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/1701
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1701/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1701/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1701/events
|
https://github.com/materialsproject/pymatgen/pull/1701
| 534,931,638
|
MDExOlB1bGxSZXF1ZXN0MzUwNzE1MjEx
| 1,701
|
Bump tqdm from 4.40.0 to 4.40.1
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[
"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [build (3.7)](https://developer.github.com/actions/)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-09T13:28:23
| 2019-12-09T14:23:15
|
2019-12-09T14:23:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.40.0 to 4.40.1.
<details>
<summary>Commits</summary>
- [`4276147`](https://github.com/tqdm/tqdm/commit/42761473f9edf276937cc3a28a6fcabc59f5f97d) bump version, merge branch 'devel'
- [`ffb706e`](https://github.com/tqdm/tqdm/commit/ffb706ec9ecdadfb5cbaa826dfa48c22e04d58eb) add tests for float total < n
- [`f422502`](https://github.com/tqdm/tqdm/commit/f4225020380eafaaeb8f4328271381d4fdecb1df) fix floating point imprecision raising errors
- [`03f8300`](https://github.com/tqdm/tqdm/commit/03f830070ec15c9ff99f78c5e698c476c7bdfa95) fix auto gh releases
- [`085cc0a`](https://github.com/tqdm/tqdm/commit/085cc0ad98a7f131c68d3aa039cf52b000095bf6) update CONTRIBUTING
- See full diff in [compare view](https://github.com/tqdm/tqdm/compare/v4.40.0...v4.40.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.40.0&new-version=4.40.1)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</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/1701/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1701/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1701",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1701",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1701.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1701.patch",
"merged_at": "2019-12-09T14:23:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1702
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1702/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1702/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1702/events
|
https://github.com/materialsproject/pymatgen/pull/1702
| 534,981,297
|
MDExOlB1bGxSZXF1ZXN0MzUwNzU2MDIx
| 1,702
|
Fix bug in lobsterout
|
{
"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 |
[] | 2019-12-09T14:49:55
| 2019-12-09T23:47:34
|
2019-12-09T23:47:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello,
I have fixed a bug in the Lobsterout class. Before this bug fix, "lobsterout" files which were created with only one thread could not be read and this bug led to an exception. I have included this option now and added an additional test to avoid this problem in the future. I ran into this bug by running Lobster with only one thread by accident.
Best
JG
## 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:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] 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 existing 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/1702/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1702/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1702",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1702",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1702.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1702.patch",
"merged_at": "2019-12-09T23:47:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1703
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1703/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1703/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1703/events
|
https://github.com/materialsproject/pymatgen/issues/1703
| 535,403,899
|
MDU6SXNzdWU1MzU0MDM4OTk=
| 1,703
|
Illegal Instruction when importing find_points_in_spheres
|
{
"login": "gmfricke",
"id": 3946771,
"node_id": "MDQ6VXNlcjM5NDY3NzE=",
"avatar_url": "https://avatars.githubusercontent.com/u/3946771?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gmfricke",
"html_url": "https://github.com/gmfricke",
"followers_url": "https://api.github.com/users/gmfricke/followers",
"following_url": "https://api.github.com/users/gmfricke/following{/other_user}",
"gists_url": "https://api.github.com/users/gmfricke/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gmfricke/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gmfricke/subscriptions",
"organizations_url": "https://api.github.com/users/gmfricke/orgs",
"repos_url": "https://api.github.com/users/gmfricke/repos",
"events_url": "https://api.github.com/users/gmfricke/events{/privacy}",
"received_events_url": "https://api.github.com/users/gmfricke/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 what's the issue with conda installation on Linux. But for linux, perhaps you can just try using `pip install pymatgen`. That usually forces a compile using whatever compiler you have on your system and works fine.",
"Thanks for the reply. The illegal instruction does not occur with Clang 9.0.0 and Python 8, but does occur with gcc 7.3.0 and Pyton 3.7.3. The pymatgen versions are both 2019.12.3. \r\n\r\nPython 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:19) \r\n[Clang 9.0.0 (tags/RELEASE_900/final)] :: Anaconda, Inc. on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from pymatgen.optimization.neighbors import find_points_in_spheres\r\n>>> \r\n",
"Hmm... Python 3.8 cannot be the issue. We have tested on Python 3.7x and it works. It is probably the c compiler then. Does pip installing solve the problem?",
"I tried pip which we use fairly regularly, this is at an HPC center. For example \r\npip3 install --user pyramid installs correctly\r\n\r\nhowever\r\npip3 install --user pymatgen yields,\r\n\r\ngcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python3.6m -I/users/mfricke/.local/lib/python3.6/site-packages/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.linux-x86_64-3.6/pymatgen/optimization/linear_assignment.o\r\n pymatgen/optimization/linear_assignment.c:4:20: fatal error: Python.h: No such file or directory\r\n compilation terminated.\r\n error: command 'gcc' failed with exit status 1\r\n\r\ngcc --version\r\ngcc (GCC) 5.4.0\r\n\r\nPython.h is in the path as specified by CPATH.\r\n\r\nI am trying the spack recipe for pymatgen to see if that works better. Is there a specific GNU or intel compiler version you recommend? ",
"As far as I can tell, the problem is that the header files are missing. I would suggest you do not just type pip3 in the command line. It is probably the system Python (I see Python 3.6, not 3.7 in your output) and pip that is being used.\r\n\r\nI suggest you use the gcc from conda itself. And then use pip from within your conda env. ie..,\r\n\r\n```\r\nconda create -n test_pymatgen python=3.7\r\nconda activate test_pymatgen\r\nconda install gcc\r\npip install pymatgen\r\n```\r\n\r\nI tested this on a HPC and it works.",
"That worked beautifully. Thank you for the help."
] | 2019-12-09T23:43:51
| 2019-12-10T01:38:16
|
2019-12-10T01:38:16Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
An illegal instruction occurs when importing find_points_in_spheres from pymatgen.optimization.neighbors. The code was built with anaconda 5.2.0.
To reproduce:
$ conda create -n test_pymatgen -c conda-forge pymatgen
$ conda activate test_pymatgen
(test_pymatgen) $ python
Python 3.7.3 | packaged by conda-forge | (default, Dec 6 2019, 08:54:18)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pymatgen.optimization.neighbors import find_points_in_spheres
Illegal instruction (core dumped)
|
{
"login": "gmfricke",
"id": 3946771,
"node_id": "MDQ6VXNlcjM5NDY3NzE=",
"avatar_url": "https://avatars.githubusercontent.com/u/3946771?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/gmfricke",
"html_url": "https://github.com/gmfricke",
"followers_url": "https://api.github.com/users/gmfricke/followers",
"following_url": "https://api.github.com/users/gmfricke/following{/other_user}",
"gists_url": "https://api.github.com/users/gmfricke/gists{/gist_id}",
"starred_url": "https://api.github.com/users/gmfricke/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/gmfricke/subscriptions",
"organizations_url": "https://api.github.com/users/gmfricke/orgs",
"repos_url": "https://api.github.com/users/gmfricke/repos",
"events_url": "https://api.github.com/users/gmfricke/events{/privacy}",
"received_events_url": "https://api.github.com/users/gmfricke/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1703/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1703/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1704
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1704/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1704/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1704/events
|
https://github.com/materialsproject/pymatgen/pull/1704
| 536,106,044
|
MDExOlB1bGxSZXF1ZXN0MzUxNjk2MjI2
| 1,704
|
Add missing information to docstrings
|
{
"login": "rwoodsrobinson",
"id": 7270689,
"node_id": "MDQ6VXNlcjcyNzA2ODk=",
"avatar_url": "https://avatars.githubusercontent.com/u/7270689?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rwoodsrobinson",
"html_url": "https://github.com/rwoodsrobinson",
"followers_url": "https://api.github.com/users/rwoodsrobinson/followers",
"following_url": "https://api.github.com/users/rwoodsrobinson/following{/other_user}",
"gists_url": "https://api.github.com/users/rwoodsrobinson/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rwoodsrobinson/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rwoodsrobinson/subscriptions",
"organizations_url": "https://api.github.com/users/rwoodsrobinson/orgs",
"repos_url": "https://api.github.com/users/rwoodsrobinson/repos",
"events_url": "https://api.github.com/users/rwoodsrobinson/events{/privacy}",
"received_events_url": "https://api.github.com/users/rwoodsrobinson/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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!"
] | 2019-12-11T02:38:16
| 2019-12-11T02:43:16
|
2019-12-11T02:43:16Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Adds units and reference for atomic orbital dataset
|
{
"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/1704/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1704/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1704",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1704",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1704.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1704.patch",
"merged_at": "2019-12-11T02:43:16Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1705
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1705/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1705/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1705/events
|
https://github.com/materialsproject/pymatgen/pull/1705
| 536,427,203
|
MDExOlB1bGxSZXF1ZXN0MzUxOTU4NjMw
| 1,705
|
Fix bug of missing sp2 N-N bond data
|
{
"login": "kwaters4",
"id": 5183028,
"node_id": "MDQ6VXNlcjUxODMwMjg=",
"avatar_url": "https://avatars.githubusercontent.com/u/5183028?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/kwaters4",
"html_url": "https://github.com/kwaters4",
"followers_url": "https://api.github.com/users/kwaters4/followers",
"following_url": "https://api.github.com/users/kwaters4/following{/other_user}",
"gists_url": "https://api.github.com/users/kwaters4/gists{/gist_id}",
"starred_url": "https://api.github.com/users/kwaters4/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/kwaters4/subscriptions",
"organizations_url": "https://api.github.com/users/kwaters4/orgs",
"repos_url": "https://api.github.com/users/kwaters4/repos",
"events_url": "https://api.github.com/users/kwaters4/events{/privacy}",
"received_events_url": "https://api.github.com/users/kwaters4/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Can you add a small unittest in the existing unittests to make sure this additional data works as intended? There are already tests there - so it is just copying and pasting one or two lines and changing it to the N-N bond. Thanks.",
"THanks!",
"Hi @kwaters4, please feel welcome to add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately for your contribution in the [pymatgen docs](https://pymatgen.org/team.html). We want to make sure we credit all contributors, even for small additions or bug fixes."
] | 2019-12-11T15:00:39
| 2020-01-13T22:07:15
|
2019-12-11T17:14:07Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Added data for an sp2 N-N bonds in bond_lengths.json
Use value of 1.25 from the following source
http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1705/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1705/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1705",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1705",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1705.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1705.patch",
"merged_at": "2019-12-11T17:14:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1706
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1706/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1706/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1706/events
|
https://github.com/materialsproject/pymatgen/pull/1706
| 536,444,024
|
MDExOlB1bGxSZXF1ZXN0MzUxOTcyNjQz
| 1,706
|
Non-standard setting for magnetic spacegroup & Site property deserialization
|
{
"login": "guycmoore",
"id": 29589087,
"node_id": "MDQ6VXNlcjI5NTg5MDg3",
"avatar_url": "https://avatars.githubusercontent.com/u/29589087?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/guycmoore",
"html_url": "https://github.com/guycmoore",
"followers_url": "https://api.github.com/users/guycmoore/followers",
"following_url": "https://api.github.com/users/guycmoore/following{/other_user}",
"gists_url": "https://api.github.com/users/guycmoore/gists{/gist_id}",
"starred_url": "https://api.github.com/users/guycmoore/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/guycmoore/subscriptions",
"organizations_url": "https://api.github.com/users/guycmoore/orgs",
"repos_url": "https://api.github.com/users/guycmoore/repos",
"events_url": "https://api.github.com/users/guycmoore/events{/privacy}",
"received_events_url": "https://api.github.com/users/guycmoore/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @guymoore13! One thing I noticed was missing is a test for the site property serialization fix. Doing a round-trip as_dict from_dict would probably be sufficient.",
"Sounds good @mkhorton, thank you for the tip!",
"@mkhorton should I add coordinate wrapping for all symmops? In other words, for translations I tried adding np.mod(x,1.0), where x is a translation component in fractional lattice coordinates. This appeared to work well but I want to check with you first. This mod() operation appears to map the following: x -> x+1.0 if x<0.0, and x -> x-1.0 if 1.0 <= x < 2.0.",
"Thanks @guymoore13 ! Yes, co-ordinate wrapping sounds sensible. Thanks for adding the missing module docstrings also. The `jf_in` keyword arg can probably be renamed to `setting_transformation` or something more descriptive (verbosity is fine).\r\n\r\nIf in doubt about something like `mod` you can always check the documentation, for the NumPy modulo that's [here](https://docs.scipy.org/doc/numpy/reference/generated/numpy.mod.html). Otherwise this all looks good.",
"Great, thanks @guymoore13 ! Will merge once continuous integration tests pass.\r\n\r\nAlso, since this is your first pymatgen code addition, please make sure to add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html).",
"Thank you @mkhorton! I just submitted the developer information form."
] | 2019-12-11T15:27:38
| 2020-01-14T05:35:12
|
2020-01-14T05:35:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Added "Jones Faithful transformation" as an optional input for the MagneticSpaceGroup constructor, allowing the user to define the space-group in non-standard coordinates
* CIF file reader uses non-standard transformation in BNS setting as input to MagneticSpaceGroup constructor
* Fixed Monty deserialization of site properties using Matt Horton's suggestion
## Additional dependencies introduced (if any)
* Added dependency to json module in core/sites.py. This dependency was added in order to decode site properties. This dependency is modeled after core/structure.py.
## TODO (if any)
* At the moment, Jones Faithful transformation applies only to the MagSymmOp output of symmetry_ops() attribute of MagneticSpaceGroup. The transformation isn't applied to the operator "data" directly.
## Checklist
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] 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 existing tests pass.
|
{
"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/1706/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1706/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1706",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1706",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1706.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1706.patch",
"merged_at": "2020-01-14T05:35:12Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1707
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1707/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1707/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1707/events
|
https://github.com/materialsproject/pymatgen/issues/1707
| 536,467,016
|
MDU6SXNzdWU1MzY0NjcwMTY=
| 1,707
|
W_pv not included in newer POTCAR versions
|
{
"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 |
[
"I would suggest we simply use have a different YAML setting file that specifies W instead of W_pv as the PSP.",
"We noticed this ourselves recently -- the immediate fix is simply to add `user_potcar_settings={\"W\":\"W_sv\"}` I believe. The _sv seems like the better pseudo potential anyway.\r\n\r\nMore broadly, we're working to rigorously benchmark and improve on MVLScanSet (@rkingsbury) and this will likely see a new base set with different potcar choices. @rkingsbury has recently been adding potcar hash checking to the input sets also, so that we can have more robust checking against using incorrect potcars.",
"Thank you very much for the ideas. I will try to find a solution for the LobsterSet. It should however still allow to use the old PBE POTCARs. Lobster will work with them as well. I might need to change the config depending on which POTCAR version is chosen."
] | 2019-12-11T16:04:43
| 2023-06-01T00:41:02
|
2023-06-01T00:41:02Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
W_pv POTCAR does not exist in the newer POTCAR versions (PBE_54). Using the MVLScanRelaxSet or the LobsterSet for compounds including W will therefore result in an error:
**To Reproduce**
`from pymatgen.ext.matproj import MPRester`
`from pymatgen.io.vasp.sets import MVLScanRelaxSet`
`a = MPRester()`
`struct = a.get_structure_by_material_id('mp-1191364')`
`set = MVLScanRelaxSet(structure=struct, potcar_functional="PBE_54")`
`set.write_input(output_dir=".")`
Does anyone have a suggestion how to fix this? Since a change would affect standard configurations, I wanted to ask for help.
Best,
JG
|
{
"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/1707/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/1707/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1708
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1708/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1708/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1708/events
|
https://github.com/materialsproject/pymatgen/pull/1708
| 536,523,185
|
MDExOlB1bGxSZXF1ZXN0MzUyMDM4Njg5
| 1,708
|
MP SCAN input set
|
{
"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 |
[
"Hmm... why don't you just edit the current input set rather than having yet another one?",
"Failing with `No library stub file for module 'pytest`",
"> Hmm... why don't you just edit the current input set rather than having yet another one?\r\n\r\n@shyuep my thought (informed by my experience as I've learned pymatgen) was that it's more transparent to users to have a single .yaml file to look at that defines the key INCAR parameters, rather than having to follow multiple steps of inheritance that each modifies a few parameters. This can make it hard to understand what INCAR settings you are ultimately getting. \r\n\r\nWhile we could inherit from `MPRelaxSet` or `MVLScanRelaxSet`, we are changing enough of the parameters that we thought it more transparent to define a new set, especially since SCAN calculations may be central to our core workflows in coming years",
"This could also replace the current `MVLScanRelaxSet`",
"@shyuep it's also important to have separation of concerns. Things related to MP, and data that will be on the website should be explicitly `MP blah blah`, with the expectation that they only get modified by group consent. This doesn't seem to be the case for the MIT or MVL parameters which have changed in the past and caused headaches for MP.",
"I would say we have no reason to have two different SCAN input sets unless there is a goal that they are substantially different. Just integrate the new parameters into the MVLScanSet for now. As far as I know, changes to either MIT or MVL sets are rare. In fact, changes to MP sets occur more frequently. And Matt and I are always gatekeepers to ensure no strange parameters are added.",
"In the rare cases it happens, we should have a procedure in place. Unfortunately we cannot protect individual files on GitHub. We did have a serious issue with one of the MD sets a year or so ago (Prec set to Low and the relevant individuals were not notified/did not notice the change, resulting in a lot of lost compute time).\r\n\r\nI'm not sure how best to avoid this -- we've discussed hashing the .yaml files, the key issue seems to be notifying the end user if the input set has changed. One idea could be to store the input set hashes in .pmgrc.yaml, and then if a set is initialized and the hash doesn't match the one previously stored, the user would be notified that the set has changed. This perhaps seems over-complex.",
"I think hashing is overly complex and rigid. There are parameters that we care about, and there are those that we don't or are more lenient on. E.g., we are fine with mixing ISMEAR=-5 and ISMEAR=0 runs for the most part depending on the kpoints. Custodian also modifies some inputs based on errors. Hashing would mean that even if say, VASP decides to add a new parameter to tune convergence and we add it to an input set, the hashes would be different.\r\n\r\nI personally think the best way is to expand the compatibility engine. Instead of just PSP that is being checked right now, we will add parameters that we care about. Right now, I can't really think of what I would add. Maybe PREC, ENCUT and ISPIN for starters since those obviously will have an effect on comparability. U is treated as a special case since we are modifying energy values based on that.",
"Also, I am not aware of the PREC issue on the MD sets, but I would say that if this is a rare occurrence, we shouldn't be designing systems to handle it. I think the original MITMD set was indeed set to prec=low to save computing costs.",
"Hi all, the yaml file for MVLScanRelaxSet was constructed based on the PSP52 recommendations in vasp online manual, which is now no longer updated. Later the VASP developer removed `W_pv` \"because of s ghoststate above E-fermi\" and add `W_sv`. \r\n\r\nI hope you have noticed that there is no `W_sv` in PBE52. If preset `W_sv` in yaml for SCAN, there will be a problem when using PBE52 for W. \r\n\r\nFor the MPSCAN default settings, I am not sure if you have been tested these two params\r\n`ALGO = All ; LMIXTAU = True`. In my experience, these two params (suggested by SCAN developers) work much better in energy convergence than \"ALGO = Fast/Normal\". I would also suggest `ICHARG = 2` instead of 0/1 because I have seen convergence issues when using `ICHARG = 0/1`\r\n\r\n ",
"Thanks @zbwang . \r\n\r\n@rkingsbury @mkhorton @shyamd I suggest we try to solve this problem once and for all. The input sets should define not just the symbol for each element, but also the PSP set it comes from. I.e., we add something in the yaml that says this is from PBE and that one is from PBE_52. This should apply to all prior input sets as well.\r\n\r\nFor the purposes of SCAN, I suggest we just move to PBE_54 and stick with that, unless we have a reason to keep PBE_52? You'd probably want to look into the parameters suggested by @zbwang as well. It is a new enough functional that I am not too worried about backward compatibility.",
"Thank you for those suggestions, @zbwang ! We will investigate.\r\n\r\nI agree that defining the functional within the InputSets alongside the PSPs and INCAR parameters makes sense. For SCAN I think we're comfortable defaulting to PBE_54. If so, I can drop the `potcar_functional` argument so that the 54's are always used, and then we don't need to worry about toggling W_pv and W_sv.",
"Ok with me. I think you should keep the potcar_functional argument (but set it to default to None). The idea being that sometimes I just want to run something with an input set but I want to change the potcar functional. That should be allowed. But the default should be the one specified in the yaml itself.",
"> Ok with me. I think you should keep the potcar_functional argument (but set it to default to None). The idea being that sometimes I just want to run something with an input set but I want to change the potcar functional. That should be allowed. But the default should be the one specified in the yaml itself.\r\n\r\nBut if we allow changing of the potcar_functional, there is the potential for potcar symbols in the .yaml file not to match (e.g., W_pv vs. W_sv). Are you comfortable relying on the user to override the potcar symbols in those cases?",
"Users can do whatever they want.... The rule is that we specify defaults that we think makes the most sense for 99% of the population. For the 1% who wants to mess around with the potcar functional as well as the specific symbols, they can do so....",
"> Users can do whatever they want.... The rule is that we specify defaults that we think makes the most sense for 99% of the population. For the 1% who wants to mess around with the potcar functional as well as the specific symbols, they can do so....\r\n\r\nOK, so to clarify what is being proposed (@shyuep correct me if I'm misunderstanding): \r\n\r\n- add a `POTCAR_FUNCTIONAL` key to each .yaml file\r\n- retain `potcar_functional` as a kwarg in `DictSet` but default to `None`\r\n- [Ryan's proposal]: rename `potcar_functional` to `user_potcar_functional` for consistency with other args that override defaults, like `user_kpoints_settings`.\r\n- InputSets will read the value from the .yaml files unless the user specifies something else.\r\n\r\n@shyuep since this would affect all InputSets I'd prefer to handle via a separate PR / branch. Ok?",
"Ok. Thanks!",
"@shyuep The issue with parameters changing might be a rare occurrence, but it can have significant consequences. The PREC change was part of a larger PR for other reasons and as a result, was not caught. The consequence was 13M CPU hours being lost. We're also putting SCAN on the MP Website. Thus there should be an MP input set for this. This is a simple sociological fix rather than a technical fix.\r\n\r\nEverything else I like. ",
"@shyamd The proposed solution does not solve the \"rare problem\" at all. It really doesn't matter whether something is called MVLScanSet or MPScanSet. In either of these, someone can make a change as part of a bigger PR and there is a non-zero probability that it does not get caught. If you really want to solve this problem, by all means fix the compatibility checks.",
"Compatability checks come after the calculations are finished, so they won't fix the issue of just wasting CPU time. Having an MP set gives @mkhorton something to watch out for. :>",
"@zbwang I'm incorporating your suggestions about `ALGO=ALL` and `ICHARG=2`. We'll likely add `LMIXTAU=TRUE` as well, but want to run a couple of benchmarks first (in progress now). \r\n\r\nWe originally set `ICHARG=1` because our SCAN workflow employs a PBE preconditioning calculation, so we always start SCAN from a CHGCAR, but you make a good point that this set should be designed to facilitate standalone SCAN calculations. We can override ICHARG in our atomate workflow.",
"I am somewhat confused as to why you'd want to use PBE as a preconditioner. Is the PBE doing relaxation or just a static charge calculation?",
"> I am somewhat confused as to why you'd want to use PBE as a preconditioner. Is the PBE doing relaxation or just a static charge calculation?\r\n\r\n@shyuep We've tried workflows with both a PBE static and a PBE relaxation prior to SCAN, but have settled on using a PBE relaxation as our first step. It's main purpose is to accelerate convergence by initializing the wavefunctions.",
"I would argue you should not use a PBE relaxation unless your results show that it is indeed faster. SCAN gets lattice parameters close to the expt. PBE does not.\r\n\r\nIn fact, our experience with HSE is that if you have expt lattice parameters, directly computing from the expt structure is usually faster than relaxing with PBE to wrong lattice parameters and then re-relaxing it with HSE.\r\n\r\nOf course, this assumes you are starting from expt structures. I would actually argue for a PBE static -> SCAN low -> SCAN high sequence of runs.",
"@shyuep I'm not commenting on the workflow here, but just a note on SCAN itself: convergence is nasty, and as currently formulated it's numerically badly conditioned. I'm told that *internally* inside VASP they generate a PBE wavefunction first before generating the SCAN one, and this is at every SCF step resulting in a ~30% performance penalty. But overall convergence is also bad enough that pre-conditioning with a self-consistent PBE WAVECAR is itself necessary (whether PBE *specifically* is important I couldn't say).",
"> I would argue you should not use a PBE relaxation unless your results show that it is indeed faster. SCAN gets lattice parameters close to the expt. PBE does not.\r\n> \r\n> In fact, our experience with HSE is that if you have expt lattice parameters, directly computing from the expt structure is usually faster than relaxing with PBE to wrong lattice parameters and then re-relaxing it with HSE.\r\n> \r\n> Of course, this assumes you are starting from expt structures. I would actually argue for a PBE static -> SCAN low -> SCAN high sequence of runs.\r\n\r\nWe thought so too. We did a series of benchmarks comparing PBE > SCAN > SCAN workflows, and found that the second SCAN relaxation changed the output very little, hence the two step PBE>SCAN that we plan to adopt. That said, we are generally starting from PBE relaxed structures from MP rather than experimental ones.",
"> > Users can do whatever they want.... The rule is that we specify defaults that we think makes the most sense for 99% of the population. For the 1% who wants to mess around with the potcar functional as well as the specific symbols, they can do so....\r\n> \r\n> OK, so to clarify what is being proposed (@shyuep correct me if I'm misunderstanding):\r\n> \r\n> * add a `POTCAR_FUNCTIONAL` key to each .yaml file\r\n> \r\n> * retain `potcar_functional` as a kwarg in `DictSet` but default to `None`\r\n> \r\n> * [Ryan's proposal]: rename `potcar_functional` to `user_potcar_functional` for consistency with other args that override defaults, like `user_kpoints_settings`.\r\n> \r\n> * InputSets will read the value from the .yaml files unless the user specifies something else.\r\n> \r\n> \r\n> @shyuep since this would affect all InputSets I'd prefer to handle via a separate PR / branch. Ok?\r\n\r\n\r\n> Ok. Thanks!\r\n\r\n@shyuep I've implemented this as part of #1698. I'll update this inputset to use the new method of defining `potcar_functional` once we finalize that PR.",
"@shyuep starting from some code contributed by @mkhorton , I added a unittest that checks the hashes of all `InputSet` .yaml files to address some of the concerns raised above about changing parameters. The test will fail if anything in the .yaml changes, and raise a warning that the user needs to contact you or @mkhorton about the change.",
"Just to clarify, this new hash is *not* something that runs at run-time, it's purely for CI -- I wanted an explicit test that would fail if someone changes an input set .yaml file, to make it more likely we would catch a change if it was part of a large PR.",
"Well, I can confirm that the new `SetChangeCheckTest` works! This is a good safeguard.\r\n\r\nENCUT value was updated to 680 eV per an internal discussion with @mkhorton, @shyamd , and @kristinpersson this morning."
] | 2019-12-11T17:47:17
| 2019-12-17T19:37:04
|
2019-12-17T19:37:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This is a new VASP input set for the SCAN metaGGA functional. Compared to previous input sets, we have adjusted a number of INCAR tags based on internal benchmarking of energy convergence, and utilized some modernized features of VASP such as KSPACING.
This input set is utilized in a forthcoming atomate workflow (see [PR](https://github.com/hackingmaterials/atomate/pull/345))
@mkhorton and @shyamd have been involved in the benchmarking and decision making regarding parameters.
|
{
"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/1708/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1708/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1708",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1708",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1708.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1708.patch",
"merged_at": "2019-12-17T19:37:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1709
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1709/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1709/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1709/events
|
https://github.com/materialsproject/pymatgen/pull/1709
| 538,411,886
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYyMjk4
| 1,709
|
Bump tqdm from 4.40.1 to 4.40.2
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:27:41
| 2019-12-16T14:10:04
|
2019-12-16T14:10:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.40.1 to 4.40.2.
<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.40.2 stable
> - fix `pandas` unhashable func ([#862](https://github-redirect.dependabot.com/tqdm/tqdm/issues/862) -> [#863](https://github-redirect.dependabot.com/tqdm/tqdm/issues/863))
> + add tests
</details>
<details>
<summary>Commits</summary>
- [`571aa7f`](https://github.com/tqdm/tqdm/commit/571aa7f2516efd8f9c811af70ce92dcffab4b286) bump version, merge branch 'devel'
- [`a7c565e`](https://github.com/tqdm/tqdm/commit/a7c565ec64c7add40baeecdae32077c020ef2f35) add pandas unhashable test
- [`d8152a4`](https://github.com/tqdm/tqdm/commit/d8152a4618e6487de4428dcb235413829657035c) fix pandas unhashable func
- See full diff in [compare view](https://github.com/tqdm/tqdm/compare/v4.40.1...v4.40.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.40.1&new-version=4.40.2)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1709/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1709/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1709",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1709",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1709.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1709.patch",
"merged_at": "2019-12-16T14:10:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1710
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1710/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1710/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1710/events
|
https://github.com/materialsproject/pymatgen/pull/1710
| 538,412,058
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYyNDQ1
| 1,710
|
Bump pydocstyle from 5.0.0 to 5.0.1
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:27:59
| 2019-12-16T14:13:34
|
2019-12-16T14:13:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [pydocstyle](https://github.com/PyCQA/pydocstyle) from 5.0.0 to 5.0.1.
<details>
<summary>Changelog</summary>
*Sourced from [pydocstyle's changelog](https://github.com/PyCQA/pydocstyle/blob/master/docs/release_notes.rst).*
> 5.0.1 - December 9th, 2019
> ==========================
>
> Bug Fixes
>
> - Fixed an issue where AttributeError was raised when parsing the parameter section of a class docstring ([#434](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/434), [#436](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/436)).
</details>
<details>
<summary>Commits</summary>
- [`05e6205`](https://github.com/PyCQA/pydocstyle/commit/05e6205630569452fa13799783641153ea6cb7c6) Bump version: 5.0.1rc → 5.0.1
- [`4d27748`](https://github.com/PyCQA/pydocstyle/commit/4d27748f8197ef3558baf8167397961368cd6940) Fix the AttributeError bug when parsing parameter lists in a class docstring ...
- [`d1c06c6`](https://github.com/PyCQA/pydocstyle/commit/d1c06c6b1c606c7b03522e5bc321d62f656e7f62) Bump version: 5.0.0 → 5.0.1rc
- See full diff in [compare view](https://github.com/PyCQA/pydocstyle/compare/5.0.0...5.0.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pydocstyle&package-manager=pip&previous-version=5.0.0&new-version=5.0.1)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1710/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1710/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1710",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1710",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1710.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1710.patch",
"merged_at": "2019-12-16T14:13:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1711
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1711/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1711/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1711/events
|
https://github.com/materialsproject/pymatgen/pull/1711
| 538,412,287
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYyNjQw
| 1,711
|
Bump pytest from 5.3.1 to 5.3.2
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:28:22
| 2019-12-16T17:05:45
|
2019-12-16T17:05:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.3.1 to 5.3.2.
<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.3.2
> No release notes provided.
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
</details>
<details>
<summary>Commits</summary>
- [`7f24cc2`](https://github.com/pytest-dev/pytest/commit/7f24cc2feb87af41e95d2c0aee59fc81a44dbea8) Remove duplicated user from announcement
- [`10fcac7`](https://github.com/pytest-dev/pytest/commit/10fcac7f908b792264c3e6a402aa1aa01345acc4) Preparing release version 5.3.2
- [`8942a05`](https://github.com/pytest-dev/pytest/commit/8942a05cfec4b97d7aa94e55d08e41a08397e78e) Change 4639 from feature to improvement
- [`66c1a12`](https://github.com/pytest-dev/pytest/commit/66c1a120ba42983285d5102237fd973de0c5606e) Bugfix 5430 pass logs to junit report ([#6274](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6274))
- [`8cdf9d4`](https://github.com/pytest-dev/pytest/commit/8cdf9d43a9f277782310bedd7431fad20474085f) Fixes [#6326](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6326): Typo in the Security section docs home page. ([#6327](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6327))
- [`2ddc330`](https://github.com/pytest-dev/pytest/commit/2ddc330b626705fc83a01d87e40d584ab33af625) Fixes [#6326](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6326): Typo in the Security section docs home page.
- [`1c0ab3c`](https://github.com/pytest-dev/pytest/commit/1c0ab3c2a32f7932378a1c37106d082784cb4700) Add 4.6.7 changelog to master (Wait until [#6318](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6318)) ([#6319](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6319))
- [`7ff91d8`](https://github.com/pytest-dev/pytest/commit/7ff91d81277f92a9fa0910133b61f9eb80a0a8c0) Merge pull request [#6313](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6313) from nicoddemus/egg-rewrite-6301
- [`64c71da`](https://github.com/pytest-dev/pytest/commit/64c71daa21ba58ca6e960dc0744b9d7b32ecd633) Add 4.6.7 changelog to master
- [`c7f9fda`](https://github.com/pytest-dev/pytest/commit/c7f9fda42d475a5579aa988d8b491be3de53925b) Fix assertion rewriting module detection for egg dists
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.3.1...5.3.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.3.1&new-version=5.3.2)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1711/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1711/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1711",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1711",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1711.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1711.patch",
"merged_at": "2019-12-16T17:05:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1712
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1712/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1712/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1712/events
|
https://github.com/materialsproject/pymatgen/pull/1712
| 538,412,481
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYyODAy
| 1,712
|
Bump coverage from 4.5.4 to 5.0
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:28:42
| 2019-12-16T16:21:35
|
2019-12-16T16:21:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [coverage](https://github.com/nedbat/coveragepy) from 4.5.4 to 5.0.
<details>
<summary>Changelog</summary>
*Sourced from [coverage's changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst).*
> Version 5.0 --- 2019-12-14
> ==========================
>
> Nothing new beyond 5.0b2.
>
> Version 5.0b2 --- 2019-12-08
> ============================
>
> - An experimental `[run] relative_files` setting tells coverage to store relative file names in the data file. This makes it easier to run tests in one (or many) environments, and then report in another. It has not had much real-world testing, so it may change in incompatible ways in the future.
> - When constructing a coverage.Coverage object, data\_file can be specified as None to prevent writing any data file at all. In previous versions, an explicit data\_file=None argument would use the default of ".coverage". Fixes [issue 871](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/871).
> - Python files run with `-m` now have `__spec__` defined properly. This fixes [issue 745](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/745) (about not being able to run unittest tests that spawn subprocesses), and [issue 838](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/838), which described the problem directly.
> - The `[paths]` configuration section is now ordered. If you specify more than one list of patterns, the first one that matches will be used. Fixes [issue 649](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/649).
> - The .coverage.numbits.register\_sqlite\_functions function now also registers numbits\_to\_nums for use in SQLite queries. Thanks, Simon Willison.
> - Python 3.9a1 is supported.
> - Coverage.py has a mascot: Sleepy Snake <sleepy>.
>
> Version 5.0b1 --- 2019-11-11
> ============================
>
> - The HTML and textual reports now have a `--skip-empty` option that skips files with no statements, notably `__init__.py` files. Thanks, Reya B.
