing the `inputs` and not the kwargs. Therefore, I added a custom `__eq__` method to ensure that `InputSet` are considered equal only if both the `inputs` and all kwargs are equal.
Note that a small change in some of the pre-existing tests was required due to the changed behavior of `__iter__`.
Thanks @orionarcher for identifying this bug. Also flagging @utf in case the changed behavior of `__iter__` will affect your new input sets in atomate2
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2575/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2575/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2575",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2575",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2575.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2575.patch",
"merged_at": "2022-07-06T21:03:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2576
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2576/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2576/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2576/events
|
https://github.com/materialsproject/pymatgen/issues/2576
| 1,296,558,298
|
I_kwDOACgets5NR-ja
| 2,576
|
Sign convention inconsistency between pymatgen and atomate2
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Fixed in #2577 "
] | 2022-07-06T22:32:05
| 2022-07-08T06:12:18
|
2022-07-08T06:12:18Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Here the sign convention is more electrons bigger number:
https://github.com/materialsproject/pymatgen/blob/723260b181734337cbd75fc4ec8f55382b91dc90/pymatgen/io/vasp/outputs.py#L1170
Here `nelect` is the number computed from the potcar so it is exactly the opposite of the definition above:
https://github.com/materialsproject/atomate2/blob/e11f3d2c7f943d012b80b935a9585bee7d18a645/src/atomate2/vasp/sets/base.py#L478-L484
Just wanna flag this issue before making a PR.
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2576/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2576/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2577
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2577/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2577/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2577/events
|
https://github.com/materialsproject/pymatgen/pull/2577
| 1,296,608,608
|
PR_kwDOACgets46-paL
| 2,577
|
changed charge convention
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Unittest needed.",
"\n[](https://coveralls.io/builds/50656286)\n\nCoverage decreased (-0.001%) to 63.589% when pulling **5f2ce21b223837d300624cdf1fb16bf0be4f490d on jmmshn:charge_sign** into **72d6e8b4df2a7e76ac5bba4ccc834df3683637c0 on materialsproject:master**.\n",
"The unit tests already exist but used the wrong convention?\r\n@mkhorton and I had a chat and think we should use negative throughout to avoid these issues in the future.\r\nThe unit tests have been updated to reflect this.",
"Thanks.",
"This convention change silently broke the code that I use. I think it's a bit irresponsible to change conventions like this without properly warning your users, especially for such a large, dynamic, and widely used library such as this. The only reason I was able to find out that something was wrong with my code was because I had old data that wasn't matching; if this were not the case, this change might have gone unnoticed, resulting in bad calculations and data. This is very concerning. @shyuep @mkhorton ",
"I think the original implementation was wrong to begin with. It is perfectly reasonable that a negative charge corresponds to an electron (otherwise we violate almost all conventions used in physics and chemistry?). This PR fixes that problem.\n\nAs with all cases, we document the changes in the release. But perhaps it would be useful to add a warning to users that the convention has changed if there is a charge. @jmmshn can you just add a warning?",
"@shyuep ok I'll add a warning. Thanks for bringing this up @mturiansky.",
"\r\n\r\n\r\n\r\n> I think the original implementation was wrong to begin with. It is perfectly reasonable that a negative charge corresponds to an electron (otherwise we violate almost all conventions used in physics and chemistry?). This PR fixes that problem.\r\n\r\nI can't speak to why this convention was chosen for the original implementation, but it was and people developed on top of that using that convention. I can't imagine I'm the only one who used it, and I suspect by adding a warning someone else may be surprised to find that it has changed.\r\n\r\nI understand you can't put a warning for every tiny change, but a convention change like this, where previous code could work just fine within the old convention, seems like a good case for one."
] | 2022-07-06T23:52:46
| 2023-01-03T01:06:13
|
2022-07-07T14:15:13Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## The sign convention of the net charge parsed by Vasprun should be changed.
The current value of the parsed charge for Vasprun.structure is more positive if NELECT is higher.
If we used the electron -> negative charge convention then this expression should have the other sign
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2577/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2577/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2577",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2577",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2577.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2577.patch",
"merged_at": "2022-07-07T14:15:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2578
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2578/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2578/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2578/events
|
https://github.com/materialsproject/pymatgen/issues/2578
| 1,298,567,560
|
I_kwDOACgets5NZpGI
| 2,578
|
Missing Charge in Vasprun.final_structure
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"addressed in #2579 "
] | 2022-07-08T06:45:24
| 2022-07-08T06:58:39
|
2022-07-08T06:58:39Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/d10c460b2b20b8802e345491bfe2301d1376650e/pymatgen/io/vasp/outputs.py#L1348-L1355
The charge is missing in `Vasprun.final_structure` and `Vasprun.initial_structure`.
Is it possible to just use `Vasprun.structures[-1]` and `Vasprun.structures[0]` for these as opposed to reading them explicitly?
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2578/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2578/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2579
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2579/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2579/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2579/events
|
https://github.com/materialsproject/pymatgen/pull/2579
| 1,298,578,513
|
PR_kwDOACgets47FZT-
| 2,579
|
Apply the structure charge to initial and final structure
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50701699)\n\nCoverage increased (+0.003%) to 63.593% when pulling **29706c90fc55d6aec4f0be4b9d09f7da2091d84d on jmmshn:charge_sign** into **d10c460b2b20b8802e345491bfe2301d1376650e on materialsproject:master**.\n"
] | 2022-07-08T06:57:09
| 2022-07-08T11:27:31
|
2022-07-08T11:27:30Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Bug Fix in Vasprun
The current code does not decorate the initial and final structures in `Vasprun` with the charge. This affects Atomate2
https://github.com/materialsproject/atomate2/issues/154
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2579/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2579/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2579",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2579",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2579.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2579.patch",
"merged_at": "2022-07-08T11:27:30Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2580
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2580/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2580/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2580/events
|
https://github.com/materialsproject/pymatgen/pull/2580
| 1,298,865,456
|
PR_kwDOACgets47GXpz
| 2,580
|
Brillouin sone -> Brillouin zone
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50707453)\n\nCoverage remained the same at 63.591% when pulling **f9d38dfee844b0017ee4121cc030b6958fa66939 on janosh:typo** into **d10c460b2b20b8802e345491bfe2301d1376650e on materialsproject:master**.\n"
] | 2022-07-08T11:02:31
| 2022-07-08T11:55:17
|
2022-07-08T11:34:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Also replaces unicode character U+2013 "–" with regular minus sign U+002d "-" as the latter is more commonly used in source code.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2580/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2580/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2580",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2580",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2580.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2580.patch",
"merged_at": "2022-07-08T11:34:46Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2581
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2581/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2581/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2581/events
|
https://github.com/materialsproject/pymatgen/pull/2581
| 1,299,656,562
|
PR_kwDOACgets47JAXP
| 2,581
|
Add "External tools" section to `docs_rst/addons.rst`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51098196)\n\nCoverage decreased (-0.001%) to 63.579% when pulling **078479d67967ef6af4cd22edb8362ffa635d9e23 on janosh:pymatviz-addon** into **780788270550fe4febeeac50ae00dbc2167a1b47 on materialsproject:master**.\n",
"The add-ons page is specifically for packages within the pymatgen namespace, so this is not appropriate here.\r\n\r\nWe can definitely add a page on complementary codes, or codes that use pymatgen, somewhere else in the docs though, perhaps under a heading \"Third-party codes that use pymatgen\" and list `pymatviz` there.",
"A new list for 3rd party tools built with/for `pymatgen` sounds like a cool idea. @JaGeo Might be interested in listing https://github.com/JaGeo/LobsterPy and I'm sure there are many more.\r\n\r\n@mkhorton Just to confirm, you're suggesting this as a new section on the same docs page?",
"Ambivalent about location, same page sounds fine.\r\n\r\nMaybe could be renamed to “Add-ons and External Tools” and have a new\r\nsubheading and a little text to clarify the distinction. Also add some text\r\nto say that if anyone would like their own tool listed to submit a PR, and\r\nalso include a link to\r\nhttps://github.com/materialsproject/pymatgen/network/dependents.\r\n\r\nOn Mon, Jul 18, 2022 at 18:00, Janosh Riebesell ***@***.***>\r\nwrote:\r\n\r\n> A new list for 3rd party tools built with/for pymatgen sounds like a cool\r\n> idea. @JaGeo <https://github.com/JaGeo> Might be interested in listing\r\n> https://github.com/JaGeo/LobsterPy and I'm sure there are many more.\r\n>\r\n> @mkhorton <https://github.com/mkhorton> Just to confirm, you're\r\n> suggesting this as a new section on the same docs page?\r\n>\r\n> —\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/materialsproject/pymatgen/pull/2581#issuecomment-1188481712>,\r\n> or unsubscribe\r\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRD7BK73N7PM3HA66IDVUX4ZXANCNFSM53DJFMTA>\r\n> .\r\n> You are receiving this because you were mentioned.Message ID:\r\n> ***@***.***>\r\n>\r\n"
] | 2022-07-09T12:08:48
| 2022-07-28T18:00:30
|
2022-07-28T17:58:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Add https://github.com/janosh/pymatviz to https://pymatgen.org/addons.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2581/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2581/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2581",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2581",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2581.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2581.patch",
"merged_at": "2022-07-28T17:58:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2582
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2582/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2582/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2582/events
|
https://github.com/materialsproject/pymatgen/pull/2582
| 1,301,162,265
|
PR_kwDOACgets47N6TI
| 2,582
|
Preparing to replace defects module
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50804688)\n\nCoverage increased (+0.05%) to 63.64% when pulling **30e0977f9c3f9357503d6e090377960cd1f16c78 on jmmshn:replace_defects** into **23421524e1ac567358144b74825be14b2b1a7af6 on materialsproject:master**.\n",
"Before this merge goes ahead, can I have comment from @nwinner; will this affect any of the atomate workflows you've been developing for defects, are there any changes we might need to make to atomate to mitigate?\r\n\r\n(Edit to clarify: Asking more broadly with respect to the movement of the defects module and changes therein.)",
"that makes sense. @nwinner please also make sure that these two pieces of code are not used for anything in your workflows\r\n\r\n> #. :code:`pymatgen.transformations.defect_transformations`\r\n> #. :code:`pymatgen.analysis.structure_matcher.PointDefectComparator`\r\n\r\n",
"Before we can merge, we also need to ensure that there are no conflict in versions, i.e., if we delete the current pymatgen.analysis.defects, we then need the new pymatgen-analysis-defects to require the latest version of pymatgen (after we release). Otherwise, there is a namespace collision.\r\n",
"I don't think we need to have a deprecation step. Just remove the defects package entirely and move to add-on.",
"> Just remove the defects package entirely and move to add-on.\r\n\r\nYes, that was my suggestion too -- but we still ideally need a way to communicate with people that they need to install a new package. I'm not sure there's an appropriate place for such a warning though.",
"I think it is fine. When people suddenly realize that import pymatgen.analysis.defects gives an error, they will figure out why. I suspect the people using the defects package is a much smaller subset of people.\r\n",
"We can of course put large warnings in the change log and the release notes.",
"The only other alternative is to rename the pymatgen-analysis-defects to something else, e.g., pymatgen-analysis-defect (no s) and put deprecation messages in the original \"defects\" package. This will be more friendly, but at the same time, I am not sure I want to spend the effort doing this.",
"> that makes sense. @nwinner please also make sure that these two pieces of code are not used for anything in your workflows\r\n> \r\n> > #. :code:`pymatgen.transformations.defect_transformations`\r\n> > #. :code:`pymatgen.analysis.structure_matcher.PointDefectComparator`\r\n\r\nBoth my workflows and the legacy workflow use these, but that shouldn't be an issue. Those workflows can just require the presence of this add-on module I think.",
"@nwinner \r\n> Both my workflows and the legacy workflow use these, but that shouldn't be an issue. Those workflows can just require the presence of this add-on module I think.\r\n\r\nThe add-on module is basically a complete rewrite and those functionalities are no longer needed.\r\nThat is why I wanted to have an \"intermediate\" period where someone has the possibility of installing the new module on top of the old one and neither will disrupt the other.\r\n\r\nOne thing I can do is to leave the old import locations in and print an error message so you know where to import the updated version of the old code.",
"@shyuep I think that because the new package is a complete rewrite we should have at least a few releases (maybe even like 6 months) of lead up to deleting the code specifically for cases like @nwinner's",
"@mkhorton @jmmshn I have made a decision. Let's just delete the old defects old. Note that if people want to use the old one, they simply just install \"pymatgen==2022.7.8\". People who are developing additional functionality on top of pymatgen should be doing that anyway. ",
"@shyuep, OK I will updated the docs the the add-on package a bit and get this deleted.",
" @jmmshn \r\n \r\n> The add-on module is basically a complete rewrite and those functionalities are no longer needed.\r\n\r\nWell I see that the functionality has been moved to your new module, but it's still there in your `defects.core` file and your new `defect_transformations` file. It would just be a change of import for codes like mine. Anyway a slower rollout is fine by me, but just changing imports won't be too much inconvenience for codes like mine.\r\n\r\nNot sure I like putting a transformation in a file that isn't in the transformations module, but I guess its the only way to make it an add-on.",
"Great! Let's go ahead and do it then, and cleanly remove the old `defects`. I'll make sure we have some loud notices in the docs.",
"Looks like the [defects module removal](https://github.com/materialsproject/pymatgen/blob/master/CHANGES.rst#v2022719) is causing [errors in `atomate` CI](https://github.com/hackingmaterials/atomate/runs/7550197522?check_suite_focus=true#step:7:185). \r\n\r\nI think https://github.com/hackingmaterials/atomate/pull/760 should fix it. Is it just a matter of adding `pymatgen-analysis-defects` to `setup.py` `install_requires`?",
"Just a note that install_requires is not meant for optional requirements. If someone is not interested in defect workflows, they should not be forced to install pymatgen-analysis-defects to run atomate. ",
"Fair point. Was considering putting it in optional but not sure how central it was. I'll create a new `extras_require` for it.",
"@jmmshn What happened to the `ChargeInsertionAnalyzer`?\r\n\r\n```py\r\nE ImportError: cannot import name 'ChargeInsertionAnalyzer' from 'pymatgen.analysis.defects.utils'\r\n(/opt/hostedtoolcache/Python/3.8.13/x64/lib/python3.8/site-packages/pymatgen/analysis/defects/utils.py)\r\n```\r\n\r\n[CI Logs](https://github.com/hackingmaterials/atomate/runs/7550582186?check_suite_focus=true#step:7:31)",
"@janosh heard you are in Bay Area. If you find yourself in the South Bay, happy to meet up for a coffee or lunch. ",
"Cool, you're here too? I thought you were in San Diego? I'm meeting someone in Palo Alto for lunch (date tbd). Is that close to you? Let's carry on via email.",
"This bug is due to the fact that the insertion workflow needs the defects\nutils package to analyze interstitial positions I already told the folks\nusing that code to lock the pymatgen version for a bit while everything\ngets migrated. And that Chagrdensityanalyzer needs to be rewritten at some\npoint anyways.\n\nBut I forgot about the atomate CI, we can probably just skip that test for\nnow.\n\nOn Wed, Jul 27, 2022 at 5:18 PM Janosh Riebesell ***@***.***>\nwrote:\n\n> Cool, you're here too? I thought you were in San Diego? I'm meeting\n> someone in Palo Alto for lunch (date tbd). Is that close to you? Let's\n> carry on via email.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/2582#issuecomment-1197511043>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/ADK233JSB25XXJS4S7LA5J3VWHGTXANCNFSM53IVF2HQ>\n> .\n> You are receiving this because you were mentioned.Message ID:\n> ***@***.***>\n>\n-- \n*Jimmy-Xuan Shen*\n",
"So I’m on paternity leave right now and won’t get to this until mid\nAugust. The ChargeDensityAnlyzer was really messy old code that needed a\nclean up … but it was being used by my insertion workflow. Maybe we should\nleave the old defect code in the code base a bit longer and\n pymatgen-analysis-defects can just be installed on top to replace the\nmodule? I will fix this when I come back from leave.\n\nOn Thu, Jul 28, 2022 at 8:25 AM Jimmy Shen ***@***.***> wrote:\n\n> This bug is due to the fact that the insertion workflow needs the defects\n> utils package to analyze interstitial positions I already told the folks\n> using that code to lock the pymatgen version for a bit while everything\n> gets migrated. And that Chagrdensityanalyzer needs to be rewritten at some\n> point anyways.\n>\n> But I forgot about the atomate CI, we can probably just skip that test for\n> now.\n>\n> On Wed, Jul 27, 2022 at 5:18 PM Janosh Riebesell ***@***.***>\n> wrote:\n>\n>> Cool, you're here too? I thought you were in San Diego? I'm meeting\n>> someone in Palo Alto for lunch (date tbd). Is that close to you? Let's\n>> carry on via email.\n>>\n>> —\n>> Reply to this email directly, view it on GitHub\n>> <https://github.com/materialsproject/pymatgen/pull/2582#issuecomment-1197511043>,\n>> or unsubscribe\n>> <https://github.com/notifications/unsubscribe-auth/ADK233JSB25XXJS4S7LA5J3VWHGTXANCNFSM53IVF2HQ>\n>> .\n>> You are receiving this because you were mentioned.Message ID:\n>> ***@***.***>\n>>\n> --\n> *Jimmy-Xuan Shen*\n>\n> --\n*Jimmy-Xuan Shen*\n",
"@jmmshn Thanks for the update. Like you suggested, I'll skip that test for now with a link to this issue.",
"I think the easiest solution is to peg atomate to the correct version of pymatgen. There is no need for atomate to always follow the latest pyamtgen. ",
"True but unpinned deps have the advantage that breaking changes lead to downstream errors quickly. That usually means the people who are familiar with what happened are still around and know how to resolve. Half a year later, it's usually harder to follow the trace of why sth broke."
] | 2022-07-11T20:04:39
| 2022-07-28T16:14:41
|
2022-07-13T18:02:49Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Moving code that overlap the current defects module
Some parts of the current defect module have parts that leak into other parts of our code.
This PR moves all the codes and tests inside the current (old) defects module.
The warning message has also been moved into the `core` submodule. This allows the old code to become an implicit namespace package that only loads if a source package (`pymatgen-analysis-defects` in this case) is not present.
I think this is the exact behavior we want since if the the `pymatgen-analysis-defects` is not present we would want to make sure NOTHING in the old module is loaded
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2582/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2582/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2582",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2582",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2582.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2582.patch",
"merged_at": "2022-07-13T18:02:49Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2583
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2583/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2583/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2583/events
|
https://github.com/materialsproject/pymatgen/issues/2583
| 1,306,100,461
|
I_kwDOACgets5N2YLt
| 2,583
|
Scaling of velocities in Poscar file
|
{
"login": "gVallverdu",
"id": 5417018,
"node_id": "MDQ6VXNlcjU0MTcwMTg=",
"avatar_url": "https://avatars.githubusercontent.com/u/5417018?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gVallverdu",
"html_url": "https://github.com/gVallverdu",
"followers_url": "https://api.github.com/users/gVallverdu/followers",
"following_url": "https://api.github.com/users/gVallverdu/following{/other_user}",
"gists_url": "https://api.github.com/users/gVallverdu/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gVallverdu/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gVallverdu/subscriptions",
"organizations_url": "https://api.github.com/users/gVallverdu/orgs",
"repos_url": "https://api.github.com/users/gVallverdu/repos",
"events_url": "https://api.github.com/users/gVallverdu/events{/privacy}",
"received_events_url": "https://api.github.com/users/gVallverdu/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks. I agree and I have made the change."
] | 2022-07-15T14:23:46
| 2022-07-30T15:47:31
|
2022-07-30T15:47:25Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi
I have a question about the sampling of velocities on this line. It corresponds to the `set_temperature()` method in the Poscar class.
https://github.com/materialsproject/pymatgen/blob/23421524e1ac567358144b74825be14b2b1a7af6/pymatgen/io/vasp/inputs.py#L597
I wonder why, the velocities are scaled before the center of mass velocity is removed ? To precise, I would invert line 597 and line 600. It does not change a lot the results but I think if the velocities are scaled before computing the center of mass velocities, the quantity which is subtracted is not exactly the center of mass velocity.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2583/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2583/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2584
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2584/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2584/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2584/events
|
https://github.com/materialsproject/pymatgen/pull/2584
| 1,306,306,090
|
PR_kwDOACgets47fDkF
| 2,584
|
Structure __eq__ bugfix
|
{
"login": "KirbyBroderick",
"id": 57768514,
"node_id": "MDQ6VXNlcjU3NzY4NTE0",
"avatar_url": "https://avatars.githubusercontent.com/u/57768514?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/KirbyBroderick",
"html_url": "https://github.com/KirbyBroderick",
"followers_url": "https://api.github.com/users/KirbyBroderick/followers",
"following_url": "https://api.github.com/users/KirbyBroderick/following{/other_user}",
"gists_url": "https://api.github.com/users/KirbyBroderick/gists{/gist_id}",
"starred_url": "https://api.github.com/users/KirbyBroderick/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/KirbyBroderick/subscriptions",
"organizations_url": "https://api.github.com/users/KirbyBroderick/orgs",
"repos_url": "https://api.github.com/users/KirbyBroderick/repos",
"events_url": "https://api.github.com/users/KirbyBroderick/events{/privacy}",
"received_events_url": "https://api.github.com/users/KirbyBroderick/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I can reproduce in `pymatgen==2022.7.8`\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\n\r\ncoords = [[0.5, 0.5, 0.5], [0, 0, 0]]\r\nspecies = [\"Na\", \"Cl\"]\r\nlattice = Lattice.from_parameters(a=4, b=4, c=4, alpha=90, beta=90, gamma=90)\r\nstructure = Structure(lattice, species, coords)\r\n\r\nstructure == \"Na\"\r\n```\r\n\r\nraises\r\n\r\n```py\r\npymatgen/core/structure.py in __eq__(self, other)\r\n 1053 if len(self) != len(other):\r\n 1054 return False\r\n-> 1055 if self.lattice != other.lattice:\r\n 1056 return False\r\n 1057 for site in self:\r\n\r\nAttributeError: 'str' object has no attribute 'lattice'\r\n```\r\n\r\nMight be worth adding a test case in this PR that verifies the fix.\r\n",
"Thanks @KirbyBroderick! What an interesting bug : ) Will merge once checks pass.",
"\n[](https://coveralls.io/builds/51037616)\n\nCoverage decreased (-0.003%) to 63.638% when pulling **c4adc378b3e3ae8cd4ee238db208be7fb01883a1 on KirbyBroderick:patch-1** into **58b8bd589ec6b39b22007e536d5a8a38281d824f on materialsproject:master**.\n"
] | 2022-07-15T17:27:19
| 2022-07-21T01:28:13
|
2022-07-21T01:28:13Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Ran into an obscure bug where `other` was a length-18 string and `self` was a structure with 18 atoms
## Summary
Include a summary of major changes in bullet points:
* Check that the structure being compared against has a lattice parameter before trying to access the lattice parameter.