> - Configuration can now be read from [TOML](https://github.com/toml-lang/toml#readme) files. This requires installing coverage.py with the `[toml]` extra. The standard "pyproject.toml" file will be read automatically if no other configuration file is found, with settings in the `[tool.coverage.]` namespace. Thanks to Frazer McLean for implementation and persistence. Finishes [issue 664](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/664).
> - The `[run] note` setting has been deprecated. Using it will result in a warning, and the note will not be written to the data file. The corresponding .CoverageData methods have been removed.
> - The HTML report has been reimplemented (no more table around the source code). This allowed for a better presentation of the context information, hopefully resolving [issue 855](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/855).
> - Added sqlite3 module version information to `coverage debug sys` output.
> - Asking the HTML report to show contexts (`[html] show_contexts=True` or `coverage html --show-contexts`) will issue a warning if there were no contexts measured ([issue 851](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/851)).
>
> Version 5.0a8 --- 2019-10-02
> ============================
>
> - The .CoverageData API has changed how queries are limited to specific contexts. Now you use .CoverageData.set\_query\_context to set a single exact-match string, or .CoverageData.set\_query\_contexts to set a list of regular expressions to match contexts. This changes the command-line `--contexts` option to use regular expressions instead of filename-style wildcards.
>
> Version 5.0a7 --- 2019-09-21
> ============================
>
> - Data can now be "reported" in JSON format, for programmatic use, as requested in [issue 720](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/720). The new `coverage json` command writes raw and summarized data to a JSON file. Thanks, Matt Bachmann.
> - Dynamic contexts are now supported in the Python tracer, which is important for PyPy users. Closes [issue 846](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/846).
> - The compact line number representation introduced in 5.0a6 is called a "numbits." The coverage.numbits module provides functions for working with them.
> - The reporting methods used to permanently apply their arguments to the configuration of the Coverage object. Now they no longer do. The arguments affect the operation of the method, but do not persist.
> - A class named "test\_something" no longer confuses the `test_function` dynamic context setting. Fixes [issue 829](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/829).
> - Fixed an unusual tokenizing issue with backslashes in comments. Fixes [issue 822](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/822).
> - `debug=plugin` didn't properly support configuration or dynamic context plugins, but now it does, closing [issue 834](https://github-redirect.dependabot.com/nedbat/coveragepy/issues/834).
>
> Version 5.0a6 --- 2019-07-16
> ============================
>
> - Reporting on contexts. Big thanks to Stephan Richter and Albertas Agejevas for the contribution.
> - The `--contexts` option is available on the `report` and `html` commands. It's a comma-separated list of shell-style wildcards, selecting the contexts to report on. Only contexts matching one of the wildcards will be included in the report.
> - The `--show-contexts` option for the `html` command adds context information to each covered line. Hovering over the "ctx" marker at the end of the line reveals a list of the contexts that covered the line.
> - Database changes:
> - Line numbers are now stored in a much more compact way. For each file and context, a single binary string is stored with a bit per line number. This greatly improves memory use, but makes ad-hoc use difficult.
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`bde3130`](https://github.com/nedbat/coveragepy/commit/bde31306de4ff2b6e4945683e5deb821c85984e8) Sample html report for 5.0
- [`b92a84c`](https://github.com/nedbat/coveragepy/commit/b92a84c8e5ec9eca615bd5a481b491f6865072a9) Prep for 5.0
- [`5379317`](https://github.com/nedbat/coveragepy/commit/5379317ad73694099b7876797695bc76bd9cdce5) Clarify the connection between subprocesses and --concurrency
- [`eebc1e9`](https://github.com/nedbat/coveragepy/commit/eebc1e9c93f97d03c481336607668e93b926c181) Forgot to mention Sleepy Snake in the changelog
- [`da8aace`](https://github.com/nedbat/coveragepy/commit/da8aaceb4da7c6ba958c6687bbef102800e72065) Better wording on the Sleepy page
- [`abbbd7d`](https://github.com/nedbat/coveragepy/commit/abbbd7dea7ebab412c2a73046436017ce18d277d) Bump version
- [`b68d147`](https://github.com/nedbat/coveragepy/commit/b68d14755fd8882483be1f02e4b96d33ed4c8636) Bumping version before readthedocs works better
- [`225dd7c`](https://github.com/nedbat/coveragepy/commit/225dd7cd63336b90c6e0b55fbe800a9241b3695b) Prep for 5.0b2
- [`aec4473`](https://github.com/nedbat/coveragepy/commit/aec4473cdcf2fdd4acde6a4314ba912f25cb0a55) Sleepy Snake
- [`b4a4626`](https://github.com/nedbat/coveragepy/commit/b4a46264fa0d029591c368ac95af692afc2bf471) A little easier to read in contributing.rst
- Additional commits viewable in [compare view](https://github.com/nedbat/coveragepy/compare/coverage-4.5.4...coverage-5.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=coverage&package-manager=pip&previous-version=4.5.4&new-version=5.0)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1712/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1712/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1712",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1712",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1712.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1712.patch",
"merged_at": "2019-12-16T16:21:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1713
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1713/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1713/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1713/events
|
https://github.com/materialsproject/pymatgen/pull/1713
| 538,412,653
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYyOTU4
| 1,713
|
Bump sympy from 1.4 to 1.5
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:29:00
| 2019-12-16T14:50:18
|
2019-12-16T14:50:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [sympy](https://sympy.org) from 1.4 to 1.5.
[](https://dependabot.com/compatibility-score.html?dependency-name=sympy&package-manager=pip&previous-version=1.4&new-version=1.5)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1713/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1713/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1713",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1713",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1713.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1713.patch",
"merged_at": "2019-12-16T14:50:16Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1714
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1714/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1714/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1714/events
|
https://github.com/materialsproject/pymatgen/pull/1714
| 538,413,078
|
MDExOlB1bGxSZXF1ZXN0MzUzNTYzMzIz
| 1,714
|
Bump ase from 3.18.1 to 3.18.2
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-16T13:29:44
| 2019-12-16T15:13:09
|
2019-12-16T15:13:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [ase](https://gitlab.com/ase/ase) from 3.18.1 to 3.18.2.
<details>
<summary>Changelog</summary>
*Sourced from [ase's changelog](https://gitlab.com/ase/ase/blob/master/CHANGELOG.rst).*
</details>
<details>
<summary>Commits</summary>
- [`87d1492`](https://gitlab.com/ase/ase/commit/87d1492a3706378e74de47aa228782add806c4fd) ASE version 3.18.2
- [`0b60ba8`](https://gitlab.com/ase/ase/commit/0b60ba86c267d51b6d1b422b3ceeaaefdde73558) newrelease script: delete the build/ directory; create release from current b...
- See full diff in [compare view](https://gitlab.com/ase/ase/compare/3.18.1...3.18.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=ase&package-manager=pip&previous-version=3.18.1&new-version=3.18.2)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1714/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1714/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1714",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1714",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1714.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1714.patch",
"merged_at": "2019-12-16T15:13:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1715
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1715/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1715/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1715/events
|
https://github.com/materialsproject/pymatgen/pull/1715
| 538,591,685
|
MDExOlB1bGxSZXF1ZXN0MzUzNzEwOTQz
| 1,715
|
Add fast `Structure.get_neighbor_list` method
|
{
"login": "chc273",
"id": 22353204,
"node_id": "MDQ6VXNlcjIyMzUzMjA0",
"avatar_url": "https://avatars.githubusercontent.com/u/22353204?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chc273",
"html_url": "https://github.com/chc273",
"followers_url": "https://api.github.com/users/chc273/followers",
"following_url": "https://api.github.com/users/chc273/following{/other_user}",
"gists_url": "https://api.github.com/users/chc273/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chc273/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chc273/subscriptions",
"organizations_url": "https://api.github.com/users/chc273/orgs",
"repos_url": "https://api.github.com/users/chc273/repos",
"events_url": "https://api.github.com/users/chc273/events{/privacy}",
"received_events_url": "https://api.github.com/users/chc273/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Fantastic! Thanks @chc273 \r\n\r\nCould you comment a little on the change in the C++ compile args? Is this going to be any easier/more difficult to compile than previously?",
"@mkhorton `c++0x` is an older standard than `c++11`. Some supercomputer platforms (like tscc we are using) are still using the old gcc version that is not compatible with `c++11`. The code I wrote actually does not use new c++ features, and hence the compilation flags can be set to older c++ standards without affecting the results. ",
"Ok, sounds good"
] | 2019-12-16T18:56:40
| 2019-12-16T20:06:13
|
2019-12-16T20:06:13Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added a Structure method to construct neighbor list without using Neighbor class. Previously this is achieved by using `get_all_neighbors` method, which is much slower than the proposed methods. It may become a problem when the structure is very large, e.g., >10,000 atoms.
Here I am adding a new method `get_neighbor_list` to `Structure`, that returns the full information about neighbors without the use of many python native objects. This new method returns a tuple of numpy array `(center_indices, points_indices, offset_vectors, distances)` as the neighbors. Here atom `center_indices[i]` has neighbor atom index `points_indices[i]` that is translated by `offset_vectors[i]` lattice vectors, and the distance between them is `distances[i]`.
For a Mo structure with atom numbers of `1000` ([10, 10, 10] supercell), `10,000` ([10, 10, 100] supercell) and `100,000 ` ([10, 10, 1000] supercells), constructing the neighbor list of radius 4 in this way takes about `0.04`, `0.24` and `2.37` seconds, respectively using 2.7 GHz Dual-Core Intel Core i5. `get_all_neighbors` (not including the time it takes to convert neighbors to numpy format) is about five times slower. I think this method is highly needed for high-performance materials computations, for example, in the construction of force fields, machine learning, etc.
Before a pull request can be merged, the following items must be checked:
- [Y] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [Y] 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.
- [Y ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [ Y] Tests have been added for any new functionality or bug fixes.
- [ Y] All existing 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/1715/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1715/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1715",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1715",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1715.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1715.patch",
"merged_at": "2019-12-16T20:06:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1716
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1716/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1716/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1716/events
|
https://github.com/materialsproject/pymatgen/pull/1716
| 539,390,021
|
MDExOlB1bGxSZXF1ZXN0MzU0Mzc2MTAz
| 1,716
|
determine kspacing and smearing from bandgap in MPScanRelaxSet
|
{
"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 |
[
"@mkhorton @shyamd this is how E_gap maps to KSPACING. The VASP default value is 0.5. Should we cap the value at 0.5, or allow it to increase beyond that? (Would change the k-point density of materials with Egap > 6 eV)\r\n\r\n\r\n",
"I think we'd bound it. Anything over say 0.5 eV, we pin it to 0.44 all the way down to 0.22 for metallic?",
"Thanks @rkingsbury !"
] | 2019-12-18T00:52:52
| 2019-12-19T00:38:20
|
2019-12-19T00:38:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This morning @mkhorton @shyamd @kristinpersson and I decided to compute the KSPACING value based on the bandgap of the input material in our SCAN workflow. At the time I thought this functionality would be part of atomate, but later learned it needs to be in MPScanRelaxSet.
I also identified and corrected a potential bug / unintended behavior when a user tries to override KSPACING, ISMEAR, or SIGMA.
|
{
"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/1716/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1716/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1716",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1716",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1716.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1716.patch",
"merged_at": "2019-12-19T00:38:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1717
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1717/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1717/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1717/events
|
https://github.com/materialsproject/pymatgen/issues/1717
| 539,988,010
|
MDU6SXNzdWU1Mzk5ODgwMTA=
| 1,717
|
Reaction Calculator -- better stoichiometry coefficient balancing
|
{
"login": "mattmcdermott",
"id": 40469694,
"node_id": "MDQ6VXNlcjQwNDY5Njk0",
"avatar_url": "https://avatars.githubusercontent.com/u/40469694?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mattmcdermott",
"html_url": "https://github.com/mattmcdermott",
"followers_url": "https://api.github.com/users/mattmcdermott/followers",
"following_url": "https://api.github.com/users/mattmcdermott/following{/other_user}",
"gists_url": "https://api.github.com/users/mattmcdermott/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mattmcdermott/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mattmcdermott/subscriptions",
"organizations_url": "https://api.github.com/users/mattmcdermott/orgs",
"repos_url": "https://api.github.com/users/mattmcdermott/repos",
"events_url": "https://api.github.com/users/mattmcdermott/events{/privacy}",
"received_events_url": "https://api.github.com/users/mattmcdermott/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 with commit #1718. "
] | 2019-12-18T23:46:21
| 2020-05-22T00:14:16
|
2020-05-22T00:14:16Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The current Reaction class’s stoichiometry/balancing code allows for the automatic shuffling of reactants/products to opposite sides -- or even deleting the reactants/products entirely. While this is occasionally a nice feature for underdetermined systems, it can lead to undesirable/unexpected solutions. For example, when we run:
```
reactants = ["Mn(HO)2", "Li2CO3", "Ni(HO)2", "O2"]
products = ["Li2MnO3", "Li2MnNiO4", "CO2", "H2O"]
reactants = [Composition(r) for r in reactants]
products = [Composition(p) for p in products]
rxn = Reaction(reactants, products)
print(rxn)
```
We get the following reaction:
_2 Mn(HO)2 + 2 Li2CO3 + Ni(HO)2 + O2 -> Li2MnO3 + Li2MnNiO4 + 2 CO2 + 3 H2O_
However, when we simply reverse the reaction via `Reaction(products, reactants)`, we get:
_Li2MnNiO4 + CO2 + 2 H2O -> Mn(HO)2 + Li2CO3 + Ni(HO)2 + 0.5 O2_
In the above example, Li2MnO3 is unexpectedly removed, just by simply changing the direction of the reaction. Albeit not that common, I feel like this is very counterintuitive result to a user.
To fix this issue, I suggest we change the starting constraints and iterate until we find the “best” solution, i.e. the solution which causes the fewest number of swaps/deletions. I am submitting a PR with a proposed fix!
|
{
"login": "mattmcdermott",
"id": 40469694,
"node_id": "MDQ6VXNlcjQwNDY5Njk0",
"avatar_url": "https://avatars.githubusercontent.com/u/40469694?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mattmcdermott",
"html_url": "https://github.com/mattmcdermott",
"followers_url": "https://api.github.com/users/mattmcdermott/followers",
"following_url": "https://api.github.com/users/mattmcdermott/following{/other_user}",
"gists_url": "https://api.github.com/users/mattmcdermott/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mattmcdermott/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mattmcdermott/subscriptions",
"organizations_url": "https://api.github.com/users/mattmcdermott/orgs",
"repos_url": "https://api.github.com/users/mattmcdermott/repos",
"events_url": "https://api.github.com/users/mattmcdermott/events{/privacy}",
"received_events_url": "https://api.github.com/users/mattmcdermott/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1717/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1717/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1718
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1718/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1718/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1718/events
|
https://github.com/materialsproject/pymatgen/pull/1718
| 539,991,480
|
MDExOlB1bGxSZXF1ZXN0MzU0ODc0Nzk1
| 1,718
|
Reaction Calculator -- better stoichiometry/balancing
|
{
"login": "mattmcdermott",
"id": 40469694,
"node_id": "MDQ6VXNlcjQwNDY5Njk0",
"avatar_url": "https://avatars.githubusercontent.com/u/40469694?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mattmcdermott",
"html_url": "https://github.com/mattmcdermott",
"followers_url": "https://api.github.com/users/mattmcdermott/followers",
"following_url": "https://api.github.com/users/mattmcdermott/following{/other_user}",
"gists_url": "https://api.github.com/users/mattmcdermott/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mattmcdermott/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mattmcdermott/subscriptions",
"organizations_url": "https://api.github.com/users/mattmcdermott/orgs",
"repos_url": "https://api.github.com/users/mattmcdermott/repos",
"events_url": "https://api.github.com/users/mattmcdermott/events{/privacy}",
"received_events_url": "https://api.github.com/users/mattmcdermott/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 looks excellent, thanks @mattmcdermott !\r\n\r\nBefore merging could you comment a little on the test changes, e.g. is `test_singular_case` still testing a singular case? It's not clear to me how the old test was correct in any case.",
"@mkhorton Yeah! All changes I made to the tests were because the previous solutions were either not optimal, or in some cases, not even given (i.e. components were changing sides or being deleted more than necessary).\r\n\r\nIt does seems weird in general to create a test which enforces a specific solution when many exist, as in the case of underdetermined systems. At least now though we know it is looking for the best solution, instead of just what is found first when iterating through possible constraints.\r\n\r\nAs for the singular case -- I think the original composition matrix is singular, but as far as I know, this isn't really that special of a case. The Moore-Penrose pseudoinverse will always be defined and unique so it shouldn't really matter.",
"Ok, that makes sense. Thanks for the additional info!",
"Hey @mattmcdermott, not sure why this wasn't caught in CI but there are some missing docstrings that should be added to the ReactionCalculator: https://travis-ci.org/materialsproject/pymatgen/builds/627925624#L2734\r\n\r\nI understand these are not methods you've added, but whenever you touch a file that causes the doc checks for that file to be run.",
"@mkhorton Haha I was wondering about that... thought it was weird that those old functions had none. Should I add docstrings to all the functions? And should I open a new PR or can we tag it into this? ",
"You should open a PR since this has already been merged now",
"Hi @mattmcdermott I noticed you were missing from our developer list, please fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html).",
"@mkhorton Thanks so much -- done! Also I haven't forgotten about the docstrings, it is on my to-do :) "
] | 2019-12-18T23:58:14
| 2020-01-13T22:09:36
|
2019-12-20T22:22:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This PR references the issue described in #1717: i.e. that the stoichiometric coefficient solver in the _Reaction_ class often finds solutions which are unexpected/undesirable.
The fix adds tracking for the `num_errors`, which counts how many components flip sides or are deleted entirely. The `_balance_coeffs()` method loops through different combinations of constraints and keeps track of the best solution (that which minimizes the number of errors).
Note that I use _pinv_ from numpy instead of _lstsq_, however the code functions similarly and is a little easier to follow I think.
Also note that I altered a few tests that were enforcing less than optimal solutions, and added the solutions found by the new method.
Regarding possible increase in computational time -- I am already using this code for high-throughput generation of hundreds of thousands of reactions and it seems to be roughly equivalent timing wise for reactions which have 1,2 reactants going to 1,2 products (this might not hold for much larger reactions).
|
{
"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/1718/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/1718/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1718",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1718",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1718.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1718.patch",
"merged_at": "2019-12-20T22:22:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1719
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1719/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1719/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1719/events
|
https://github.com/materialsproject/pymatgen/pull/1719
| 540,431,764
|
MDExOlB1bGxSZXF1ZXN0MzU1MjQxODM5
| 1,719
|
add missing docstring to symbol in PotcarSingle
|
{
"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!"
] | 2019-12-19T16:48:14
| 2019-12-19T16:58:01
|
2019-12-19T16:57:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Adds a missing docstring to the 'symbol' property of 'PotcarSingle'. Also updates .gitignore to ignore VS code settings files.
|
{
"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/1719/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1719/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1719",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1719",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1719.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1719.patch",
"merged_at": "2019-12-19T16:57:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1720
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1720/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1720/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1720/events
|
https://github.com/materialsproject/pymatgen/pull/1720
| 540,656,810
|
MDExOlB1bGxSZXF1ZXN0MzU1NDM3NzUz
| 1,720
|
Bug fix: remove occasional blank line that makes CHGCAR unreadable
|
{
"login": "LindaHung-TRI",
"id": 35808296,
"node_id": "MDQ6VXNlcjM1ODA4Mjk2",
"avatar_url": "https://avatars.githubusercontent.com/u/35808296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/LindaHung-TRI",
"html_url": "https://github.com/LindaHung-TRI",
"followers_url": "https://api.github.com/users/LindaHung-TRI/followers",
"following_url": "https://api.github.com/users/LindaHung-TRI/following{/other_user}",
"gists_url": "https://api.github.com/users/LindaHung-TRI/gists{/gist_id}",
"starred_url": "https://api.github.com/users/LindaHung-TRI/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/LindaHung-TRI/subscriptions",
"organizations_url": "https://api.github.com/users/LindaHung-TRI/orgs",
"repos_url": "https://api.github.com/users/LindaHung-TRI/repos",
"events_url": "https://api.github.com/users/LindaHung-TRI/events{/privacy}",
"received_events_url": "https://api.github.com/users/LindaHung-TRI/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @LindaHung-TRI !",
"Hi @LindaHung-TRI, I forgot to mention, please do add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html). We want to make sure we credit all contributors, even if they're just small additions or bug fixes."
] | 2019-12-20T00:15:12
| 2020-01-13T22:02:34
|
2019-12-20T01:01:25Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Fix 1: When writing CHGCAR files, if a full line is already output in the last step of the for loop, additional blank line is no longer added.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/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/1720/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1720/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1720",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1720",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1720.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1720.patch",
"merged_at": "2019-12-20T01:01:25Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1721
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1721/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1721/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1721/events
|
https://github.com/materialsproject/pymatgen/issues/1721
| 541,054,710
|
MDU6SXNzdWU1NDEwNTQ3MTA=
| 1,721
|
PhaseDiagram/PDPlotter may rotate endpoints when elements are not explicitly specified.
|
{
"login": "JosephMontoya-TRI",
"id": 45643466,
"node_id": "MDQ6VXNlcjQ1NjQzNDY2",
"avatar_url": "https://avatars.githubusercontent.com/u/45643466?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JosephMontoya-TRI",
"html_url": "https://github.com/JosephMontoya-TRI",
"followers_url": "https://api.github.com/users/JosephMontoya-TRI/followers",
"following_url": "https://api.github.com/users/JosephMontoya-TRI/following{/other_user}",
"gists_url": "https://api.github.com/users/JosephMontoya-TRI/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JosephMontoya-TRI/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JosephMontoya-TRI/subscriptions",
"organizations_url": "https://api.github.com/users/JosephMontoya-TRI/orgs",
"repos_url": "https://api.github.com/users/JosephMontoya-TRI/repos",
"events_url": "https://api.github.com/users/JosephMontoya-TRI/events{/privacy}",
"received_events_url": "https://api.github.com/users/JosephMontoya-TRI/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I don’t have a problem with this. I guess the simplest solution is to add a elements = sorted(elements) somewhere. Feel free to implement, with tests, and submit PR.",
"@JosephMontoya-TRI @montoyjh just checking, this issue is fixed with your PR from a couple of years ago and can be closed right?",
"Yep."
] | 2019-12-20T15:35:42
| 2022-02-25T21:34:54
|
2022-02-25T21:34:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
PhaseDiagram/PDPlotter may rotate endpoints when elements are not explicitly specified.
**To Reproduce**
Steps to reproduce the behavior:
1. Make list of entries
2. PhaseDiagram(entries)
3. PhaseDiagram(entries.shuffle())
4. PDPlot both
5. One may be rotated relative to other
**Expected behavior**
Endpoints of PDPlot to be consistent
**Additional context**
Specifically, this cropped up when we were plotting differences between successive iterations of an algorithm which augmented a list of entries on the same plot. One was rotated, but the endpoints didn't show up. One can remedy this by supplying an explicit list of elements, but it's a bit surprising that you would need to do so for ordering purposes.
|
{
"login": "JosephMontoya-TRI",
"id": 45643466,
"node_id": "MDQ6VXNlcjQ1NjQzNDY2",
"avatar_url": "https://avatars.githubusercontent.com/u/45643466?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JosephMontoya-TRI",
"html_url": "https://github.com/JosephMontoya-TRI",
"followers_url": "https://api.github.com/users/JosephMontoya-TRI/followers",
"following_url": "https://api.github.com/users/JosephMontoya-TRI/following{/other_user}",
"gists_url": "https://api.github.com/users/JosephMontoya-TRI/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JosephMontoya-TRI/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JosephMontoya-TRI/subscriptions",
"organizations_url": "https://api.github.com/users/JosephMontoya-TRI/orgs",
"repos_url": "https://api.github.com/users/JosephMontoya-TRI/repos",
"events_url": "https://api.github.com/users/JosephMontoya-TRI/events{/privacy}",
"received_events_url": "https://api.github.com/users/JosephMontoya-TRI/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1721/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1721/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1722
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1722/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1722/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1722/events
|
https://github.com/materialsproject/pymatgen/pull/1722
| 541,389,484
|
MDExOlB1bGxSZXF1ZXN0MzU2MDQyNTAw
| 1,722
|
Element sorting in Phase Diagram
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2019-12-22T00:30:49
| 2020-01-06T14:15:53
|
2020-01-06T14:15:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Sorts elements determined from entries, if elements are not explicitly specified. Adds test for to ensure that specified element order is respected and that unspecified element orderings result in the same ordering. Addresses #1721 .
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1722/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1722/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1722",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1722",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1722.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1722.patch",
"merged_at": "2020-01-06T14:15:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1723
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1723/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1723/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1723/events
|
https://github.com/materialsproject/pymatgen/pull/1723
| 541,755,937
|
MDExOlB1bGxSZXF1ZXN0MzU2MzI5ODY3
| 1,723
|
Bump coverage from 5.0 to 5.0.1
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-23T13:29:30
| 2019-12-23T14:10:33
|
2019-12-23T14:10:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [coverage](https://github.com/nedbat/coveragepy) from 5.0 to 5.0.1.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst">coverage's changelog</a>.</em></p>
<blockquote>
<h1>Version 5.0.1 --- 2019-12-22</h1>
<ul>
<li>If a 4.x data file is the cause of a "file is not a database" error, then use a more specific error message, "Looks like a coverage 4.x data file, are you mixing versions of coverage?" Helps diagnose the problems described in <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/886">issue 886</a>.</li>
<li>Measurement contexts and relative file names didn't work together, as reported in <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/899">issue 899</a> and <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/900">issue 900</a>. This is now fixed, thanks to David Szotten.</li>
<li>When using <code>coverage run --concurrency=multiprocessing</code>, all data files should be named with parallel-ready suffixes. 5.0 mistakenly named the main process' file with no suffix when using <code>--append</code>. This is now fixed, closing <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/880">issue 880</a>.</li>
<li>Fixed a problem on Windows when the current directory is changed to a different drive (<a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/895">issue 895</a>). Thanks, Olivier Grisel.</li>
<li>Updated Python 3.9 support to 3.9a2.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/nedbat/coveragepy/commit/d2ae0e2d04f77350ff0fb40847089655f2c00362"><code>d2ae0e2</code></a> Prep for 5.0.1</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/7e747a3e2d50138474a0ac5ecc766c9399a27e2b"><code>7e747a3</code></a> Re-order windows CI jobs to get more useful information earlier</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/0d6a8784cdafd46409fe187ad87b7c38772d6d1b"><code>0d6a878</code></a> Detect when a 4.x data file is being read. <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/886">#886</a></li>
<li><a href="https://github.com/nedbat/coveragepy/commit/d66d496b53e3fd8ba891a2704d82e0b6a0be1502"><code>d66d496</code></a> Don't need to check for JSON-era bad-data messages any more</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/77dc37fca441705dd6f8560a3f57cad13ee43302"><code>77dc37f</code></a> Tweak some coverage details of switch_context code</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/cecc5ddc2d1a95223ad708a3dcc27f7a7f4d54b9"><code>cecc5dd</code></a> One more adjustment for Python 3.9a2</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/28c29a72242e76dab658fe07f104961889c85c12"><code>28c29a7</code></a> bpo 39114 broke 3.9, but maybe it's their bug</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/31f7280b5f9a8fcd4b36f23f5b058deee602c4db"><code>31f7280</code></a> Cleanup and changelog for <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/899">#899</a> <a href="https://github-redirect.dependabot.com/nedbat/coveragepy/issues/900">#900</a></li>
<li><a href="https://github.com/nedbat/coveragepy/commit/ade1f2c534d1b85c8b465ce302ab345b316ec3ef"><code>ade1f2c</code></a> fix context reporting for relative_files</li>
<li><a href="https://github.com/nedbat/coveragepy/commit/7dc37728d3ddddd12115bb94c58ad0dc67dcfb3e"><code>7dc3772</code></a> Python 3.9a2 reverted how argv[0] is handled</li>
<li>Additional commits viewable in <a href="https://github.com/nedbat/coveragepy/compare/coverage-5.0...coverage-5.0.1">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=coverage&package-manager=pip&previous-version=5.0&new-version=5.0.1)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1723/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1723/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1723",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1723",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1723.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1723.patch",
"merged_at": "2019-12-23T14:10:31Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1724
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1724/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1724/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1724/events
|
https://github.com/materialsproject/pymatgen/pull/1724
| 541,756,108
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwMDIy
| 1,724
|
Bump phonopy from 1.11.12.121 to 2.4.2
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[
"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [build (ubuntu-latest, 3.6)](https://help.github.com/en/actions)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-23T13:29:50
| 2021-02-13T17:29:09
|
2020-02-12T04:41:14Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [phonopy](http://atztogo.github.io/phonopy/) from 1.11.12.121 to 2.4.2.
[](https://dependabot.com/compatibility-score.html?dependency-name=phonopy&package-manager=pip&previous-version=1.11.12.121&new-version=2.4.2)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"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/1724/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1724/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1724",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1724",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1724.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1724.patch",
"merged_at": "2020-02-12T04:41:14Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1725
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1725/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1725/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1725/events
|
https://github.com/materialsproject/pymatgen/pull/1725
| 541,756,329
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwMjE0
| 1,725
|
Bump mypy from 0.750 to 0.761
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[
"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [continuous-integration/travis-ci/pr](https://travis-ci.org/materialsproject/pymatgen/builds/628727408?utm_source=github_status&utm_medium=notification)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-23T13:30:21
| 2019-12-24T00:14:58
|
2019-12-24T00:14:47Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [mypy](https://github.com/python/mypy) from 0.750 to 0.761.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/python/mypy/commit/f53b718bdf5935443332a43d8c1b448af8b80b57"><code>f53b718</code></a> Bump version to 0.761</li>
<li><a href="https://github.com/python/mypy/commit/54447c6068f13326ec18dd4efb81ae3ab83b5ab4"><code>54447c6</code></a> Bump version to 0.760</li>
<li><a href="https://github.com/python/mypy/commit/ba73352af39a44bd8dbdc03e8c1b4e1c8e613787"><code>ba73352</code></a> Sync typeshed (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8139">#8139</a>)</li>
<li><a href="https://github.com/python/mypy/commit/bbd56278f8b6c2798fe5ae96dbd07c5e1a2ad80d"><code>bbd5627</code></a> Don't mark a module as stale if its children change (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8134">#8134</a>)</li>
<li><a href="https://github.com/python/mypy/commit/a2ab97badc0db97b6d639af0157a12357c12c91d"><code>a2ab97b</code></a> Produce error when assigning Enum or TypedDict as attribute (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8107">#8107</a>)</li>
<li><a href="https://github.com/python/mypy/commit/bc3e9d44aa8f61858ff48b667e38cc5c4f9a317a"><code>bc3e9d4</code></a> [mypyc] Actually increment lambda_counter (<a href="https://github-redirect.dependabot.com/python/mypy/issues/7889">#7889</a>)</li>
<li><a href="https://github.com/python/mypy/commit/29252f853127409780b005aca1e12639a83b14a8"><code>29252f8</code></a> Bugfix/fix failing tests on windows due to relpath (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8094">#8094</a>)</li>
<li><a href="https://github.com/python/mypy/commit/63057d8df78b7e0f0a02058a10291b8edcbcd672"><code>63057d8</code></a> Stubgen: split <a href="https://github.com/abstractproperty">@abstractproperty</a> (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8066">#8066</a>)</li>
<li><a href="https://github.com/python/mypy/commit/4fc7400435460d86277479cbb68f113fcda616f6"><code>4fc7400</code></a> Fix error code of binary operation involving overload (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8124">#8124</a>)</li>
<li><a href="https://github.com/python/mypy/commit/7e65f1e4ed1cb9489bc3fc1fa12fd7659a02e8e6"><code>7e65f1e</code></a> [mypyc] Respect declared metaclasses for non-extension classes (<a href="https://github-redirect.dependabot.com/python/mypy/issues/8119">#8119</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/python/mypy/compare/v0.750...v0.761">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=mypy&package-manager=pip&previous-version=0.750&new-version=0.761)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</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/1725/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1725/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1725",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1725",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1725.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1725.patch",
"merged_at": "2019-12-24T00:14:47Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1726
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1726/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1726/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1726/events
|
https://github.com/materialsproject/pymatgen/pull/1726
| 541,756,596
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwNDU1
| 1,726
|
Bump ase from 3.18.2 to 3.19.0
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-23T13:30:57
| 2019-12-23T15:49:08
|
2019-12-23T15:49:06Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [ase](https://gitlab.com/ase/ase) from 3.18.2 to 3.19.0.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://gitlab.com/ase/ase/blob/master/CHANGELOG.rst">ase's changelog</a>.</em></p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://gitlab.com/ase/ase/commit/fcdb47ceb2905604fc45c07cec1f331869079d12"><code>fcdb47c</code></a> ASE version 3.19.0</li>
<li><a href="https://gitlab.com/ase/ase/commit/6d3c8f5cdaa5af20b6e235d2167c2de2fcfd7c3e"><code>6d3c8f5</code></a> newrelease script: delete the build/ directory; create release from current b...</li>
<li><a href="https://gitlab.com/ase/ase/commit/e32c3cf335d7b3439ed813c0f7bdff0b4f9232ec"><code>e32c3cf</code></a> big update of release notes</li>
<li><a href="https://gitlab.com/ase/ase/commit/9fe18854390079711a314b0ce4bf34109b0eb19a"><code>9fe1885</code></a> Merge branch 'amber_read_coord_fix' into 'master'</li>
<li><a href="https://gitlab.com/ase/ase/commit/8ebf2c86453079ea1cd89888aa11eb1426e7be5c"><code>8ebf2c8</code></a> Merge branch 'default-atoms-tags' into 'master'</li>
<li><a href="https://gitlab.com/ase/ase/commit/3c05510680840289a232708644fcff70ddd962b8"><code>3c05510</code></a> Merge branch 'casedness-of-xc-in-siesta' into 'master'</li>
<li><a href="https://gitlab.com/ase/ase/commit/7f5a15dfb4727af41af5ccb7f95c29eae5a1d2f1"><code>7f5a15d</code></a> case insensitive matching in SIESTA calculator</li>
<li><a href="https://gitlab.com/ase/ase/commit/34340c8d6730df085aee4d64347eda71c3dd83d1"><code>34340c8</code></a> handle occupancies=None</li>
<li><a href="https://gitlab.com/ase/ase/commit/9ae5d64bf26859b3f2241d057db478ceba4ccd90"><code>9ae5d64</code></a> python compatability</li>
<li><a href="https://gitlab.com/ase/ase/commit/fb600dbc7517b9c9ada96ac6a5a8dc750a6284bc"><code>fb600db</code></a> set atom tags only for partial occupancies</li>
<li>Additional commits viewable in <a href="https://gitlab.com/ase/ase/compare/3.18.2...3.19.0">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=ase&package-manager=pip&previous-version=3.18.2&new-version=3.19.0)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1726/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1726/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1726",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1726",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1726.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1726.patch",
"merged_at": "2019-12-23T15:49:06Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1727
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1727/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1727/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1727/events
|
https://github.com/materialsproject/pymatgen/pull/1727
| 541,756,624
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwNDc4
| 1,727
|
Bump tqdm from 4.40.2 to 4.41.0
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-23T13:31:01
| 2019-12-23T16:30:09
|
2019-12-23T16:30:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.40.2 to 4.41.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/tqdm/tqdm/releases">tqdm's releases</a>.</em></p>
<blockquote>
<h2>tqdm v4.41.0 stable</h2>
<ul>
<li>trim on <code>ncols</code> overflow with ANSI handling (<a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/850">#850</a>, <a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/716">#716</a> <- <a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/690">#690</a>)</li>
<li>add <code>notebook.reset()</code> (<a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/864">#864</a>)</li>
<li>add <code>keras.TqdmCallback</code> (<a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/867">#867</a> <- <a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/835">#835</a>)</li>
<li>documentation updates
<ul>
<li>document newly added features (above)</li>
<li>notebook <code>ncols</code> percentage/pixels (<a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/276">#276</a>)</li>
</ul>
</li>
<li>test updates
<ul>
<li>test newly added features (above)</li>
<li>add CI for <code>win</code> and <code>osx</code> (<a href="https://github-redirect.dependabot.com/tqdm/tqdm/issues/841">#841</a>)</li>
<li><code>py2</code> threading</li>
</ul>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/tqdm/tqdm/commit/194b9261eab5fc2bcce45d2c536931e3453e0fbb"><code>194b926</code></a> bump version, merge branch 'devel'</li>
<li><a href="https://github.com/tqdm/tqdm/commit/b7dcfbf20eb3297d56b86773399f2c2445e2cd56"><code>b7dcfbf</code></a> fix batch scaling</li>
<li><a href="https://github.com/tqdm/tqdm/commit/3c42b02f50d7c090538258891d7600f6987f4d24"><code>3c42b02</code></a> better keras tests</li>
<li><a href="https://github.com/tqdm/tqdm/commit/1435d102be858f28a07c89aaf55fe3d76694ef31"><code>1435d10</code></a> refix py2 tests</li>
<li><a href="https://github.com/tqdm/tqdm/commit/b45f24868d1f6faffe718f94092e1a15ab676aa3"><code>b45f248</code></a> document keras <code>fit(verbose=0)</code></li>
<li><a href="https://github.com/tqdm/tqdm/commit/69699dadda558edfdc68012499e48e862f393300"><code>69699da</code></a> Merge branch 'keras' into devel</li>
<li><a href="https://github.com/tqdm/tqdm/commit/dadb81732d99a39948a08a1439d5e1c77eb65453"><code>dadb817</code></a> minor tidy</li>
<li><a href="https://github.com/tqdm/tqdm/commit/aa7e631eddf453189a066ae128314ef046e3c304"><code>aa7e631</code></a> keras notebook auto-epochs</li>
<li><a href="https://github.com/tqdm/tqdm/commit/8431d2c58b9e91db01b7af858a53ff06ec9d02a0"><code>8431d2c</code></a> patch py2 threading tests</li>
<li><a href="https://github.com/tqdm/tqdm/commit/133f2a6fae14dbbb30da7539bbe82a65656c7467"><code>133f2a6</code></a> CI test keras</li>
<li>Additional commits viewable in <a href="https://github.com/tqdm/tqdm/compare/v4.40.2...v4.41.0">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.40.2&new-version=4.41.0)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1727/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1727/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1727",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1727",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1727.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1727.patch",
"merged_at": "2019-12-23T16:30:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1728
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1728/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1728/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1728/events
|
https://github.com/materialsproject/pymatgen/pull/1728
| 541,756,942
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwNzU4
| 1,728
|
Bump scipy from 1.3.3 to 1.4.1
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[
"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [build (ubuntu-latest, 3.6)](https://help.github.com/en/actions)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-23T13:31:40
| 2019-12-24T00:14:42
|
2019-12-24T00:14:34Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [scipy](https://github.com/scipy/scipy) from 1.3.3 to 1.4.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
<blockquote>
<h1>SciPy 1.4.1 Release Notes</h1>
<p>SciPy <code>1.4.1</code> is a bug-fix release with no new features
compared to <code>1.4.0</code>. Importantly, it aims to fix a problem
where an older version of <code>pybind11</code> may cause a segmentation
fault when imported alongside incompatible libraries.</p>
<h1>Authors</h1>
<ul>
<li>Ralf Gommers</li>
<li>Tyler Reddy</li>
</ul>
<h1>SciPy 1.4.0 Release Notes</h1>
<p>SciPy <code>1.4.0</code> is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with <code>python -Wd</code> and check for <code>DeprecationWarning</code> s).