## Additional dependencies introduced (if any)
* None
## TODO (if any)
None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ X] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to allowing commits.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2584/reactions",
"total_count": 2,
"+1": 2,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2584/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2584",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2584",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2584.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2584.patch",
"merged_at": "2022-07-21T01:28:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2585
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2585/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2585/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2585/events
|
https://github.com/materialsproject/pymatgen/pull/2585
| 1,306,720,789
|
PR_kwDOACgets47gcp-
| 2,585
|
Added 'get_ir_reciprocal_mesh_map'-method
|
{
"login": "nheinsdorf",
"id": 43240144,
"node_id": "MDQ6VXNlcjQzMjQwMTQ0",
"avatar_url": "https://avatars.githubusercontent.com/u/43240144?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/nheinsdorf",
"html_url": "https://github.com/nheinsdorf",
"followers_url": "https://api.github.com/users/nheinsdorf/followers",
"following_url": "https://api.github.com/users/nheinsdorf/following{/other_user}",
"gists_url": "https://api.github.com/users/nheinsdorf/gists{/gist_id}",
"starred_url": "https://api.github.com/users/nheinsdorf/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/nheinsdorf/subscriptions",
"organizations_url": "https://api.github.com/users/nheinsdorf/orgs",
"repos_url": "https://api.github.com/users/nheinsdorf/repos",
"events_url": "https://api.github.com/users/nheinsdorf/events{/privacy}",
"received_events_url": "https://api.github.com/users/nheinsdorf/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/50922191)\n\nCoverage decreased (-0.01%) to 63.627% when pulling **6fe9396b8e3491b4327f53631ce4a6e290ddcf68 on nheinsdorf:master** into **58b8bd589ec6b39b22007e536d5a8a38281d824f on materialsproject:master**.\n",
"Thanks @nheinsdorf, this looks useful!"
] | 2022-07-16T06:08:44
| 2022-07-21T00:50:47
|
2022-07-21T00:50:46Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
In physical simulations it is often desirable to make use of the lattice symmetries to save computational time. The 'get_ir_reciprocal_mesh' function (which is basically an interface to spglib) returns an irreducible mesh and the weight, which just tells how many other kpoints a given irreducible kpoint is mapped to.
This function does the same, but instead of returning the irreducible kpoints and their weights it returns the full grid and the mapping that is used to generate the irreducible grid. This is useful if physical objects are calculated that do not include a summation over all kpoints, because in that case the weight of an irreducible kpoint is not enough and the mapping is needed to relate any kpoint to the irreducible mesh.
## TODO (if any)
It would be nice if that function could also return a list of symmetry operations that show which symmetry maps a given k-point to its irreducible counterpart. This would be very useful if the properties calculated do not transform as scalars.
## Checklist
Implemented a test that compares to the already tested 'get_ir_reciprocal_mesh'-method.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2585/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2585/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2585",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2585",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2585.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2585.patch",
"merged_at": "2022-07-21T00:50:46Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2587
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2587/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2587/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2587/events
|
https://github.com/materialsproject/pymatgen/issues/2587
| 1,313,376,988
|
I_kwDOACgets5OSIrc
| 2,587
|
`IStructure.__eq__` fails for integers
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I am confused. Isn't comparing Structure and a string/int/whatever that is not Structure-like supposed to fail?",
"Comparison across types is supposed to return false. E.g.\r\n\r\n```py\r\n'foo' == 5\r\n>>> False\r\n```",
"Then the current PR implementation is not correct. I would actually do something like \r\n\r\ntry:\r\n ...\r\nexcept TypeError:\r\n return False",
"By returning `NotImplemented`, the equality check is handed over from `IStructure.__eq__()` to the other, i.e. `int.__eq__()` or `str.__eq__()`, where Python knows to return `False`.",
"That is fine. But I would still do the try except rather than the instance check. There is no reason why we need to ban say a Structure == something very much structure like with all the features but not exactly a Structure. This is afterall the principle of ducktyping in python.\r\n",
"I was considering using `SiteCollection`.\r\n\r\n```py\r\ndef __eq__(self, other: object) -> bool:\r\n if not isinstance(other, SiteCollection):\r\n```\r\n\r\nHappy to change to that if you think it's more appropriate. Beyond `SiteCollection`, I'm not sure what would qualify as being equal to structure. Bear in mind, we're not banning equality with other stuff here, we're just handing off to the other object's equality. If that other thing knows how to compare with structure, it can still return `True`.",
"@shyuep Actually, looking at the [`functools.total_ordering` docs](https://docs.python.org/3/library/functools.html#functools.total_ordering), I think what we should really do is return `NotImplemented` if any of the attributes required for equality checking are missing. See this `class Student` example:\r\n\r\n```py\r\n@total_ordering\r\nclass Student:\r\n def _is_valid_operand(self, other):\r\n return (hasattr(other, \"lastname\") and\r\n hasattr(other, \"firstname\"))\r\n def __eq__(self, other):\r\n if not self._is_valid_operand(other):\r\n return NotImplemented\r\n # ...\r\n```"
] | 2022-07-21T14:45:16
| 2022-07-21T17:07:39
|
2022-07-21T17:07:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
There are more edge cases like #2584 in `IStructure.__eq__`. E.g. comparing against `int`s also throws.
```py
from pymatgen.core import Lattice, Structure
coords = [[0.5, 0.5, 0.5], [0, 0, 0]]
species = ["Na", "Cl"]
lattice = Lattice.from_parameters(a=4, b=4, c=4, alpha=90, beta=90, gamma=90)
structure = Structure(lattice, species, coords)
structure == 42
```
```py
def __eq__(self, other) -> bool:
if other is self:
return True
if other is None:
return False
> if len(self) != len(other):
E TypeError: object of type 'int' has no len()
```
I think a fix to handle all such edge cases would be to start with an `isinstance` check that returns `NotImplemented` if `other` is not a `(I)Structure`.
```py
def __eq__(self, other: object) -> bool:
if not isinstance(other, IStructure):
return NotImplemented
```
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2587/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2587/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2588
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2588/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2588/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2588/events
|
https://github.com/materialsproject/pymatgen/pull/2588
| 1,313,393,264
|
PR_kwDOACgets473K5w
| 2,588
|
Fix edge cases in Structure equality
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51060609)\n\nCoverage decreased (-0.0007%) to 63.571% when pulling **fb45c40867fff0413d7bb21cc2bdb609128ec5ae on janosh:test-structure-equality** into **c4e0552c2fdb14bb02152fced8ef7fcbb0de8007 on materialsproject:master**.\n",
"Thanks @janosh!"
] | 2022-07-21T14:54:39
| 2022-07-21T17:21:02
|
2022-07-21T17:07:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #2587.
Related #2584.
Also adds tests for `IStructure.__eq__()`.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2588/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2588/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2588",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2588",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2588.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2588.patch",
"merged_at": "2022-07-21T17:07:39Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2589
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2589/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2589/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2589/events
|
https://github.com/materialsproject/pymatgen/pull/2589
| 1,313,834,327
|
PR_kwDOACgets474rGJ
| 2,589
|
fixed serialization bug
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51069669)\n\nCoverage decreased (-0.0008%) to 63.58% when pulling **ff4696c29a81888bec93828da28db8c363027686 on jmmshn:symm_fix** into **cd47594bab856ecc70e427e99ed77e9990f14d8b on materialsproject:master**.\n"
] | 2022-07-21T21:39:15
| 2022-07-21T22:18:01
|
2022-07-21T22:18:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This should fix the underlying serialization bug related to this PR:
https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/pull/264
I think the other PR
https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/pull/312
still fails if `symm_structure` is provided due to this bug.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2589/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2589/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2589",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2589",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2589.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2589.patch",
"merged_at": "2022-07-21T22:18:01Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2590
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2590/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2590/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2590/events
|
https://github.com/materialsproject/pymatgen/pull/2590
| 1,315,303,610
|
PR_kwDOACgets479zJ7
| 2,590
|
Update absorption coefficient
|
{
"login": "yang-ruoxi",
"id": 13646711,
"node_id": "MDQ6VXNlcjEzNjQ2NzEx",
"avatar_url": "https://avatars.githubusercontent.com/u/13646711?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yang-ruoxi",
"html_url": "https://github.com/yang-ruoxi",
"followers_url": "https://api.github.com/users/yang-ruoxi/followers",
"following_url": "https://api.github.com/users/yang-ruoxi/following{/other_user}",
"gists_url": "https://api.github.com/users/yang-ruoxi/gists{/gist_id}",
"starred_url": "https://api.github.com/users/yang-ruoxi/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/yang-ruoxi/subscriptions",
"organizations_url": "https://api.github.com/users/yang-ruoxi/orgs",
"repos_url": "https://api.github.com/users/yang-ruoxi/repos",
"events_url": "https://api.github.com/users/yang-ruoxi/events{/privacy}",
"received_events_url": "https://api.github.com/users/yang-ruoxi/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51094622)\n\nCoverage remained the same at 63.58% when pulling **3acc67b6d66c6c02e423c6728d94b40d528b3d5b on yang-ruoxi:absorption** into **780788270550fe4febeeac50ae00dbc2167a1b47 on materialsproject:master**.\n",
"Thanks for catching this @yang-ruoxi !"