Our development attention will now shift to bug-fix releases on the
1.4.x branch, and on adding new features on the master branch.</p>
<p>This release requires Python <code>3.5+</code> and NumPy <code>>=1.13.3</code> (for Python <code>3.5</code>, <code>3.6</code>),
<code>>=1.14.5</code> (for Python <code>3.7</code>), <code>>= 1.17.3</code> (for Python <code>3.8</code>)</p>
<p>For running on PyPy, PyPy3 <code>6.0+</code> and NumPy <code>1.15.0</code> are required.</p>
<h2>Highlights of this release</h2>
<ul>
<li>a new submodule, <code>scipy.fft</code>, now supersedes <code>scipy.fftpack</code>; this
means support for <code>long double</code> transforms, faster multi-dimensional
transforms, improved algorithm time complexity, release of the global
intepreter lock, and control over threading behavior</li>
<li>support for <code>pydata/sparse</code> arrays in <code>scipy.sparse.linalg</code></li>
<li>substantial improvement to the documentation and functionality of
several <code>scipy.special</code> functions, and some new additions</li>
<li>the generalized inverse Gaussian distribution has been added to
<code>scipy.stats</code></li>
<li>an implementation of the Edmonds-Karp algorithm in
<code>scipy.sparse.csgraph.maximum_flow</code></li>
<li><code>scipy.spatial.SphericalVoronoi</code> now supports n-dimensional input,
has linear memory complexity, improved performance, and
supports single-hemisphere generators</li>
</ul>
</tr></table> ... (truncated)
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/scipy/scipy/commit/adc4f4f7bab120ccfab9383aba272954a0a12fb0"><code>adc4f4f</code></a> REL: SciPy 1.4.1 release commit</li>
<li><a href="https://github.com/scipy/scipy/commit/470c16d34603122c95f9bf0fe1bb938c93a2bb11"><code>470c16d</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/scipy/scipy/issues/11240">#11240</a> from tylerjereddy/treddy_prep_141</li>
<li><a href="https://github.com/scipy/scipy/commit/87b5c3084e3513467f4a8fc7db1ec405e3c1a85d"><code>87b5c30</code></a> DOC: 1.4.1 release notes revision</li>
<li><a href="https://github.com/scipy/scipy/commit/29bf2cdbed4fd7a328e45764abb1b07d025f2859"><code>29bf2cd</code></a> BLD: update minimum pybind11 version to 2.4.0.</li>
<li><a href="https://github.com/scipy/scipy/commit/d45fb7e4389cf952a48efc399e3955b8e5f06718"><code>d45fb7e</code></a> MAINT, REL: prepare for SciPy 1.4.1</li>
<li><a href="https://github.com/scipy/scipy/commit/f533e9103e249ac56654626621aca3ec1bffff0e"><code>f533e91</code></a> REL: set version to 1.4.0</li>
<li><a href="https://github.com/scipy/scipy/commit/2d85bb2876daec08a3ad0a097268e6b3d464b8fd"><code>2d85bb2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/scipy/scipy/issues/11221">#11221</a> from tylerjereddy/scipy-140-rel-prep</li>
<li><a href="https://github.com/scipy/scipy/commit/c705210bbe79ab9ad242cdfaa184f12621c7790a"><code>c705210</code></a> DOC: update 1.4.0 release notes</li>
<li><a href="https://github.com/scipy/scipy/commit/be5fe99a8bf3bc79162d82b1b06e4228025e983f"><code>be5fe99</code></a> BUG: sparse.linalg: mistake in unsymm. real shift-invert ARPACK eigenvalue se...</li>
<li><a href="https://github.com/scipy/scipy/commit/119bf01c2d2581a8b4007b6babd4437df888887e"><code>119bf01</code></a> TST: Bump up tolerance for test_maxiter_worsening</li>
<li>Additional commits viewable in <a href="https://github.com/scipy/scipy/compare/v1.3.3...v1.4.1">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=scipy&package-manager=pip&previous-version=1.3.3&new-version=1.4.1)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</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/1728/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1728/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1728",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1728",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1728.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1728.patch",
"merged_at": "2019-12-24T00:14:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1729
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1729/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1729/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1729/events
|
https://github.com/materialsproject/pymatgen/pull/1729
| 541,757,165
|
MDExOlB1bGxSZXF1ZXN0MzU2MzMwOTUx
| 1,729
|
Bump numpy from 1.17.4 to 1.18.0
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%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 |
[] | 2019-12-23T13:32:07
| 2019-12-23T15:16:24
|
2019-12-23T15:16:22Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [numpy](https://github.com/numpy/numpy) from 1.17.4 to 1.18.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.18.0</h2>
<h1>NumPy NumPy 1.18.0 Release Notes</h1>
<p>In addition to the usual bug fixes, this NumPy release cleans up and
documents the new random C-API, expires a large number of old
deprecations, and improves the appearance of the documentation. The
Python versions supported are 3.5-3.8. This is the last NumPy release
series that will support Python 3.5.</p>
<p>Downstream developers should use Cython >= 0.29.14 for Python 3.8
support and OpenBLAS >= 3.7 to avoid problems on the Skylake
architecture.</p>
<h2>Highlights</h2>
<ul>
<li>The C-API for <code>numpy.random</code> has been defined and documented.</li>
<li>Basic infrastructure for linking with 64 bit BLAS and LAPACK
libraries.</li>
<li>Many documentation improvements.</li>
</ul>
<h2>New functions</h2>
<h3>Multivariate hypergeometric distribution added to <code>numpy.random</code></h3>
<p>The method <code>multivariate_hypergeometric</code> has been added to the class
[numpy.random.Generator]{.title-ref}. This method generates random
variates from the multivariate hypergeometric probability distribution.
(<a href="https://github-redirect.dependabot.com/numpy/numpy/pull/13794">gh-13794</a>)</p>
<h2>Deprecations</h2>
<h3><code>np.fromfile</code> and <code>np.fromstring</code> will error on bad data</h3>
<p>In future numpy releases, the functions <code>np.fromfile</code> and
<code>np.fromstring</code> will throw an error when parsing bad data. This will now
give a <code>DeprecationWarning</code> where previously partial or even invalid
data was silently returned. This deprecation also affects the C defined
functions <code>PyArray_FromString</code> and <code>PyArray_FromFile</code>
(<a href="https://github-redirect.dependabot.com/numpy/numpy/pull/13605">gh-13605</a>)</p>
<h3>Deprecate non-scalar arrays as fill values in <code>ma.fill_value</code></h3>
<p>Setting a <code>MaskedArray.fill_value</code> to a non-scalar array is deprecated
since the logic to broadcast the fill value to the array is fragile,
especially when slicing.
(<a href="https://github-redirect.dependabot.com/numpy/numpy/pull/13698">gh-13698</a>)</p>
</tr></table> ... (truncated)
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/numpy/numpy/commit/2410c6d0a63cb56455fc9ab6affcf1a776c82134"><code>2410c6d</code></a> REL: NumPy 1.18.0 release.</li>
<li><a href="https://github.com/numpy/numpy/commit/457b4302ed997e7e6a5470d49ca45237d095c269"><code>457b430</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/15146">#15146</a> from charris/prepare-1.18.0-release</li>
<li><a href="https://github.com/numpy/numpy/commit/b0913d12a7df0f624bf1b152a47ba08b018f23b3"><code>b0913d1</code></a> REL: Prepare for 1.18.0 release.</li>
<li><a href="https://github.com/numpy/numpy/commit/791bbba554410e9afb1502e26e819296d08d5c7e"><code>791bbba</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/15114">#15114</a> from charris/backport-15069</li>
<li><a href="https://github.com/numpy/numpy/commit/ed41774bbf24cfaa934672a969b042c82d5c6125"><code>ed41774</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/15113">#15113</a> from charris/backport-15106</li>
<li><a href="https://github.com/numpy/numpy/commit/912a9ccbac09eca47283b2059cfe85fbd5f3b83a"><code>912a9cc</code></a> DOC: explain NPY_*_ILP64_ORDER default values</li>
<li><a href="https://github.com/numpy/numpy/commit/5cb81304441d2e2e89a286d57b6414a1ca69e6f5"><code>5cb8130</code></a> DOC: adjust ILP64 openblas release note</li>
<li><a href="https://github.com/numpy/numpy/commit/97610ffa39f5a8114e3b143a06890bde79c0b35a"><code>97610ff</code></a> DOC: site.cfg: add note about 64-bit openblas library names</li>
<li><a href="https://github.com/numpy/numpy/commit/9466d31bd846e47f14ba0f22087cd7c420589a1e"><code>9466d31</code></a> BUG: core: use blas_ilp64 also for *_matmul, *_dot, and *_vdot</li>
<li><a href="https://github.com/numpy/numpy/commit/8d64296510d5b95ba696fd05bb861cf7d6bf9c46"><code>8d64296</code></a> DOC: document 64-bit BLAS/LAPACK build-time variables</li>
<li>Additional commits viewable in <a href="https://github.com/numpy/numpy/compare/v1.17.4...v1.18.0">compare view</a></li>
</ul>
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=numpy&package-manager=pip&previous-version=1.17.4&new-version=1.18.0)
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)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (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)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
- Update frequency (including time of day and day of week)
- Pull request limits (per update run and/or open at any time)
- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
</details>
|
{
"login": "dependabot-preview[bot]",
"id": 27856297,
"node_id": "MDM6Qm90Mjc4NTYyOTc=",
"avatar_url": "https://avatars.githubusercontent.com/in/2141?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot-preview%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot-preview",
"followers_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot-preview%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1729/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1729/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1729",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1729",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1729.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1729.patch",
"merged_at": "2019-12-23T15:16:22Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1730
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1730/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1730/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1730/events
|
https://github.com/materialsproject/pymatgen/issues/1730
| 543,513,205
|
MDU6SXNzdWU1NDM1MTMyMDU=
| 1,730
|
Add new spacegroup names
|
{
"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 |
[
"Thanks, I pushed a fix to include all renames of the \"e\" operation and added tests. Let me know if there are other issues."
] | 2019-12-29T18:32:38
| 2019-12-30T01:52:33
|
2019-12-30T01:51:56Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
In `pymatgen/symmetry/symm_data.json`, there is the `Cmma` spacegroup (num. 67), but this spacegroup has [been renamed](https://hal.archives-ouvertes.fr/hal-00963925/document) (see top of page 00006-p.26) to `Cmme`, which is not found in the json file. Similarly, there is support for `Ccca` (num. 68), but this spacegroup has been renamed `Ccce`, which is not supported. Interestingly, spacegroup num. 64 is included with its new name of `Cmce`, but its old name of `Cmca` is not included as a possible synonym.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1730/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1730/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1731
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1731/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1731/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1731/events
|
https://github.com/materialsproject/pymatgen/pull/1731
| 545,221,293
|
MDExOlB1bGxSZXF1ZXN0MzU5MTY4MDcy
| 1,731
|
add potcar_spec option to write_input
|
{
"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 |
[
"How about you remove the existing `write_spec` method (which hasn't been there long in any case) and add a `zip` flag to `write_input` also?\r\n\r\nThe `write_spec` was added to formalize some functionality that previously existed in Materials Project, but was only present in the website code, and since pymatgen has an option to reconstruct from a spec (via its command-line interface) it seemed to make sense to have it here.",
"Otherwise this looks good.",
"Great, thanks!"
] | 2020-01-04T01:03:50
| 2020-01-07T17:42:26
|
2020-01-06T19:32:25Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Adds a boolean `potcar_spec` option to the `write_input` method of a `VaspInputSet`. When this option is enabled, `write_input` generates a POTCAR.spec file rather than a POTCAR file (similar to the existing `write_spec` method, which outputs a .zip file containing all the inputs.) The purpose of this option is to facilitate sharing of inputs and automated testing in environments where POTCAR files are not available due to licensing.
In this particular case, I developed some tests for a new atomate workflow in which the input set utilized POTCAR files that are not distributed with pymatgen (see https://github.com/hackingmaterials/atomate/pull/345). It was not possible for the CI testing to call `write_input` on my inputset because of the missing POTCARs. A similar issue affects some of the Ferroelectric workflow tests in atomate.
With this new option in pymatgen, a powerup can be added to atomate to enable the `potcar_spec` option in unittests and avoid problems with missing POTCARs. The existing `write_spec` method is less desirable for this because it outputs a zip file rather than just writing the files into a directory.
@utf and @computron were consulted on this solution.
|
{
"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/1731/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1731/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1731",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1731",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1731.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1731.patch",
"merged_at": "2020-01-06T19:32:25Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1732
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1732/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1732/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1732/events
|
https://github.com/materialsproject/pymatgen/pull/1732
| 547,367,589
|
MDExOlB1bGxSZXF1ZXN0MzYwODY3MTYw
| 1,732
|
Connectivity analysis using chemenv
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-01-09T09:52:07
| 2020-01-09T19:20:33
|
2020-01-09T19:20:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Connectivity of environments. Allows to target specific environments in order e.g. to find isolated columns/planes of a given type of environment.
Unit tests and documentation for this connectivity analysis.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1732/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1732/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1732",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1732",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1732.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1732.patch",
"merged_at": "2020-01-09T19:20:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1733
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1733/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1733/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1733/events
|
https://github.com/materialsproject/pymatgen/pull/1733
| 547,611,236
|
MDExOlB1bGxSZXF1ZXN0MzYxMDY4NTgz
| 1,733
|
Added horizontal line in DosPlotter
|
{
"login": "uthpalaherath",
"id": 28810161,
"node_id": "MDQ6VXNlcjI4ODEwMTYx",
"avatar_url": "https://avatars.githubusercontent.com/u/28810161?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/uthpalaherath",
"html_url": "https://github.com/uthpalaherath",
"followers_url": "https://api.github.com/users/uthpalaherath/followers",
"following_url": "https://api.github.com/users/uthpalaherath/following{/other_user}",
"gists_url": "https://api.github.com/users/uthpalaherath/gists{/gist_id}",
"starred_url": "https://api.github.com/users/uthpalaherath/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/uthpalaherath/subscriptions",
"organizations_url": "https://api.github.com/users/uthpalaherath/orgs",
"repos_url": "https://api.github.com/users/uthpalaherath/repos",
"events_url": "https://api.github.com/users/uthpalaherath/events{/privacy}",
"received_events_url": "https://api.github.com/users/uthpalaherath/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-01-09T17:13:25
| 2020-01-09T17:21:40
|
2020-01-09T17:21:21Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Added a horizontal line in DosPlotter. This is helpful when we have spin polarized DOS.
|
{
"login": "uthpalaherath",
"id": 28810161,
"node_id": "MDQ6VXNlcjI4ODEwMTYx",
"avatar_url": "https://avatars.githubusercontent.com/u/28810161?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/uthpalaherath",
"html_url": "https://github.com/uthpalaherath",
"followers_url": "https://api.github.com/users/uthpalaherath/followers",
"following_url": "https://api.github.com/users/uthpalaherath/following{/other_user}",
"gists_url": "https://api.github.com/users/uthpalaherath/gists{/gist_id}",
"starred_url": "https://api.github.com/users/uthpalaherath/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/uthpalaherath/subscriptions",
"organizations_url": "https://api.github.com/users/uthpalaherath/orgs",
"repos_url": "https://api.github.com/users/uthpalaherath/repos",
"events_url": "https://api.github.com/users/uthpalaherath/events{/privacy}",
"received_events_url": "https://api.github.com/users/uthpalaherath/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1733/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1733/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1733",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1733",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1733.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1733.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1734
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1734/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1734/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1734/events
|
https://github.com/materialsproject/pymatgen/pull/1734
| 547,620,613
|
MDExOlB1bGxSZXF1ZXN0MzYxMDc2Mjgw
| 1,734
|
DOS Horizontal Line
|
{
"login": "uthpalaherath",
"id": 28810161,
"node_id": "MDQ6VXNlcjI4ODEwMTYx",
"avatar_url": "https://avatars.githubusercontent.com/u/28810161?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/uthpalaherath",
"html_url": "https://github.com/uthpalaherath",
"followers_url": "https://api.github.com/users/uthpalaherath/followers",
"following_url": "https://api.github.com/users/uthpalaherath/following{/other_user}",
"gists_url": "https://api.github.com/users/uthpalaherath/gists{/gist_id}",
"starred_url": "https://api.github.com/users/uthpalaherath/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/uthpalaherath/subscriptions",
"organizations_url": "https://api.github.com/users/uthpalaherath/orgs",
"repos_url": "https://api.github.com/users/uthpalaherath/repos",
"events_url": "https://api.github.com/users/uthpalaherath/events{/privacy}",
"received_events_url": "https://api.github.com/users/uthpalaherath/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thank you!",
"Thanks @uthpalah ! Make sure to add your name to [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can credit you appropriately in the [pymatgen docs](https://pymatgen.org/team.html). We want to make sure we credit all contributors, even if it's just a small addition."
] | 2020-01-09T17:32:24
| 2020-01-10T23:35:20
|
2020-01-09T19:12:46Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Added a horizontal line at y=0 for the DOS plotter. This is helpful when we have spin polarized DOS plots.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1734/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1734/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1734",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1734",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1734.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1734.patch",
"merged_at": "2020-01-09T19:12:46Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1735
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1735/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1735/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1735/events
|
https://github.com/materialsproject/pymatgen/pull/1735
| 548,987,092
|
MDExOlB1bGxSZXF1ZXN0MzYyMTYzMTY3
| 1,735
|
Fixed minor issue in connected_components.
|
{
"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 |
[] | 2020-01-13T15:01:09
| 2020-01-15T15:35:44
|
2020-01-15T15:35:44Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Bad check on a peculiar case (which in the latest version of the connected component code, could actually not occur anymore) that was actually wrong in other cases. => removed that check.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1735/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1735/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1735",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1735",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1735.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1735.patch",
"merged_at": "2020-01-15T15:35:44Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1736
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1736/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1736/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1736/events
|
https://github.com/materialsproject/pymatgen/pull/1736
| 550,455,137
|
MDExOlB1bGxSZXF1ZXN0MzYzMzU4OTMx
| 1,736
|
Refactor write_input() when potcar_spec=True
|
{
"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 |
[] | 2020-01-15T22:03:11
| 2020-02-18T21:28:23
|
2020-01-17T22:37:45Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This commit refactors 'write_input' so that 'get_vasp_input' is not called when `write_spec` is True. Avoiding the call to `get_vasp_input` is important for testing in systems where no POTCARs are installed. @utf was consulted on this fix as well. See https://github.com/hackingmaterials/atomate/pull/345
|
{
"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/1736/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/1736/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1736",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1736",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1736.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1736.patch",
"merged_at": "2020-01-17T22:37:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1737
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1737/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1737/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1737/events
|
https://github.com/materialsproject/pymatgen/issues/1737
| 552,356,465
|
MDU6SXNzdWU1NTIzNTY0NjU=
| 1,737
|
Add optional n parameters to all "Get neighbours" functions in structure
|
{
"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 |
[
"While this is possible, but it would be highly inefficient since it is not possible to a priori know what r should be to get n neigbors. The easier way is simply to use `nn = get_all_neighbors(..)` with a reasonable r (say 5A), and then just take the first n neighbors. E.g., `nn[:n]`.",
"@shyuep we could add that functionality as a convenience method (e.g. pick r, trim the list)? I can see why people might find it useful. However, *exactly* n sites would be impossible to guarantee. N neighbor shells might be more generally useful.",
"@mkhorton I am in general not supportive of convenience methods that implement a one-liner in python (it is literally just nn[:n] as I wrote, since the nn returned is in increasing order of distance), unless it is supremely unintuitive for people to figure out and is used by > 80% of people. \r\n\r\nAs for N neighbor shells, that is potentially useful but non-trivial to implement. You'd have to use some form of clustering (similar to what was used in determining surface sites) because atoms that are r and r+-0.001 A should be considered in the same shell due to numerical considerations. That delta tolerance is non-trivial. Scipy cluster can do it of course. Not clear how many people would use it.",
"We might be able to add on N neighbor shells to the NearNeighbor class, i.e. define shells by number of bonds, rather than geometric distance. For use cases, I've see this for extracting clusters from a larger supercell e.g. for multiscale QM/MM simulations etc. \r\n\r\nFair point on the convenience method, let's leave that alone then."
] | 2020-01-20T15:07:10
| 2020-01-21T00:51:20
|
2020-01-20T15:41:37Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello
As it stands there are many methods to get all sites within a radius r of some co-ordinates / site in a crystal. I notice that there is no way to specify 'n' instead where r is chosen to give exactly n sites. this functionality seems intuitive and I imagine fairly easy to add would it be possible to include this in an update?
Thanks
Mike
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1737/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1737/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1738
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1738/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1738/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1738/events
|
https://github.com/materialsproject/pymatgen/issues/1738
| 553,318,115
|
MDU6SXNzdWU1NTMzMTgxMTU=
| 1,738
|
Cython wrapper problem for zeo++
|
{
"login": "ws517037749",
"id": 43861983,
"node_id": "MDQ6VXNlcjQzODYxOTgz",
"avatar_url": "https://avatars.githubusercontent.com/u/43861983?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ws517037749",
"html_url": "https://github.com/ws517037749",
"followers_url": "https://api.github.com/users/ws517037749/followers",
"following_url": "https://api.github.com/users/ws517037749/following{/other_user}",
"gists_url": "https://api.github.com/users/ws517037749/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ws517037749/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ws517037749/subscriptions",
"organizations_url": "https://api.github.com/users/ws517037749/orgs",
"repos_url": "https://api.github.com/users/ws517037749/repos",
"events_url": "https://api.github.com/users/ws517037749/events{/privacy}",
"received_events_url": "https://api.github.com/users/ws517037749/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-01-22T05:28:50
| 2020-01-30T00:25:30
|
2020-01-30T00:25:30Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
For Macos version at or than 10.15, the voronoi and zeo++ could be compiled successfully but could not be wrapped
**To Reproduce**
Steps to reproduce the behavior:
mkdir Voro++
mkdir Voro++/voro
cd Voro++/voro
svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk
cd trunk
make
mkdir Zeo++
mkdir Zeo++/zeo
cd Zeo++/zeo
svn checkout --username anonsvn https://code.lbl.gov/svn/zeo/trunk # password is 'anonsvn'
cd trunk
make dylib
pip install cython
cd cython_wrapper
python setup_alt.py develop
**Expected behavior**
Any modification to the setup.py or other actions could be taken to include the zeo++ function into python
A**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: Macos
- Version [Catalina 10.15.2]
**Additional context**
I try to find solutions online but it seems that the new-version gcc in Mac lack stdlibc++ and would use libc++ standard library instead, the compiled file is executable for voronoi and zeo++ but failed to be wrapped in cython
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1738/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1738/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1739
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1739/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1739/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1739/events
|
https://github.com/materialsproject/pymatgen/pull/1739
| 553,631,592
|
MDExOlB1bGxSZXF1ZXN0MzY1OTI5Mjkx
| 1,739
|
automatic setting for NEDOS in MPNonSCFSet
|
{
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fraricci/followers",
"following_url": "https://api.github.com/users/fraricci/following{/other_user}",
"gists_url": "https://api.github.com/users/fraricci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fraricci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fraricci/subscriptions",
"organizations_url": "https://api.github.com/users/fraricci/orgs",
"repos_url": "https://api.github.com/users/fraricci/repos",
"events_url": "https://api.github.com/users/fraricci/events{/privacy}",
"received_events_url": "https://api.github.com/users/fraricci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-01-22T15:53:06
| 2020-01-22T16:00:27
|
2020-01-22T16:00:27Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
As discussed with @mkhorton, here an implemention of
an automatic setting for NEDOS for "uniform" mode in MPNonSCFSet.
It reads the max and min of eigenvalues from previous vasprun and use
a default energy step, called dedos, set at 0.005eV.
It works setting nedos=0 in from_prev_calc() method:
mpset = MPNonSCFSet.from_prev_calc(prev_static_dir,mode="uniform",nedos=0)
Let me know if it's ok or it need to be implemented differently.
|
{
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fraricci/followers",
"following_url": "https://api.github.com/users/fraricci/following{/other_user}",
"gists_url": "https://api.github.com/users/fraricci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fraricci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fraricci/subscriptions",
"organizations_url": "https://api.github.com/users/fraricci/orgs",
"repos_url": "https://api.github.com/users/fraricci/repos",
"events_url": "https://api.github.com/users/fraricci/events{/privacy}",
"received_events_url": "https://api.github.com/users/fraricci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1739/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1739/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1739",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1739",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1739.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1739.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1740
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1740/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1740/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1740/events
|
https://github.com/materialsproject/pymatgen/pull/1740
| 553,637,061
|
MDExOlB1bGxSZXF1ZXN0MzY1OTMzODc1
| 1,740
|
Automatic setting for NEDOS in MPNonSCFSet
|
{
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fraricci/followers",
"following_url": "https://api.github.com/users/fraricci/following{/other_user}",
"gists_url": "https://api.github.com/users/fraricci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fraricci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fraricci/subscriptions",
"organizations_url": "https://api.github.com/users/fraricci/orgs",
"repos_url": "https://api.github.com/users/fraricci/repos",
"events_url": "https://api.github.com/users/fraricci/events{/privacy}",
"received_events_url": "https://api.github.com/users/fraricci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Many thanks @fraricci ",
"Seems there are failing tests.",
"Merging the master to my auto_nedos branch deleted my changes.\r\nI pushed back the new features in auto_nedos branch. \r\nTests were passing in my computer. They should pass here too now."
] | 2020-01-22T16:01:37
| 2020-01-29T00:41:23
|
2020-01-29T00:41:23Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
As discussed with @mkhorton, here an implemention of
an automatic setting for NEDOS for "uniform" mode in MPNonSCFSet.
It reads the max and min of eigenvalues from previous vasprun and use
a default energy step, called dedos, set at 0.005eV.
It works setting nedos=0 in from_prev_calc() method:
mpset = MPNonSCFSet.from_prev_calc(prev_static_dir,mode="uniform",nedos=0)
Let me know if it's ok or it need to be implemented differently.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1740/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1740/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1740",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1740",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1740.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1740.patch",
"merged_at": "2020-01-29T00:41:23Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1741
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1741/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1741/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1741/events
|
https://github.com/materialsproject/pymatgen/pull/1741
| 553,641,266
|
MDExOlB1bGxSZXF1ZXN0MzY1OTM3NDIw
| 1,741
|
Isym uniform bug fix
|
{
"login": "fraricci",
"id": 17427517,
"node_id": "MDQ6VXNlcjE3NDI3NTE3",
"avatar_url": "https://avatars.githubusercontent.com/u/17427517?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fraricci",
"html_url": "https://github.com/fraricci",
"followers_url": "https://api.github.com/users/fraricci/followers",
"following_url": "https://api.github.com/users/fraricci/following{/other_user}",
"gists_url": "https://api.github.com/users/fraricci/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fraricci/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fraricci/subscriptions",
"organizations_url": "https://api.github.com/users/fraricci/orgs",
"repos_url": "https://api.github.com/users/fraricci/repos",
"events_url": "https://api.github.com/users/fraricci/events{/privacy}",
"received_events_url": "https://api.github.com/users/fraricci/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks @fraricci! Can we use ISYM = 2 as this should be more efficient. See https://www.vasp.at/wiki/index.php/ISYM",
"I am fine with this, but please implement tests.",
"@utf , thanks for the suggestion, that's preferable indeed.\r\n@shyuep test on isym added as well.",
"Thanks @fraricci !"
] | 2020-01-22T16:08:21
| 2020-01-23T21:30:48
|
2020-01-23T21:30:47Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
As discussed in issue #1453, ISYM has to be set to 1 in case of uniform mode in MPNonSCFSet.
This pull request should fix the problem.
|
{
"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/1741/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1741/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1741",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1741",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1741.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1741.patch",
"merged_at": "2020-01-23T21:30:47Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1742
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1742/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1742/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1742/events
|
https://github.com/materialsproject/pymatgen/pull/1742
| 554,781,312
|
MDExOlB1bGxSZXF1ZXN0MzY2ODczODY3
| 1,742
|
Small fix in connected components
|
{
"login": "davidwaroquiers",
"id": 3625296,
"node_id": "MDQ6VXNlcjM2MjUyOTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/3625296?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/davidwaroquiers",
"html_url": "https://github.com/davidwaroquiers",
"followers_url": "https://api.github.com/users/davidwaroquiers/followers",
"following_url": "https://api.github.com/users/davidwaroquiers/following{/other_user}",
"gists_url": "https://api.github.com/users/davidwaroquiers/gists{/gist_id}",
"starred_url": "https://api.github.com/users/davidwaroquiers/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/davidwaroquiers/subscriptions",
"organizations_url": "https://api.github.com/users/davidwaroquiers/orgs",
"repos_url": "https://api.github.com/users/davidwaroquiers/repos",
"events_url": "https://api.github.com/users/davidwaroquiers/events{/privacy}",
"received_events_url": "https://api.github.com/users/davidwaroquiers/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks @davidwaroquiers "
] | 2020-01-24T14:53:49
| 2020-01-24T21:46:38
|
2020-01-24T21:46:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* Fixing a small error in serialization of connected components.
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/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/1742/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1742/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1742",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1742",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1742.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1742.patch",
"merged_at": "2020-01-24T21:46:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1743
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1743/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1743/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1743/events
|
https://github.com/materialsproject/pymatgen/pull/1743
| 555,293,019
|
MDExOlB1bGxSZXF1ZXN0MzY3MjY1MDcz
| 1,743
|
Update xas
|
{
"login": "yimingchen-eng",
"id": 27871258,
"node_id": "MDQ6VXNlcjI3ODcxMjU4",
"avatar_url": "https://avatars.githubusercontent.com/u/27871258?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/yimingchen-eng",
"html_url": "https://github.com/yimingchen-eng",
"followers_url": "https://api.github.com/users/yimingchen-eng/followers",
"following_url": "https://api.github.com/users/yimingchen-eng/following{/other_user}",
"gists_url": "https://api.github.com/users/yimingchen-eng/gists{/gist_id}",
"starred_url": "https://api.github.com/users/yimingchen-eng/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/yimingchen-eng/subscriptions",
"organizations_url": "https://api.github.com/users/yimingchen-eng/orgs",
"repos_url": "https://api.github.com/users/yimingchen-eng/repos",
"events_url": "https://api.github.com/users/yimingchen-eng/events{/privacy}",
"received_events_url": "https://api.github.com/users/yimingchen-eng/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @yimingchen95 !\r\n\r\n@shyamd is there anything else you need from this for the builders/api?",
"I don't think we need separate classes for XANES and EXAFS, since both have the same init. I think you can add a name arg to the XAS to allow you to specify whether it is K,L XANES or EXAFS.\r\n\r\nThen, what you need is as XAS.stitch(other) method that does the stitching, rather than two individual methods that violate OOP for no reason. I do not quite understand why the stiching is different for XANES+EXAFS vs L2 + L3. Is it simply because one is an addition? If so, Spectrum already implements linear addition? Surely we can also enable interpolated addition?",
"I agree to merge the XANES and EXAFS module, which makes things more concise, and also move stitching methods inside class. \r\n\r\nYes, while Spectrum has the linear addition and interpolated addition is doable, things are bit more complicated for stitching L2+L3. This is because fill value needs to be added to prevent sudden change in mu. This fill value when x-axis is out of range is more tricky and less common. Hence I would like to have another method for stitching L2 and L3.\r\n\r\nFor stitching XANES+EXAFS, extra math are required and this is unique for this process. \r\n",
"Also, pls have type hints for all the methods.",
"Thanks."