] | 2022-07-22T18:29:54
| 2022-07-22T23:09:19
|
2022-07-22T23:08:51Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
### Summary
The previous absorption coefficient lack a 2*pi constant. It is corrected in this PR and the results compare well with experiments.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2590/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2590/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2590",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2590",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2590.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2590.patch",
"merged_at": "2022-07-22T23:08:51Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2591
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2591/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2591/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2591/events
|
https://github.com/materialsproject/pymatgen/issues/2591
| 1,318,106,385
|
I_kwDOACgets5OkLUR
| 2,591
|
Atom position overlap after repairing the slab
|
{
"login": "ganfisher",
"id": 72131770,
"node_id": "MDQ6VXNlcjcyMTMxNzcw",
"avatar_url": "https://avatars.githubusercontent.com/u/72131770?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ganfisher",
"html_url": "https://github.com/ganfisher",
"followers_url": "https://api.github.com/users/ganfisher/followers",
"following_url": "https://api.github.com/users/ganfisher/following{/other_user}",
"gists_url": "https://api.github.com/users/ganfisher/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ganfisher/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ganfisher/subscriptions",
"organizations_url": "https://api.github.com/users/ganfisher/orgs",
"repos_url": "https://api.github.com/users/ganfisher/repos",
"events_url": "https://api.github.com/users/ganfisher/events{/privacy}",
"received_events_url": "https://api.github.com/users/ganfisher/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I could confirm I'm able to reproduce this issue with the provided structure and code in `v2023.12.18`, and I'm looking into this.\r\n\r\nIn the following generated `POSCAR-1`, there are at least a pair of overlapped atoms (didn't check the others):\r\n<details>\r\n <summary>POSCAR-1 with overlap atoms</summary>\r\n\r\n ```POSCAR\r\n Al36 O54\r\n 1.0\r\n 4.1432315010944283 0.0000000000000000 -2.3920958224718043\r\n 0.0000000000000021 13.0584997064738300 0.0000000000000008\r\n 0.0000000000000000 0.0000000000000000 33.4893415146052718\r\n Al O\r\n 36 54\r\n direct\r\n 0.0000000000000000 0.8520410609510133 0.1190476190476190 Al\r\n 0.6666666666666667 0.9812922723823201 0.0238095238095239 Al\r\n 0.6666666666666667 0.6853743942843467 0.0238095238095239 Al\r\n 0.3333333333333335 0.8146256057156533 0.0714285714285714 Al\r\n 0.3333333333333335 0.5187077276176800 0.0714285714285714 Al\r\n 0.0000000000000000 0.6479589390489868 0.1190476190476190 Al\r\n 0.0000000000000000 0.3520410609510135 0.1190476190476190 Al\r\n 0.6666666666666667 0.4812922723823201 0.0238095238095239 Al\r\n 0.6666666666666667 0.1853743942843467 0.0238095238095239 Al\r\n 0.3333333333333335 0.3146256057156533 0.0714285714285714 Al\r\n 0.3333333333333335 0.0187077276176800 0.0714285714285714 Al\r\n 0.0000000000000000 0.1479589390489868 0.1190476190476190 Al\r\n 0.0000000000000000 0.8520410609510133 0.2619047619047619 Al\r\n 0.6666666666666667 0.9812922723823201 0.1666666666666667 Al\r\n 0.6666666666666667 0.6853743942843467 0.1666666666666667 Al\r\n 0.3333333333333335 0.8146256057156533 0.2142857142857143 Al\r\n 0.3333333333333335 0.5187077276176800 0.2142857142857143 Al\r\n 0.0000000000000000 0.6479589390489868 0.2619047619047619 Al-OVERLAP\r\n 0.0000000000000000 0.3520410609510135 0.2619047619047619 Al\r\n 0.6666666666666667 0.4812922723823201 0.1666666666666667 Al\r\n 0.6666666666666667 0.1853743942843467 0.1666666666666667 Al\r\n 0.3333333333333335 0.3146256057156533 0.2142857142857143 Al\r\n 0.3333333333333335 0.0187077276176800 0.2142857142857143 Al\r\n 0.0000000000000000 0.1479589390489868 0.2619047619047619 Al\r\n 0.0000000000000000 0.8520410609510133 0.2619047619047619 Al\r\n 0.6666666666666667 0.9812922723823201 0.3095238095238095 Al\r\n 0.6666666666666667 0.6853743942843467 0.3095238095238095 Al\r\n 0.3333333333333335 0.8146256057156533 0.3571428571428571 Al\r\n 0.3333333333333335 0.5187077276176800 0.3571428571428571 Al\r\n 0.0000000000000000 0.6479589390489868 0.2619047619047619 Al-OVERLAP\r\n 0.0000000000000000 0.3520410609510135 0.2619047619047619 Al\r\n 0.6666666666666667 0.4812922723823201 0.3095238095238095 Al\r\n 0.6666666666666667 0.1853743942843467 0.3095238095238095 Al\r\n 0.3333333333333335 0.3146256057156533 0.3571428571428571 Al\r\n 0.3333333333333335 0.0187077276176800 0.3571428571428571 Al\r\n 0.0000000000000000 0.1479589390489868 0.2619047619047619 Al\r\n 0.6936636505992461 0.7500000000000000 0.1190476190476190 O\r\n 0.3333333333333334 0.9166666666666667 0.1151909070572505 O\r\n 0.0000000000000000 0.7500000000000000 0.0752852834189399 O\r\n 0.3063363494007539 0.7500000000000000 0.0199528118191553 O\r\n 0.0269969839325794 0.9166666666666667 0.0276662357998923 O\r\n 0.6396696827340873 0.9166666666666667 0.0714285714285714 O\r\n 0.0269969839325794 0.4166666666666669 0.0714285714285714 O\r\n 0.6666666666666667 0.5833333333333334 0.0675718594382029 O\r\n 0.3333333333333334 0.4166666666666669 0.0276662357998923 O\r\n 0.6396696827340873 0.4166666666666669 0.1151909070572505 O\r\n 0.3603303172659127 0.5833333333333334 0.1229043310379875 O\r\n 0.9730030160674206 0.5833333333333334 0.0238095238095238 O\r\n 0.3603303172659126 0.0833333333333335 0.0238095238095238 O\r\n 0.0000000000000000 0.2500000000000001 0.0199528118191553 O\r\n 0.6666666666666665 0.0833333333333335 0.1229043310379875 O\r\n 0.9730030160674206 0.0833333333333335 0.0675718594382029 O\r\n 0.6936636505992462 0.2500000000000001 0.0752852834189399 O\r\n 0.3063363494007540 0.2500000000000001 0.1190476190476190 O\r\n 0.6936636505992461 0.7500000000000000 0.2619047619047619 O\r\n 0.3333333333333334 0.9166666666666667 0.2580480499143934 O\r\n 0.0000000000000000 0.7500000000000000 0.2181424262760828 O\r\n 0.3063363494007539 0.7500000000000000 0.1628099546762982 O\r\n 0.0269969839325794 0.9166666666666667 0.1705233786570351 O\r\n 0.6396696827340873 0.9166666666666667 0.2142857142857143 O\r\n 0.0269969839325794 0.4166666666666669 0.2142857142857142 O\r\n 0.6666666666666667 0.5833333333333334 0.2104290022953458 O\r\n 0.3333333333333334 0.4166666666666669 0.1705233786570351 O\r\n 0.6396696827340873 0.4166666666666669 0.2580480499143934 O\r\n 0.3603303172659127 0.5833333333333334 0.2657614738951304 O\r\n 0.9730030160674206 0.5833333333333334 0.1666666666666667 O\r\n 0.3603303172659126 0.0833333333333335 0.1666666666666667 O\r\n 0.0000000000000000 0.2500000000000001 0.1628099546762982 O\r\n 0.6666666666666665 0.0833333333333335 0.2657614738951304 O\r\n 0.9730030160674206 0.0833333333333335 0.2104290022953458 O\r\n 0.6936636505992462 0.2500000000000001 0.2181424262760827 O\r\n 0.3063363494007540 0.2500000000000001 0.2619047619047619 O\r\n 0.6936636505992461 0.7500000000000000 0.4047619047619048 O\r\n 0.3333333333333334 0.9166666666666667 0.4009051927715362 O\r\n 0.0000000000000000 0.7500000000000000 0.3609995691332256 O\r\n 0.3063363494007539 0.7500000000000000 0.3056670975334410 O\r\n 0.0269969839325794 0.9166666666666667 0.3133805215141780 O\r\n 0.6396696827340873 0.9166666666666667 0.3571428571428571 O\r\n 0.0269969839325794 0.4166666666666669 0.3571428571428571 O\r\n 0.6666666666666667 0.5833333333333334 0.3532861451524886 O\r\n 0.3333333333333334 0.4166666666666669 0.3133805215141779 O\r\n 0.6396696827340873 0.4166666666666669 0.4009051927715362 O\r\n 0.3603303172659127 0.5833333333333334 0.4086186167522732 O\r\n 0.9730030160674206 0.5833333333333334 0.3095238095238095 O\r\n 0.3603303172659126 0.0833333333333335 0.3095238095238095 O\r\n 0.0000000000000000 0.2500000000000001 0.3056670975334410 O\r\n 0.6666666666666665 0.0833333333333335 0.4086186167522732 O\r\n 0.9730030160674206 0.0833333333333335 0.3532861451524886 O\r\n 0.6936636505992462 0.2500000000000001 0.3609995691332256 O\r\n 0.3063363494007540 0.2500000000000001 0.4047619047619048 O\r\n ```\r\n\r\n</details>\r\n"
] | 2022-07-26T11:31:50
| 2024-01-15T05:37:19
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hey, I'm trying to generate the (010) facet structures of α-Al2O3 with pymatgen 2022.5.26
```python
from pymatgen.core.surface import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.structure import Structure
struct = Structure.from_file('Al2O3CONTCAR')
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
slab = SlabGenerator(struct, miller_index=[0, 1, 0], min_slab_size=10,min_vacuum_size=15)
for n, s in enumerate(slab.get_slabs(bonds = {('Al','O'):2.1},repair=True)):
s=s.get_sorted_structure()
s.to(filename='POSCAR-'+str(n),fmt='poscar')
```
When I opened one of the generated POSCAR with VESTA, I found the label of the 30th Al atom is invisible because of the overlap,
which caused the failure of the subsequent calculation by VASP
It is strange that such a problem will not happen when there is no bond constraints and repair requirement.
Here is the input CONTCAR and the generated POSCAR
[Al2O3CONTCAR.txt](https://github.com/materialsproject/pymatgen/files/9189365/Al2O3CONTCAR.txt)
[POSCAR-0.txt](https://github.com/materialsproject/pymatgen/files/9189368/POSCAR-0.txt)
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2591/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2591/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2592
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2592/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2592/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2592/events
|
https://github.com/materialsproject/pymatgen/issues/2592
| 1,321,901,357
|
I_kwDOACgets5Oyp0t
| 2,592
|
Please add to README how to run tests
|
{
"login": "yurivict",
"id": 271906,
"node_id": "MDQ6VXNlcjI3MTkwNg==",
"avatar_url": "https://avatars.githubusercontent.com/u/271906?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yurivict",
"html_url": "https://github.com/yurivict",
"followers_url": "https://api.github.com/users/yurivict/followers",
"following_url": "https://api.github.com/users/yurivict/following{/other_user}",
"gists_url": "https://api.github.com/users/yurivict/gists{/gist_id}",
"starred_url": "https://api.github.com/users/yurivict/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/yurivict/subscriptions",
"organizations_url": "https://api.github.com/users/yurivict/orgs",
"repos_url": "https://api.github.com/users/yurivict/repos",
"events_url": "https://api.github.com/users/yurivict/events{/privacy}",
"received_events_url": "https://api.github.com/users/yurivict/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I am not sure how your pymatgen is installed. But tests are included only in the dev version of pymatgen cloned from Github. After that, it is just `pytest pymatgen` like all other codes."
] | 2022-07-29T08:04:44
| 2022-07-30T15:09:57
|
2022-07-30T15:09:57Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
pytest used to run tests, but now it fails to find any tests:
```
==================================================================================== test session starts =====================================================================================
platform freebsd13 -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0 -- /usr/local/bin/python3.9
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/disk-samsung/freebsd-ports/science/py-pymatgen/work-py39/pymatgen-2022.7.19/.hypothesis/examples')
rootdir: /disk-samsung/freebsd-ports/science/py-pymatgen/work-py39/pymatgen-2022.7.19, configfile: setup.cfg
plugins: forked-1.4.0, rerunfailures-10.1, hypothesis-6.51.0, xdist-2.5.0, cov-2.9.0, typeguard-2.13.3
collected 0 items
=================================================================================== no tests ran in 0.62s ====================================================================================
*** Error code 5
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2592/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2592/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2593
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2593/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2593/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2593/events
|
https://github.com/materialsproject/pymatgen/issues/2593
| 1,322,721,734
|
I_kwDOACgets5O1yHG
| 2,593
|
Faster structure matching via `StructureMatcher` (and by extension, `group_structures`)
|
{
"login": "sgbaird",
"id": 45469701,
"node_id": "MDQ6VXNlcjQ1NDY5NzAx",
"avatar_url": "https://avatars.githubusercontent.com/u/45469701?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/sgbaird",
"html_url": "https://github.com/sgbaird",
"followers_url": "https://api.github.com/users/sgbaird/followers",
"following_url": "https://api.github.com/users/sgbaird/following{/other_user}",
"gists_url": "https://api.github.com/users/sgbaird/gists{/gist_id}",
"starred_url": "https://api.github.com/users/sgbaird/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/sgbaird/subscriptions",
"organizations_url": "https://api.github.com/users/sgbaird/orgs",
"repos_url": "https://api.github.com/users/sgbaird/repos",
"events_url": "https://api.github.com/users/sgbaird/events{/privacy}",
"received_events_url": "https://api.github.com/users/sgbaird/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Speed ups are always welcome. But I want to note a few things:\r\n1. Hashing is already done. E.g., if the fractional composition are not equal, two structures would immediately evaluate to not being equal without any matrix comparisons.\r\n2. Most of the code is already vectorized in numpy. Any GPU optimizations that work with numpy would work with structure matcher.\r\n\r\nIf any further optimizations are implemented, it should not be at the cost of code maintainability or support for simple single CPU machines. \r\n\r\nI should add that as implemented, StructureMatcher is meant for simple one-off comparisons. When we actually run matching across large structure sets (e.g., entire ICSD), we use various tricks to speed it up. Pre-grouping by composition. Reducing to primitive cell. All these allow us to disable some of the more costly aspects of the general structure matcher, e.g., generating supercells. Of course, the only people who really care about performance in this regard are people working with large databases of materials. That's not a huge population to begin with.",
"Thanks for creating this issue @sgbaird.\r\n\r\nI agree with @shyuep's general points, but note that I don't think this is the easiest code to maintain as it is currently written either (eg, we do use the custom Cython linear assignment code that's quite difficult to understand), so I hope that there's good scope for improvements!\r\n\r\nWhile large-scale usage may be comparatively rare, I certainly think the number of people needing to do large numbers of comparisons is increasing, and it's often been a bottleneck.",
"For the specific suggestions:\r\n\r\n> we should be able to run `_preprocess` on all structures once and short-circuit it during later match matrix calculations\r\n\r\nYes, this seems like an obvious optimization if this is being repeated. It's probably not the most critical piece (since it only has to be done once for each structure) but perhaps `get_niggli_reduced_lattice` can be accelerated too.\r\n\r\n> precompute several common supercells for each structure and use a lookup instead of generating it on the fly.\r\n\r\nThink we'd have to try this out to see how useful it'd be in practice; it's not obvious to me how many supercells are needed to be generated.\r\n\r\n> _cart_dists is probably the easiest to replace or numba-fy, e.g. by implementing a jit-ed version of the Kabsch algorithm\r\n\r\nAgreed, I do want to point out [this](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/optimization/neighbors.pyx) for examples of where else optimized code in pymatgen lives (this was for neighbor finding). I note that `numba` is both excellent and a really troublesome dependency, since it typically lags behind the latest `numpy` and Python versions, so might err towards a Cython solution if feasible. Perhaps a simpler `numpy`-vectorized solution might also be a better option -- as @shyuep notes this is done in several places already, but perhaps we've missed an opportunity.",
"Let me mention that `StructureMatcher.group_structures` calls `_preprocess` for each structure only once (https://github.com/materialsproject/pymatgen/pull/2490).\r\nSo, it is a little improvement, but using `StructureMatcher.group_structures` will reduce `_preprocess` part of the flame graph from O(n^2) to O(n), and ~150% faster as a whole.\r\n",
"That's fantastic @lan496! Sometimes the key to big speed improvements is lots of \"small\" optimizations, this is definitely appreciated :)",
"Just to second the discussions here, any form of further optimisation for `StructureMatcher` (particularly the `_cart_dists()` function which tends to be the bottleneck for large cells -- `Cython`?) would be really amazing"
] | 2022-07-29T22:19:38
| 2024-10-09T19:13:25
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
Using `StructureMatcher` repeatedly causes a large overhead (in my use-case, ~40 hrs to check the performance of a generative benchmark via [`matbench-genmetrics`](https://github.com/sparks-baird/matbench-genmetrics)).
**Describe the solution you'd like**
Explore speeding up bottlenecks in the `StructureMatcher` algorithm, pre-screening, leveraging GPU for distributed calculation of matches, etc.
**Describe alternatives you've considered**
These are in active discussion at https://github.com/sparks-baird/matbench-genmetrics/issues/9, e.g. [AFLOW's `XtalFinder`](https://www.nature.com/articles/s41524-020-00483-4), [`dscribe` kernels](https://singroup.github.io/dscribe/latest/tutorials/similarity_analysis/kernels.html)
**Additional context**
As a follow-up to @mkhorton 's https://github.com/sparks-baird/matbench-genmetrics/issues/9#issuecomment-1199738568, here are some flame graphs on repeated evaluations of `StructureMatcher().fit(...)`:
```bash
%pip install matbench-genmetrics
```
```python
from mp_time_split.utils.gen import DummyGenerator
from matbench_genmetrics.core import MPTSMetrics
from tqdm import tqdm
mptm = MPTSMetrics(dummy=True, verbose=False)
for fold in tqdm(mptm.folds):
train_val_inputs = mptm.get_train_and_val_data(fold)
dg = DummyGenerator()
dg.fit(train_val_inputs)
gen_structures = dg.gen(n=50)
mptm.evaluate_and_record(fold, gen_structures)
print(mptm.recorded_metrics)
```
@mkhorton figured we could chat about bottlenecks and the potential for precomputing things and speedups. Here are some of my initial thoughts:
- we should be able to run `_preprocess` on all structures once and short-circuit it during later match matrix calculations
- precompute several common supercells for each structure and use a lookup instead of generating it on the fly. Not exactly clear to me how to implement that in: https://github.com/materialsproject/pymatgen/blob/6d1eae91dfbf996ed472de49ce5fe0fae985884d/pymatgen/analysis/structure_matcher.py#L469-L492
- `_cart_dists` is probably the easiest to replace or `numba`-fy, e.g. by implementing a `jit`-ed version of the Kabsch algorithm (@kjappelbaum)
Would be good to know how much memory is taken up by each calculation and whether or not these could be calculated in parallel on typical consumer GPUs.
Happy to move this to discussions if that's a better place.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2593/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2593/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2594
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2594/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2594/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2594/events
|
https://github.com/materialsproject/pymatgen/pull/2594
| 1,322,898,660
|
PR_kwDOACgets48Wjem
| 2,594
|
Change lattice equality
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51284315)\n\nCoverage increased (+0.003%) to 63.547% when pulling **f178d555ae5762d49ca490116807446398bddf9e on janosh:change-lattice-equality** into **1335a14ffc9ef0f50d782316cd6a8abfdfad1b54 on materialsproject:master**.\n"
] | 2022-07-30T04:38:21
| 2022-07-30T15:06:57
|
2022-07-30T15:06:57Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Same treatment for `Lattice` as `IStructure` received in #2588, i.e. return `NotImplemented` rather than `False` in `Lattice.__eq__()` if other lacks expected attributes.
Related #2587, #2584.
Also adds test to `Lattice.__eq__()` plus some `flake8` fixes.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2594/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2594/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2594",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2594",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2594.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2594.patch",
"merged_at": "2022-07-30T15:06:57Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2595
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2595/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2595/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2595/events
|
https://github.com/materialsproject/pymatgen/pull/2595
| 1,322,926,498
|
PR_kwDOACgets48Wowx
| 2,595
|
Correct doc description of electron affinity
|
{
"login": "755452800",
"id": 18474386,
"node_id": "MDQ6VXNlcjE4NDc0Mzg2",
"avatar_url": "https://avatars.githubusercontent.com/u/18474386?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/755452800",
"html_url": "https://github.com/755452800",
"followers_url": "https://api.github.com/users/755452800/followers",
"following_url": "https://api.github.com/users/755452800/following{/other_user}",
"gists_url": "https://api.github.com/users/755452800/gists{/gist_id}",
"starred_url": "https://api.github.com/users/755452800/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/755452800/subscriptions",
"organizations_url": "https://api.github.com/users/755452800/orgs",
"repos_url": "https://api.github.com/users/755452800/repos",
"events_url": "https://api.github.com/users/755452800/events{/privacy}",
"received_events_url": "https://api.github.com/users/755452800/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51284823)\n\nCoverage increased (+0.005%) to 63.549% when pulling **176495aceb9d8bfdfca0e12786a09f1554cd7693 on 755452800:master** into **1335a14ffc9ef0f50d782316cd6a8abfdfad1b54 on materialsproject:master**.\n",
"thanks."
] | 2022-07-30T07:34:54
| 2022-07-30T15:06:41
|
2022-07-30T15:06:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The electron affinity description is duplicate with ionization energy. Updated the definition according to wiki (https://en.wikipedia.org/wiki/Electron_affinity).
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2595/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2595/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2595",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2595",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2595.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2595.patch",
"merged_at": "2022-07-30T15:06:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2596
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2596/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2596/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2596/events
|
https://github.com/materialsproject/pymatgen/pull/2596
| 1,323,265,325
|
PR_kwDOACgets48Xydh
| 2,596
|
Fix for loop reassigning its iterable
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51288725)\n\nCoverage increased (+0.002%) to 63.549% when pulling **00d81f1fe22ca669cc72de81d9d40a0f2a91731d on janosh:fix-for-loop-assigning-its-iterable** into **fd88d820820d57cd370eaf88ce89e9283dc19f11 on materialsproject:master**.\n"
] | 2022-07-30T19:18:12
| 2022-07-31T01:38:27
|
2022-07-31T01:37:52Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Two small bug fixes in a7f5fb226ede0cfc57fc81b71b61ce98cf310f58 and 5246c19845f9ef7ddfa366b1bf0510d1bc8e663e.