] | 2020-01-26T21:49:17
| 2020-01-29T00:34:13
|
2020-01-29T00:34:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Update XAS module with EXAFS module and stitching code
* Add EXAFS module
* Add stitching method for XANES and EXAFS
* Add stitching method for L2 and L3 edge XANES
## 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)
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:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] 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 existing 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/1743/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1743/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1743",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1743",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1743.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1743.patch",
"merged_at": "2020-01-29T00:34:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1744
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1744/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1744/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1744/events
|
https://github.com/materialsproject/pymatgen/issues/1744
| 555,436,132
|
MDU6SXNzdWU1NTU0MzYxMzI=
| 1,744
|
About a min-pymatgen version including core classes
|
{
"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
}
|
[
{
"id": 4646275120,
"node_id": "LA_kwDOACgets8AAAABFPCIMA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/discussion",
"name": "discussion",
"color": "AA9790",
"default": false,
"description": ""
},
{
"id": 5585018768,
"node_id": "LA_kwDOACgets8AAAABTOSfkA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/pkg",
"name": "pkg",
"color": "EFE8DB",
"default": false,
"description": "Package health and distribution related stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @gVallverdu,\r\n\r\nThis is certainly something we’ve (@shyuep) talked about but have not reached a decision on yet.\r\n\r\nI will note that the situation is not quite as bad as it might seem: the large repo size is due to extensive test files, the actual source distribution on PyPI is just 2.6 MB. Also, the dependencies of pymatgen are fairly slim and/or standard (numpy, script, pandas, matplotlib, etc. — packages that are usually installed by a typical scientific python user regardless).\r\n\r\nSo we would definitely still encourage use of pymatgen for its core classes alone. The pymatgen core classes are also now completely type hinted and type checked and have been around for a long time with very few backwards-incompatible changes, so in this sense they are well suited for use from another code (in fact, off hand, I can’t remember the last backwards incompatible change that was made to a core class, and even if this did happen we would make sure to deprecate in a responsible manner).\r\n\r\nWith this said, the idea of separating pymatgen into pymatgen-core and then a plugin system for additional components is something we will likely need to consider as pymatgen grows in size. The problem here is that it comes with an added maintenance burden etc.",
"Hi,\r\nI understand and agree that splitting pymatgen will certainly lead to more stuff ... \r\n\r\n> So we would definitely still encourage use of pymatgen for its core classes alone.\r\n\r\nI will do that ! As you said I just don't have to hesitate putting pymatgen as requierments !\r\n\r\nThanks for the comment",
"Thanks. As @mkhorton said, we considered this carefully. The size of pymatgen is mainly an issue for people who need to clone the entire repo, which has gotten quite sizable due to the test files. While we can prune the test files a little and start the repo from scratch, it is not going to make a meaningfully large difference.\r\n\r\nThe problem is that I know of no good way to implement a plugin system for Python packages. Ideally, I would want to be able to release pymatgen.core (and perhaps a few other critical functionality like entries and electronic structure) as one package, and have pymatgen.analysis.anything as plugins. But the only way I know this works is for other packages to have different package names, e.g., pymatgen_diffusion is an example. I would very much rather it be pymatgen.diffusion to be consistent with everything pymatgen.\r\n\r\nIf anyone knows a good solution, we can revisit this.",
"I thought about it a bit more. I am going to implement something now that might help ",
"There is a plugin architecture available for Python in the standard library, https://packaging.python.org/guides/creating-and-discovering-plugins/ so we do have options.\r\n\r\nThere's also setup.py \"extras\" https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-extras so you can e.g. `pip install pymatgen[core]` with a separate set of dependencies, that's also an option.\r\n\r\nTo do this robustly we should look at the dependency graph between the various pymatgen subpackages/submodules, I think extracting core (perhaps with electronic_structure) should be fairly clean but I'm not sure about some of the others.",
"@mkhorton By all means you can try. I tried getting the plugin to work but it is difficult.",
"Yeah, likewise, which is why I've left it on the back burner for now.",
"I figured out how to get this to work in some way. Pushed a minimal implementation. More details to follow.",
"An alternative here is namespace packages. @tschaume has been building MPContribs with this and we're switching emmet to those. See [PEP420](https://www.python.org/dev/peps/pep-0420/)",
"Several namespace packages exist at this point:\r\n\r\n- https://github.com/materialsproject/pymatgen-analysis-alloys\r\n- https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion\r\n- https://github.com/materialsproject/pymatgen-analysis-defects\r\n- https://github.com/JuDFTteam/pymatgen-io-fleur\r\n\r\nwhich are also listed are here:\r\n\r\nhttps://pymatgen.org/addons\r\n\r\n`pymatgen.core` is still not installable, but I think we'd like to keep it that way. Closing this as not planned."
] | 2020-01-27T08:55:56
| 2023-06-05T18:13:24
|
2023-06-05T18:13:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi !
I wonder if it could be possible in any way to distribute a kind of small/min/light version of pymatgen including only core classes ? Now pymatgen is a quite large python packages (git repo is about 1.5 Go). All different modules are really interesting but sometimes, if you want to develop a new application, what you need essentially are the `Molecule` and `Structure` classes. These classes are really convenient, easy to use and as you said "fairly robust" ;). Thus setting pymatgen as requirements will increase a log the size of needed library only for core classes.
Another goal could be the use of pymatgen for server applications. Thus a light version of the package may be appreciable.
Thus, the idea/proposition is to talk about the possibility to extract mainly the contains of the core module and the `Molecule` and `Structure` classes in a min/light pymatgen version ? On the contrary if there is a current way or python strategy in order to do that, I am really interesting. Maybe I am completely wrong and I should write pymatgen as requirements without considering the size.
|
{
"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/1744/reactions",
"total_count": 3,
"+1": 3,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1744/timeline
| null |
not_planned
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1745
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1745/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1745/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1745/events
|
https://github.com/materialsproject/pymatgen/issues/1745
| 556,009,037
|
MDU6SXNzdWU1NTYwMDkwMzc=
| 1,745
|
Numerical error produces lattice with values close to 0, but negative
|
{
"login": "felentovic",
"id": 13416944,
"node_id": "MDQ6VXNlcjEzNDE2OTQ0",
"avatar_url": "https://avatars.githubusercontent.com/u/13416944?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/felentovic",
"html_url": "https://github.com/felentovic",
"followers_url": "https://api.github.com/users/felentovic/followers",
"following_url": "https://api.github.com/users/felentovic/following{/other_user}",
"gists_url": "https://api.github.com/users/felentovic/gists{/gist_id}",
"starred_url": "https://api.github.com/users/felentovic/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/felentovic/subscriptions",
"organizations_url": "https://api.github.com/users/felentovic/orgs",
"repos_url": "https://api.github.com/users/felentovic/repos",
"events_url": "https://api.github.com/users/felentovic/events{/privacy}",
"received_events_url": "https://api.github.com/users/felentovic/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 report @felentovic, Negative values are not intrinsically incorrect and somewhat inevitable given the nature of floating point arithmetic -- can you give a specific example of error accumulation leading to a bug?\r\n\r\nThis said, I agree it's unfortunate there are these small-non-zero values in this very simple case. It's possible to initialize directly from the matrix, since this is the internal representation of the lattice, to avoid this issue. I'll take a look at the math we're using also in case there's a cleaner solution here.",
"This isn’t a bug but rather a reality of floating point arithmetic. I have yet to encounter a real world situation that this matters. Closing this. "
] | 2020-01-28T06:27:23
| 2020-01-28T14:08:51
|
2020-01-28T14:08:51Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
In the class `Lattice` the method `from parameters` in some cases creates lattice vectors which have a value close to zero, but negative. E.g [5.61018515, 0.0, 3.435247643285757e-16]. This accumulates errors later in calculations.
**To Reproduce**
Steps to reproduce the behavior:
Create a lattice from parameters with the following arguments:
a = {float64} 5.61018515
b = {float64} 5.61018515
c = {float64} 20.95050049
alpha = {float64} 90.0
beta = {float64} 90.0
gamma = {float64} 90.0
The result is:
Lattice vectors: [a,b,c]
<class 'list'>: [[5.61018515, 0.0, 3.435247643285757e-16], [-3.435247643285757e-16, 5.61018515, 3.435247643285757e-16], [0.0, 0.0, 20.95050049]]
**Expected behaviour**
Lattice vectors: [a,b,c]
<class 'list'>: [[5.61018515, 0.0, 0.0], [0.0, 5.61018515, 0.0], [0.0, 0.0, 20.95050049]]
**Desktop:**
- OS: Mac,Linux
- Version: 2020.1.10
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1745/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1745/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1746
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1746/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1746/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1746/events
|
https://github.com/materialsproject/pymatgen/issues/1746
| 556,138,269
|
MDU6SXNzdWU1NTYxMzgyNjk=
| 1,746
|
POTCAR file hashes appear to be incorrect
|
{
"login": "bjmorgan",
"id": 1182923,
"node_id": "MDQ6VXNlcjExODI5MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/1182923?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/bjmorgan",
"html_url": "https://github.com/bjmorgan",
"followers_url": "https://api.github.com/users/bjmorgan/followers",
"following_url": "https://api.github.com/users/bjmorgan/following{/other_user}",
"gists_url": "https://api.github.com/users/bjmorgan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/bjmorgan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/bjmorgan/subscriptions",
"organizations_url": "https://api.github.com/users/bjmorgan/orgs",
"repos_url": "https://api.github.com/users/bjmorgan/repos",
"events_url": "https://api.github.com/users/bjmorgan/events{/privacy}",
"received_events_url": "https://api.github.com/users/bjmorgan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks for reporting this.\r\n@mkhorton @shyamd I honestly dislike the file hash approach to dealing with POTCARs. Should we just do away with this? I think basic checks such as the functional, date and parameters would suffice?",
"These aren't supposed to be file hashes, but rather data hashes, so this is the expected behavior. \r\n\r\nEdit: NVM, I didn't realize file hashes were included as well. I like the data hash, not the file hash. That will have too many issues. A different `mtime` will alter the file hash, which is problematic. ",
"From my testing, the data hashes work as intended. But these are only currently included for Materials Project compatible pseudopotential sets. Other PP choices fall back to file hashes.",
"This check was to ensure that when non-MP researchers ran calculations they could be sure those pseudopotentials were the same as what we ran our calculations with. This should just be a warning that maybe can be toggled off via `PMG_` environment variable?",
"@rkingsbury can you check the docstring here https://github.com/materialsproject/pymatgen/blob/3189eb225831f90db61c296ac1175e1811031a97/pymatgen/io/vasp/sets.py#L2856 ?\r\n\r\nIs it correct that the data hashes (`pymatgen_hashes`) are only available for the old PP set, I thought these were added for all PPs?\r\n\r\n@shyuep There are only a handful of pseudopotentials distributed with VASP, in principle hashing shouldn't be causing grief unless users manually edit or generate their own POTCARs, however we may have a bug here.",
"@mkhorton I'm investigating now. I believe we do have a bug in the file hashes. Will update shortly.",
"As best I can tell, the original hash files were generated on an incomplete set of POTCARs. For example, the \"PBE\" set was not included in the original files. I've recomputed the hash files to include every PSP currently installed on Cori (Vasp 5.4.4). \r\n\r\nAs @bjmorgan pointed out, the data hashes were correct (just incomplete), while it appears some of the file hashes were incorrect, possibly due to the changes to the metadata noted by Paul_Fons in the related [discussion thread](https://discuss.matsci.org/t/hash-failure-for-potcar/3461).",
"Thanks for submitting the fix so promptly @rkingsbury ",
"Thanks for reporting @bjmorgan! Please let us know if you have any further problems after the fix is merged.",
"If it helps for checking, I have what I believe to be a full set of file hashes at https://github.com/bjmorgan/vasppy/tree/master/vasppy/data (`*_md5.yaml`)",
"@bjmorgan thanks, that might help. We're leaning on the \"data\" hashes more that literal md5 checksums because VASP did make a revision release of one of their POTCAR sets where they changed metadata (typos/incorrect strings in TITEL) but the POTCARs themselves were functionally equivalent. I believe this only happened once, but we do need to catch it.",
"@mkhorton I actually updated my dataset today when I learned about this from the discussion thread. The new-metadata \"recommended\" PPs are listed in the `PBE_54r_md5.yaml` and `LDA_54r_md5.yaml` files. Testing against only the PP data seems more robust, and avoids this issue.",
"The updated hashes in https://github.com/materialsproject/pymatgen/pull/1749 do not appear to include the examples given in my original comment (and are possibly all the same hashes as in `master`; with the exception of the PP sets added during this commit).",
"@bjmorgan do you mean the file hashes? Yes, I was checking our recomputed hashes against yours and noticed the same thing. Did you compute your hashes from the `.data` attribute of the `PotcarSingle` object (as in your example) or directly from the file itself?\r\n\r\n",
"@bjmorgan it appears that you get a different hash depending upon whether you hash a Potcar or a PotcarSingle object. For example:\r\n\r\n```\r\nfrom hashlib import md5\r\n\r\npath = Path(\"POTCAR.Ac.gz\")\r\n\r\npsingle = PotcarSingle.from_file(path)\r\npotcar = Potcar.from_file(path)\r\n\r\nhash1 = md5(psingle.data.encode('utf-8')).hexdigest()\r\nhash2 = md5(potcar[0].data.encode('utf-8')).hexdigest()\r\n\r\nprint(hash1)\r\nprint(hash2)\r\n```\r\ngives\r\n```\r\ncb0e0b98d520a284cf11d1161f25e6a5\r\n61fb9dcc007c8d625d77210ebc269828\r\n```\r\n\r\nWe used the second approach to compute the hashes, which is why they are not equal to those you computed. We're revisiting whether this is the best approach though as it clearly leads to confusion!",
"The difference is because the final `\\n` has been stripped in the case of `potcar[0].data`.",
"In which case there is a bug in `validate_potcar_hash()` https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/sets.py#L2879\r\nwhere the `PotcarSingle` hash is generated for comparison.",
"Thank you @bjmorgan , we're making progress. Yes, thanks to our discussion I just recognized that bug and have pushed a recomputed set of hashes using PotcarSingle. This bug was causing some extra warnings during our tests that we assumed were due to some of the POTCARs distributed with pymatgen having old / out of date metadata.\r\n\r\nOut of about 3,000 file hashes, I now show only about 650 that differ from yours. I'll reply shortly when I figure out which files those differences are coming from",
"There are 622 files in the PBE_54r and LDA_54r sets combined, so those account for most of the missing hashes. We apparently don't have those PPs installed on our system.\r\n\r\nHashes differ for the following PBE PPs:\r\n\r\n```\r\nPBE B_h\r\nPBE C_h\r\nPBE Ce\r\nPBE Eu\r\nPBE F_h\r\nPBE Gd\r\nPBE Ge_d\r\nPBE H_h\r\nPBE Li_sv\r\nPBE Lu\r\nPBE Mg_pv\r\nPBE N_h\r\nPBE Na_pv\r\nPBE Nd\r\nPBE O_h\r\nPBE Pd\r\nPBE Pm\r\nPBE Pr\r\nPBE Si_h\r\nPBE Sm\r\nPBE Sm_3\r\nPBE Tm\r\nPBE Yb\r\n```\r\n\r\nAnd finally, there are discrepancies for Mg_pv and Si_h that I think are related to the fact that both of these PPs have multiple versions (on our system at least) with filenames like `POTCAR.Mg_pv.gz', 'POTCAR.Mg_pv.old.gz', 'POTCAR.Mg_pv_GW.gz'",
"For `PBE B_h` I get\r\n```python\r\nfrom pymatgen.io.vasp.inputs import PotcarSingle\r\npsingle = PotcarSingle.from_file(filename='POTCAR_PBE_B_h')\r\n\r\nfrom hashlib import md5\r\nprint(md5(psingle.data.encode(\"utf-8\")).hexdigest())\r\n```\r\n```\r\n501131776b38fb29fe50c430b72d2643\r\n```\r\nand\r\n```\r\n$ md5 POTCAR_PBE_B_h \r\nMD5 (POTCAR_PBE_B_h) = 501131776b38fb29fe50c430b72d2643\r\n```",
"@bjmorgan thanks for all the assistance in troubleshooting this. We've merged a provisional fix that uses the more complete set of `PotcarSingle` hashes and changes the `BadHashError` into a warning so that it won't be fatal. \r\n\r\nPlease test and let us know how things are working. We need to continue investigating whether the PP's that we have available on Cori have the most up to date metadata (based on your contributions it sounds like they are not). If that's the case, we'll try to update them and get a more complete set of hashes pushed soon."
] | 2020-01-28T11:10:47
| 2020-01-30T00:25:16
|
2020-01-30T00:25:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The `vasp_potcar_file_hashes.json` ([here](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/vasp/vasp_potcar_file_hashes.json)) is supposed to contain md5 hashes of POTCAR files (if I have this understood correctly). But the hashes in the file do not match the hashes generated from `md5sum POTCAR` from the command line.
e.g. using the PBE_54 Ac POTCAR
```python
from pymatgen.io.vasp.inputs import PotcarSingle
psingle = PotcarSingle.from_file(filename='POTCAR_PBE54_Ac')
print(psingle.hash)
# note: this hash is included in the vasp_potcar_pymatgen_hashes.json file
from hashlib import md5
print(md5(psingle.data.encode("utf-8")).hexdigest())
# This is the same hash generated using `md5sum POTCAR` from the command line.
# it is *not* included in the vasp_potcar_file_hashes.json file
```
produces
```
4175a0a39300f5c90c84142814f8cc72
cb0e0b98d520a284cf11d1161f25e6a5
```
The first hash is included in the `vasp_potcar_pymatgen_hashes.json` file:
```
grep -c 4175a0a39300f5c90c84142814f8cc72 vasp_potcar_pymatgen_hashes.json
1
```
The second hash is *not* included in the `vasp_potcar_file_hashes.json` file:
```
grep -c cb0e0b98d520a284cf11d1161f25e6a5 vasp_potcar_file_hashes.json
0
```
Note: this is using the "original unvie release version" PBE_54 pseudopotential files.
Using the updated PBE_54 pseudopotentials gives:
```
md5 POTCAR
MD5 (POTCAR) = 2837362d49736e188edb5cc8d2a39c71
grep -c 2837362d49736e188edb5cc8d2a39c71 vasp_potcar_file_hashes.json
0
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1746/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1746/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1747
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1747/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1747/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1747/events
|
https://github.com/materialsproject/pymatgen/issues/1747
| 556,320,986
|
MDU6SXNzdWU1NTYzMjA5ODY=
| 1,747
|
Fail to build python bindings to Zeo++ with Cython
|
{
"login": "ws517037749",
"id": 43861983,
"node_id": "MDQ6VXNlcjQzODYxOTgz",
"avatar_url": "https://avatars.githubusercontent.com/u/43861983?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ws517037749",
"html_url": "https://github.com/ws517037749",
"followers_url": "https://api.github.com/users/ws517037749/followers",
"following_url": "https://api.github.com/users/ws517037749/following{/other_user}",
"gists_url": "https://api.github.com/users/ws517037749/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ws517037749/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ws517037749/subscriptions",
"organizations_url": "https://api.github.com/users/ws517037749/orgs",
"repos_url": "https://api.github.com/users/ws517037749/repos",
"events_url": "https://api.github.com/users/ws517037749/events{/privacy}",
"received_events_url": "https://api.github.com/users/ws517037749/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls contact the developers of Zeo++ as we do not maintain that code. "
] | 2020-01-28T16:23:10
| 2020-01-28T16:26:48
|
2020-01-28T16:26:47Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
Successful compilation of Zeo++ but fail to build the python bindings , the return error is ''command 'gcc' failed with exit status 1'', I am not sure whether it is the problem for the gcc or something else. I successfully do it only once in a cluster but failed in my Macbook (Macos.10.15.2) and on the other cluster.
**To Reproduce**
Steps to reproduce the behavior:
mkdir Voro++
mkdir Voro++/voro
cd Voro++/voro
svn checkout --username anonsvn https://code.lbl.gov/svn/voro/trunk # password is 'anonsvn'
Add -fPIC to the CFLAGS variable in config.mk
mkdir Zeo++
mkdir Zeo++/zeo
cd Zeo++/zeo
svn checkout --username anonsvn https://code.lbl.gov/svn/zeo/trunk # password is 'anonsvn'
cd trunk
make dylib
make
pip install cython
cd cython_wrapper
python setup_alt.py develop
**Expected behavior**
Clear the python binding problem, actually the compiled binary file could run successfully
**Screenshots**
**Desktop (please complete the following information):**
- OS: Red Hat
- Version: 4.8.5-28
**Additional context**
Add any other context about the problem here.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1747/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1747/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1748
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1748/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1748/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1748/events
|
https://github.com/materialsproject/pymatgen/pull/1748
| 556,341,253
|
MDExOlB1bGxSZXF1ZXN0MzY4MTIzNTY2
| 1,748
|
XYZ reader
|
{
"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 |
[] | 2020-01-28T16:56:32
| 2020-01-28T19:57:21
|
2020-01-28T19:57:21Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I just change two characters in the regex used to read XYZ files in order to allow more flexibility (again).
For example, I got some files such as:
```
32
C32-C2-1
C 2.70450 1.16090 -0.14630 1 3 23 2
C 1.61930 1.72490 -0.79330 2 1 5 26
C 2.34210 1.02670 1.14620 3 1 8 6
C -0.68690 2.16170 -0.13790 4 5 18 7
C 0.67160 2.15830 0.14350 5 4 2 6
```
The integers at the end of the lines correspond to the connectivity. Thus I change the regex in order to ignore this but read the xyz file. I add tests also.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1748/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1748/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1748",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1748",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1748.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1748.patch",
"merged_at": "2020-01-28T19:57:21Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1749
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1749/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1749/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1749/events
|
https://github.com/materialsproject/pymatgen/pull/1749
| 556,375,133
|
MDExOlB1bGxSZXF1ZXN0MzY4MTUxNjY0
| 1,749
|
update POTCAR hashes
|
{
"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 @rkingsbury, can you double-check that *all* the potcar hash in the .json file I provided way back are now included in this? because that should have been almost complete"
] | 2020-01-28T18:00:11
| 2020-01-29T01:03:28
|
2020-01-29T01:03:28Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Addresses #1746
Hashes have been recomputed using the complete set of POTCARs distributed with VASP 5.4.4 on Cori.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1749/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1749/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1749",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1749",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1749.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1749.patch",
"merged_at": "2020-01-29T01:03:28Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1750
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1750/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1750/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1750/events
|
https://github.com/materialsproject/pymatgen/issues/1750
| 556,638,535
|
MDU6SXNzdWU1NTY2Mzg1MzU=
| 1,750
|
Point cloud from structure
|
{
"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 |
[
"[[*site.coords, site.specie.symbol, site.specie.oxi_state] for site in structure]\r\n\r\nI don’t think there is a need to use the as_dict method.",
"I had tried this I believe but I didn't want the 'sites' for partial occupancies I wanted a raw list of atoms which I struggled to achieve without hacky list comprehensions that took a long time to complete.\r\n\r\nDirectly calling species broke for partial occupancies and directly calling sites gave inconsistent dtypes.",
"Perhaps I am unclear what is the output you want. By nature, partial occupancies have an arbitrary number of elements and occupancies. ",
"Yes, I wanted to expand them out and treat them as independant points, my main issue has been that the neighbour class seems to erase access to the occupancy.\r\n\r\nSo I'd want to represent the site H0.25O0.75 at x,y,z = 1,2,3 as\r\n\r\n[1,2,3,H,0.25]\r\n[1,2,3,O,0.75]\r\n\r\nMy apologies if doing this with the library is actually trivial the structure module just seems to be fighting me on getting a raw array of species and getting rid of the grouping into a site",
"I see. This is actually not difficult (and the Neighbor class functions just like a PeriodicSite in most instances).\r\n\r\n```python\r\ndata = []\r\nfor site in structure:\r\n for el, occu in site.species.items():\r\n row = list(site.coords)\r\n row.append(str(el))\r\n row.append(occu)\r\n data.append(row)\r\n```\r\nshould provide what you need.\r\n\r\nFor future reference, pls post questions on usage at http://discuss.matsci.org . The Github Issues is meant for bug reports and feature requests. Thanks.",
"Ah thank you, I was unaware of the generic items method and was looking in the documentation which led me to believe the information was missing. I'll take note to assume I'm the prolem and head to masci before posting here again then thank you for your time!"
] | 2020-01-29T05:05:01
| 2020-01-29T23:32:55
|
2020-01-29T22:55:52Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
In order to get a raw point cloud from a pymatgen structure I've found I've had to use the as dict method and list comprehensions which is computationally expensive, a quick command to extract a 2d list of every species in the from [x,y,z,element, oxidation,occupancy] or something similar would be invaluable for geometric machine learning on crystal structures.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1750/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1750/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1751
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1751/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1751/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1751/events
|
https://github.com/materialsproject/pymatgen/pull/1751
| 557,072,353
|
MDExOlB1bGxSZXF1ZXN0MzY4NzMwMDU4
| 1,751
|
MPScanRelaxSet: fix bug and add write_input test
|
{
"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 |
[] | 2020-01-29T19:36:38
| 2020-05-05T23:15:48
|
2020-01-29T21:22:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Recent changes to `write_input` contained a bug regarding cases in which there was no KPOINTS file. In such cases, `write_input` would still write an empty file, causing problems with downstream logic.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1751/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1751/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1751",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1751",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1751.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1751.patch",
"merged_at": "2020-01-29T21:22:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1752
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1752/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1752/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1752/events
|
https://github.com/materialsproject/pymatgen/issues/1752
| 557,423,630
|
MDU6SXNzdWU1NTc0MjM2MzA=
| 1,752
|
unintended for/else in validate_poscar()?
|
{
"login": "bjmorgan",
"id": 1182923,
"node_id": "MDQ6VXNlcjExODI5MjM=",
"avatar_url": "https://avatars.githubusercontent.com/u/1182923?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/bjmorgan",
"html_url": "https://github.com/bjmorgan",
"followers_url": "https://api.github.com/users/bjmorgan/followers",
"following_url": "https://api.github.com/users/bjmorgan/following{/other_user}",
"gists_url": "https://api.github.com/users/bjmorgan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/bjmorgan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/bjmorgan/subscriptions",
"organizations_url": "https://api.github.com/users/bjmorgan/orgs",
"repos_url": "https://api.github.com/users/bjmorgan/repos",
"events_url": "https://api.github.com/users/bjmorgan/events{/privacy}",
"received_events_url": "https://api.github.com/users/bjmorgan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 ",
"Discussing this in the lab, thanks -- @rkingsbury will be implementing a further update to this",
"Good catch @bjmorgan , thank you for reporting!"
] | 2020-01-30T11:11:22
| 2020-02-02T21:57:54
|
2020-02-02T21:57:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The `validate_poscar` function [https://github.com/materialsproject/pymatgen/blob/4d9bfd9915b818cf61113e9402112c302a958aae/pymatgen/io/vasp/sets.py#L2860](here) contains a `for/else` construction, that looks like it is supposed to be indented differently to give `if/else`:
```python
for psingle in potcar:
if psingle.hash != pymatgen_hashes[key][psingle.symbol]:
warnings.warn(
"POTCAR data hash for POTCAR {} did not pass \
validation. Verify the integrity of your \
POTCAR files. ".format(
psingle.symbol
),
BadHashWarning
)
else:
file_hash = md5(psingle.data.encode("utf-8")).hexdigest()
if file_hash != file_hashes[key][psingle.symbol]:
warnings.warn(
"POTCAR file hash for POTCAR {} did not pass validation. \
It is possible that the metadata in the POTCAR has changed. \
We will continue loading the POTCAR because the hash of \
the data itself has passed validation.".format(
psingle.symbol
),
BadHashWarning
)
```
At the moment it is possible to trigger *both* `BadHashWarning`s, which means the messages contradict each other.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1752/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1752/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1753
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1753/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1753/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1753/events
|
https://github.com/materialsproject/pymatgen/pull/1753
| 557,681,060
|
MDExOlB1bGxSZXF1ZXN0MzY5MjI4NDk5
| 1,753
|
Update OpenBabel; Fix NN classes, graph classes
|
{
"login": "espottesmith",
"id": 17201238,
"node_id": "MDQ6VXNlcjE3MjAxMjM4",
"avatar_url": "https://avatars.githubusercontent.com/u/17201238?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/espottesmith",
"html_url": "https://github.com/espottesmith",
"followers_url": "https://api.github.com/users/espottesmith/followers",
"following_url": "https://api.github.com/users/espottesmith/following{/other_user}",
"gists_url": "https://api.github.com/users/espottesmith/gists{/gist_id}",
"starred_url": "https://api.github.com/users/espottesmith/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/espottesmith/subscriptions",
"organizations_url": "https://api.github.com/users/espottesmith/orgs",
"repos_url": "https://api.github.com/users/espottesmith/repos",
"events_url": "https://api.github.com/users/espottesmith/events{/privacy}",
"received_events_url": "https://api.github.com/users/espottesmith/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks for the quick fix @espottesmith ",
"Once tests pass, will merge",
"Thanks @espottesmith , have made a note of the pandas issue to re-visit once pandas 1.0 has settled down",
"Got a tonne of linter errors on this: https://circleci.com/gh/materialsproject/pymatgen/9592?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link\r\n\r\nMissing docstrings for the new properties.\r\n\r\nNot sure why it wasn't caught in CI during the PR"
] | 2020-01-30T18:45:23
| 2020-01-31T04:31:36
|
2020-01-31T03:38:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR addresses two major issues:
* The recent OpenBabel release 3.0.0 breaks the previous API in several ways, most notably in how the Python interface is imported
* A bug was found in which certain NearNeighbors classes failed to approrpriately detect bonds in molecules
With respect to the second change, all NearNeighbor classes now have properties describing if they can be used with Molecules, Structures, or both. MoleculeGraph and StructureGraph now prevent the user from using with_local_env_strategy with an inappropriate strategy.
Additionally, the bug which caused an automatic re-indexing of Molecules has been identified and fixed.
## Additional dependencies introduced (if any)
* openbabel 3.0.0
## Checklist
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [X] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). (exceptions for some properties)
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.
- [X] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
|
{
"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/1753/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1753/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1753",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1753",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1753.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1753.patch",
"merged_at": "2020-01-31T03:38:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1754
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1754/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1754/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1754/events
|
https://github.com/materialsproject/pymatgen/pull/1754
| 558,277,399
|
MDExOlB1bGxSZXF1ZXN0MzY5Njk3MTQz
| 1,754
|
Added docstrings to new NearNeighbors properties make the linters happy
|
{
"login": "espottesmith",
"id": 17201238,
"node_id": "MDQ6VXNlcjE3MjAxMjM4",
"avatar_url": "https://avatars.githubusercontent.com/u/17201238?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/espottesmith",
"html_url": "https://github.com/espottesmith",
"followers_url": "https://api.github.com/users/espottesmith/followers",
"following_url": "https://api.github.com/users/espottesmith/following{/other_user}",
"gists_url": "https://api.github.com/users/espottesmith/gists{/gist_id}",
"starred_url": "https://api.github.com/users/espottesmith/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/espottesmith/subscriptions",
"organizations_url": "https://api.github.com/users/espottesmith/orgs",
"repos_url": "https://api.github.com/users/espottesmith/repos",
"events_url": "https://api.github.com/users/espottesmith/events{/privacy}",
"received_events_url": "https://api.github.com/users/espottesmith/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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"
] | 2020-01-31T17:54:50
| 2020-01-31T18:02:01
|
2020-01-31T18:01:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Extremely small change - just adds docstrings in pymatgen/analysis/local_env.py
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1754/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1754/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1754",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1754",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1754.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1754.patch",
"merged_at": "2020-01-31T18:01:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1755
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1755/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1755/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1755/events
|
https://github.com/materialsproject/pymatgen/pull/1755
| 558,309,029
|
MDExOlB1bGxSZXF1ZXN0MzY5NzIyODI4
| 1,755
|
Bugfix for validate_potcar_hashes
|
{
"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 |
[] | 2020-01-31T18:49:59
| 2020-02-18T21:27:59
|
2020-02-02T21:57:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Fix #1752 in validate_potcar_hashes.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1755/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1755/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1755",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1755",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1755.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1755.patch",
"merged_at": "2020-02-02T21:57:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1756
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1756/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1756/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1756/events
|
https://github.com/materialsproject/pymatgen/issues/1756
| 558,622,222
|
MDU6SXNzdWU1NTg2MjIyMjI=
| 1,756
|
Improve error messages in MPRester for unknown materials or missing material properties
|
{
"login": "paulneves77",
"id": 14657273,
"node_id": "MDQ6VXNlcjE0NjU3Mjcz",
"avatar_url": "https://avatars.githubusercontent.com/u/14657273?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/paulneves77",
"html_url": "https://github.com/paulneves77",
"followers_url": "https://api.github.com/users/paulneves77/followers",
"following_url": "https://api.github.com/users/paulneves77/following{/other_user}",
"gists_url": "https://api.github.com/users/paulneves77/gists{/gist_id}",
"starred_url": "https://api.github.com/users/paulneves77/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/paulneves77/subscriptions",
"organizations_url": "https://api.github.com/users/paulneves77/orgs",
"repos_url": "https://api.github.com/users/paulneves77/repos",
"events_url": "https://api.github.com/users/paulneves77/events{/privacy}",
"received_events_url": "https://api.github.com/users/paulneves77/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @paulneves77,\r\n\r\nNot all materials have band structures associated with them. If you visit this [materials details page](https://materialsproject.org/materials/mp-756234) you can see there is no band structure supplied, which is why you have the error. The error message could be more useful however! Later in the year, we're planning a big data release with a lot of new band structures available.\r\n\r\nIt looks like for this material, we have calculated a band structure (see [here](https://materialsproject.org/tasks/mp-756234#mp-844812)), but for whatever reason it's not currently available on the website or via the API -- maybe @shyamd can comment?\r\n\r\nSince this is a Materials Project data question, a more appropriate place to ask would be on the [Materials Project discussion forum](https://discuss.matsci.org/c/materials-project/).\r\n\r\nI'll leave this issue open here however to make a note that we should improve the error messages for materials where band structures are not available.",
"Thanks for the information @mkhorton!\r\n\r\nI thought I saw a band structure calculation for this material on the materials project, but I must have been mistaken.\r\n\r\nI am still confused about one point though: I was able to run **get_bandstructure_by_material_id** on many materials that do not have a band structure calculated in the materials project (to pick a random example, [mp-767194](https://materialsproject.org/materials/mp-767194/)), and it does not error and end the program. Instead, get_bandstructure_by_material_id just returns None. I am unclear on the difference between querying mp-767194 and mp-769885: why does one error while the other does not? Perhaps it is that there is a band structure calculated for mp-769885, as you mentioned.\r\n\r\nAt any rate, returning None instead of giving an Error if there is no available band-structure makes more sense in my mind. I am running a search based on a list of selected material IDs, looking at all the available band structures (that data release of new band structures sounds exciting!). If it crashes when it gets to materials like mp-769885, the program will never complete!\r\n\r\nAlso, in the spirit of unclear error messages, I am getting a different error when I try to use get_bandstructure_by_material_id on [mp-756234](https://materialsproject.org/materials/mp-756234/), which does have a calculated bandstructure. It says:\r\n\r\n```\r\nIn [51]: m.get_bandstructure_by_material_id('mp-767633')\r\nTraceback (most recent call last):\r\n\r\n File \"<ipython-input-51-363b57d22dbb>\", line 1, in <module>\r\n m.get_bandstructure_by_material_id('mp-767633')\r\n\r\n File \"C:\\Users\\pmneves\\Anaconda3\\lib\\site-packages\\pymatgen\\ext\\matproj.py\", line 624, in get_bandstructure_by_material_id\r\n data = self.get_data(material_id, prop=prop)\r\n\r\n File \"C:\\Users\\pmneves\\Anaconda3\\lib\\site-packages\\pymatgen\\ext\\matproj.py\", line 241, in get_data\r\n return self._make_request(sub_url)\r\n\r\n File \"C:\\Users\\pmneves\\Anaconda3\\lib\\site-packages\\pymatgen\\ext\\matproj.py\", line 188, in _make_request\r\n raise MPRestError(msg)\r\n\r\nMPRestError: REST query returned with error status code 504. Content: b\"<html><body><h1>504 Gateway Time-out</h1>\\nThe server didn't respond in time.\\n</body></html>\\n\\n\"\r\n```\r\n\r\nDo you think I should open a thread on the MP forum about these concerns?",
"> Do you think I should open a thread on the MP forum about these concerns?\r\n\r\nIn general, yes, but since this thread is already open don't worry about it -- a similar group of people read both places, it's mostly an organizational thing to help us keep track.\r\n\r\n> If it crashes when it gets to materials like mp-769885, the program will never complete!\r\n\r\nA remedy here, for now, is to wrap it in a try/except:\r\n\r\n```\r\ntry:\r\n with MPRester(<API_KEY>) as m:\r\n bs = m.get_bandstructure_by_material_id('mp-769885')\r\nexcept MPRestError: # you may need to `import MPRestError` from the relevant module\r\n pass\r\n```\r\n\r\nIn this way, you could also keep a list of mp-ids for which band structures are not available.\r\n\r\nRegarding the issue itself, I'll raise this at our weekly meeting to discuss.",
"This issue has been outstanding for a number of years. So I am closing it. Feel free to reopen in the mp-api repo if still valid."