Plus address some linter errors in 86d08dcfe46bca993d06519e6c4a392f7deefde0.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2596/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2596/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2596",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2596",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2596.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2596.patch",
"merged_at": "2022-07-31T01:37:51Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2597
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2597/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2597/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2597/events
|
https://github.com/materialsproject/pymatgen/issues/2597
| 1,323,492,276
|
I_kwDOACgets5O4uO0
| 2,597
|
Process for verifying a pull request is correct?
|
{
"login": "mm04926412",
"id": 21348397,
"node_id": "MDQ6VXNlcjIxMzQ4Mzk3",
"avatar_url": "https://avatars.githubusercontent.com/u/21348397?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mm04926412",
"html_url": "https://github.com/mm04926412",
"followers_url": "https://api.github.com/users/mm04926412/followers",
"following_url": "https://api.github.com/users/mm04926412/following{/other_user}",
"gists_url": "https://api.github.com/users/mm04926412/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mm04926412/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mm04926412/subscriptions",
"organizations_url": "https://api.github.com/users/mm04926412/orgs",
"repos_url": "https://api.github.com/users/mm04926412/repos",
"events_url": "https://api.github.com/users/mm04926412/events{/privacy}",
"received_events_url": "https://api.github.com/users/mm04926412/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks for the contribution. You can simply create a pull request and we will provide feedback on it. The steps are in the pymatgen documentation under the \"contributing\" section. ",
"Thanks, would that be under the master branch?",
"Doesn't matter what branch. Whatever you prefer on your fork. The master branch at the origin is only accessible to only two people in any case. So whatever you do on your fork does not affect it unti we merge it."
] | 2022-07-31T15:27:12
| 2022-08-01T03:22:47
|
2022-08-01T03:22:47Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello
As part of my research I created a unit cell transformation algorithm that I thought might be useful to others. I'm not used to working on collaberative open source projects like this. I'd like to ask if there is anywhere / anyone I should send my code to for the purposes of getting external confirmation my code does what I say it does. Any advice on this matter would be appreciated.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2597/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2597/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2598
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2598/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2598/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2598/events
|
https://github.com/materialsproject/pymatgen/pull/2598
| 1,324,959,832
|
PR_kwDOACgets48dXiq
| 2,598
|
[pre-commit.ci] pre-commit autoupdate
|
{
"login": "pre-commit-ci[bot]",
"id": 66853113,
"node_id": "MDM6Qm90NjY4NTMxMTM=",
"avatar_url": "https://avatars.githubusercontent.com/in/68672?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D",
"html_url": "https://github.com/apps/pre-commit-ci",
"followers_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/pre-commit-ci%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51328233)\n\nCoverage remained the same at 63.549% when pulling **e83f546ea995fa60c291065ca7cc516aa8b58f6c on pre-commit-ci-update-config** into **013b70530ead3ede744dbda3b691f9c502036f7d on master**.\n"
] | 2022-08-01T20:43:38
| 2022-08-01T21:31:06
|
2022-08-01T21:31:06Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.34.0 → v2.37.3](https://github.com/asottile/pyupgrade/compare/v2.34.0...v2.37.3)
- [github.com/PyCQA/flake8: 4.0.1 → 5.0.2](https://github.com/PyCQA/flake8/compare/4.0.1...5.0.2)
- [github.com/pre-commit/mirrors-mypy: v0.961 → v0.971](https://github.com/pre-commit/mirrors-mypy/compare/v0.961...v0.971)
<!--pre-commit.ci end-->
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2598/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2598/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2598",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2598",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2598.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2598.patch",
"merged_at": "2022-08-01T21:31:06Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2599
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2599/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2599/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2599/events
|
https://github.com/materialsproject/pymatgen/issues/2599
| 1,325,188,605
|
I_kwDOACgets5O_MX9
| 2,599
|
Allow the user to set SpacegroupAnalyzer parameters when writing FEFF input files
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Since it is a relatively quick fix, I have implemented it. Pls see latest commits.",
"@shyuep Perfect thank you. Quick followup question: are you open to using the FEFF writers to handle amorphous materials and clusters (i.e. very low symmetry systems)? I think that would be quite useful for people (though perhaps out of scope). Curious to know what you think.",
"Yes, that would be great. I personally think the tools themselves (FEFF input generation etc.) should be general to any structure and treat crystalline structures as a special case. I think all that is needed is an option to turn off symmetry checking completely. ",
"@shyuep I'm happy to take a shot at this if you'd like. Give me the green light and I'll open an issue (which you can assign me to if possible). I can then work on this a bit and open a PR down the road.",
"Yes, pls open an issue and submit a PR when you are ready. Many thanks."
] | 2022-08-02T02:07:29
| 2022-08-02T14:31:10
|
2022-08-02T03:39:52Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
Currently when writing FEFF input files, if [SpacegroupAnalyzer](https://github.com/materialsproject/pymatgen/blob/baf62b77788fc43387e15b1e0b60094132815c47/pymatgen/io/feff/inputs.py#L177) fails at any point, it prevents the user from writing anything. I've encountered a few cases where relaxing `symprec` slightly allows everything proceed. It would be great to have a few extra arguments added to the [FEFFDictSet](https://github.com/materialsproject/pymatgen/blob/738b52a17426eff3b8fb5c4dcf8c8e363284794b/pymatgen/io/feff/sets.py#L120) (which then propagate through to the other FEFF objects) which would let the user set these parameters.
**Describe the solution you'd like**
Described above. I'm happy to do it in a PR.
**Describe alternatives you've considered**
This seems like a straightforward request without another reasonable alternative. The user should be able to control the keywords to `SpacegroupAnalyzer` when writing FEFF input files.
**Additional context**
None.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2599/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2599/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2600
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2600/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2600/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2600/events
|
https://github.com/materialsproject/pymatgen/issues/2600
| 1,326,310,451
|
I_kwDOACgets5PDeQz
| 2,600
|
Add low-symmetry structure/cluster support for FEFF writers
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
] | null |
[] | 2022-08-02T19:27:34
| 2022-08-03T19:47:41
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
# Is your feature request related to a problem? Please describe
Currently, the `FEFFDictSet` object utilizes the `SpacegroupAnalyzer` in various contexts to produce header files. The `is_ordered` property is also called quite a few times. I don't think any of these will work properly if the provided structure is either amorphous or a cluster (such as a molecule). It would be nice to have a few flags that would allow the user to "turn off" the pieces of this that depend on the structure having high symmetry. Since FEFF works on clusters, not periodic systems, this seem to be a reasonable feature, since it would allow people to write FEFF input files for low-symmetry systems in general. See #2599 for more details.
# Describe the solution you'd like
Augment the functionality of `FEFFDictSet` and all of it's dependencies to allow for low-symmetry structures.
# Describe alternatives you've considered
I don't really see any alternatives other than to write these new features.
# Additional context
@shyuep please feel free to assign me. I will try to open a PR sometime soon!
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2600/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2600/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2601
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2601/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2601/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2601/events
|
https://github.com/materialsproject/pymatgen/pull/2601
| 1,327,639,942
|
PR_kwDOACgets48mVoH
| 2,601
|
Remove `__ne__` methods
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"To quote [this SO answer](https://stackoverflow.com/a/30676267): \r\n\r\n> should I implement `__ne__()` operator based on `__eq__`?\r\n> \r\n> Short Answer: Don't implement it, but if you must, use `==`, not `__eq__`",
"Wait! Still need to fix a test. :)",
"Don't worry about it.",
"I'm in a call atm, will do it after.",
"I already fixed it.\r\n"
] | 2022-08-03T18:39:37
| 2022-08-03T19:47:41
|
2022-08-03T19:24:05Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Since they're auto-defined by python as `not __eq__()`.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2601/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2601/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2601",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2601",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2601.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2601.patch",
"merged_at": "2022-08-03T19:24:05Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2602
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2602/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2602/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2602/events
|
https://github.com/materialsproject/pymatgen/pull/2602
| 1,327,701,804
|
PR_kwDOACgets48mjBb
| 2,602
|
Fix CI AssertionError: `False` is not `True` in `self.assertTrue(Magmom([0, 0, 10]) == 10)`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-08-03T19:37:14
| 2022-08-03T23:41:59
|
2022-08-03T23:41:25Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Follow up to #2601.
Fixes `pymatgen/electronic_structure/tests/test_core.py:131: AssertionError`.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2602/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2602/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2602",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2602",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2602.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2602.patch",
"merged_at": "2022-08-03T23:41:25Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2603
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2603/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2603/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2603/events
|
https://github.com/materialsproject/pymatgen/pull/2603
| 1,328,550,417
|
PR_kwDOACgets48pVot
| 2,603
|
Add option for 90 degree "cubic" supercells
|
{
"login": "JaGeo",
"id": 22094846,
"node_id": "MDQ6VXNlcjIyMDk0ODQ2",
"avatar_url": "https://avatars.githubusercontent.com/u/22094846?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JaGeo",
"html_url": "https://github.com/JaGeo",
"followers_url": "https://api.github.com/users/JaGeo/followers",
"following_url": "https://api.github.com/users/JaGeo/following{/other_user}",
"gists_url": "https://api.github.com/users/JaGeo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JaGeo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JaGeo/subscriptions",
"organizations_url": "https://api.github.com/users/JaGeo/orgs",
"repos_url": "https://api.github.com/users/JaGeo/repos",
"events_url": "https://api.github.com/users/JaGeo/events{/privacy}",
"received_events_url": "https://api.github.com/users/JaGeo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51417780)\n\nCoverage increased (+0.008%) to 63.533% when pulling **d7aba46501cc07e8ca6b3627f3901960f8cd51fc on JaGeo:supercell_transformation** into **6ea3ec8d055dd7cd4e8e0e4008e866e288c693a1 on materialsproject:master**.\n",
"Thanks."
] | 2022-08-04T12:31:51
| 2022-08-04T19:03:27
|
2022-08-04T18:44:26Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
I have added an additional option to the CubicSupercellTransformation to only return cells with three 90 degree angles. I think this might be useful for tasks where supercells are required.
I have also added two test cases and documentation.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2603/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2603/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2603",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2603",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2603.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2603.patch",
"merged_at": "2022-08-04T18:44:26Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2604
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2604/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2604/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2604/events
|
https://github.com/materialsproject/pymatgen/pull/2604
| 1,328,792,598
|
PR_kwDOACgets48qKVx
| 2,604
|
Change default number of significant digits to write VASP POSCAR file
|
{
"login": "henriquemiranda",
"id": 5531862,
"node_id": "MDQ6VXNlcjU1MzE4NjI=",
"avatar_url": "https://avatars.githubusercontent.com/u/5531862?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/henriquemiranda",
"html_url": "https://github.com/henriquemiranda",
"followers_url": "https://api.github.com/users/henriquemiranda/followers",
"following_url": "https://api.github.com/users/henriquemiranda/following{/other_user}",
"gists_url": "https://api.github.com/users/henriquemiranda/gists{/gist_id}",
"starred_url": "https://api.github.com/users/henriquemiranda/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/henriquemiranda/subscriptions",
"organizations_url": "https://api.github.com/users/henriquemiranda/orgs",
"repos_url": "https://api.github.com/users/henriquemiranda/repos",
"events_url": "https://api.github.com/users/henriquemiranda/events{/privacy}",
"received_events_url": "https://api.github.com/users/henriquemiranda/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks @henriquemiranda. This change breaks quite a number of tests. They need to be fixed before I can merge it.",
"Ok, I see... I don't see where to start to fix those issues.\r\n@shyuep Do you think any of the devs could help me?\r\n",
"Click on the failed tests and look at the logs. There will be error messages indicating what test failed. From that, you just need to correct the tests. Most of it is likely due to the fact that you changed the number of significant figures and that changed all the output file comparisons. ",
"Actually... It seems the error is triggered by a test where the lattice parameters must not match because of the precision of the POSCAR files...\r\nhttps://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/defects/tests/test_core.py#L33\r\nThat's certainly a useful test to have\r\n",
"\n[](https://coveralls.io/builds/51501144)\n\nCoverage increased (+0.005%) to 63.518% when pulling **cf0abc579f4d080587106bfd6bd3f5e3909941f8 on henriquemiranda:master** into **ebfdde14598795a90ad3e6b7a2f0bf2ae6a36858 on materialsproject:master**.\n",
"@shyuep I think I fixed all the tests that were failing because of the change in the precision of the POSCAR.\r\nThe checks here on GitHub actions are failing but I am not sure if it's related to the changes in this PR.",
"Great. Thanks. I will merge now."
] | 2022-08-04T15:14:43
| 2022-08-08T21:31:04
|
2022-08-08T21:31:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Changed the default number of significant digits to be used when writing the POSCAR file.
Writing the POSCAR with the current default can cause all kinds of different nasty issues in VASP for example:
- VASP might not be able to find the correct space group
- VASP might lose the symmetry during relaxation
- Might lead to a slightly different number of G vectors for symmetry equivalent k-points
- ...
https://www.vasp.at/wiki/index.php/Precision,_symmetry_and_POSCAR
These issues are particularly painful for beginners.
Since there is not much to be gained by using a low number of digits I propose to use 16 significant digits.
Then, when a user starts off with a POSCAR with low precision he can symmetrize the structure using spglib and write a new POSCAR with higher precision with a simple python script using pymatgen before starting the VASP calculation:
https://gist.github.com/henriquemiranda/e4a1b616693aac339ef011af6484f890
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2604/reactions",
"total_count": 4,
"+1": 4,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2604/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2604",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2604",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2604.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2604.patch",
"merged_at": "2022-08-08T21:31:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2605
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2605/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2605/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2605/events
|
https://github.com/materialsproject/pymatgen/issues/2605
| 1,329,216,259
|
I_kwDOACgets5POjsD
| 2,605
|
What is the best way to rearrange the lattice vectors?
|
{
"login": "mm04926412",
"id": 21348397,
"node_id": "MDQ6VXNlcjIxMzQ4Mzk3",
"avatar_url": "https://avatars.githubusercontent.com/u/21348397?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mm04926412",
"html_url": "https://github.com/mm04926412",
"followers_url": "https://api.github.com/users/mm04926412/followers",
"following_url": "https://api.github.com/users/mm04926412/following{/other_user}",
"gists_url": "https://api.github.com/users/mm04926412/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mm04926412/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mm04926412/subscriptions",
"organizations_url": "https://api.github.com/users/mm04926412/orgs",
"repos_url": "https://api.github.com/users/mm04926412/repos",
"events_url": "https://api.github.com/users/mm04926412/events{/privacy}",
"received_events_url": "https://api.github.com/users/mm04926412/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-08-04T22:00:52
| 2022-08-26T14:58:48
|
2022-08-26T14:58:48Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I'm testing a methodology where the ordering of the lattice paramaters matters, is is possibel to rearrange a b and c?
|
{
"login": "mm04926412",
"id": 21348397,
"node_id": "MDQ6VXNlcjIxMzQ4Mzk3",
"avatar_url": "https://avatars.githubusercontent.com/u/21348397?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mm04926412",
"html_url": "https://github.com/mm04926412",
"followers_url": "https://api.github.com/users/mm04926412/followers",
"following_url": "https://api.github.com/users/mm04926412/following{/other_user}",
"gists_url": "https://api.github.com/users/mm04926412/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mm04926412/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mm04926412/subscriptions",
"organizations_url": "https://api.github.com/users/mm04926412/orgs",
"repos_url": "https://api.github.com/users/mm04926412/repos",
"events_url": "https://api.github.com/users/mm04926412/events{/privacy}",
"received_events_url": "https://api.github.com/users/mm04926412/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2605/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2605/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2606
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2606/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2606/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2606/events
|
https://github.com/materialsproject/pymatgen/pull/2606
| 1,330,223,261
|
PR_kwDOACgets48u7s7
| 2,606
|
Bit more code clean up
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@shyuep Not sure the remaining CI error is related to my changes.\r\n\r\n<details>\r\n<summary>CI logs</summary>\r\n\r\n```py\r\n================================== FAILURES ===================================\r\n____________________________ TestQCOutput.test_all ____________________________\r\n\r\nself = <qchem.tests.test_outputs.TestQCOutput testMethod=test_all>\r\n\r\n def test_all(self):\r\n self.maxDiff = None\r\n single_outs = {}\r\n for file in single_job_out_names:\r\n> single_outs[file] = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, \"molecules\", file)).data\r\n\r\npymatgen\\io\\qchem\\tests\\test_outputs.py:228: \r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\r\npymatgen\\io\\qchem\\outputs.py:[27](https://github.com/materialsproject/pymatgen/runs/7697121700?check_suite_focus=true#step:5:28)9: in __init__\r\n self._read_optimization_data()\r\npymatgen\\io\\qchem\\outputs.py:898: in _read_optimization_data\r\n self.data[\"structure_change\"] = check_for_structure_changes(\r\npymatgen\\io\\qchem\\outputs.py:1497: in check_for_structure_changes\r\n initial_mol_graph = MoleculeGraph.with_local_env_strategy(mol_list[0], OpenBabelNN())\r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _\r\n\r\nargs = (<pymatgen.analysis.local_env.OpenBabelNN object at 0x000002002A7FDEE0>,)\r\nkwargs = {}\r\n\r\n @functools.wraps(_callable)\r\n def decorated(*args, **kwargs):\r\n if not self.condition:\r\n> raise RuntimeError(self.message)\r\nE RuntimeError: BabelMolAdaptor requires openbabel to be installed with Python bindings. Please get it at http://openbabel.org (version >=3.0.0).\r\n\r\nC:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64\\lib\\site-packages\\monty\\dev.py:96: RuntimeError\r\n============================== warnings summary ===============================\r\nC:\\hostedtoolcache\\windows\\Python\\3.9.13\\x64\\lib\\site-packages\\past\\builtins\\misc.py:[45](https://github.com/materialsproject/pymatgen/runs/7697121700?check_suite_focus=true#step:5:46)\r\n```\r\n</details>"
] | 2022-08-05T18:07:39
| 2022-08-05T19:59:58
|
2022-08-05T19:33:32Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Remove unneeded `dict.keys()` calls for conciseness. Finishes up some loose ends from #2596.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2606/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2606/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2606",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2606",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2606.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2606.patch",
"merged_at": "2022-08-05T19:33:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2607
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2607/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2607/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2607/events
|
https://github.com/materialsproject/pymatgen/pull/2607
| 1,330,617,011
|
PR_kwDOACgets48wEew
| 2,607
|
unittest2pytest pymatgen/core/tests --write --nobackups
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I do not have a super strong opinion. The only thing is that unittest is included as part of python and I don't find a big problem with it. Pytest is used right now as a dev requirement, but there is no guarantee that we will continue to use it in future.",
"> but there is no guarantee that we will continue to use it in future.\r\n\r\nThere were already 18 test files importing `pytest` prior to this PR. Dropping it from dev deps would take some work.",
"I understand that. But dropping it from 100+ test files would take even more work. We already did a unittest -> nosetests -> pytest switch. I do not know what comes after pytest. At the same time, the default unittest in Python presumably will always be supported for any decent test protocol. PymatgenTest actually inherits from unittest.TestCase and adds support for things like numpy array comparisons and useful structure and test directory tools. I would actually recommend people just use PymatgenTest. ",
"I see. My bets are on `pytest` not going anywhere. On GitHub, it has [8x more](https://github.com/pytest-dev/pytest) stars and 4x more repos using it (512k vs 123k) than [nose](https://github.com/nose-devs/nose).\r\n\r\nThe thing with `PymatgenTest` is many people likely don't know about it. It provides functionality that might be better left to a test framework. E.g. `pytest` has [`approx()`](https://docs.pytest.org/en/7.1.x/reference/reference.html#pytest-approx) for array comparison.",
"It wasn't that long ago that I thought nose wouldn't go anywhere too. As for PymatgenTest, I agree some of the functionality are better left to a test framework (e.g., array comparisons, and in fact, PymatgenTest's array comparisons simply delegate to numpy's). But it is not just array comparisons. It is test directory specification, convenience structures, etc. \r\n\r\nIn any case, I am by no means objecting to pytest. If someone submits new tests in pytest, I will just accept the PR. I just don't think it is a fruitful use of time to migrate old tests based on perfectly fine unittest.TestCase to pytest. Ultimately, the unittests are subject to less stringent code quality criteria than the actual code, e.g., you don't document unittest methods and until black came about, we don't bother with linting quality on tests. ",
"> I just don't think it is a fruitful use of time to migrate old tests based on perfectly fine unittest.TestCase to pytest.\r\n\r\nThe time investment is actually quite small considering all I did was run `unittest2pytest pymatgen/core/tests --write --nobackups` and fix a few linter errors. But I see your point. There's still overhead re-running the tests to make sure nothing broke and with reviewing.",
"\n[](https://coveralls.io/builds/51714770)\n\nCoverage increased (+0.03%) to 63.269% when pulling **fcb2a98eafddbc62515290b69fabf54d85a4d167 on janosh:unittest2pytest** into **dda4cd31af37e1488d3c4f280d96bcda4aeabc97 on materialsproject:master**.\n",
"@shyuep I resolved the merge conflicts."
] | 2022-08-06T02:44:34
| 2022-08-17T01:43:27
|
2022-08-17T01:43:27Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
@shyuep What's your stance on converting `pymatgen` tests from `unittest` to `pytest`?
I find `pytest`'s functional style to be more concise and easier to read than `unittest`.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2607/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2607/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2607",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2607",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2607.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2607.patch",
"merged_at": "2022-08-17T01:43:27Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2608
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2608/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2608/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2608/events
|
https://github.com/materialsproject/pymatgen/issues/2608
| 1,330,668,239
|
I_kwDOACgets5PUGLP
| 2,608
|
some wrong with the BSDOSPlotter
|
{
"login": "she529",
"id": 75371769,
"node_id": "MDQ6VXNlcjc1MzcxNzY5",
"avatar_url": "https://avatars.githubusercontent.com/u/75371769?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/she529",
"html_url": "https://github.com/she529",
"followers_url": "https://api.github.com/users/she529/followers",
"following_url": "https://api.github.com/users/she529/following{/other_user}",
"gists_url": "https://api.github.com/users/she529/gists{/gist_id}",
"starred_url": "https://api.github.com/users/she529/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/she529/subscriptions",
"organizations_url": "https://api.github.com/users/she529/orgs",
"repos_url": "https://api.github.com/users/she529/repos",
"events_url": "https://api.github.com/users/she529/events{/privacy}",
"received_events_url": "https://api.github.com/users/she529/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-08-06T06:34:08
| 2022-08-06T06:34:08
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
when I use the BSDosPlotter model to draw BAND and DOS figure,I am fail with a “band = cast(list[float], band)” . then I modified the code with "band = cast(list band) " and got a result.