] | 2020-02-02T00:48:40
| 2023-08-10T15:00:33
|
2023-08-10T15:00:06Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Description:**
I get an error when calling **get_bandstructure_by_material_id** on material **mp-769885**. I do not know if this error is also present in other materials, nor whether the error is due to the get_bandstructure_by_material_id function or in the material itself. I have been able to use get_bandstructure_by_material_id with over 30 other materials without issue.
**To Reproduce:**
```
with MPRester(<API_KEY>) as m:
bs = m.get_bandstructure_by_material_id('mp-769885')
```
**Error Message:**
```
File "<FOO.PY>", line 71, in <module>
bs = m.get_bandstructure_by_material_id('mp-769885')
File "C:\Users\<USERNAME>\Anaconda3\lib\site-packages\pymatgen\ext\matproj.py", line 625, in get_bandstructure_by_material_id
return data[0][prop]
IndexError: list index out of range
```
**Desktop (please complete the following information):**
- OS: Windows
- Version: Current as of Feb 2, 2020
Any guidance would be much 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/1756/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1756/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1757
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1757/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1757/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1757/events
|
https://github.com/materialsproject/pymatgen/pull/1757
| 558,764,000
|
MDExOlB1bGxSZXF1ZXN0MzcwMDYwNDI5
| 1,757
|
Parse NPLWV, NPLWVs at kpoints from OUTCAR-files into Outcar.data dictionary.
|
{
"login": "stichri",
"id": 24986870,
"node_id": "MDQ6VXNlcjI0OTg2ODcw",
"avatar_url": "https://avatars.githubusercontent.com/u/24986870?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/stichri",
"html_url": "https://github.com/stichri",
"followers_url": "https://api.github.com/users/stichri/followers",
"following_url": "https://api.github.com/users/stichri/following{/other_user}",
"gists_url": "https://api.github.com/users/stichri/gists{/gist_id}",
"starred_url": "https://api.github.com/users/stichri/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/stichri/subscriptions",
"organizations_url": "https://api.github.com/users/stichri/orgs",
"repos_url": "https://api.github.com/users/stichri/repos",
"events_url": "https://api.github.com/users/stichri/events{/privacy}",
"received_events_url": "https://api.github.com/users/stichri/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls add a unittest for the new functionality. Thanks.",
"Thanks",
"Hi @stichri, thanks for this PR. Could you fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can acknowledge your contribution appropriately in the [pymatgen documentation](https://pymatgen.org/team.html)? I have been checking our acknowledgments and I realized we'd missed some contributions."
] | 2020-02-02T21:51:03
| 2020-08-05T06:09:53
|
2020-02-03T04:06:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Parse NPLWV from OUTCAR file using the read_pattern method of Outcar class
* Parse numbers of plane waves at each kpoint from OUTCAR file using the read_table_pattern method of Outcar class
## 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/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] All existing 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/1757/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1757/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1757",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1757",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1757.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1757.patch",
"merged_at": "2020-02-03T04:06:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1758
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1758/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1758/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1758/events
|
https://github.com/materialsproject/pymatgen/pull/1758
| 559,774,799
|
MDExOlB1bGxSZXF1ZXN0MzcwODgzMTQ1
| 1,758
|
Coordination Sequences in Connected Components + Serialization of Structure Connectivity
|
{
"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 |
[
"I don't understand why the travis-ci failed here."
] | 2020-02-04T14:57:35
| 2020-02-05T13:04:45
|
2020-02-05T13:04:45Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Fixed as_dict/from_dict of StructureConnectivity
* Computation of Coordination sequences in connected components.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1758/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1758/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1758",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1758",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1758.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1758.patch",
"merged_at": "2020-02-05T13:04:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1759
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1759/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1759/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1759/events
|
https://github.com/materialsproject/pymatgen/pull/1759
| 559,917,117
|
MDExOlB1bGxSZXF1ZXN0MzcwOTk5NzE3
| 1,759
|
Allow list of species to determine supercell_size in structure_matcher
|
{
"login": "lbluque",
"id": 9788715,
"node_id": "MDQ6VXNlcjk3ODg3MTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/9788715?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/lbluque",
"html_url": "https://github.com/lbluque",
"followers_url": "https://api.github.com/users/lbluque/followers",
"following_url": "https://api.github.com/users/lbluque/following{/other_user}",
"gists_url": "https://api.github.com/users/lbluque/gists{/gist_id}",
"starred_url": "https://api.github.com/users/lbluque/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/lbluque/subscriptions",
"organizations_url": "https://api.github.com/users/lbluque/orgs",
"repos_url": "https://api.github.com/users/lbluque/repos",
"events_url": "https://api.github.com/users/lbluque/events{/privacy}",
"received_events_url": "https://api.github.com/users/lbluque/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @lbluque !",
"If this is your first contribution to pymatgen, please also fill out our [developer's form](https://forms.gle/JnisFb38QDR8QTFTA) so we can [credit you appropriately](https://pymatgen.org/team.html), thanks!"
] | 2020-02-04T19:03:03
| 2020-02-12T04:11:32
|
2020-02-12T04:08:59Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Include a summary of major changes in bullet points:
* Allow to use a list/tuple of species as the supercell_size kwarg for StructureMatcher. This allows to use 'sublattices' (for example a anion sublattice in a cathode material) to determine the formula units in a supercell.
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/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [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.
- [ ] All existing tests pass. Errors elsewhere from current state of master.
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/1759/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1759/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1759",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1759",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1759.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1759.patch",
"merged_at": "2020-02-12T04:08:59Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1760
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1760/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1760/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1760/events
|
https://github.com/materialsproject/pymatgen/pull/1760
| 561,948,342
|
MDExOlB1bGxSZXF1ZXN0MzcyNjYzNDA4
| 1,760
|
Revise POTCAR hash checking
|
{
"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 |
[
"@mkhorton the only test failure left arises in `MPNonSCFSet`. Can you please inspect this error and help me understand what's happening? \r\n\r\nBecause of the hash checking, whenever we init a `DictSet` or derived class we now loop through each of the potcars. Doing so causes a call to `self.potcar_symbols`, which in turn calls `self.poscar`, which is built from the structure. For some reason, the `standardize=True` argument in `MPNonSCFSet` is causing this init process to fail (other tests use this inputset without the standardize argument, and those tests pass).\r\n\r\nI've confirmed using print statements that the `get_refined_structure` method is receiving all its expected arguments, and none of them is `None`. So I'm not sure where the `TypeError` is coming from.\r\n\r\n\r\n```__________________________________________________________________________________________________________________________________________________________________________________________ MPNonSCFSetTest.test_init ___________________________________________________________________________________________________________________________________________________________________________________________\r\n\r\nself = <pymatgen.io.vasp.tests.test_sets.MPNonSCFSetTest testMethod=test_init>\r\n\r\n def test_init(self):\r\n prev_run = self.TEST_FILES_DIR / \"relaxation\"\r\n # check boltztrap mode\r\n vis = MPNonSCFSet.from_prev_calc(prev_calc_dir=prev_run, mode=\"Boltztrap\")\r\n self.assertEqual(vis.incar[\"ISMEAR\"], 0)\r\n \r\n # check uniform mode\r\n vis = MPNonSCFSet.from_prev_calc(prev_calc_dir=prev_run, mode=\"Uniform\")\r\n self.assertEqual(vis.incar[\"ISMEAR\"], -5)\r\n self.assertEqual(vis.incar[\"ISYM\"], 2)\r\n \r\n # check uniform mode with automatic nedos\r\n vis = MPNonSCFSet.from_prev_calc(prev_calc_dir=prev_run, mode=\"Uniform\",\r\n nedos=0)\r\n self.assertEqual(vis.incar[\"NEDOS\"], 12217)\r\n \r\n # test line mode\r\n vis = MPNonSCFSet.from_prev_calc(\r\n prev_calc_dir=prev_run,\r\n mode=\"Line\",\r\n copy_chgcar=False,\r\n user_incar_settings={\"SIGMA\": 0.025},\r\n )\r\n \r\n self.assertEqual(vis.incar[\"NSW\"], 0)\r\n # Check that the ENCUT has been inherited.\r\n self.assertEqual(vis.incar[\"ENCUT\"], 600)\r\n # Check that the user_incar_settings works\r\n self.assertEqual(vis.incar[\"SIGMA\"], 0.025)\r\n self.assertEqual(vis.kpoints.style, Kpoints.supported_modes.Reciprocal)\r\n \r\n # Check as from dict.\r\n vis = MPNonSCFSet.from_dict(vis.as_dict())\r\n self.assertEqual(vis.incar[\"NSW\"], 0)\r\n # Check that the ENCUT has been inherited.\r\n self.assertEqual(vis.incar[\"ENCUT\"], 600)\r\n self.assertEqual(vis.kpoints.style, Kpoints.supported_modes.Reciprocal)\r\n \r\n vis.write_input(self.tmp)\r\n self.assertFalse(os.path.exists(os.path.join(self.tmp, \"CHGCAR\")))\r\n \r\n vis = MPNonSCFSet.from_prev_calc(\r\n prev_calc_dir=prev_run, mode=\"Line\", copy_chgcar=True\r\n )\r\n # check ISMEAR set correctly for line mode\r\n self.assertEqual(vis.incar[\"ISMEAR\"], 0)\r\n vis.write_input(self.tmp)\r\n self.assertTrue(os.path.exists(os.path.join(self.tmp, \"CHGCAR\")))\r\n os.remove(os.path.join(self.tmp, \"CHGCAR\"))\r\n \r\n vis = MPNonSCFSet.from_prev_calc(\r\n> prev_calc_dir=prev_run, standardize=True, mode=\"Line\", copy_chgcar=True\r\n )\r\n\r\ntests/test_sets.py:650: \r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \r\nsets.py:1541: in from_prev_calc\r\n input_set = cls(_dummy_structure, **kwargs)\r\nsets.py:1337: in __init__\r\n super().__init__(structure, **kwargs)\r\nsets.py:772: in __init__\r\n super().__init__(structure, MPRelaxSet.CONFIG, **kwargs)\r\nsets.py:439: in __init__\r\n for psingle in self.potcar:\r\nsets.py:129: in potcar\r\n potcar = Potcar(self.potcar_symbols, functional=self.potcar_functional)\r\nsets.py:111: in potcar_symbols\r\n elements = self.poscar.site_symbols\r\nsets.py:603: in poscar\r\n return Poscar(self.structure)\r\nsets.py:463: in structure\r\n international_monoclinic=self.international_monoclinic,\r\nsets.py:2845: in standardize_structure\r\n international_monoclinic=international_monoclinic\r\n../../symmetry/analyzer.py:423: in get_primitive_standard_structure\r\n international_monoclinic=international_monoclinic)\r\n../../symmetry/analyzer.py:480: in get_conventional_standard_structure\r\n struct = self.get_refined_structure()\r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ \r\n\r\nself = <pymatgen.symmetry.analyzer.SpacegroupAnalyzer object at 0x8200f2f28>\r\n\r\n def get_refined_structure(self):\r\n \"\"\"\r\n Get the refined structure based on detected symmetry. The refined\r\n structure is a *conventional* cell setting with atoms moved to the\r\n expected symmetry positions.\r\n \r\n Returns:\r\n Refined structure.\r\n \"\"\"\r\n # Atomic positions have to be specified by scaled positions for spglib.\r\n lattice, scaled_positions, numbers \\\r\n> = spglib.refine_cell(self._cell, self._symprec, self._angle_tol)\r\nE TypeError: 'NoneType' object is not iterable\r\n\r\n../../symmetry/analyzer.py:314: TypeError```",
"Actually, I see that in the CI testing everything is failing with, for example, `E OSError: You do not have the right POTCAR with functional PBE and label F in your VASP_PSP_DIR`. So the CI is not finding the potcars. This doesn't occur on my local testing, and I can't see how my changes would have triggered this. Has anything changed recently with the pymatgen CI test env?",
"Make sjure you are up to date with master.",
"Yes @shyuep I am",
"@shyuep I pulled the latest master to catch the changes you made today, but am still seeing VASP tests fail with `E OSError: You do not have the right POTCAR with functional PBE and label F in your VASP_PSP_DIR`. Do you have any other ideas about what might be happening?",
"Not sure. I don’t see this error.\n\nOn Tue, Feb 11, 2020 at 12:01 Ryan Kingsbury <notifications@github.com>\nwrote:\n\n> @shyuep <https://github.com/shyuep> I pulled the latest master to catch\n> the changes you made today, but am still seeing VASP tests fail with E\n> OSError: You do not have the right POTCAR with functional PBE and label F\n> in your VASP_PSP_DIR. Do you have any other ideas about what might be\n> happening?\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1760?email_source=notifications&email_token=AAEM4U2ADHQQUJIQMCYI2RLRCL7ZVA5CNFSM4KRXJQ62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELN3KQQ#issuecomment-584824130>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAEM4UY4CPEUZAD5QRDNVETRCL7ZVANCNFSM4KRXJQ6Q>\n> .\n>\n-- \nShyue Ping\n",
"@shyuep @mkhorton I've identified the cause of the failures and am seeking your input on the best workaround.\r\n\r\nBy placing hash checking in the `init` of each input set, we cause the `.potcar` attribute to be called when an `InputSet` is created. As a result, we get a bunch of new test failures b/c many of the `InputSet`s in the tests require POTCARs that aren't in the test folders. The tests themselves don't call `.potcar`, so this was not an issue before.\r\n\r\nOne solution would be to use the `potcar_spec=True` option to all `InputSet` in the test files. We developed that option specifically to address this problem. However, there are some tests that may require actually inspecting the POTCAR file, and using the `potcar_spec` flag might defeat the purpose.\r\n\r\nA second solution would be to move hash checking to occur when the `.potcar` attribute is called rather than in `init`.",
"> @shyuep @mkhorton I've identified the cause of the failures and am seeking your input on the best workaround.\r\n> \r\n> By placing hash checking in the `init` of each input set, we cause the `.potcar` attribute to be called when an `InputSet` is created. As a result, we get a bunch of new test failures b/c many of the `InputSet`s in the tests require POTCARs that aren't in the test folders. The tests themselves don't call `.potcar`, so this was not an issue before.\r\n> \r\n> One solution would be to use the `potcar_spec=True` option to all `InputSet` in the test files. We developed that option specifically to address this problem. However, there are some tests that may require actually inspecting the POTCAR file, and using the `potcar_spec` flag might defeat the purpose.\r\n> \r\n> A second solution would be to move hash checking to occur when the `.potcar` attribute is called rather than in `init`.\r\n\r\nI opted to move the hash checking into the `.potcar` attribute of `VaspInputSet`, as this seemed both easier and safer to implement without accidentally breaking something.",
"@bjmorgan Can you test this branch and let us know if you see any other unexpected behavior related to the POTCAR hashes?",
"@rkingsbury thanks for this -- I would still say the most appropriate place for this is in `Potcar` init, happy to compromise on the .potcar attribute however.",
"Thanks @rkingsbury !"
] | 2020-02-08T01:24:37
| 2020-02-18T21:26:32
|
2020-02-18T19:32:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
By way for further response to #1746 and related discussions, this PR revises the way POTCAR hash checking is implemented. Specifically:
* md5 hashes of the POTCAR files and the POTCAR data itself (`potcar.hash`) were recomputed against the complete set of freshly-downloaded files distributed with VASP 5.4.4.
* The recomputed file hashes were checked against the data compiled by @bjmorgan in vasppy. Our hash database now contains every hash in the vasppy set except for `0c04467f51b768cef1567df3e2794f25`, plus 103 additional hashes that are not present in the vasppy set.
* added an `identify_potcar` method to `PotcarSingle` that reports which potcar_functionals (e.g. PBE, PBE_54, LDA, etc.) a given POTCAR is known to be associated with. The method also includes descriptions of each functional that closely mirror what is shown on the VASP portal, to minimize confusion.
* Moved POTCAR hash checking from InputSets to `PotcarSingle`. Now, anytime a `PotcarSingle` is instantiated, its hash is checked against the database. If either the POTCAR data or the metadata are not known to match a VASP potcar, a descriptive warning is raised. The warning is not fatal.
* When the `.potcar` attribute of any `VaspInputSet` is called, `identify_potcar` is used to retrieve the functionals that the POTCARs are known to correspond to. If the functional specified in the input set does not match the functional of the POTCAR, a `BadInputSetWarning` is raised
|
{
"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/1760/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/1760/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1760",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1760",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1760.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1760.patch",
"merged_at": "2020-02-18T19:32:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1761
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1761/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1761/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1761/events
|
https://github.com/materialsproject/pymatgen/issues/1761
| 561,950,409
|
MDU6SXNzdWU1NjE5NTA0MDk=
| 1,761
|
Improve input set warnings
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "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
}
|
[
{
"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
}
] | null |
[] | 2020-02-08T01:37:43
| 2023-08-13T16:32:56
|
2023-08-13T16:32:56Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The current if statement is insufficient and can raise a false positive.
https://github.com/materialsproject/pymatgen/blob/749ee4dacab0698acf60120ac35b5065a4ad1f0a/pymatgen/io/vasp/sets.py#L573
Edit: Actually, the logic seems fine, however still getting the error on an MPStaticSet (eg of Al).
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1761/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1761/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1762
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1762/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1762/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1762/events
|
https://github.com/materialsproject/pymatgen/issues/1762
| 562,202,496
|
MDU6SXNzdWU1NjIyMDI0OTY=
| 1,762
|
visualize multiple molecules
|
{
"login": "Chen-Cai-OSU",
"id": 47577816,
"node_id": "MDQ6VXNlcjQ3NTc3ODE2",
"avatar_url": "https://avatars.githubusercontent.com/u/47577816?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Chen-Cai-OSU",
"html_url": "https://github.com/Chen-Cai-OSU",
"followers_url": "https://api.github.com/users/Chen-Cai-OSU/followers",
"following_url": "https://api.github.com/users/Chen-Cai-OSU/following{/other_user}",
"gists_url": "https://api.github.com/users/Chen-Cai-OSU/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Chen-Cai-OSU/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Chen-Cai-OSU/subscriptions",
"organizations_url": "https://api.github.com/users/Chen-Cai-OSU/orgs",
"repos_url": "https://api.github.com/users/Chen-Cai-OSU/repos",
"events_url": "https://api.github.com/users/Chen-Cai-OSU/events{/privacy}",
"received_events_url": "https://api.github.com/users/Chen-Cai-OSU/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I think your original post already answers the question. I think (1) can be done with nglview and you can make sure all the molecule plots are the same size. (2) Once you have 100 images from (1), you can easily use the Pillow package to stitch images. See https://stackoverflow.com/questions/10657383/stitching-photos-together for an example.",
"Sure thing I can do that myself. But this often requires taking care out input/ouput and convert matplotlib figures to images and then stitch images together. Taking care of those things usually takes quite some time and my intention is simply take a look at data before doing any analysis. \n\nI feels that this is better done in pymatgen instead by users.\n\n> On Feb 9, 2020, at 11:33 AM, Shyue Ping Ong <notifications@github.com> wrote:\n> \n> Closed #1762 <https://github.com/materialsproject/pymatgen/issues/1762>.\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/1762?email_source=notifications&email_token=ALK7VWC3K5Z2UH5FONCSXNLRCAV47A5CNFSM4KSCYBC2YY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOWQGGIQQ#event-3020710978>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALK7VWFSWB2ROTWJQCOSCCLRCAV47ANCNFSM4KSCYBCQ>.\n> \n\n"
] | 2020-02-09T16:29:22
| 2020-02-10T15:12:15
|
2020-02-10T15:12:15Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello,
I am trying to visualize multiple molecules to get the sense of the whole dataset. First, I tried [nglview](https://github.com/arose/nglview/issues/864) it works for single-molecule but not work for multiple ones. From this [post](https://github.com/materialsproject/pymatgen/issues/1310) , pymatgen.vis.structure_chemview is also not the right way.
I was wondering would you like to suggest some quick visualization tools that can 1) plot and save a single molecule as a png and 2) plot all many molecules, say 100, into a 10*10 grid very easily?
I am a computer scientist who doesn't know much about chemistry and material science. The two above requirements seem to be very reasonable and I am having a hard time finding an easy way to achieve this. Hopefully, this make sense to you. Thank you very much for your help!
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1762/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1762/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1763
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1763/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1763/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1763/events
|
https://github.com/materialsproject/pymatgen/pull/1763
| 562,280,547
|
MDExOlB1bGxSZXF1ZXN0MzcyOTA0NTgy
| 1,763
|
Minor fixes to structure mactcher and volumetric data
|
{
"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 |
[
"References #1665 "
] | 2020-02-10T01:42:20
| 2020-02-11T15:09:19
|
2020-02-11T15:09:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
- Allow the fit function in structure matcher to be symmetric
- Updated the from_hdf5 function so that inherited classes can use it more readily.
- Changed the way Chgcar objects are initialized so work with the above change
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1763/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1763/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1763",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1763",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1763.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1763.patch",
"merged_at": "2020-02-11T15:09:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1764
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1764/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1764/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1764/events
|
https://github.com/materialsproject/pymatgen/issues/1764
| 562,302,297
|
MDU6SXNzdWU1NjIzMDIyOTc=
| 1,764
|
MaterialsProjectCompatibility method process_entries fails if symmetry determination of any entry fails
|
{
"login": "LuciusV",
"id": 11925386,
"node_id": "MDQ6VXNlcjExOTI1Mzg2",
"avatar_url": "https://avatars.githubusercontent.com/u/11925386?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/LuciusV",
"html_url": "https://github.com/LuciusV",
"followers_url": "https://api.github.com/users/LuciusV/followers",
"following_url": "https://api.github.com/users/LuciusV/following{/other_user}",
"gists_url": "https://api.github.com/users/LuciusV/gists{/gist_id}",
"starred_url": "https://api.github.com/users/LuciusV/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/LuciusV/subscriptions",
"organizations_url": "https://api.github.com/users/LuciusV/orgs",
"repos_url": "https://api.github.com/users/LuciusV/repos",
"events_url": "https://api.github.com/users/LuciusV/events{/privacy}",
"received_events_url": "https://api.github.com/users/LuciusV/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Hmmm interesting. But it is very rare that symmetry detection fails. Typically the worst case scenario is that the structure returns a P1. Failure usually occurs only when you have colliding atoms, in which case the calculation is completely useless....\r\n\r\nDo you have an example where this failure occured on a normal structure?",
"You are right, I just checked, this is because of bad structure, it exploded during optimization and also has overlapped atoms like you mentioned. Actually its only one structure in about 30000 entries, so considering mentioned above I don't expect this happen in normal structure now."
] | 2020-02-10T03:26:29
| 2020-02-11T14:47:47
|
2020-02-11T14:47:47Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I process a lot of calculated entries collected by BorgQueen and put them in all_entries list. Then when I use
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
processed_entries = compat.process_entries(all_entries)
I got exception
`/home/youjin/.local/lib64/python3.6/site-packages/pymatgen/symmetry/analyzer.py in get_space_group_symbol(self)
105 (str): Spacegroup symbol for structure.
106 """
--> 107 return self._space_group_data["international"]
108
109 def get_space_group_number(self):
TypeError: 'NoneType' object is not subscriptable`
Obviously because symmetry determination in
`/home/youjin/.local/lib64/python3.6/site-packages/pymatgen/analysis/structure_analyzer.py in sulfide_type(structure)
620
621 finder = SpacegroupAnalyzer(structure, symprec=0.1)
--> 622 symm_structure = finder.get_symmetrized_structure()`
fails.
I suggest changing
`/home/youjin/.local/lib64/python3.6/site-packages/pymatgen/entries/compatibility.py in process_entry(self, entry)
438 """
439 try:
--> 440 corrections = self.get_corrections_dict(entry)
441 except CompatibilityError:
442 return None`
to also catch TypeError.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1764/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1764/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1765
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1765/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1765/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1765/events
|
https://github.com/materialsproject/pymatgen/issues/1765
| 562,314,763
|
MDU6SXNzdWU1NjIzMTQ3NjM=
| 1,765
|
visualization
|
{
"login": "Chen-Cai-OSU",
"id": 47577816,
"node_id": "MDQ6VXNlcjQ3NTc3ODE2",
"avatar_url": "https://avatars.githubusercontent.com/u/47577816?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Chen-Cai-OSU",
"html_url": "https://github.com/Chen-Cai-OSU",
"followers_url": "https://api.github.com/users/Chen-Cai-OSU/followers",
"following_url": "https://api.github.com/users/Chen-Cai-OSU/following{/other_user}",
"gists_url": "https://api.github.com/users/Chen-Cai-OSU/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Chen-Cai-OSU/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Chen-Cai-OSU/subscriptions",
"organizations_url": "https://api.github.com/users/Chen-Cai-OSU/orgs",
"repos_url": "https://api.github.com/users/Chen-Cai-OSU/repos",
"events_url": "https://api.github.com/users/Chen-Cai-OSU/events{/privacy}",
"received_events_url": "https://api.github.com/users/Chen-Cai-OSU/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Check out StructureVis: https://pymatgen.org/pymatgen.vis.structure_vtk.html"
] | 2020-02-10T04:18:40
| 2020-02-13T02:39:47
|
2020-02-13T02:39:47Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello,
Sorry I have to reopen this issue. https://github.com/materialsproject/pymatgen/issues/1762. It turns out that ngl cannot save visualization of a single molecule in python script. (only support Jupiter notebook) So right now I don't even know how to visualize a single molecule (cif file) in a python script.
I am not asking for a simple solution to visualize multiple molecules. (I can do this my self by stitching a bunch of png files myself) Would you like to provide a working example to visualize a cif file?
Thank you very much!
|
{
"login": "Chen-Cai-OSU",
"id": 47577816,
"node_id": "MDQ6VXNlcjQ3NTc3ODE2",
"avatar_url": "https://avatars.githubusercontent.com/u/47577816?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Chen-Cai-OSU",
"html_url": "https://github.com/Chen-Cai-OSU",
"followers_url": "https://api.github.com/users/Chen-Cai-OSU/followers",
"following_url": "https://api.github.com/users/Chen-Cai-OSU/following{/other_user}",
"gists_url": "https://api.github.com/users/Chen-Cai-OSU/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Chen-Cai-OSU/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Chen-Cai-OSU/subscriptions",
"organizations_url": "https://api.github.com/users/Chen-Cai-OSU/orgs",
"repos_url": "https://api.github.com/users/Chen-Cai-OSU/repos",
"events_url": "https://api.github.com/users/Chen-Cai-OSU/events{/privacy}",
"received_events_url": "https://api.github.com/users/Chen-Cai-OSU/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1765/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1765/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1766
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1766/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1766/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1766/events
|
https://github.com/materialsproject/pymatgen/pull/1766
| 562,767,264
|
MDExOlB1bGxSZXF1ZXN0MzczMzAyODI4
| 1,766
|
Minor fixes to Zeo++ interface
|
{
"login": "dskoda",
"id": 17065914,
"node_id": "MDQ6VXNlcjE3MDY1OTE0",
"avatar_url": "https://avatars.githubusercontent.com/u/17065914?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dskoda",
"html_url": "https://github.com/dskoda",
"followers_url": "https://api.github.com/users/dskoda/followers",
"following_url": "https://api.github.com/users/dskoda/following{/other_user}",
"gists_url": "https://api.github.com/users/dskoda/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dskoda/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dskoda/subscriptions",
"organizations_url": "https://api.github.com/users/dskoda/orgs",
"repos_url": "https://api.github.com/users/dskoda/repos",
"events_url": "https://api.github.com/users/dskoda/events{/privacy}",
"received_events_url": "https://api.github.com/users/dskoda/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-02-10T19:10:20
| 2020-02-11T15:09:04
|
2020-02-11T15:09:03Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fixes minor bugs on Zeo++ interface.
* `from_parameters(structure.lattice.parameters)` -> `from_parameters(*structure.lattice.parameters)` (starred)
* `self._mol` does not exist in `pymatgen.io.xyz.XYZ` anymore. Replaced by `self._mols[0]`.
* Test for getting free sphere parameters skipped, as file `free_sph.cif` does not exist anymore. All other tests for the zeopp file are ok.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1766/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1766/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1766",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1766",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1766.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1766.patch",
"merged_at": "2020-02-11T15:09:03Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1767
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1767/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1767/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1767/events
|
https://github.com/materialsproject/pymatgen/pull/1767
| 563,747,799
|
MDExOlB1bGxSZXF1ZXN0Mzc0MTAzMDIx
| 1,767
|
[WIP] Allow pandas 1.0+
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-02-12T04:39:55
| 2021-02-13T17:26:30
|
2020-03-27T19:23:01Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Pandas 1.0 introduced a lot of breaking changes, need to update pymatgen to accommodate these.
|
{
"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/1767/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1767/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1767",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1767",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1767.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1767.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1768
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1768/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1768/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1768/events
|
https://github.com/materialsproject/pymatgen/pull/1768
| 563,899,465
|
MDExOlB1bGxSZXF1ZXN0Mzc0MjI2MDM5
| 1,768
|
Two small bugfixes
|
{
"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 |
[
"I will work on a test.",
"Travis CI is complaining about missing docstrings. Do I need to change this?\r\nThanks.",
"Should I add the docstrings? If so, let me know.",
"Yes pls. Thanks.",
"I think it is ready to be merged.",
"Thanks!"
] | 2020-02-12T10:26:45
| 2020-02-18T19:32:33
|
2020-02-18T19:32:28Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
I am commiting two very small bug fixes. One allows to open gzipped ICOHPLIST.lobster files. The other one closes the plt after saving a plot with a phonon dos with the PhononDosPlotter. This is done similar to "save_plot" in PhononBSPlotter.
|
{
"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/1768/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1768/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1768",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1768",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1768.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1768.patch",
"merged_at": "2020-02-18T19:32:28Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1769
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1769/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1769/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1769/events
|
https://github.com/materialsproject/pymatgen/pull/1769
| 566,629,728
|
MDExOlB1bGxSZXF1ZXN0Mzc2NDA0NzQw
| 1,769
|
Replace deprecated modules
|
{
"login": "CifLord",
"id": 8036054,
"node_id": "MDQ6VXNlcjgwMzYwNTQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/8036054?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/CifLord",
"html_url": "https://github.com/CifLord",
"followers_url": "https://api.github.com/users/CifLord/followers",
"following_url": "https://api.github.com/users/CifLord/following{/other_user}",
"gists_url": "https://api.github.com/users/CifLord/gists{/gist_id}",
"starred_url": "https://api.github.com/users/CifLord/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/CifLord/subscriptions",
"organizations_url": "https://api.github.com/users/CifLord/orgs",
"repos_url": "https://api.github.com/users/CifLord/repos",
"events_url": "https://api.github.com/users/CifLord/events{/privacy}",
"received_events_url": "https://api.github.com/users/CifLord/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks!\r\n\r\nYes, I think they're unrelated -- I was trying to track those down too but the noisy tests were making it difficult, so thanks for fixing :-)"
] | 2020-02-18T03:55:52
| 2020-02-18T04:46:41
|
2020-02-18T04:46:41Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Replace all deprecated use of scipy for linear algebra with numpy in wulff.py.
@mkhorton I think this should fix the noisy py3test issue on CircleCi, as I didn't see the previous messages from my tests flooding CircleCi anymore, but I did see some errors in things like test_molecule_matcher.py, though I don't think that is related to this pull right?
|
{
"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/1769/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1769/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1769",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1769",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1769.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1769.patch",
"merged_at": "2020-02-18T04:46:41Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1770
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1770/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1770/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1770/events
|
https://github.com/materialsproject/pymatgen/pull/1770
| 568,077,032
|
MDExOlB1bGxSZXF1ZXN0Mzc3NTcxNjk3
| 1,770
|
Critic2 updates
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-02-20T06:18:30
| 2021-02-13T17:29:15
|
2020-04-20T20:27:56Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Adaptor for critic2 analysis code, deprecating the old parsing method (from stdout) and adding a new method to parse from JSON.
Have a few changes before merging.
|
{
"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/1770/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1770/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1770",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1770",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1770.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1770.patch",
"merged_at": "2020-04-20T20:27:56Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1771
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1771/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1771/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1771/events
|
https://github.com/materialsproject/pymatgen/pull/1771
| 568,505,026
|
MDExOlB1bGxSZXF1ZXN0Mzc3OTIyMTg0
| 1,771
|
[WIP] Implement units using pint
|
{
"login": "ayushsgupta",
"id": 16586331,
"node_id": "MDQ6VXNlcjE2NTg2MzMx",
"avatar_url": "https://avatars.githubusercontent.com/u/16586331?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ayushsgupta",
"html_url": "https://github.com/ayushsgupta",
"followers_url": "https://api.github.com/users/ayushsgupta/followers",
"following_url": "https://api.github.com/users/ayushsgupta/following{/other_user}",
"gists_url": "https://api.github.com/users/ayushsgupta/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ayushsgupta/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ayushsgupta/subscriptions",
"organizations_url": "https://api.github.com/users/ayushsgupta/orgs",
"repos_url": "https://api.github.com/users/ayushsgupta/repos",
"events_url": "https://api.github.com/users/ayushsgupta/events{/privacy}",
"received_events_url": "https://api.github.com/users/ayushsgupta/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @ayushsgupta, this looks like a good start but there's a lot of items that will need to be addressed:\r\n\r\n* you should move the unit registry out of the root pymatgen init, this should live in pymatgen.core.units\r\n\r\n* this will be *much* easier to merge if it's two separate pull requests: the first pull request simply replaces current usage of units in pymatgen, the second pull request adds unit functionality to new modules -- this second case will require more discussion\r\n\r\n* in the second case, care should be taken to make sure this does not adversely affect performance\r\n\r\n* it's not clear to me why \".magnitude\" has to be used in so many places, since math can be performed on pint Quantity objects directly\r\n\r\n* I understand this is a \"work in progress / WIP\" PR so it's not a problem right now, but there are a lot of print statements and commented out blocks here -- as a guideline, these should never be committed to start with, it's easier to keep commits clean than to go back and tidy them later\r\n\r\nThanks for your work on this!",
"Thanks @mkhorton , we know this still has a ways to go. I asked @ayushsgupta to go ahead and open a WIP PR to facilitate feedback as his work progresses. \r\n\r\nRe: bullet 2 - This was our initial goal, but due to some idiosyncratic differences between pymatgen's `XXWithUnit` classes and `Quantity` objects, it wasn't as straightforward where to draw the boundary as we expected. We were trying to completely eliminate, e.g., `FloatWithUnit` rather than have to write a wrapper around `Quantity`, which is how we wound up with a bit deeper integration than we first expected. But I agree it makes sense to have separate PRs for the initial migration to pint vs. a more comprehensive integration. What exactly do you have in mind when you say \"replaces current usage in pymatgen\"?\r\n\r\nRe: point 3 - Ayush has done some performance testing and so far it's a mixed bag - certain methods are slower but a few are somehow faster with Quantity!\r\n\r\nRe: point 4 - you are right that math can be done on `Quantity` objects directly, but don't we need to be concerned about breaking existing scripts that are expecting floats? We consider using .magnitude the shortest, safest path to getting the initial `Quantity` support working. ",
"> I asked @ayushsgupta to go ahead and open a WIP PR to facilitate feedback as his work progresses.\r\n\r\nExcellent -- definitely appreciate the open PR, I agree it makes feedback a lot easier!\r\n\r\n> What exactly do you have in mind when you say \"replaces current usage in pymatgen\"?\r\n\r\nI meant one PR where it replaces current `FloatWithUnit` usage (etc.), and a second PR if you want to add it to any new classes.\r\n\r\n> certain methods are slower but a few are somehow faster with Quantity!\r\n\r\nReally interested in what the faster ones might be! Could reveal some easy performance optimizations we could make.\r\n\r\n> We consider using .magnitude the shortest, safest path to getting the initial Quantity support working.\r\n\r\nPossibly -- I think it just makes the code a lot more difficult to parse. If you have to get the magnitude conversion, you could convert relevant quantities at the top of the function/method/wherever rather than inline. Also make sure to check [this page](https://pint.readthedocs.io/en/0.11/wrapping.html) in the pint docs which might be useful, as well as the second section [here](https://pint.readthedocs.io/en/0.11/performance.html).\r\n\r\n> but don't we need to be concerned about breaking existing scripts that are expecting floats? \r\n\r\nDefinitely concerned, I'm not entirely sure though. Maybe there's a clean way to do it -- I'm interested to see how this PR turns out. It could definitely break type hints too, depending on implementation. I'm optimistic we can find a good solution though.",
"@rkingsbury feel free to correct me on anything I say here or if you have something else to add. @mkhorton thanks for the feedback. \r\n\r\n> Really interested in what the faster ones might be! Could reveal some easy performance optimizations we could make.\r\n\r\nFile | Time_Q | Time_O | Std_Dev_Q | Std_Dev_O\r\n-- | -- | -- | -- | --\r\nanalysis/elastic | 89 | 90 | 4.35 | 2.37\r\nanalysis/local_env | 112 | 119 | 9.98 | 8.18\r\nanalysis/nmr | 2.71 | 2.25 | 1.45E-04 | 5.35E-05\r\nanalysis/quasiharmonic | 3.16 | 2.64 | 1.69E-04 | 7.66E-05\r\ncore/lattice | 6.53 | 5.7 | 7.18E-05 | 1.14E-04\r\ncore/periodic_table | 6.66 | 6.12 | 1.31E-04 | 2.66E-04\r\ncore/structure | 120 | 121 | 3.94E+00 | 5.75E+00\r\ncore/surface | 84 | 102 | 2.71 | 6.07\r\nentries/compatibility | 3.29 | 2.45 | 1.45E-04 | 4.39E-05\r\nentries/computed_entry | 3.86 | 3.8 | 4.23E-04 | 1.10E-04\r\n\r\nThis is the timing data for 10 files I chose because I had modified them to use Quantity instead of FloatWithUnit. I used %timeit from jupyter on the test files, 7 trials each. Q = Quantity, O = original, everything's in seconds.",
"Just a note that breaking existing scripts is NOT an option. I would rather have whatever suboptimal implementation in pymatgen currently that is completely compatible with normal Float use, than to try to replace it with pint and break everything expecting a float. Note that most people do not even care that the things are properly unitized and they just want the float value and they can deal with units separately themselves. ",
"Yes, agreed, requiring a type cast to float after every functional call is clearly not an acceptable outcome. But I'm optimistic we can find a good solution, this PR is intended to explore the idea of what it could look like.\r\n\r\n> Note that most people do not even care that the things are properly unitized and they just want the float value and they can deal with units separately themselves.\r\n\r\nI don't really agree with this, I think we can be *much* better as a community with unit handling. Angstroms and eVs are fine, but anything more complex than that is how mistakes are made (and I've seen eV vs eV/atom mistakes myself, that would be caught by a more rigorous unit system).",
"Or, I think you're right that most people probably don't care, but I think we're in a position we can push to raise the bar a little on this.",
"Just to clarify, it is not that I don't think units are useful. They are. I cannot recall how many times I have to do the eV/atom to J/mol conversion. A proper unit system makes this a lot more painless.\r\n\r\nWhat I meant is that most people just take the float value and run with it. Because most people work with whatever existing unit system is from the output. The only time units matter is when you have to compute the capacity in mAh/g or something that an experimentalist uses. So an unacceptable outcome is that all outputs from pymatgen require someone to do `.magnitude` or `float(x)` to use. \r\n\r\nIf you can solve this in a way that is completely transparent and bug free to the user, I am fine with moving to pint. Otherwise, there is no value proposition from pint that would convince me it is a good idea. I would rather have a much less powerful system that doesn't kill usability.",
"Thanks @ayushsgupta for digging into the details of this; we're eager to hear everyone's thoughts on the best way forward. Here is a synopsis of the challenge we face:\r\n\r\n#### Difference between `Quantity` and `FloatWithUnit`\r\n\r\nPart of the reason for so many internal calls to `.magnitude` is that pint `Quantity` has stricter units handling than `FloatWithUnit`. For example, a `FloatWithUnit` will allow you to add a regular float (which drops the unit and changes the return type to a regular float), whereas `Quantity` will not. \r\n\r\n`FloatWithUnit` allows arithmetic with heterogeneous units (regular floats) by dropping units information:\r\n\r\n```\r\n>>> from pymatgen.core.units import FloatWithUnit\r\n>>> e = FloatWithUnit(1.1, \"eV\")\r\n>>> print(e)\r\n1.1 eV\r\n>>> e + 2\r\n3.1\r\n```\r\n\r\n`Quantity` only allows math in consistent units:\r\n```\r\n>>> from pint import UnitRegistry\r\n>>> ureg = UnitRegistry()\r\n>>> Q=ureg.Quantity\r\n>>> e = Q(1, 'eV')\r\n>>> print(e)\r\n1 electron_volt\r\n>>> e+2\r\n---------------------------------------------------------------------------\r\nDimensionalityError Traceback (most recent call last)\r\n~/pymatgen/pymatgen/entries/compatibility.py in \r\n 4 e = Q(1, 'eV')\r\n 5 print(e)\r\n----> 6 e+2\r\n\r\n~/miniconda3/envs/mp/lib/python3.6/site-packages/pint/quantity.py in __add__(self, other)\r\n 752 return self.to_timedelta() + other\r\n 753 else:\r\n--> 754 return self._add_sub(other, operator.add)\r\n 755 \r\n 756 __radd__ = __add__\r\n\r\n~/miniconda3/envs/mp/lib/python3.6/site-packages/pint/quantity.py in wrapped(self, *args, **kwargs)\r\n 73 elif isinstance(other, list) and isinstance(other[0], type(self)):\r\n 74 return NotImplemented\r\n---> 75 result = f(self, *args, **kwargs)\r\n 76 return result\r\n 77 return wrapped\r\n\r\n~/miniconda3/envs/mp/lib/python3.6/site-packages/pint/quantity.py in _add_sub(self, other, op)\r\n 663 _to_magnitude(other, self.force_ndarray))\r\n 664 else:\r\n--> 665 raise DimensionalityError(self._units, 'dimensionless')\r\n 666 return self.__class__(magnitude, units)\r\n 667 \r\n\r\nDimensionalityError: Cannot convert from 'electron_volt' to 'dimensionless'\r\n```\r\n\r\nI think the more robust approach taken by `pint` will definitely benefit pymatgen in the long run, but we'll have to think carefully about the best way to make the transition without breaking too many existing scripts. That said, in my opinion we *should* be breaking existing scripts that only work because they ignore units. For example, Ayush discovered that pymatgen's `CostEntry` class actually uses the `.energy` attribute to store cost information, so you are doing computations with a \"cost\" in energy units even though it's supposed to be $/mol. These types of inconsistencies will only become visible when we have something like pint tracking all the calculations and those inconsistent things start to break. We can of course use deprecation warnings and other means to transition gradually though.\r\n\r\n#### Units in pymatgen\r\n\r\nIn the pymatgen codebase, most of the methods that return `FloatWithUnit` are in the `periodic_table` module, which is heavily utilized throughout the rest of pymatgen. So clearly these methods are intended to pass units information to downstream methods. However, almost nothing calls the `._unit` attribute of `FloatWithUnit`, so the returned values are more or less behaving as floats. \r\n\r\nGiven the above difference between `Quantity` and `FloatWithUnit`, we have a couple of options for how to migrate to pint:\r\n\r\n1. Change the return type of everything in `periodic_table` to `Quantity` (as done here), and use pint's wrapper to enforce specific units on downstream methods without having to modify the downstream methods themselves. We have the option here of either requiring input arguments to be `Quantity` or allowing floats as inputs (and assuming they have the correct units). We also have the option to return either `Quantity` or Float.\r\n\r\n2. Use `Quantity` internally in `periodic_table` but return `.magnitude` (losing any units information in downstream code, e.g. the `._unit` attribute)\r\n\r\n3. Keep `FloatWithUnit` as a lightweight wrapper around `Quantity` that mimics existing behavior (which would not enforce the more rigorous units handling)\r\n\r\nThere are some more complicated approaches we could use to make this more transparent to users. For example, we could try to 4. add a `unit=` kwarg to pymatgen methods, with an expected default, and then construct `Quantity` internally, e.g.:\r\n\r\n```def some_func(float, unit='eV'):\r\n self.q = Q(float, unit)\r\n <do math with self.q>\r\n return self.q OR self.q.magnitude\r\n```\r\n\r\nAlternatively, 5. we could use type checking so that the method call signatures would either be Quantity -> Quantity or Float -> Float.\r\n\r\nPersonally I am in favor of Option 1, where we pass `Quantity` within pymatgen but also allow floats (and assume correct units) for compatibility reasons. We might introduce a deprecation warning at some point and eventually require `Quantity` inputs to those methods. This way, methods in pymatgen outside of `periodic_table` will still work with floats as inputs, and it will be easy for us to move to more robust handling in the future.",
"Thanks @rkingsbury . I am not in favor of stricter checking. I agree of course that if we fully adopt pint, it will help avoid certain errors. But it is *not* the role for pymatgen to play. Most people do not want someone else to be babysitting units for them.\r\n\r\nFor example, a fairly accomplished users knows that VASP returns energies in eV. When I am lazy and I want to convert that to joule, I just do X * 1.6e-19. I do not want it such that I have to do X.to(“J”) or X.magnitude * 1.6e-19. That violates what people mostly think of as a float construct.\r\n\r\nPersonally, I’d rather have pymatgen return no unitized quantity whatsoever, and when people actually want to use units, they can pass those quantities to pint to manipulate them.",
"Just a note that something like e+2 throwing an error is precisely why I do not want to enforce unit checking. I may have in my head that I need to shift something by 2eV. I want to just do e+2. It is not your business to check on my units.",
"Thanks @shyuep. I understand your concerns about being able to do basic arithmetic such as `e+2` without errors. I'm confident we can find some kind of workaround or compromise there.\r\n\r\n> I agree of course that if we fully adopt pint, it will help avoid certain errors. But it is _not_ the role for pymatgen to play. Most people do not want someone else to be babysitting units for them.\r\n\r\nI see this differently. It makes sense to me that the entire DFT community is \"standardized\" on eV and angstroms, but from my perspective as someone with 1) an experimental background and 2) visions of using pymatgen for analysis beyond DFT results, I absolutely do want someone else checking units for me. I have seen (and committed) many errors due to wrong units, and I think avoiding those kinds of mistakes is something that codes such as pymatgen are well-suited for.\r\n\r\nI'm optimistic we can find a solution that's flexible enough to satisfy both use cases. Stay tuned!",
"@shyuep @mkhorton can you give us some feedback on a creative solution @ayushsgupta came up with? This work is not complete yet, but before we continue in this direction we wanted to get your opinion.\r\n\r\n- Ayush created a custom class from `pint.Quantity` called `CompatibleQuantity` that allows one to add floats to Quantity (similar to the original `FloatWithUnit`). However, if you try to add a float to a Quantity, the float is assumed to have the same units as the Quantity. Therefore (unlike `FloatWithUnit`), units information is preserved. For example:\r\n\r\n```\r\nfrom pymatgen.core.units import CompatibleQuantity\r\na=CompatibleQuantity(1, 'eV')\r\nprint(a)\r\n1 electron_volt\r\nb=2\r\nprint(a+b)\r\n3 electron_volt\r\n```\r\n\r\n- We propose to replace `FloatWithUnit` with `CompatibleQuantity` in all classes in `pymatgen.core`. This means that many attributes of `Element`, `Structure,` etc. will now return `CompatibleQuantity` instead of `FloatWithUnit`.\r\n- Outside of `pymatgen.core`, anytime a method calls something from a core method, we would use the returned `CompatibleQuantity` to convert the value to an appropriate unit, and then pass the magnitude to the rest of the method. You can see a nice example of this in my next comment\r\n- Methods outside of `pymatgen.core` will continue to return floats for the time being\r\n\r\nPlease let us know what you think.\r\n\r\n",
"What happens if you try to use CompatibleQuantity with numpy operations?",
"> What happens if you try to use CompatibleQuantity with numpy operations?\r\n\r\n@mkhorton it should be the same behavior as `Quantity`, which means most np operations should work as expected; although I know there are a few that aren't supported by `Quantity` Did you have specific cases in mind?",
"Hi @ayushsgupta, I'm not sure if @rkingsbury relayed the message on this, but basically I think `CompatibleQuantity` (as a concept) is a good direction to try, but the implementation (over-riding` __add__`, `__mul__` etc.) is going to be brittle and likely won't play nicely with numpy.\r\n\r\nOne approach that may be worth attempting is to over-ride `__getattr__`, check if units exist then (1) if they do exist, apply the operations with Quantities as normal, (2) if units do not exist, apply the operations on the underlying `.magnitude`, and cast the result back to the appropriate units, and issue a warning.\r\n\r\nIf this approach is viable depends, ultimately, on performance and robustness. Note that we would also need a global option for unit checking (e.g. that we can put in the .pmgrc.yaml), which can be set to `STRICT`, `WARN` or `IGNORE` respectively. This could open the door for us to be strict when doing internal testing, but ignore issues for end users who want to use existing scripts as normal. ",
"Closing this since work seems to have stalled. Please feel welcome to re-open if you want to take another go at this. Thanks for helping to explore this idea!"
] | 2020-02-20T19:01:18
| 2020-12-01T16:34:42
|
2020-12-01T16:34:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The goal of this project is to replace the current pymatgen unit system with that of pint, which will allow for more comprehensive and robust unit handling
* Replace all instances of FloatWithUnit with the Quantity class from pint
* Calculations in pymatgen use Quantity.magnitude
* TODO: Lots of tests still fail, will be fixed
## Additional dependencies introduced (if any)
* Pint - whole project based on the Quantity class from pint
|
{
"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/1771/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1771/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1771",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1771",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1771.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1771.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1772
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1772/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1772/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1772/events
|
https://github.com/materialsproject/pymatgen/issues/1772
| 569,021,711
|
MDU6SXNzdWU1NjkwMjE3MTE=
| 1,772
|
PointGroupAnalyzer gets totally wrong point group
|
{
"login": "fxcoudert",
"id": 1980544,
"node_id": "MDQ6VXNlcjE5ODA1NDQ=",
"avatar_url": "https://avatars.githubusercontent.com/u/1980544?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fxcoudert",
"html_url": "https://github.com/fxcoudert",
"followers_url": "https://api.github.com/users/fxcoudert/followers",
"following_url": "https://api.github.com/users/fxcoudert/following{/other_user}",
"gists_url": "https://api.github.com/users/fxcoudert/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fxcoudert/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fxcoudert/subscriptions",
"organizations_url": "https://api.github.com/users/fxcoudert/orgs",
"repos_url": "https://api.github.com/users/fxcoudert/repos",
"events_url": "https://api.github.com/users/fxcoudert/events{/privacy}",
"received_events_url": "https://api.github.com/users/fxcoudert/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Forget about it. The default eigenvalue tolerance is just too low for something like this. I have:\r\n\r\n```\r\nDEBUG:pymatgen.symmetry.analyzer:Spherical top molecule detected\r\nDEBUG:pymatgen.symmetry.analyzer:Accidental speherical top!\r\nDEBUG:pymatgen.symmetry.analyzer:Eigenvalues = [0.66670374 0.66659252 0.66670374].\r\nDEBUG:pymatgen.symmetry.analyzer:Rotation symmetries = [(array([-0.16868303, -0.60751073, 0.77619376]), 1)]\r\nDEBUG:pymatgen.symmetry.analyzer:Accidental speherical top!\r\nDEBUG:pymatgen.symmetry.analyzer:Eigenvalues = [0.66670374 0.66659252 0.66670374].\r\nDEBUG:pymatgen.symmetry.analyzer:Rotation symmetries = [(array([-0.16868303, -0.60751073, 0.77619376]), 1), (array([-0.16868303, -0.60751073, 0.77619376]), 1)]\r\n```\r\n\r\nwhich lead me to lower the tolerance:\r\n\r\n```\r\npg = pymatgen.symmetry.analyzer.PointGroupAnalyzer(mol, eigen_tolerance=0.000001)\r\n```\r\n\r\nwhich lead to the correct `C3v` point group.",
"Re-opening because we’ve had another issue with this recently where the eigenval tolerance didn’t help. I’ll try to find it to paste here.\r\n\r\nOn investigation, it seemed strange because the detected symmetry ops were still correct even though the label was wrong. We suspect a logic bug, and want to investigate alternatives to the current labelling algorithm.",
"I am seeing more trouble. I was trying to get the symmetrized molecule into a good frame of reference, since it appears that `symmetrize_molecule` does not do any orientation.\r\n\r\nHowever, I am finding that the principal axes as calculated by `PointGroupAnalyzer` are not orthogonal, which I don't understand:\r\n\r\n```\r\n#!/usr/bin/env python3\r\n\r\nimport numpy as np\r\nimport pymatgen\r\n\r\nmol = pymatgen.Molecule.from_file(\"Cluster_Zr_1H.xyz\")\r\npg = pymatgen.symmetry.analyzer.PointGroupAnalyzer(mol, eigen_tolerance=0.000001)\r\nprint('Point group: ' + str(pg.get_pointgroup()))\r\nprint(np.dot(pg.principal_axes, pg.principal_axes.T))\r\n```\r\n\r\nis giving:\r\n\r\n```\r\nPoint group: C3v\r\n[[ 1.00000000e+00 -1.04189128e-14 3.97365516e-01]\r\n [-1.04189128e-14 1.00000000e+00 -7.17973577e-13]\r\n [ 3.97365516e-01 -7.17973577e-13 1.00000000e+00]]\r\n```\r\n\r\nwhich is not the identity matrix (see xz and zx terms).",
"It does seem like the answer is approximately an identity. But just to clarify, the principal axes are just the eigenvectors of the inertia tensor. This is straight from a numpy.linalg.eig calculation. THis molecule is rather large, so it is rather sensitive to numerical errors.",
"Adding another example upon encouragement from @mkhorton. Just tried using the PointGroupAnalyzer on the following molecule:\r\n\r\n5\r\nLi1 C2 O2\r\nO 1.466022 0.260061 0.857948\r\nC 1.199389 0.074416 2.036307\r\nC 0.920374 -0.114814 3.237086\r\nO 0.648901 -0.305195 4.442436\r\nLi 0.266687 -0.563754 6.096545\r\n\r\nIt didn't actually return the wrong point group. Instead, I got a ValueError from _get_smallest_set_not_on_axis:\r\n\r\nValueError: min() arg is an empty sequence\r\n\r\nI guess this makes sense since it's trying to find a set of molecules not on the axis, but the molecule is linear?\r\n\r\nThis is on version '2020.12.31', by the way.",
"I cannot reproduce the last error. \r\n\r\n```python\r\nfrom pymatgen import Molecule\r\nm = Molecule.from_str(\"\"\"5\r\nLi1 C2 O2\r\nO 1.466022 0.260061 0.857948\r\nC 1.199389 0.074416 2.036307\r\nC 0.920374 -0.114814 3.237086\r\nO 0.648901 -0.305195 4.442436\r\nLi 0.266687 -0.563754 6.096545\"\"\", fmt=\"xyz\")\r\nfrom pymatgen.symmetry.analyzer import PointGroupAnalyzer\r\na = PointGroupAnalyzer(m)\r\nprint(a.get_pointgroup())\r\n```\r\n\r\nspits out C*v, which is correct? This is based on default parameters.",
"Ah, I should have mentioned in my original post. This was with eigen_tolerance=0.000001 (trying to ensure that there wouldn't be issues with tolerance as the original issue mentioned). That is interesting that by using the default tolerance you don't get an issue.",
"@espottesmith Tolerances work both ways. Too strict and you are unable to detect certain symmetries when they exist. Too loose and certain atoms/symmetry operations get lumped together. There is no way around this unless you are always inputting an idealized molecule at perfect symmetry positions at the limits of floating point precision. The best we can do is to tweak the default settings such that it works in most cases."
] | 2020-02-21T15:27:05
| 2023-08-13T16:32:57
|
2023-08-13T16:32:57Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
pymatgen 2020.1.28 fails to identify proper point group with pymatgen.symmetry.analyzer.PointGroupAnalyzer
**To Reproduce**
1. Create a file called `Cluster_H.xyz` with this content: https://gist.github.com/fxcoudert/def477b148e95b8cad61804e26e89271
2. Run the following code:
```
import pymatgen
mol = pymatgen.Molecule.from_file("Cluster_H.xyz")
pg = pymatgen.symmetry.analyzer.PointGroupAnalyzer(mol)
print(pg.get_pointgroup())
```
3. The point group identified is `D1d`, which is wrong.
**Expected behavior**
The point group should be `C3v`, not `D1d`. Changing tolerances will not help, since the symmetry is exactly C3v in this case.
This is a significant mistake, since D1d (which is also C2h with a different choice of orientation) is actually not a subgroup of C3v at all.
**Desktop**
- OS: macOS 10.15.3
- Version: pymatgen 2020.1.28
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1772/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1772/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1773
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1773/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1773/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1773/events
|
https://github.com/materialsproject/pymatgen/pull/1773
| 569,378,818
|
MDExOlB1bGxSZXF1ZXN0Mzc4NjIxMjYy
| 1,773
|
Raise MemoryError in the case of memory allocation failure in get_neighbors cython code
|
{
"login": "chc273",
"id": 22353204,
"node_id": "MDQ6VXNlcjIyMzUzMjA0",
"avatar_url": "https://avatars.githubusercontent.com/u/22353204?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chc273",
"html_url": "https://github.com/chc273",
"followers_url": "https://api.github.com/users/chc273/followers",
"following_url": "https://api.github.com/users/chc273/following{/other_user}",
"gists_url": "https://api.github.com/users/chc273/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chc273/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chc273/subscriptions",
"organizations_url": "https://api.github.com/users/chc273/orgs",
"repos_url": "https://api.github.com/users/chc273/repos",
"events_url": "https://api.github.com/users/chc273/events{/privacy}",
"received_events_url": "https://api.github.com/users/chc273/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-02-22T19:06:14
| 2020-02-24T03:34:02
|
2020-02-24T03:34:02Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Added wrappers to the c memory allocation functions malloc and realloc. In the case memory allocation failure, the cython code will raise MemoryError instead of relying on c behavior.
* Reduced the theoretical amortized time by doubling the neighbor size everytime maximum number is hit. Previously a constant is added to the maximum number of neighbors everytime the maximum is hit.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1773/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1773/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1773",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1773",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1773.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1773.patch",
"merged_at": "2020-02-24T03:34:02Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1774
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1774/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1774/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1774/events
|
https://github.com/materialsproject/pymatgen/issues/1774
| 570,135,514
|
MDU6SXNzdWU1NzAxMzU1MTQ=
| 1,774
|
Extracting the asymmetric single molecule from the CIF file
|
{
"login": "misterblonde",
"id": 35377468,
"node_id": "MDQ6VXNlcjM1Mzc3NDY4",
"avatar_url": "https://avatars.githubusercontent.com/u/35377468?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/misterblonde",
"html_url": "https://github.com/misterblonde",
"followers_url": "https://api.github.com/users/misterblonde/followers",
"following_url": "https://api.github.com/users/misterblonde/following{/other_user}",
"gists_url": "https://api.github.com/users/misterblonde/gists{/gist_id}",
"starred_url": "https://api.github.com/users/misterblonde/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/misterblonde/subscriptions",
"organizations_url": "https://api.github.com/users/misterblonde/orgs",
"repos_url": "https://api.github.com/users/misterblonde/repos",
"events_url": "https://api.github.com/users/misterblonde/events{/privacy}",
"received_events_url": "https://api.github.com/users/misterblonde/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @misterblonde, can you be more specific about what you mean by \"extract the single molecule in the asymmetric unit of a .cif file\"?\r\n\r\n> the entire function is not documented anywhere.\r\n\r\nFunctions with leading underscores in Python are considered \"private\" so may not contain docstrings. They're there for ease of maintenance, rather than to be called by the end user.\r\n\r\nIt's a little convoluted, but there is one method to extract molecules from an arbitrary CIF file, see https://pymatgen.org/pymatgen.analysis.graphs.html#pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules -- this requires prior bond detection using one of the bonding algorithms in pymatgen.analysis.local_env, and then it uses the bonding information to extract individual molecules (even if they straddle periodic boundaries). This functionality has not been used extensively, so issue reports would be welcome.",
"Hi @mkhorton! \r\n\r\nThanks for your quick response! The asymmetric molecule is the molecule in the unit cell, which all the symmetry operations are based upon. So basically the molecule that you get without any translations/rotations. Then you can use that molecule to build the supercell by translating/rotating it. \r\nI know you currently employ the opposite approach of just periodically replicating the unit cell to build the supercell. I would look for something that just returns me the single molecule, assuming a Z'=1 crystal structure, ie. only one molecule in the asymmetric unit. \r\n\r\nI had a look at the graphs module, but I guess you don't have any examples on how to use it yet? Would you just use nx to convert into the right graph format? Does Pymatgen not offer a way to convert from my _Pymatgen parsed cif_ to the _MSONable graph_ format? \r\n\r\n`from pymatgen.io.cif import CifParser\r\n\r\nparser = CifParser(filn)\r\nstruc = parser.get_structures()[0]`\r\n\r\nSorry, I tried to get into your code before because I thought it would be super useful, but none of the sample notebooks, answered the questions I had 😃 Maybe there's a new resource/sample page now? \r\n",
"> I had a look at the graphs module, but I guess you don't have any examples on how to use it yet? Would you just use nx to convert into the right graph format? Does Pymatgen not offer a way to convert from my Pymatgen parsed cif to the MSONable graph format?\r\n\r\nI don't have an example to hand, but usage is basically:\r\n\r\n```\r\nfrom pymatgen.analysis.graphs import StructureGraph\r\nfrom pymatgen.analysis.local_env import MinimumDistanceNN\r\n\r\nnn = MinimumDistanceNN()\r\nsg = StructureGraph.with_local_env_strategy(my_struct, nn)\r\nmolecules = sg.get_subgraphs_as_molecules()\r\n```\r\n\r\nbut this is a very inefficient way to do it for the \"asymmetric molecule\" you described, since this data is already in the CIF...\r\n\r\nWe should definitely have an example notebook :) ",
"Hey thank you! The code you sent works and I get a single molecule in xyz coordinates. However, when I compare the single molecule extracted to the xyz supercell generated using the `.make_supercell `function, then the single molecule is not periodically related to the supercell. I opened both in pymol to see (photos attached). Ideally, I would want to be able to extract all the possible nearest neighbour dimer pairs of the two molecules in the central unit cell/center of the supercell. Could I \"repair the broken fragments\" of the supercell somehow, or set periodic boundary conditions to false (pbc=false)? I also tried to see if the graph module offers any functionality to find all the molecules and delete broken ones instead? No luck. \r\n<img width=\"463\" alt=\"supercell_on_its_own\" src=\"https://user-images.githubusercontent.com/35377468/75617169-84526300-5b29-11ea-8d7d-0c4bc8d8b1bf.png\">\r\n<img width=\"485\" alt=\"supercell_with_misplaced_single_mol\" src=\"https://user-images.githubusercontent.com/35377468/75617170-84526300-5b29-11ea-8b1b-9830bac0b379.png\">\r\n\r\n",
"> > I had a look at the graphs module, but I guess you don't have any examples on how to use it yet? Would you just use nx to convert into the right graph format? Does Pymatgen not offer a way to convert from my Pymatgen parsed cif to the MSONable graph format?\r\n> \r\n> I don't have an example to hand, but usage is basically:\r\n> \r\n> ```\r\n> from pymatgen.analysis.graphs import StructureGraph\r\n> from pymatgen.analysis.local_env import MinimumDistanceNN\r\n> \r\n> nn = MinimumDistanceNN()\r\n> sg = StructureGraph.with_local_env_strategy(my_struct, nn)\r\n> molecules = sg.get_subgraphs_as_molecules()\r\n> ```\r\n> \r\n> but this is a very inefficient way to do it for the \"asymmetric molecule\" you described, since this data is already in the CIF...\r\n> \r\n> We should definitely have an example notebook :)\r\n\r\nHello! I faced the same problem. I've not seen any functions to get assymetric unit from CIF-file. By default string `parser.get_structures()[0]` gets all atoms within unit cell however for my purposes I need only assymetric part (i.e. only atoms which are listed inside CIF-file). I tried your example with subgraph search but it's really inefficient approach. Maybe is there more simple way to extract assymetric unit? Because as I can see it'd not be a big problem.\r\n"
] | 2020-02-24T20:43:00
| 2023-08-13T16:32:57
|
2023-08-13T16:32:57Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Is your feature request related to a problem? Please describe.**
I'm always frustrated when I try to use Pymatgen to extract the single molecule in the asymmetric unit of a .cif file. I hope that _unique_coords() inside cif.py would offer this functionality, but I don't seem to get this to work? I only have sites but it requires actual coords as input. the entire function is not documented anywhere.
**Describe the solution you'd like**
can you please show me a sample implementation of this function? If this is not the right function to do what I'm trying to do, please suggest the correct function to use.
**Describe alternatives you've considered**
I also tried the simple .cif to .xyz io/conversion, however that just gives you all the atoms inside the unit cell in cartesian coordinates, which is not very useful for my purposes.
**Additional context**
this functionality was offered by an old version of open babel, but then got deprecated, because it's not a trivial problem. I really look forward to your reply. 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/1774/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1774/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1775
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1775/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1775/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1775/events
|
https://github.com/materialsproject/pymatgen/pull/1775
| 571,025,360
|
MDExOlB1bGxSZXF1ZXN0Mzc5OTcyNDUz
| 1,775
|
Add functions to generate phonon DOS & BS from force constants
|
{
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"following_url": "https://api.github.com/users/utf/following{/other_user}",
"gists_url": "https://api.github.com/users/utf/gists{/gist_id}",
"starred_url": "https://api.github.com/users/utf/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/utf/subscriptions",
"organizations_url": "https://api.github.com/users/utf/orgs",
"repos_url": "https://api.github.com/users/utf/repos",
"events_url": "https://api.github.com/users/utf/events{/privacy}",
"received_events_url": "https://api.github.com/users/utf/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Failing tests are unrelated to this PR.",
"This should be ready to merge now.",
"Thanks @utf, planning to push a release later today"
] | 2020-02-26T02:26:37
| 2020-02-28T20:47:08
|
2020-02-28T20:47:08Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added methods for generating `CompletePhononDos`, `PhononBandStructure`, and `PhononBandStructureSymmLine` directly from phonopy force constants.
This complements existing methods for generating these objects from text files.
Tests have been added.
## 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/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [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 existing tests pass.
|
{
"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/1775/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/1775/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1775",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1775",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1775.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1775.patch",
"merged_at": "2020-02-28T20:47:08Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1776
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1776/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1776/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1776/events
|
https://github.com/materialsproject/pymatgen/pull/1776
| 571,032,648
|
MDExOlB1bGxSZXF1ZXN0Mzc5OTc4Mjg5
| 1,776
|
Add MonteCarloRattleTransformation and general refactoring
|
{
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"following_url": "https://api.github.com/users/utf/following{/other_user}",
"gists_url": "https://api.github.com/users/utf/gists{/gist_id}",
"starred_url": "https://api.github.com/users/utf/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/utf/subscriptions",
"organizations_url": "https://api.github.com/users/utf/orgs",
"repos_url": "https://api.github.com/users/utf/repos",
"events_url": "https://api.github.com/users/utf/events{/privacy}",
"received_events_url": "https://api.github.com/users/utf/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 remaining mypy errors don't seem particularly reasonable.\r\n\r\n~~EDIT: WIP while I fix a potential bug.~~",
"This should also be ready to merge now.",
"Thanks!\r\n"
] | 2020-02-26T02:51:19
| 2020-02-28T21:25:38
|
2020-02-28T21:25:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request introduces a number of miscellaneous features as part of an atomate workflow to calculate lattice thermal conductivity.
- Added MonteCarloRattleTransformation. Uses the hiPhive package to displace atomic sites according to a Monte Carlo routine which punishes small bond distances. I've added an explanation of the algorithm in the docstring of the class.
- Refactored ShengBTE Control implementation. Also added helper methods to construct a Control object from a pymatgen structure and to extract a Structure from an existing Control object.
- Added type hinting in a few places.
- Updated tests.
## Additional dependencies introduced (if any)
* `hiphive`: Added as an optional dependency. We use this package in atomate to fit the force constants and it also provides several useful functions for generating perturbed structures. This transformation must be added in Pymatgen itself, as it is used in the `TransformerFW` which is only capable of applying Pymatgen transformations.