**To Reproduce**
Steps to reproduce the behavior:
Follows are my script of DosPlotter:
from pymatgen.electronic_structure.plotter import BSDOSPlotter
from pymatgen.io.vasp.outputs import Vasprun
from matplotlib import pyplot as plt
from typing import Literal, cast
vasprun = Vasprun('vasprun.xml', parse_projected_eigen=True)
bs_data = vasprun.get_band_structure(line_mode=True)
dos_vasprun = Vasprun('vasprun.xml')
dos_data = dos_vasprun.complete_dos
print(bs_data)
band = cast(list, bs_data)
print(band)
banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements',
vb_energy_range=5, fixed_cb_energy=5)
#banddos_fig = BSDOSPlotter(bs_projection=None, dos_projection=None, vb_energy_range=-5, fixed_cb_energy=5)
banddos_fig.get_plot(bs_data,dos=dos_data)
plt.savefig( 'banddos_fig.png')
error:
TypeError Traceback (most recent call last)
Input In [4], in <cell line: 12>()
8 dos_data = vasprun.complete_dos
9 banddos_fig = BSDOSPlotter(bs_projection='elements', dos_projection='elements',
10 vb_energy_range=5, fixed_cb_energy=5)
---> 12 banddos_fig.get_plot(bs=bs_data, dos=dos_data)
13 plt.savefig(band_directory / 'banddos_fig.png')
File E:\program\conda\envs\study\lib\site-packages\pymatgen\electronic_structure\plotter.py:2419, in BSDOSPlotter.get_plot(self, bs, dos)
2417 band_energies[spin] = []
2418 for band in bs.bands[spin]:
-> 2419 band = cast(list[float], band)
2420 band_energies[spin].append([e - bs.efermi for e in band]) # type: ignore
2422 # renormalize the DOS energies to Fermi level
the result after modified:
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
A clear and concise description of what you expected to happen.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: [e.g. Mac,Windows,Linux]
- Version [e.g. 2019.9.16]
**Additional context**
Add any other context about the problem here.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2608/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2608/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2609
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2609/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2609/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2609/events
|
https://github.com/materialsproject/pymatgen/pull/2609
| 1,330,812,129
|
PR_kwDOACgets48wqTg
| 2,609
|
metal_edge_extender enhancements
|
{
"login": "rkingsbury",
"id": 1908695,
"node_id": "MDQ6VXNlcjE5MDg2OTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/1908695?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rkingsbury",
"html_url": "https://github.com/rkingsbury",
"followers_url": "https://api.github.com/users/rkingsbury/followers",
"following_url": "https://api.github.com/users/rkingsbury/following{/other_user}",
"gists_url": "https://api.github.com/users/rkingsbury/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rkingsbury/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rkingsbury/subscriptions",
"organizations_url": "https://api.github.com/users/rkingsbury/orgs",
"repos_url": "https://api.github.com/users/rkingsbury/repos",
"events_url": "https://api.github.com/users/rkingsbury/events{/privacy}",
"received_events_url": "https://api.github.com/users/rkingsbury/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The test failures seem to be related to `bader` installation (which afaik is not related to the changes here)",
"Thanks"
] | 2022-08-06T18:04:24
| 2022-08-10T14:01:15
|
2022-08-06T22:24:24Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Assorted enhancements to `metal_edge_extender` to increase its flexibility for use in contexts beyond the LIBE dataset (e.g., water-ion coordination)
* Adds `metals`, `coordinators`, and `cutoff` as keyword arguments so that metal edge extender settings can be customized for different applications (e.g., including additional metal species)
* Expand docstring of `metal_edge_extender` and add type hinting
* Adds the ability to automatically detect metals in the structure based on `Species.is_metal`
* Adds tests for all new kwargs and expands testing of original functionality
## Additional dependencies introduced (if any)
None
## TODO (if any)
Feedback from @espottesmith and @samblau
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2609/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2609/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2609",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2609",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2609.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2609.patch",
"merged_at": "2022-08-06T22:24:24Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2610
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2610/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2610/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2610/events
|
https://github.com/materialsproject/pymatgen/pull/2610
| 1,330,857,516
|
PR_kwDOACgets48wzBy
| 2,610
|
Correct link to Fleur website in addon entry for `pymatgen-io-fleur`
|
{
"login": "janssenhenning",
"id": 11249470,
"node_id": "MDQ6VXNlcjExMjQ5NDcw",
"avatar_url": "https://avatars.githubusercontent.com/u/11249470?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janssenhenning",
"html_url": "https://github.com/janssenhenning",
"followers_url": "https://api.github.com/users/janssenhenning/followers",
"following_url": "https://api.github.com/users/janssenhenning/following{/other_user}",
"gists_url": "https://api.github.com/users/janssenhenning/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janssenhenning/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janssenhenning/subscriptions",
"organizations_url": "https://api.github.com/users/janssenhenning/orgs",
"repos_url": "https://api.github.com/users/janssenhenning/repos",
"events_url": "https://api.github.com/users/janssenhenning/events{/privacy}",
"received_events_url": "https://api.github.com/users/janssenhenning/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks,"
] | 2022-08-06T22:03:18
| 2022-08-13T07:22:16
|
2022-08-06T22:22:48Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The link in the docs was mistakenly interpreted as relative inside the pymatgen documentation. Also added `rel/`, which will always point to the documentation for the latest version of the code
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2610/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2610/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2610",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2610",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2610.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2610.patch",
"merged_at": "2022-08-06T22:22:48Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/2611
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2611/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2611/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2611/events
|
https://github.com/materialsproject/pymatgen/pull/2611
| 1,330,868,591
|
PR_kwDOACgets48w1GD
| 2,611
|
Add option to skip SpacegroupAnalyzer in FEFFDictSet
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"A few suggestions:\r\n\r\n1. Pls change low_symmetry to just skip_symmetry.\r\n2. Pls add a unittest (in test_sets.py) to test the new argument functionality.\r\n\r\nA note about the rest. A symmetry calculation is actually fast. By specifying symmetry, we reduce the cost of the FEFF calculation itself. It is true you can put settings in the init instead of yaml. The reason why this is done this way is to have the parameters in a glance in a file. One can also modify the parameters quickly. The rationale is probably more valid in very complicated input files like VASP. I guess we will keep it here for now.",
"> 1. Pls change low_symmetry to just skip_symmetry.\r\n> 2. Pls add a unittest (in test_sets.py) to test the new argument functionality.\r\n\r\n@shyuep sure will do.\r\n\r\n> A note about the rest. A symmetry calculation is actually fast. By specifying symmetry, we reduce the cost of the FEFF calculation itself. \r\n\r\nHow so? It appears that the symmetry information from `SpacegroupAnalyzer` only comes into play in constructing the header comments. Did I miss something?\r\n\r\n> It is true you can put settings in the init instead of yaml. The reason why this is done this way is to have the parameters in a glance in a file. One can also modify the parameters quickly. The rationale is probably more valid in very complicated input files like VASP. I guess we will keep it here for now.\r\n\r\nThe issue I take with this is that the `yaml` files are not exposed in the [documentation](https://pymatgen.org/pymatgen.io.feff.sets.html). It's not available at a glance for the average user who might not that the parameter files are there.\r\n\r\nDo you mind if I take a shot at improving this? I think it'll be much clearer as default arguments in the `__init__` of the e..g `XANESDictSet`.\r\n\r\n\r\n",
"@shyuep just bumping the conversation. I'd like your feedback on what I mentioned in my above comment before I proceed.",
"@x94carbone please see also #2505 and issue #2624 . Neither is directly related to this but you may wish to provide feedback.",
"@x94carbone @rkingsbury I am happy to revisit but I just want to highlight that there are good reasons to use YAML formats, not least because it is far easier at a glance to know what settings are used than parsing python code. As a compromise, I suggest you use RST literalinclude e.g., https://dannguyen.github.io/danssphinx-template/content/001-examples/500-partials.html to insert the YAML file? ",
"@shyuep I'm not sure I agree, but ultimately it's your decision. \r\n\r\nBefore I make any further changes though, can you provide some feedback on my blocking question?\r\n\r\n>> A note about the rest. A symmetry calculation is actually fast. By specifying symmetry, we reduce the cost of the FEFF calculation itself.\r\n\r\n> How so? It appears that the symmetry information from SpacegroupAnalyzer only comes into play in constructing the header comments. Did I miss something?\r\n\r\nThanks!",
"@x94carbone I think it is fine. Pls go ahead and make the changes. Re yaml vs in code, I think this is really a matter of judgment depending on how familiar one is with Python code. Of course you and I are not going to have an issue reading python code. But for someone new, it is easier to read yaml. Even I find it helpful to quickly just pull up two YAML files if I want to say, figure out what the differences between a MPXANESSet and MPEXAFSSet are. I should note that the documentation actually does show the settings. See the pasted doc from pymatgen.org today. You see CONFIG\r\n\r\n<img width=\"709\" alt=\"CleanShot 2022-09-28 at 14 38 43@2x\" src=\"https://user-images.githubusercontent.com/577107/192893523-bfcabadb-d0fd-4c9f-b9b1-51cfde742b23.png\">\r\n"
] | 2022-08-06T23:24:47
| 2024-08-03T19:01:57
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
# Summary
Allows passing of a `low_symmetry_system` keyword argument to `FEFFDictSet` which skips the `SpacegroupAnalyzer` runs in constructing the header.
# Comments
* Frankly I think the entire feature should be deprecated. There's no reason to do such a heavy calculation just for a header comment. If the user wants to perhaps they should just pass this directly to the comment themselves? If you want, I can make these changes.
* It's unrelated, but I noticed that default parameters are stored in `.yaml` files. This is really confusing- why not just store these as default cards in the `__init__`s? I'm also happy to modify if desired.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2611/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2611/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2611",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2611",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2611.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2611.patch",
"merged_at": null
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/2612
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2612/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2612/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2612/events
|
https://github.com/materialsproject/pymatgen/issues/2612
| 1,332,303,559
|
I_kwDOACgets5PaVbH
| 2,612
|
`IndexError` when unassigned ID passed to `MPRester().get_entry_by_material_id()`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2022-08-08T19:30:15
| 2022-08-08T21:31:48
|
2022-08-08T21:31:48Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
```py
from pymatgen.ext.matproj import MPRester
MPRester().get_entry_by_material_id("mp-2022")
```
raises
```py
777 """
778 data = self.get_entries(
779 material_id,
780 compatible_only=compatible_only,
(...)
783 conventional_unit_cell=conventional_unit_cell,
784 )
--> 785 return data[0]
IndexError: list index out of range
```
Should raise
```py
MPRestError: material_id = 'mp-2202' does not exist
```
instead.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2612/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2612/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/2613
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2613/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2613/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2613/events
|
https://github.com/materialsproject/pymatgen/pull/2613
| 1,332,308,474
|
PR_kwDOACgets481llF
| 2,613
|
Fix `MPRester.get_entry_by_material_id()` for missing ID
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"\n[](https://coveralls.io/builds/51504706)\n\nCoverage increased (+0.003%) to 63.516% when pulling **f469cbe587e006816631849d8f268a8b39ee37f5 on janosh:fix-get-entry-by-id-for-missing-id** into **ebfdde14598795a90ad3e6b7a2f0bf2ae6a36858 on materialsproject:master**.\n"
] | 2022-08-08T19:34:51
| 2022-08-08T21:31:48
|
2022-08-08T21:31:48Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #2612.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/2613/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/2613/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/2613",
"html_url": "https://github.com/materialsproject/pymatgen/pull/2613",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/2613.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/2613.patch",
"merged_at": "2022-08-08T21:31:48Z"
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.