## 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/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [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 existing tests pass.
|
{
"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/1776/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/1776/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1776",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1776",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1776.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1776.patch",
"merged_at": "2020-02-28T21:25:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1777
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1777/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1777/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1777/events
|
https://github.com/materialsproject/pymatgen/pull/1777
| 571,153,143
|
MDExOlB1bGxSZXF1ZXN0MzgwMDc2ODU0
| 1,777
|
get_neihgbours returns PeriodicNeighbor objects
|
{
"login": "mfherbst",
"id": 11157893,
"node_id": "MDQ6VXNlcjExMTU3ODkz",
"avatar_url": "https://avatars.githubusercontent.com/u/11157893?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mfherbst",
"html_url": "https://github.com/mfherbst",
"followers_url": "https://api.github.com/users/mfherbst/followers",
"following_url": "https://api.github.com/users/mfherbst/following{/other_user}",
"gists_url": "https://api.github.com/users/mfherbst/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mfherbst/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mfherbst/subscriptions",
"organizations_url": "https://api.github.com/users/mfherbst/orgs",
"repos_url": "https://api.github.com/users/mfherbst/repos",
"events_url": "https://api.github.com/users/mfherbst/events{/privacy}",
"received_events_url": "https://api.github.com/users/mfherbst/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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!"
] | 2020-02-26T08:31:50
| 2020-02-26T15:19:18
|
2020-02-26T15:09:20Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
* Bugfix for StructureVis.add_structure: New `get_neighbors` returns PeriodicNeighbor object.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1777/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1777/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1777",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1777",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1777.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1777.patch",
"merged_at": "2020-02-26T15:09:20Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1778
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1778/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1778/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1778/events
|
https://github.com/materialsproject/pymatgen/issues/1778
| 571,528,052
|
MDU6SXNzdWU1NzE1MjgwNTI=
| 1,778
|
Error in reading PROCAR file with SOC
|
{
"login": "rajibul645",
"id": 42172554,
"node_id": "MDQ6VXNlcjQyMTcyNTU0",
"avatar_url": "https://avatars.githubusercontent.com/u/42172554?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rajibul645",
"html_url": "https://github.com/rajibul645",
"followers_url": "https://api.github.com/users/rajibul645/followers",
"following_url": "https://api.github.com/users/rajibul645/following{/other_user}",
"gists_url": "https://api.github.com/users/rajibul645/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rajibul645/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rajibul645/subscriptions",
"organizations_url": "https://api.github.com/users/rajibul645/orgs",
"repos_url": "https://api.github.com/users/rajibul645/repos",
"events_url": "https://api.github.com/users/rajibul645/events{/privacy}",
"received_events_url": "https://api.github.com/users/rajibul645/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Same issue currently."
] | 2020-02-26T17:01:25
| 2024-09-13T02:30:50
|
2023-08-13T16:33:40Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I got following error in reading PROCAR file. Could you please suggest me, how should I deal with this problem?
C:\ProgramData\Anaconda3\envs\Pymatgen\lib\site-packages\pymatgen\io\vasp\outputs.py in __init__(self, filename)
3477 for orb in range(len(headers)):
3478 phase_factors[spin][current_kpoint, current_band,
-> 3479 index, orb] = complex(num_data[2 * orb], num_data[2 * orb + 1])
3480 else:
3481 # old format of PROCAR (vasp 5.4.1 and before)
IndexError: index 10 is out of bounds for axis 0 with size 10
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1778/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1778/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1779
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1779/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1779/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1779/events
|
https://github.com/materialsproject/pymatgen/pull/1779
| 572,447,516
|
MDExOlB1bGxSZXF1ZXN0MzgxMTQzMjY4
| 1,779
|
[WIP] mcsqs_caller scratch dir
|
{
"login": "dongsenfo",
"id": 7142440,
"node_id": "MDQ6VXNlcjcxNDI0NDA=",
"avatar_url": "https://avatars.githubusercontent.com/u/7142440?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dongsenfo",
"html_url": "https://github.com/dongsenfo",
"followers_url": "https://api.github.com/users/dongsenfo/followers",
"following_url": "https://api.github.com/users/dongsenfo/following{/other_user}",
"gists_url": "https://api.github.com/users/dongsenfo/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dongsenfo/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dongsenfo/subscriptions",
"organizations_url": "https://api.github.com/users/dongsenfo/orgs",
"repos_url": "https://api.github.com/users/dongsenfo/repos",
"events_url": "https://api.github.com/users/dongsenfo/events{/privacy}",
"received_events_url": "https://api.github.com/users/dongsenfo/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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!"
] | 2020-02-28T00:38:54
| 2020-03-09T19:20:43
|
2020-03-09T19:20:43Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
run mcsqs in scratch dir to deal with multiple files better
## 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:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] 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 existing 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/1779/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1779/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1779",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1779",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1779.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1779.patch",
"merged_at": "2020-03-09T19:20:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1780
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1780/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1780/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1780/events
|
https://github.com/materialsproject/pymatgen/pull/1780
| 573,603,003
|
MDExOlB1bGxSZXF1ZXN0MzgyMDg1NDc2
| 1,780
|
Refactor ComputedEntry and PDEntry with new Entry class
|
{
"login": "ayushsgupta",
"id": 16586331,
"node_id": "MDQ6VXNlcjE2NTg2MzMx",
"avatar_url": "https://avatars.githubusercontent.com/u/16586331?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ayushsgupta",
"html_url": "https://github.com/ayushsgupta",
"followers_url": "https://api.github.com/users/ayushsgupta/followers",
"following_url": "https://api.github.com/users/ayushsgupta/following{/other_user}",
"gists_url": "https://api.github.com/users/ayushsgupta/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ayushsgupta/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ayushsgupta/subscriptions",
"organizations_url": "https://api.github.com/users/ayushsgupta/orgs",
"repos_url": "https://api.github.com/users/ayushsgupta/repos",
"events_url": "https://api.github.com/users/ayushsgupta/events{/privacy}",
"received_events_url": "https://api.github.com/users/ayushsgupta/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @ayushsgupta ! I'll just add some additional context, as I think this has value to pymatgen users regardless of what we decide about the units.\r\n\r\nIn addition to facilitating the units implementation, this PR was also partly motivated by my experience learning pymatgen as a new user over the last year. I found the large number of `__Entry` classes confusing, and I also found that they did not always behave consistently or have the same method names.\r\n\r\nWhile I understand the need to have multiple types of `__Entry`, and this is not going to change anytime soon, I think minimizing the number of different classes and making their member methods as consistent as possible will really help new users while also facilitating code maintenance.\r\n\r\nThis PR is a first step in that direction that we hope to continue building on later. By inheriting as much functionality as possible from the new `Entry` class, all of the existing `__Entry` classes will become easier to maintain and more consistent. For example, the `.normalize()` method that we added to `ComputedEntry` a few months ago was never added to `PDEntry`. Now it will be available there automatically.",
"@shyuep @mkhorton , any idea why the Travis build (pydocstyle) is failing? The failures are coming from files that weren't changed in this PR. Has the pydocstyle configuration changed recently or something?",
"While I think this is a good initiative, I think perhaps you misunderstood the original organization hierarchy. The idea has always been that the PDEntry is the basic unit, and ComputedEntry (and its subclasses) inherit from that. Subsequently, the inheritance got removed but since Python works on duck typing, no functionality was broken. \r\n\r\nFor PD computations, all that is needed is composition + energy - structure and everything else are not required. Extra things like \"corrections\" etc. only apply to ComputedEntries. E.g., I can generate a phase diagram simply by generating three PDEntries with the following args: (\"Fe\", 0.0), (\"O\", 0) and (\"Fe2O3\", -0.1).\r\n\r\nSo I actually think that having a separate Entry base object serves to confuse more than help. Suddenly things like corrections become part of all entries, even when they are completely irrelevant. In fact, all the new `Entry` base class does is to take all the entire PDEntry infrastructure and adding corrections in it. That is basically a `ComputedEntry`!\r\n\r\nIn short, I am not in favor of adding complexity to the fundamental base object (whether we call it Entry or PDEntry). Corrections are an artificial construct due to the way MP chose to do its scheme. \r\n\r\nI would be fine, however, if you want to create an `Entry` abstract base class from which both PDEntry and ComputedEntry inherits from. That class would define the core methods and properties that need to be implemented for any type of entry and also implement all common functionality like energies per atom and normalize. As far as I can see, the main abstract properties needed are just energy and composition. Then the subclasses can define energy however they see fit.",
"@ayushsgupta it looks like you will also need to copy the docstring for `.normalize` into `ComputedEntry`. Here is one of the failures from the Travis build:\r\n\r\n```\r\npymatgen/entries/computed_entries.py:81 in public method `normalize`:\r\n D102: Missing docstring in public method\r\n```",
"Pls move the Entry abc to pymatgen.entries.__init__.py. I prefer less typing during imports.",
"Thanks for your feedback, @shyuep ; we're ready for you to review. Please let us know if you have any other comments. \r\n\r\nThe only reason the Travis CI is failing is because of the docstring issues introduced by a different commit; nothing in our changes is causing problems.",
"Great. Thanks."
] | 2020-03-01T19:41:57
| 2020-06-22T22:01:02
|
2020-03-03T23:18:29Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
* Creates a new Entry class from which ComputedEntry and PDEntry now inherit
* If some form of pull request #1771 (units with pint) is implemented, this will simplify the integration of units into pymatgen
* In general, will make pymatgen easier to maintain by reducing redundancy in the various entry classes
* Currently only covers ComputedEntry and PDEntry, but can be expanded in the future
* No new dependencies
@rkingsbury please add any other comments/corrections as necessary
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1780/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1780/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1780",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1780",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1780.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1780.patch",
"merged_at": "2020-03-03T23:18:29Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1781
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1781/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1781/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1781/events
|
https://github.com/materialsproject/pymatgen/pull/1781
| 574,211,787
|
MDExOlB1bGxSZXF1ZXN0MzgyNTc4OTQ3
| 1,781
|
[WIP] Read WAVECAR from gamma-point only executable
|
{
"login": "bernstei",
"id": 1202357,
"node_id": "MDQ6VXNlcjEyMDIzNTc=",
"avatar_url": "https://avatars.githubusercontent.com/u/1202357?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/bernstei",
"html_url": "https://github.com/bernstei",
"followers_url": "https://api.github.com/users/bernstei/followers",
"following_url": "https://api.github.com/users/bernstei/following{/other_user}",
"gists_url": "https://api.github.com/users/bernstei/gists{/gist_id}",
"starred_url": "https://api.github.com/users/bernstei/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/bernstei/subscriptions",
"organizations_url": "https://api.github.com/users/bernstei/orgs",
"repos_url": "https://api.github.com/users/bernstei/repos",
"events_url": "https://api.github.com/users/bernstei/events{/privacy}",
"received_events_url": "https://api.github.com/users/bernstei/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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!",
"That was quick. Glad you approve.\n\n\t\t\t\t\t\tNoam\n",
"Hi @bernstei, thanks for this PR. Could you fill out [this form](https://forms.gle/JnisFb38QDR8QTFTA) so we can properly acknowledge you in the [pymatgen documentation](https://pymatgen.org/team.html)? I have been checking our acknowledgments and I realized we'd missed a few."
] | 2020-03-02T19:59:31
| 2020-08-05T06:47:52
|
2020-03-03T14:08:01Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Extend `pymatgen.io.vasp.outputs.Wavecar` to read from gamma-point only executable.
* New bool gamma argument for `Wavecar.__init__()`, otherwise tries to guess from file contents.
* Test comparing H2 WAVECARs from regular and gamma-point only executables
## Additional dependencies introduced (if any)
None
## TODO (if any)
Fix tests, make sure pre-commit hook passes lint
## Checklist
- [X] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [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 existing tests pass. [NB tested with pytest test_output.py since changes are so localized]
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1781/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1781/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1781",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1781",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1781.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1781.patch",
"merged_at": "2020-03-03T14:08:00Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1782
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1782/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1782/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1782/events
|
https://github.com/materialsproject/pymatgen/pull/1782
| 574,336,071
|
MDExOlB1bGxSZXF1ZXN0MzgyNjc5NzQ4
| 1,782
|
automatic box size overwrite
|
{
"login": "htz1992213",
"id": 25351437,
"node_id": "MDQ6VXNlcjI1MzUxNDM3",
"avatar_url": "https://avatars.githubusercontent.com/u/25351437?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/htz1992213",
"html_url": "https://github.com/htz1992213",
"followers_url": "https://api.github.com/users/htz1992213/followers",
"following_url": "https://api.github.com/users/htz1992213/following{/other_user}",
"gists_url": "https://api.github.com/users/htz1992213/gists{/gist_id}",
"starred_url": "https://api.github.com/users/htz1992213/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/htz1992213/subscriptions",
"organizations_url": "https://api.github.com/users/htz1992213/orgs",
"repos_url": "https://api.github.com/users/htz1992213/repos",
"events_url": "https://api.github.com/users/htz1992213/events{/privacy}",
"received_events_url": "https://api.github.com/users/htz1992213/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Am I supposed to fix those docstring??? ",
"The shengbte, structure_vtk and advanced_transformations are the responsibility of other contributors. Any other errors you would have to correct, this is the result of stricter checking for docstrings on commit (if you touch a file that has bad docstrings, it will flag an error).",
"Thanks Matt! So it's good to merge?",
"Thanks! It has been merged."
] | 2020-03-03T00:21:10
| 2020-03-03T14:07:04
|
2020-03-03T14:06:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
*The box size values in the CombinedData object is now automatically updated by the min/max values of the coordinates.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1782/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1782/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1782",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1782",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1782.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1782.patch",
"merged_at": "2020-03-03T14:06:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1783
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1783/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1783/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1783/events
|
https://github.com/materialsproject/pymatgen/issues/1783
| 574,694,855
|
MDU6SXNzdWU1NzQ2OTQ4NTU=
| 1,783
|
Error in calculating Pourbaix diagram
|
{
"login": "xig126",
"id": 31936920,
"node_id": "MDQ6VXNlcjMxOTM2OTIw",
"avatar_url": "https://avatars.githubusercontent.com/u/31936920?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/xig126",
"html_url": "https://github.com/xig126",
"followers_url": "https://api.github.com/users/xig126/followers",
"following_url": "https://api.github.com/users/xig126/following{/other_user}",
"gists_url": "https://api.github.com/users/xig126/gists{/gist_id}",
"starred_url": "https://api.github.com/users/xig126/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/xig126/subscriptions",
"organizations_url": "https://api.github.com/users/xig126/orgs",
"repos_url": "https://api.github.com/users/xig126/repos",
"events_url": "https://api.github.com/users/xig126/events{/privacy}",
"received_events_url": "https://api.github.com/users/xig126/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"As people who have touched Pourbaix and reaction calculator, I'm tagging @montoyjh and @mattmcdermott for ideas.",
"Wow that's a big problem! When this is solved, I suggest adding a unittest\nfor the Pourbaix diagram for the Bi/V system, so that if something breaks\nelsewhere in Pymatgen, this is caught at the unittest level next time.\n\n\nOn Tue, Mar 3, 2020 at 1:03 PM Matthew Horton <notifications@github.com>\nwrote:\n\n> As people who have touched Pourbaix and reaction calculator, I'm tagging\n> @montoyjh <https://github.com/montoyjh> and @mattmcdermott\n> <https://github.com/mattmcdermott> for ideas.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1783?email_source=notifications&email_token=AAN4NI4GXZQ6ALFKZOAN3ELRFVBAHA5CNFSM4LALKQUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENUQXEY#issuecomment-594086803>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAN4NI5ZNYL7HH55GBTYC3TRFVBAHANCNFSM4LALKQUA>\n> .\n>\n\n\n-- \nAssistant Professor\nMaterials Science and Engineering\nUniversity of Michigan\nhttp://mse.engin.umich.edu/people/fac/whsun\nhttp://wenhaosun.github.io\n",
"Thanks for the tip and mwe, checking on it now.",
"@JosephMontoya-TRI I am guessing this is coming from my changes to reaction_calculator in December (when it's called in process_multientry).\r\n\r\nFYI the new reaction balancing code changes were to identify the \"best\" solution, since I found that many of the solutions the previous code was producing were unnecessarily flipping reactants to products, and vice versa, (when a better solution without doing this existed)",
"Ah, I see. Yeah, I think the issue is that there's a case of a multientry with VO4-/VO4[3-] leaking into the multientry pool that in the should be producing a ReactionError in pre-processing.",
"Turns out, more a bug in pourbaix_diagram than reaction - Reaction in this case was solving for a zero-coefficient product, which can happen if you can balance the reaction with everything else. Pourbaix diagram was guarding against this in the case of zero coefficients on reactants, but not on products. I have a fix for the last tagged version.\r\n\r\nIncidentally, the latest entry refactor is also causing a separate, more dramatic issue, which this fortuitously brought to my attention, so I'll work on fixing that as well and issue a PR for both.",
"@JosephMontoya-TRI awesome detective work -- thanks for working on the fix!",
"I've been investigating Pourbaix diagrams lately, and I believe this is fixed in the current master branch. When I run\r\n\r\n```\r\nwith MPRester() as m:\r\n pbx_entries = m.get_pourbaix_entries(['Bi','V'])\r\n\r\npbd = PourbaixDiagram(pbx_entries, filter_solids=True)\r\npbplot = PourbaixPlotter(pbd)\r\n#pbplot.plot_entry_stability(e[0]).show()\r\nplt=pbplot.get_pourbaix_plot()\r\nplt.gcf().set_size_inches(10,10)\r\nplt.gcf().tight_layout()\r\nplt.show()\r\n```\r\n\r\nI get \r\n\r\n\r\n\r\nwhich looks very close to the expected output. Am I missing anything?",
"Yep, forgot to tag this issue in the PR, was fixed via #1785 ",
"Thanks both"
] | 2020-03-03T14:10:06
| 2020-04-10T00:01:45
|
2020-04-10T00:01:44Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
The calculated Pourbaix diagram is wrong with pymatgen of version later than 2019.12.3.
**To Reproduce**
Steps to reproduce the behavior:
from pymatgen import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, PourbaixPlotter
%matplotlib inline
mpr = MPRester()
entries = mpr.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries, comp_dict={"Bi": 0.5, "V": 0.5},
conc_dict={"Bi": 1e-8, "V": 1e-8}, filter_solids=True)
plotter = PourbaixPlotter(pbx)
plt = plotter.get_pourbaix_plot()
**Expected behavior**
The plot should be the same with the one in following example of Bi-V-O-H system.
https://matgenb.materialsvirtuallab.org/2017/12/15/Plotting-a-Pourbaix-Diagram.html
<img width="876" alt="image" src="https://user-images.githubusercontent.com/31936920/75782469-ea452180-5d99-11ea-803a-dcfa4bc5940f.png">
Instead, we get the following plot:
<img width="717" alt="image" src="https://user-images.githubusercontent.com/31936920/75781588-73f3ef80-5d98-11ea-9338-ebe6bc8cfbbe.png">
For example, in high potential region (E > 1), the calculated stable species are VO4^{3-} and VO4^-, which is counter-intuitive. Bi and V should be conserved on Pourbaix diagram.
**Additional context**
This error is possibly caused by bugs in pymatgen.analysis.reaction_calculator. This module is used to calculate the MultiEntry using in pymatgen.analysis.pourbaix_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/1783/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1783/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1784
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1784/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1784/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1784/events
|
https://github.com/materialsproject/pymatgen/issues/1784
| 574,749,109
|
MDU6SXNzdWU1NzQ3NDkxMDk=
| 1,784
|
Structure.to(fmt='cif') Precision Issues
|
{
"login": "cpashartis",
"id": 7492783,
"node_id": "MDQ6VXNlcjc0OTI3ODM=",
"avatar_url": "https://avatars.githubusercontent.com/u/7492783?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/cpashartis",
"html_url": "https://github.com/cpashartis",
"followers_url": "https://api.github.com/users/cpashartis/followers",
"following_url": "https://api.github.com/users/cpashartis/following{/other_user}",
"gists_url": "https://api.github.com/users/cpashartis/gists{/gist_id}",
"starred_url": "https://api.github.com/users/cpashartis/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/cpashartis/subscriptions",
"organizations_url": "https://api.github.com/users/cpashartis/orgs",
"repos_url": "https://api.github.com/users/cpashartis/repos",
"events_url": "https://api.github.com/users/cpashartis/events{/privacy}",
"received_events_url": "https://api.github.com/users/cpashartis/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Can you clarify what you mean by \"CIF writer has no precision\"?\r\n\r\nIf you want to increase the number of decimal places we print in the CIF we can do that.",
"Perhaps he refers to the default format used to write floats when structure.to() is invoked.\r\n\r\nIndeed, there's no option to specify the number of digits used to print lattice vectors \r\nand atomic positions to text files so we have to rely on the default behaviour of the different `writer` instances.\r\n\r\nWe encountered a similar problem when reading POSCAR files produced by pymatgen in Abinit because, by default, the get_string method of Poscar uses significant_figures = 6.\r\n\r\nWyckoff positions such as 1/3, 2/3 are truncated and other codes may not detect all the symmetries of the system because we loose (too much) information when converting from the internal python representation to text file (especially for hexagonal and rhombohedral lattices).\r\n\r\nIt seems to me that many POSCAR files available on the materials project website have 6 significant_figures and this leads to frequent problems when new Abinit users try to use the POSCAR files to start an Abinit calculation because the code won't detect all the symmetry operations --> larger IBZ.\r\nWe have an input variable to \"refine\" the structure in Abinit when the text file is not accurate enough but not all the users are aware of this trick.\r\n\r\nIn my opinion, the default number of figures for the lattice vectors and the atomic positions should be increased in order to facilitate code interoperability.",
"> In my opinion, the default number of figures for the lattice vectors and the atomic positions should be increased in order to facilitate code interoperability.\r\n\r\nThis seems sensible to me, thanks for the exposition.",
"Six decimals seem already excessive. You mean there are symmetry codes with\nthat kind of tolerance. If u want fractions, that can be done using the\npython fractions module.\n\nOn Tue, Mar 3, 2020 at 16:58 Matthew Horton <notifications@github.com>\nwrote:\n\n> In my opinion, the default number of figures for the lattice vectors and\n> the atomic positions should be increased in order to facilitate code\n> interoperability.\n>\n> This seems sensible to me, thanks for the exposition.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1784?email_source=notifications&email_token=AAEM4UZU23ED723UBHNJ6XTRFWRTPA5CNFSM4LAM7GA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENVYTFI#issuecomment-594250133>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAEM4UY2YC3YLRRO42JWZITRFWRTPANCNFSM4LAM7GAQ>\n> .\n>\n-- \nShyue Ping\n",
"I’ve seen errors with symmetry myself when “only” six decimals are present,\nthough I’ve seen it in the context of constructing a cell from a space\ngroup.\n\nOn Tue, Mar 3, 2020 at 17:16, Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> Six decimals seem already excessive. You mean there are symmetry codes with\n> that kind of tolerance. If u want fractions, that can be done using the\n> python fractions module.\n>\n> On Tue, Mar 3, 2020 at 16:58 Matthew Horton <notifications@github.com>\n> wrote:\n>\n> > In my opinion, the default number of figures for the lattice vectors and\n> > the atomic positions should be increased in order to facilitate code\n> > interoperability.\n> >\n> > This seems sensible to me, thanks for the exposition.\n> >\n> > —\n> > You are receiving this because you are subscribed to this thread.\n> > Reply to this email directly, view it on GitHub\n> > <\n> https://github.com/materialsproject/pymatgen/issues/1784?email_source=notifications&email_token=AAEM4UZU23ED723UBHNJ6XTRFWRTPA5CNFSM4LAM7GA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENVYTFI#issuecomment-594250133\n> >,\n> > or unsubscribe\n> > <\n> https://github.com/notifications/unsubscribe-auth/AAEM4UY2YC3YLRRO42JWZITRFWRTPANCNFSM4LAM7GAQ\n> >\n> > .\n> >\n> --\n> Shyue Ping\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/1784?email_source=notifications&email_token=AAWWWRG36T3MAPGM36MXPETRFWTT3A5CNFSM4LAM7GA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENVZX4Q#issuecomment-594254834>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRGAL2LWMD5FQDTD3HDRFWTT3ANCNFSM4LAM7GAQ>\n> .\n>\n",
"Well, it seems to me that also pymatgen is trying to fix this finite precision issue\r\nwith an ad-hoc solution:\r\n\r\n```python\r\n # check for finite precision frac co-ordinates (e.g. 0.6667 instead of 0.6666666...7)\r\n # this can sometimes cause serious issues when applying symmetry operations\r\n important_fracs = (1 / 3., 2 / 3.)\r\n fracs_to_change = {}\r\n for label in ('_atom_site_fract_x', '_atom_site_fract_y', '_atom_site_fract_z'):\r\n if label in data.data.keys():\r\n for idx, frac in enumerate(data.data[label]):\r\n try:\r\n frac = str2float(frac)\r\n except Exception:\r\n # co-ordinate might not be defined e.g. '?'\r\n continue\r\n for comparison_frac in important_fracs:\r\n if abs(1 - frac / comparison_frac) < 1e-4:\r\n fracs_to_change[(label, idx)] = str(comparison_frac)\r\n if fracs_to_change:\r\n self.warnings.append(\"Some fractional co-ordinates rounded to ideal values to \"\r\n \"avoid issues with finite precision.\")\r\n for (label, idx), val in fracs_to_change.items():\r\n data.data[label][idx] = val\r\n```\r\n\r\nThe question is: why do we spend a lot of CPU-hours to obtain a relaxed structure with ab-initio quality when a significant part of the information on the crystalline structure is then lost when we present the final result to the user or when we print these results to txt file in order to restart a calculation? Note that beyond KS-DFT calculations are more sensitive to the quality of the input structure and this is the reason why we mainly use json files to perform our studies.",
"I didn't expect this to blow up as much as it did, due to my time difference I didn't follow up yet, apologies.\r\n\r\nI think @gmatteo gave a reasonable argument where the lack of precision could cause some issues (I appreciate it).\r\n\r\nIdeally in my case, the only reason I noticed this issue was creating a test for some code I have written that sorts neighbours into different shells, my precision was too high when searching for the shells, and when I tried to reproduce the bug locally by exporting as a CIF file (and then reloading it) the bug was non-existent anymore.\r\n\r\nI also agree that typically, we should not worry about extra precision, but I think from a **numerical standpoint**, the option for extra precision should be implemented and should not be hard coded. Also, from @gmatteo 's comment, it could be the case that some DFT codes might have issues restarting from a structure from a CIF file if it is not as close to what was used initially - say from a wave function restart with the previous structure loaded from a CIF. Although, I'm not sure how common this case is.",
"great discussion, \r\nI'm currently developing an other multy code workflow framework using pymatgen. Here we pull all magic numbers and parameter into a settings json file. The next parameter will be write precision. @shyuep please add the write precision in the to method. not all users have the same needs. I don't think we should be deciding what is good enough for our users.\r\nCheers,",
"I have set the default float precision to 8, and added a significant_figures arg (which also works in Structure.to and consistent with the naming used in Poscar). This should handle all these complaints. It should be noted that fundamentally cif, and all floating point translations to strings, is \"lossy\". Taking a DFT relaxed structure and transforming it to CIF before reading it back to a second DFT run is not a good practice. There are reasons why other formats (e.g., JSON) exist. \r\n\r\nFor future reference: pls be respectful during discussions and especially when asking for other people to do stuff. I am more than happy to hear feedback and we can always help. But often, it is also useful for someone to take on the mantle of simply editing the CifWriter code to implement a simple thing like float precision formatting. It was literally a few minor changes to the format strings + changes to associated tests. Generally the tone has been good, but @setten, you really shouldn't be issuing me orders. It just rubs me the wrong way.",
"Dear Shyue,\r\nPlease don't get me wrong, I never intended to order you around, anybody else would probably just have added it in a less conformal way probably even causing you even more work. The discussion just seemed to be spinning out of control.\r\nBest, Michiel "
] | 2020-03-03T15:29:38
| 2020-03-04T13:57:16
|
2020-03-04T12:35:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**It makes it difficult to reproduce bugs or get a good nearest neighbour precision when the CIF writer has no precision**
CIF writer seems to have no precision for output, can give some errors in calculations if a certain precision is needed.
**Add the number of decimals or precision to output when saving a file as CIF**
Perhaps add `**kwargs `into `.to` method for Structure. Side note: json seems to store more digits...
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1784/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1784/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1785
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1785/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1785/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1785/events
|
https://github.com/materialsproject/pymatgen/pull/1785
| 575,638,929
|
MDExOlB1bGxSZXF1ZXN0MzgzNzU5MDAz
| 1,785
|
Pourbaix fix
|
{
"login": "montoyjh",
"id": 6494516,
"node_id": "MDQ6VXNlcjY0OTQ1MTY=",
"avatar_url": "https://avatars.githubusercontent.com/u/6494516?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/montoyjh",
"html_url": "https://github.com/montoyjh",
"followers_url": "https://api.github.com/users/montoyjh/followers",
"following_url": "https://api.github.com/users/montoyjh/following{/other_user}",
"gists_url": "https://api.github.com/users/montoyjh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/montoyjh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/montoyjh/subscriptions",
"organizations_url": "https://api.github.com/users/montoyjh/orgs",
"repos_url": "https://api.github.com/users/montoyjh/repos",
"events_url": "https://api.github.com/users/montoyjh/events{/privacy}",
"received_events_url": "https://api.github.com/users/montoyjh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks!\r\n"
] | 2020-03-04T18:13:49
| 2020-03-04T19:59:24
|
2020-03-04T19:59:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Fix to two bugs in Pourbaix Diagram code
* Fixes issue where Pourbaix diagram was considering MultiEntries where reaction calculator finds a balanced reaction with no product.
* Fixes issue with MPRester PourbaixEntry processing due to Entry refactor. Specifically, `_energy`/`uncorrected_energy` mix-up.
## TODO (if any)
The regression test that I've added is heavier than I'd like (on an already too-heavy set of tests for the pourbaix_diagram module), I can create a more minimal test that encapsulates the issue more neatly, but will need a bit more time to do so, so figured I'd issue the PR in case the bug fixes are a priority.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1785/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1785/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1785",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1785",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1785.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1785.patch",
"merged_at": "2020-03-04T19:59:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1786
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1786/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1786/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1786/events
|
https://github.com/materialsproject/pymatgen/pull/1786
| 575,780,239
|
MDExOlB1bGxSZXF1ZXN0MzgzODg0MzI1
| 1,786
|
[WIP] Heisenberg
|
{
"login": "ncfrey",
"id": 19844216,
"node_id": "MDQ6VXNlcjE5ODQ0MjE2",
"avatar_url": "https://avatars.githubusercontent.com/u/19844216?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ncfrey",
"html_url": "https://github.com/ncfrey",
"followers_url": "https://api.github.com/users/ncfrey/followers",
"following_url": "https://api.github.com/users/ncfrey/following{/other_user}",
"gists_url": "https://api.github.com/users/ncfrey/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ncfrey/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ncfrey/subscriptions",
"organizations_url": "https://api.github.com/users/ncfrey/orgs",
"repos_url": "https://api.github.com/users/ncfrey/repos",
"events_url": "https://api.github.com/users/ncfrey/events{/privacy}",
"received_events_url": "https://api.github.com/users/ncfrey/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks. But can you resolve the branch conflicts first? Pls merge the latest pymatgen master to your fork.",
"Thanks @ncfrey !"
] | 2020-03-04T21:15:48
| 2020-03-10T23:27:25
|
2020-03-10T23:27:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
@mkhorton
* Added option to use an effective <J> exchange parameter from lowest energy FM and AFM configurations.
* Fixes to MSONable object handling.
## TODO
* Additional methods for obtaining exchange parameters.
* Options to fix magnetic moment magnitudes.
* Add type hints
|
{
"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/1786/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1786/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1786",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1786",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1786.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1786.patch",
"merged_at": "2020-03-10T23:27:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1787
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1787/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1787/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1787/events
|
https://github.com/materialsproject/pymatgen/issues/1787
| 577,275,146
|
MDU6SXNzdWU1NzcyNzUxNDY=
| 1,787
|
POTCAR with symbol Si has metadata that does not match any VASP POTCAR known to pymatgen.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @hongyi-zhao, it’s just a warning. If you’re comfortable you’re using the correct POTCAR you can ignore it.\r\n\r\nIt’s basically saying that the functional is compatible with those distributed as PBE_52/54 by VASP, but a specific variation we haven’t encountered before. This doesn’t mean it’s wrong.\r\n\r\n(Flagging @rkingsbury )",
"Thanks, got it.",
"Hi, \r\n\r\nI have and a couple people experience the same problem as I see from the open issues. In my case, POTCAR metadata (PSCTR file) never matches the PSCTR of PotcarSingle object. However, md5 sums of the POTCARs I have always matches the vasp_potcar_pymatgen_hashes.json file. \r\n\r\nI thought the content of the actual pseudopotential file is more important than what is inside the metadata. Why do you need to check the contents of the metadata as well?\r\n\r\nThanks,\r\nKayahan",
"Hi @kayahans , you are correct. The content of the actual pseudopotential file is what affects the calculation, so as long as the hash of the potcar **data** (which is calculated by the `get_potcar_hash` method) matches the contents of `vasp_potcar_pymatgen_hashes.json`, then your POTCAR is valid. \r\n\r\nWe track the hash of the metadata as well to provide a clearer provenance as to which POTCARs are being used, and to serve as an indicator that the contents of the POTCARs have been modified at some point. Basically, if the contents of the file (including metadata) do not match exactly what is provided by VASP, you will see a warning. ",
"Thanks! \r\n",
"@rkingsbury we're getting enough queries about these warnings that I think we should re-word the messages a little bit. I'll make a change"
] | 2020-03-07T04:20:59
| 2023-06-20T16:30:28
|
2023-06-20T16:30:28Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
I try to run the examples here:
https://ma.issp.u-tokyo.ac.jp/en/app-post/1146
With the following code to generate the band-structure plot:
```
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import BSPlotter
vaspout = Vasprun("./vasprun.xml")
bandstr = vaspout.get_band_structure(line_mode=True)
plt = BSPlotter(bandstr).get_plot(ylim=[-12,10])
plt.savefig("band.pdf")
```
I get the following warnings:
```
In [1]: runfile('/home/werner/Cd-Si/plotband.py', wdir='/home/werner/Cd-Si')
Reloaded modules: spyder
/home/werner/.pyenv/versions/hpc/lib/python3.8/site-packages/pymatgen/io/vasp/inputs.py:1855: BadPotcarWarning: POTCAR with symbol Si has metadata that does not match any VASP POTCAR known to pymatgen. The data in this POTCAR is known to match the following functionals: ['unvie_PBE_52', 'PBE_54', 'PBE_52']
warnings.warn("POTCAR with symbol {} has metadata that does not match\
```
How to solve this issue?
Regards
|
{
"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/1787/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1787/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1788
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1788/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1788/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1788/events
|
https://github.com/materialsproject/pymatgen/issues/1788
| 577,336,633
|
MDU6SXNzdWU1NzczMzY2MzM=
| 1,788
|
Need fix for the enumlib's repo url.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Done. Thanks.",
"But when I opened the website https://pymatgen.org/installation.html, it still shows the wrong url I reported here.\r\n\r\nRegards",
"Sometimes it takes a while to update on the website after a change has been made due to the content delivery networks that GitHub Pages uses (which is where pymatgen.org is hosted).",
"Sorry, there was a problem with the doc generation script. It should now be updated. For future reference, you can easily edit the docs in docs_rst and update the URLs if needed and submit a PR."
] | 2020-03-07T13:43:02
| 2020-03-09T13:49:11
|
2020-03-07T16:08:37Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
The following webpage: https://pymatgen.org/installation.html, says that:
```
2. enum:
Get it at http://enum.sourceforge.net and follow the instructions to compile multienum.x and makestr.x.
```
But this project has moved to github in 2015 as noted on the above website:
`(We have migrated this project to github [June 1 2015)] http://github.com/msg-byu/enumlib).`
Could you please fix this?
Regards
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1788/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1788/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1789
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1789/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1789/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1789/events
|
https://github.com/materialsproject/pymatgen/issues/1789
| 577,372,471
|
MDU6SXNzdWU1NzczNzI0NzE=
| 1,789
|
Space group symmetry operator issues
|
{
"login": "pietakio",
"id": 10080247,
"node_id": "MDQ6VXNlcjEwMDgwMjQ3",
"avatar_url": "https://avatars.githubusercontent.com/u/10080247?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pietakio",
"html_url": "https://github.com/pietakio",
"followers_url": "https://api.github.com/users/pietakio/followers",
"following_url": "https://api.github.com/users/pietakio/following{/other_user}",
"gists_url": "https://api.github.com/users/pietakio/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pietakio/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pietakio/subscriptions",
"organizations_url": "https://api.github.com/users/pietakio/orgs",
"repos_url": "https://api.github.com/users/pietakio/repos",
"events_url": "https://api.github.com/users/pietakio/events{/privacy}",
"received_events_url": "https://api.github.com/users/pietakio/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @pietakio,\r\n\r\nWhen building structure from space groups you have to be very careful with the precision of your inputs. Have you tried:\r\n\r\n`siha_atom_coords = [[1/3, 2/3, 0.00195], ...`\r\n\r\ninstead?\r\n\r\nWhen this happens, it's usually because 0.33333 != 1/3 from the point of view of applying a symmetry operation. If importing from a CIF file, pymatgen will try to find rational fractions for certain co-ordinates and correct as appropriate.\r\n\r\nIf this doesn't fix your issue, we can certainly look at the space group operations themselves. Errors in these are rare but certainly possible!",
"Hi @mkhorton,\r\n\r\nThank you so much! Yes, on your above advice I re-wrote the atom coordinates in fractions \r\n(wherever they were obvious) as:\r\n\r\n```\r\nsiha_atom_coords = [[1/3, 2/3, 0.00195],\r\n [0.24745, 0.99214, 1/4],\r\n [0.39747, 0.36773, 1/4],\r\n [0.32481,0.48347,1/4],\r\n [0.58394,0.46300,1/4],\r\n [0.34028,0.25607,0.07052],\r\n [0.00000,0.00000,0.20142],\r\n [0.00000,0.00000,0.01242]]\r\n```\r\n\r\nAnd now it works to give the correct structure.\r\n\r\nThanks so much!! \r\n\r\nSo nothing needs to be fixed in the space group operators for 'P6_3/m', although if it's not there already (perhaps I missed it?), it would be fantastic if a note could be made about the need to use fractions in the Structure.from_spacegroup() doc strings to save other people who might struggle with the precision issue. \r\n\r\nAny thoughts on my \"case 2\" (space group symbol and international number not generating the same structure)? \r\n\r\nThanks!\r\n",
"For your second case, you should be aware there are multiple \"settings\" available for each space group. We use the standard ITA (International Tables for Crystallography, Vol. A) settings in pymatgen, as are also used in spglib.\r\n\r\nFor the specific example of space group 14, a monoclinic group, we have to choose our unique axis (this can be either **a**, **b** or **c**) along with different choices for the oblique axes (cell choices 1, 2 or 3), and this leads to 18 different possible settings. The Bilbao Crystallographic Server is an excellent resource for this. \"P 1 2_1/a 1\" is not the same setting as \"P 1 2_1/c 1\". Likely, your reference is using the former, and pymatgen is using the latter.\r\n\r\nThe important thing here is that the overall symmetry is the same in all settings (the same symmetry operations are present), but the way we're describing the cell changes. In particular, the positions of the atoms in your motif will be different. And if you use positions for one setting while using the generators for a different system then you'll get the incorrect structure out.\r\n\r\nFinally, *pymatgen* does include a `JonesFaithfulTransformation` to help you convert atomic positions, lattices and symmetry operations between different settings. Good luck!\r\n\r\n<img width=\"1071\" alt=\"image\" src=\"https://user-images.githubusercontent.com/2976580/76156594-75335e00-60b1-11ea-971c-21849c59081c.png\">\r\nFrom International Tables for Crystallography, Vol. A\r\n\r\n<img width=\"838\" alt=\"image\" src=\"https://user-images.githubusercontent.com/2976580/76156609-aa3fb080-60b1-11ea-8bbf-2fdfc0559533.png\">\r\nFrom Bilbao Crystallographic Server, \"GENPOS\"\r\n",
"Thank you! This is extremely helpful. \r\n\r\nA few (hopefully simple requests) to help clarify these issues for others:\r\n1. Please add a note to the doc strings for Structure.from_spacegroup() about the need to use fractions, where possible, when specifying atomic coordinates. \r\n2. Would it be possible for the space group tag (i.e. what's returned from get_space_group_info()) to return the extended symbol instead of, or in addition to, the short form, as this would greatly help confirm to the user specifically what is being done in terms of symmetry operations? \r\n\r\nThank you so much! ",
"> Please add a note to the doc strings for Structure.from_spacegroup() about the need to use fractions, where possible, when specifying atomic coordinates.\r\n\r\nAgreed, that sounds sensible. Just a word of caution here though; there are many real cases of crystals where atomic positions are almost-but-not-quite at fractional co-ordinates and these do have physical meaning. At the end of the day, the user has to make a judgement call here.\r\n\r\n> Would it be possible for the space group tag (i.e. what's returned from get_space_group_info()) to return the extended symbol instead of, or in addition to, the short form, as this would greatly help confirm to the user specifically what is being done in terms of symmetry operations?\r\n\r\nWe probably won't change this -- partly because we don't want to break backwards compatibility with scripts that expect a certain output from this command, and also because the short H-M symbol is sufficient to convey setting information (P2_1/c).\r\n\r\nHowever, note that these are just convenience methods on `Structure`. If you want more information, pymatgen offers a lot more functionality via its `pymatgen.symmetry` module including `SpaceGroup` (which can give you the full symbol as an attribute) and also `SpaceGroupAnalyzer` (which can give you the structure in other settings, give you a way to retrieve Wyckoff labels etc.) "
] | 2020-03-07T17:23:54
| 2020-03-08T22:10:58
|
2020-03-08T16:03:59Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi!
Thank you for making Pymatgen -- it's a fabulously helpful and awesome program.
I've encountered two major issues when working with generation of Structures using Structure.from_spacegroup().
**First case**
In the first case (for space group 'P6_3/m', with equivalent results using the space group number 176) the generated structure is clearly not correct as it contains the incorrect number of Ca atoms (there are 14 Ca atoms instead of 10 in the unit cell).
In this case, the structure that I'm trying to generate from lattice parameters and a list of atomic positions is based on hydroxyapatite, and there are cif files available to define hydroxyapatite ([Hydroxyapatite.txt](https://github.com/materialsproject/pymatgen/files/4302192/Hydroxyapatite.txt)).
However, when I define the structure using Structure.from_file() and use the pre-defined cif files for hydroxyapatite, the unit cell has the correct formula. I noticed that if I change the spacegroup symbol
or the international spacegroup number in the hydroxyapatite cif file, that there is no change to the
structure defined by Pymatgen using Structure.from_file(). If, however, I change the space group
symmetry operations in the hydroxyapatite cif file, then the structure generated by Pymatgen has the
incorrect unit cell formula (additional atoms appear, as happens when I attempt to generate the structure using Structure.from_spacegroup(). This leads me to believe that there is an error in Pymatgen's spacegroup symmetry operators for space group 'P6_3/m' (number 176).
The symmetry operators from the hydroxyapatite cif file are:
'x,y,z'
'-x+y,-x,1/2-z'
'x-y,x,1/2+z'
'y,-x+y,-z'
'-y,x-y,z'
'x,y,1/2-z'
'-x,-y,1/2+z'
'x-y,x,-z'
'-x+y,-x,z'
'-y,x-y,1/2-z'
'y,-x+y,1/2+z'
'-x,-y,-z'
If you would please check and fix, this would be much appreciated!
To reproduce:
```
# Structure generated from cif reference file:
ref_struct = Structure.from_file(os.path.join(read_path, "Hydroxyapatite.cif"))
# Structure generated from atom list, lattice info, coords, and spacegroup (slightly different coords
# and lattice constants, but results are same using exact coords of ref cif file):
siha_atoms_list = [{'Ca':1.0},{'Ca':1.0},{'P':1.0},{'O':1.0},{'O':1.0},{'O':1.0},{'O':0.5},{'H':0.5}]
# siha_atoms_list = ['Ca','Ca','P','O','O','O','O','H']
siha_atom_coords = [[0.33333, 0.66667, 0.00195],
[0.24745, 0.99214, 0.25000],
[0.39747, 0.36773, 0.25000],
[0.32481,0.48347,0.25000],
[0.58394,0.46300,0.25000],
[0.34028,0.25607,0.07052],
[0.00000,0.00000,0.20142],
[0.00000,0.00000,0.01242]]
siha_latt = Lattice.from_parameters(a=9.43144, b=9.43144, c=6.94553,
alpha=90.00000, beta=90.0000, gamma=120.00000)
siha_struct = Structure.from_spacegroup('P6_3/m', siha_latt, siha_atoms_list, siha_atom_coords)
# Compare siha_struct to ref_struct and see that siha_struct is not correct, although it should be
# same unit cell formula to the one generated by the symmetry operators of the hydroxyapatite.cif file.
```
**Second Case**
The second case also involves generating a structure from Structure.from_spacegroup().
In this case, when attempting to generate a structure using the space group 'P 1 21/a 1', I get the correct structure, and when using xrayutilities I obtain an excellent match between the calculated and experimental xrd curve, so I believe that the structure generated by Pymatgen is correct.
The 'P 1 21/a 1' space group corresponds to international number 14 (http://img.chem.ucl.ac.uk/sgp/large/014ay1.htm), and using get_space_group_info() on the Pymatgen generated structure says the space group is ( 'P2_1/c', 14). However, if I generate the structure using 'P2_1/c' or number 14, the structure returned is incorrect, and the match to the experimental xrd spectra is terrible, and moreover, 'P2_1/c' and number 14 results are not the same (where I definitely think these two results should be the same). Again, I feel as though there must be a mistake in the underlying symmetry operators, where in this case there are different operators for items that should be mapping to the same operator (it's possible that I'm confused here too, and if this is the case, some additional documentation would be much appreciated).
**Expected behavior**
Expected structure read by cif and generated from_space group to be the same, and expected structures generated from equivalent space group symbols and numbers to be the same.
**Desktop:**
- OS: Linux
- Ubuntu 18.04.4 LTS
Thanks so much for your help!
|
{
"login": "pietakio",
"id": 10080247,
"node_id": "MDQ6VXNlcjEwMDgwMjQ3",
"avatar_url": "https://avatars.githubusercontent.com/u/10080247?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pietakio",
"html_url": "https://github.com/pietakio",
"followers_url": "https://api.github.com/users/pietakio/followers",
"following_url": "https://api.github.com/users/pietakio/following{/other_user}",
"gists_url": "https://api.github.com/users/pietakio/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pietakio/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pietakio/subscriptions",
"organizations_url": "https://api.github.com/users/pietakio/orgs",
"repos_url": "https://api.github.com/users/pietakio/repos",
"events_url": "https://api.github.com/users/pietakio/events{/privacy}",
"received_events_url": "https://api.github.com/users/pietakio/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1789/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1789/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1790
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1790/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1790/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1790/events
|
https://github.com/materialsproject/pymatgen/issues/1790
| 577,419,153
|
MDU6SXNzdWU1Nzc0MTkxNTM=
| 1,790
|
site_matching_indices in KumagaiCorrection
|
{
"login": "fermionian",
"id": 44589555,
"node_id": "MDQ6VXNlcjQ0NTg5NTU1",
"avatar_url": "https://avatars.githubusercontent.com/u/44589555?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/fermionian",
"html_url": "https://github.com/fermionian",
"followers_url": "https://api.github.com/users/fermionian/followers",
"following_url": "https://api.github.com/users/fermionian/following{/other_user}",
"gists_url": "https://api.github.com/users/fermionian/gists{/gist_id}",
"starred_url": "https://api.github.com/users/fermionian/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/fermionian/subscriptions",
"organizations_url": "https://api.github.com/users/fermionian/orgs",
"repos_url": "https://api.github.com/users/fermionian/repos",
"events_url": "https://api.github.com/users/fermionian/events{/privacy}",
"received_events_url": "https://api.github.com/users/fermionian/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2020-03-07T23:56:52
| 2023-08-13T16:33:40
|
2023-08-13T16:33:40Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I am trying to use KumagaiCorrection from pymatgen.analysis.defects.corrections.
As I did not find any tutorial or examples available, I am trying to reproduce a KumagaiCorrection using the test cases in the unittest. Basically it is the function test_kumagai [here](https://github.com/materialsproject/pymatgen/blob/890ce91491b36df15de714630f73ff66e8496def/pymatgen/analysis/defects/tests/test_corrections.py)
The associated files are [here](https://github.com/materialsproject/pymatgen/tree/890ce91491b36df15de714630f73ff66e8496def/test_files/defect)
I have no problem with reproducing the unit test assertion.
However, I do have doubt with the site_matching_indices in parameters.
If I understand correctly, the test case is a charged (-3) Ga vacancy in GaAs. The vacancy site index is 0 as in the bulk structure. And the 'site_matching_indices' written in the unittest is
`'site_matching_indices': [[ind, ind - 1] for ind in range(len(bulk_struc))]`
This would include a matching of [0,-1] ? While I thought the site_matching should exclude the defect site? and should be
`'site_matching_indices': [[ind, ind - 1] for ind in range(1, len(bulk_struc))]`
The first one gives result : `kcorr['kumagai_potential_alignment']= 2.09704862`
while the second one gives result: `kcorr['kumagai_potential_alignment']= 0.19524485`
I hope to know if this is just an arbitrary unittest or if I am understanding the site_matching_indices incorrectly...
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1790/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1790/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1791
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1791/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1791/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1791/events
|
https://github.com/materialsproject/pymatgen/issues/1791
| 577,422,522
|
MDU6SXNzdWU1Nzc0MjI1MjI=
| 1,791
|
The list of vasp's INCAR tags supported by pymatgen currently.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 use any VASP INCAR tag via pymatgen using `user_incar_settings`. ",
"I mean whether the pymatgen has already built-in usage instructions for all of these tags. The tag list is huge to some extent, so have the build-in usage instructions for them may be more useful for writing the job scripts with the help of python IDE's auto-completion functionality.",
"Pymatgen does not have instructions for VASP tags or any other software. Ultimately, VASP belongs to a completely different set of developers and they have to maintain their own documentation and help. It is certainly easy enough for us to implement something that obtains the help from the wiki....",
"Good idea. Thanks a lot.",
"I implemented a basic version for now. It should be easy to make it nicer. See pymatgen.io.vasp.help.",
"Wonderful. I tested it as following:\r\n\r\nWhen separately run on this script, it will retrieve the tags successfully: \r\n`$ python /home/werner/Public/hpc/tools/pymatgen.git/pymatgen/io/vasp/help.py`\r\n\r\nBut as for using it as a helper, I still cannot figure out how to use it. See my following usage (it should be wrong in using it), I tried some similar forms as follows but all of tries failed:\r\n\r\n```\r\nimport pymatgen\r\npymatgen.io.vasp.help.print_help('ISYM')\r\n```\r\n\r\nCould you please give me some hints for using it as a helper?\r\n \r\n\r\nBased on the vasp's wiki to retrieve the tags info in real-time, it will produce some delay in real-time. In this case, the cache mechanism should be used, anyway, the definitions for the tags won't be changed frequently. I mean, let the helper retrieve all of the tags at the first time and save it into memory and then just retrieve the needed ones for user.\r\n\r\nThe further step on this should be not only the tag itself, but also some descriptions for the tag, so may be use a dictionary, instead of the list to do the job.\r\n\r\nI'm not so familiar with it, just my ideas. \r\n\r\nRegards\r\n ",
"```python\r\nfrom pymatgen.io.vasp.help import VaspDoc\r\ndoc = VaspDoc()\r\ndoc.print_help(\"ISYM\")\r\n```\r\n\r\nPls review how to use Python classes. Sorry, but we cannot provide support for Python syntax.",
"Thanks."
] | 2020-03-08T00:30:43
| 2020-03-10T00:12:23
|
2020-03-09T14:43:45Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
The complete list of vasp INCAR tags is here:
https://www.vasp.at/wiki/index.php/Category:INCAR
I want to know which of them supported by pymatgen currently?
Regards
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1791/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1791/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1792
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1792/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1792/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1792/events
|
https://github.com/materialsproject/pymatgen/issues/1792
| 577,499,891
|
MDU6SXNzdWU1Nzc0OTk4OTE=
| 1,792
|
Abouth the kpath determining method used in pymatgen.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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're welcome to use SeeK if you want, they distribute their algorithm as a Python code too. We will not be changing the default algorithm at this time, but stay tuned for an update from MP on this later in the year.",
"Matthew Horton <notifications@github.com> 于2020年3月9日周一 上午9:34写道：\r\n\r\n> You're welcome to use SeeK if you want, they distribute their algorithm as\r\n> a Python code too. We will not be changing the default algorithm at this\r\n> time, but stay tuned for an update from MP on this later in the year.\r\n>\r\n\r\nThanks for your reply.\r\nAnother question: I've told by the developer of seekpath that it currently doesn't\r\nsupport for 1D and 2D systems for generating the corresponding kpath. I want to \r\nknow what about pymatgen for this type of job?\r\n\r\nRegards\r\n\r\n> —\r\n> You are receiving this because you authored the thread.\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/materialsproject/pymatgen/issues/1792?email_source=notifications&email_token=ACVDTDSGVHS26CGONRZWZZLRGRITPA5CNFSM4LDZMMK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOFISQQ#issuecomment-596281666>,\r\n> or unsubscribe\r\n> <https://github.com/notifications/unsubscribe-auth/ACVDTDVFU53AHUNMZVFWGO3RGRITPANCNFSM4LDZMMKQ>\r\n> .\r\n>\r\n\r\n\r\n-- \r\nHongyi Zhao <hongyi.zhao@gmail.com>\r\n",
"Generally, one usually simulates a 2D system within 3D periodic boundary conditions, and you just don't have dispersion along one of the axes. In this way, the existing k-path algorithms are fine since you're applying it to a \"3D\" system (the one you're simulating), you may just need to remove certain paths. Pymatgen does not help with this."
] | 2020-03-08T13:20:21
| 2020-03-09T02:58:01
|
2020-03-09T01:32:05Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
I noted that the HighSymmKpath class is implemented based on the paper:
http://dx.doi.org/10.1016/j.commatsci.2010.05.010
While there is another well know paper for dealing with this type of job, it's:
http://dx.doi.org/10.1016/j.commatsci.2016.10.015
The latter paper is more recent and exhaustive and it also analyzed the method given by the former paper and said that there are some shortcomings:
```
Although the concept of an automatically determined unique band path
is a significant advance, there are three major shortcomings in their work,
which obliges us to design a new scheme in band path determination.
[...]
```
So I want to know whether the latter one is more appropriate for seeking the kpath and should be adopted to substitute the currently method in pymatgen?
Regards
|
{
"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/1792/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1792/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1793
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1793/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1793/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1793/events
|
https://github.com/materialsproject/pymatgen/pull/1793
| 577,915,280
|
MDExOlB1bGxSZXF1ZXN0Mzg1NTkzMDk4
| 1,793
|
fix sites's doc (delete duplication)
|
{
"login": "dynikon",
"id": 28987801,
"node_id": "MDQ6VXNlcjI4OTg3ODAx",
"avatar_url": "https://avatars.githubusercontent.com/u/28987801?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dynikon",
"html_url": "https://github.com/dynikon",
"followers_url": "https://api.github.com/users/dynikon/followers",
"following_url": "https://api.github.com/users/dynikon/following{/other_user}",
"gists_url": "https://api.github.com/users/dynikon/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dynikon/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dynikon/subscriptions",
"organizations_url": "https://api.github.com/users/dynikon/orgs",
"repos_url": "https://api.github.com/users/dynikon/repos",
"events_url": "https://api.github.com/users/dynikon/events{/privacy}",
"received_events_url": "https://api.github.com/users/dynikon/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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."
] | 2020-03-09T13:37:44
| 2020-03-09T13:40:48
|
2020-03-09T13:40:42Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## 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:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] 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 existing 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/1793/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1793/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1793",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1793",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1793.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1793.patch",
"merged_at": "2020-03-09T13:40:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1794
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1794/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1794/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1794/events
|
https://github.com/materialsproject/pymatgen/issues/1794
| 578,262,660
|
MDU6SXNzdWU1NzgyNjI2NjA=
| 1,794
|
Some properties of the Element class not defined with decorate @property.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 @property is only used if we are using a hidden variable or it is a property that is computed on the fly. In this case, the atomic mass is important enough that we write a special decorator for it. The melting point and boiling point are much less frequently used and so we just leave it to the get_attr function to deal with it."
] | 2020-03-10T00:22:59
| 2020-03-11T13:14:33
|
2020-03-11T13:14:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
Say for the following code snippets:
```
import pymatgen as mg
fe = mg.Element("Fe")
print(fe.atomic_mass)
print(fe.melting_point)
print(fe.boiling_point)
```
The atomic_mass is defined as a property with decorate @property, but the other two are not. This will cause the property's name cannot be auto-completed within the python IDE, say pycharm.
Are they designed like this intentionally or need to some touch up for add the corresponding @property's?
Regards
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1794/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1794/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1795
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1795/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1795/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1795/events
|
https://github.com/materialsproject/pymatgen/issues/1795
| 578,617,834
|
MDU6SXNzdWU1Nzg2MTc4MzQ=
| 1,795
|
Want to make a PR for fixing the installation.rst
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Yes, submitting a PR would be fine. In fact, we prefer small PRs, even when the functionality is big, it is preferable they are broken up into simple chunks.",
"Thanks. Another issue also said on the installation page, see following:\r\n\r\n```\r\n$ pip install pymatgen[extra] \r\nLooking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple\r\nRequirement already satisfied: pymatgen[extra] in /home/werner/Public/hpc/tools/pymatgen.git (2020.3.2)\r\n WARNING: pymatgen 2020.3.2 does not provide the extra 'extra'\r\n```\r\n\r\nIs the following install option discarded for pymatgen 2020.3.2:\r\n\r\n`pymatgen[extra] `\r\n\r\nRegards\r\n",
"The word extra means one of the other extras needed. E.g., pip install pymatgen[ase]. These are defined in the setup.py under extras_require."
] | 2020-03-10T14:24:22
| 2020-03-10T16:01:52
|
2020-03-10T14:29:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hi,
I noted that the following description is outdated here:
https://github.com/materialsproject/pymatgen/blob/master/docs_rst/installation.rst
`3. Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the adapters in pymatgen.io.aseio between pymatgen's core Structure object and the Atoms object used by ASE. Get it at https://wiki.fysik.dtu.dk/ase/. Note that the ASE package is incompatible with Python 3.x at the moment.`
In fact, based on the info here: https://wiki.fysik.dtu.dk/ase/install.html, at the moment, ASE package need Python 3.5+. So, I changed the above notes into the following:
```
3. Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the
adapters in pymatgen.io.aseio between pymatgen's core Structure object and
the Atoms object used by ASE. Get it at https://wiki.fysik.dtu.dk/ase/.
Note that the ASE package is compatible with Python 3.5+ at the moment.
```
Then I want to make PR, but I'm not sure whether only change this file is enough? Please instruct me for all the changes should I do before I can make the PR.
Regards
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1795/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1795/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1796
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1796/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1796/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1796/events
|
https://github.com/materialsproject/pymatgen/issues/1796
| 578,677,340
|
MDU6SXNzdWU1Nzg2NzczNDA=
| 1,796
|
Report a bug or issue
|
{
"login": "danpho",
"id": 19391437,
"node_id": "MDQ6VXNlcjE5MzkxNDM3",
"avatar_url": "https://avatars.githubusercontent.com/u/19391437?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/danpho",
"html_url": "https://github.com/danpho",
"followers_url": "https://api.github.com/users/danpho/followers",
"following_url": "https://api.github.com/users/danpho/following{/other_user}",
"gists_url": "https://api.github.com/users/danpho/gists{/gist_id}",
"starred_url": "https://api.github.com/users/danpho/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/danpho/subscriptions",
"organizations_url": "https://api.github.com/users/danpho/orgs",
"repos_url": "https://api.github.com/users/danpho/repos",
"events_url": "https://api.github.com/users/danpho/events{/privacy}",
"received_events_url": "https://api.github.com/users/danpho/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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, but there is a lot happening in your script. Pls report the issue/bug properly with a *short* script that reproduces the problem with a minimum number of lines and inputs. We cannot debug a long script where we do not even know where the bug occurred and whether it is even in a Pymatgen related method or one of the many other packages being used."
] | 2020-03-10T15:44:40
| 2020-03-10T15:59:27
|
2020-03-10T15:59:27Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**Describe the bug**
I prefer using issue report instead of bug report. I am not fully sure it is a bug. But it shows that the inconsistent results with same input, setting, and environments.
Note: My structure has partial occupation sites.
Pymatgen was updated in February.
I built a small model using PDFgui. And then use pymatgen to generate a supercell. However, under Python >3.7 environment(I tested v3.7 and 3.81), the same input cif file and settings, I receive the inconsistent outputs. I do not which one is reasonable. Then I visualize each output to see the difference using CrystalMaker.
**To Reproduce**
Attached are my scripts, input_control file, input cif files, and output pdb files.
Please run wmake_supercell.py, and then check the number of Cs and Ba in ./pdb/*.pdb file. Rename these files and rerun the scripts. Most time, I got different numbers of Cs and Ba.
**Expected behavior**
I hope that the output is consistent with same configurations and input.
**Screenshots**
Here, I attached part of the generated structures. I ran twice my scripts, and got different number of Ba and Cs atoms.
**Desktop (please complete the following information):**
- OS: [CentOS 7.3, Kernel: Linux 3.10.0-514.16.1.el7.x86_64]
- Version [pymatgen==2020.1.28
Here are all of my files which are in pdfgui.zip.
[pdfgui.zip](https://github.com/materialsproject/pymatgen/files/4313301/pdfgui.zip)]
**Additional context**
Add any other context about the problem here.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1796/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1796/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1797
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1797/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1797/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1797/events
|
https://github.com/materialsproject/pymatgen/issues/1797
| 578,745,125
|
MDU6SXNzdWU1Nzg3NDUxMjU=
| 1,797
|
Add angle_tolerance argument to CifWriter constructor
|
{
"login": "kyledmiller",
"id": 45434005,
"node_id": "MDQ6VXNlcjQ1NDM0MDA1",
"avatar_url": "https://avatars.githubusercontent.com/u/45434005?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/kyledmiller",
"html_url": "https://github.com/kyledmiller",
"followers_url": "https://api.github.com/users/kyledmiller/followers",
"following_url": "https://api.github.com/users/kyledmiller/following{/other_user}",
"gists_url": "https://api.github.com/users/kyledmiller/gists{/gist_id}",
"starred_url": "https://api.github.com/users/kyledmiller/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/kyledmiller/subscriptions",
"organizations_url": "https://api.github.com/users/kyledmiller/orgs",
"repos_url": "https://api.github.com/users/kyledmiller/repos",
"events_url": "https://api.github.com/users/kyledmiller/events{/privacy}",
"received_events_url": "https://api.github.com/users/kyledmiller/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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 feel welcome to open a pull request if this would be useful!"
] | 2020-03-10T17:28:43
| 2020-03-11T13:05:32
|
2020-03-11T13:05:32Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Pymatgen is very useful for quickly converting between file types, e.g., POSCAR <--> cif, but the `CifWriter` constructor is lacking the `angle_tolerance` parameter which means the default `SpaceGroupAnalyzer` value of 5 degrees is used. This value is too large for many applications and should in principle be configurable.
This issue could be very easily solved by simply adding an `angle_tolerance=None` argument to the constructor and carrying it through to the `SpaceGroupAnalyzer` constructor call.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1797/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1797/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/1798
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1798/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1798/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1798/events
|
https://github.com/materialsproject/pymatgen/pull/1798
| 579,002,376
|
MDExOlB1bGxSZXF1ZXN0Mzg2NDc3OTA2
| 1,798
|
Fix the notes for python version dependent of the ASE package.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_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"
] | 2020-03-11T04:29:57
| 2020-03-11T12:14:20
|
2020-03-11T12:14:12Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
See here for more info:
https://wiki.fysik.dtu.dk/ase/install.html
Which told the following:
Note that the ASE package is compatible with Python 3.5+ at the moment.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/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/1798/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1798/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1798",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1798",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1798.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1798.patch",
"merged_at": "2020-03-11T12:14:12Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1799
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1799/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1799/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1799/events
|
https://github.com/materialsproject/pymatgen/pull/1799
| 580,132,055
|
MDExOlB1bGxSZXF1ZXN0Mzg3NDAxMTUw
| 1,799
|
Fix QChem API
|
{
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"following_url": "https://api.github.com/users/utf/following{/other_user}",
"gists_url": "https://api.github.com/users/utf/gists{/gist_id}",
"starred_url": "https://api.github.com/users/utf/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/utf/subscriptions",
"organizations_url": "https://api.github.com/users/utf/orgs",
"repos_url": "https://api.github.com/users/utf/repos",
"events_url": "https://api.github.com/users/utf/events{/privacy}",
"received_events_url": "https://api.github.com/users/utf/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Actually, I take back part of my accusation. Privatizing `check_for_structure_changes` was done by @shyuep in efd386bcdbcc5541aa01c3bb4116999ae8924f68",
"The changes made in #1753 at least were at my request -- it fixed a long-standing bug and cleaned up some of our neighbor detection, but it did also therefore make some kwargs superfluous which is why the method call changed. Apologies for breaking atomate with this one!",
"Basic principle - API means doc + test. If something does not have a doc, I treat it as something private and I can modify as I well please unless the tests fail. So, write tests and doc?",
"I've added a docstring curtsey of @espottesmith so that linting passes.\r\n\r\nI have nothing to do with the qchem module so I don't know about adding tests. I suggest @samblau or @espottesmith add one in a future pull request.\r\n\r\nThis should be ready to merge.",
"Thanks @utf!",
"Thanks. But I will wait until a test is added to that method before merging.",
"Ok, I will leave this up to someone else to fix.\r\n\r\nI was not involved in the original code and am only trying to revert changes made in pymatgen to resolve upstream breakages in atomate and custodian.\r\n\r\nI would say that implementing breaking changes should ALWAYS be avoided. Even if it comes with worse docs/testing. The solution is to add docs + tests rather than changing functionality to hide their absence."
] | 2020-03-12T18:19:04
| 2020-03-12T20:18:13
|
2020-03-12T20:13:27Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
A recent pull request ~~(#1753)~~ (efd386b) made the `check_for_structure_changes` method private. Unfortunately, custodian relies on this method so this PR broke both custodian and atomate.
Furthermore, #1753 changed the arguments for `MoleculeGraph.with_local_env_strategy` which also broke atomate.
Can I suggest that when breaking API changes are made to the qchem module, that the authors also test their changes on atomate and custodian. @espottesmith @samblau
Thanks!
|
{
"login": "utf",
"id": 1330638,
"node_id": "MDQ6VXNlcjEzMzA2Mzg=",
"avatar_url": "https://avatars.githubusercontent.com/u/1330638?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/utf",
"html_url": "https://github.com/utf",
"followers_url": "https://api.github.com/users/utf/followers",
"following_url": "https://api.github.com/users/utf/following{/other_user}",
"gists_url": "https://api.github.com/users/utf/gists{/gist_id}",
"starred_url": "https://api.github.com/users/utf/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/utf/subscriptions",
"organizations_url": "https://api.github.com/users/utf/orgs",
"repos_url": "https://api.github.com/users/utf/repos",
"events_url": "https://api.github.com/users/utf/events{/privacy}",
"received_events_url": "https://api.github.com/users/utf/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/1799/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1799/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1799",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1799",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1799.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1799.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/1800
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1800/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1800/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/1800/events
|
https://github.com/materialsproject/pymatgen/pull/1800
| 580,220,450
|
MDExOlB1bGxSZXF1ZXN0Mzg3NDcyNzQx
| 1,800
|
[WIP] New KPath and HighSymmKpath classes
|
{
"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 |
[
"Just to double-check, have you verified the original class still works as before when SeeK optional dependency is not installed?\r\n\r\nOtherwise this pull request looks essentially good. Since it's a large one, I'll take some more time to read over it, and can merge once all linting/tests pass. Happy to see it finally coming out!",
">Just to double-check, have you verified the original class still works as before when SeeK optional dependency is not installed?\r\n\r\nYes, the original class and its default behavior work even if SeeK-path is not installed. It is only when you ask HighSymmKpath to use the convention by Hinuma and coworkers, or simply ask it to use all of the conventions that an error is issued.\r\n\r\n>Otherwise this pull request looks essentially good. Since it's a large one, I'll take some more time to read over it, and can merge once all linting/tests pass. Happy to see it finally coming out!\r\n\r\nGreat! That sounds good.",
"Hi @munrojm, I'm going to merge this -- thanks for your very diligent efforts to make sure backwards compatibility wasn't broken!",
"Actually, one request first -- can you make `KPathBase` explicitly an abstract base class? Just to prevent confusion should one try to initialize it. Making it an abstract base class makes it clear to the user it shouldn't be used directly.",
"> Actually, one request first -- can you make `KPathBase` explicitly an abstract base class? Just to prevent confusion should one try to initialize it. Making it an abstract base class makes it clear to the user it shouldn't be used directly.\r\n\r\nSure! No problem. That makes sense."
] | 2020-03-12T21:07:05
| 2020-03-18T01:11:21
|
2020-03-18T01:11:20Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This pull request introduces support for generating high-symmetry k-paths using two additional conventions. Namely, the SeeK-path convention by Hinuma and coworkers [Y. Hinuma, et al. Band structure diagram paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017)], and a new "on-the-fly" convention out of the Persson group that is soon to be published.
Below is a summary of the code changes:
* New KPath classes added to handle high-symmetry k-path generation.
* Existing HighSymmKpath code to generate paths using the convention by Setyawan and Curtarolo converted to a KPath class.
* New HighSymmKpath class added which calls k-path generation classes, and provides methods for amalgamating and comparing path data across conventions.
It should be noted that the default HighSymmKpath behavior has not been altered.
## Additional dependencies
The SeeK-path package is required for the convention by Hinuma and coworkers, and has been added to the optional requirements list.
|
{
"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/1800/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/1800/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/1800",
"html_url": "https://github.com/materialsproject/pymatgen/pull/1800",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/1800.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/1800.patch",
"merged_at": "2020-03-18T01:11:20Z"
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.