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Refactor model paths #69

Open

matthewcarbone wants to merge 10 commits into dev/m3gnet from mc-dev/m3gnet

Owner

matthewcarbone commented Oct 7, 2023

@deyulu the new paths for models will look like this:

zoo/XAS_TYPE/LEVEL_OF_THEORY/EDGE/ABSORBER/models

any suggestions or is this ok?

matthewcarbone added 7 commits

October 7, 2023 12:03


          Update lightshow external with vasp postprocessing

02cedd1


          Add VASP Ti grid

e43b904


          Refactor dependencies in pyproject

5eabc3f


          Update dependencies, use broadening in vasp processing

847a466


          Refactor the model zoo

940060e

Also remove the ensemble models for now, don't want to complicate
things too quickly


          Refactor m3gnet4xas api and how models are loaded

5f39fa6


          Add scikit learn back to pyproject dependencies

543a80f

Collaborator

deyulu commented Oct 8, 2023 via email

@matthew Carbone ***@***.***> What is XAS_type? Is it XANES or EXAFS? For the folder structure, I suggest a more physics motivated order: EDGE/ABSORBER/LEVEL_OF_THEORY/models . If we have transfer learning model, will it cause confusion on "level of theory"?

On Sat, Oct 7, 2023 at 12:26 PM Matthew Carbone ***@***.***> wrote: @deyulu <https://github.com/deyulu> the new paths for models will look like this: zoo/XAS_TYPE/LEVEL_OF_THEORY/EDGE/ABSORBER/models any suggestions or is this ok? ------------------------------ You can view, comment on, or merge this pull request online at: #69 Commit Summary - 02cedd1 <02cedd1> Update lightshow external with vasp postprocessing - e43b904 <e43b904> Add VASP Ti grid - 5eabc3f <5eabc3f> Refactor dependencies in pyproject - 847a466 <847a466> Update dependencies, use broadening in vasp processing - 940060e <940060e> Refactor the model zoo - 5f39fa6 <5f39fa6> Refactor m3gnet4xas api and how models are loaded File Changes (30 files <https://github.com/matthewcarbone/Crescendo/pull/69/files>) - *M* crescendo/extern/lightshow/__init__.py <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-e32af2e55a79bb0aaab1ebbd82a4ad3eb4ef1f3376996dac3cfc56ecda707d5e> (9) - *M* crescendo/extern/lightshow/_lightshow.py <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-4034575850ef753d1ed06e1e67697dfcc988681536d35479ac9d032e3d0aff96> (217) - *M* crescendo/extern/m3gnet/m3gnet4xas.py <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-3f015d4d21851f84c4b0e5bf11d010d41f5bca474734f486b28c04932e70a8d0> (43) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_0.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-697952e575a1127cc79d98f1f5461f3b13476bd020e65dfb06e26614a01162b8> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_1.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-4ead39cc2a52858fc1d421ab6eece1f0d5d53a919d828d16ab4b2c6a9e67782d> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_10.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-1ee1c031ab50dcbe129818015a53eee8b67198230bff046f77dc475b4ade329f> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_11.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-ca77736e740bbce3b7f2fe1b8632666355e61d490debd5ccd06f1c32943cd688> (0) - 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*D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_17.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-4645c6e21d17b4a958db22256242a9744de9f2c5180070317e129d312aa764fc> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_18.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-5681dc3a59ec6cd29f4f8ab4ae1cf9016f8ec2d943ff6660afd896673d7f6a13> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_19.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-49472985e3df9977df076801bfacf80e026271e7b622e584a39deb99888b79f6> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_2.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-96aeced6c6ce96525de206c7e9804e5f117d1e08702892c16b012dd7cf1e7983> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_3.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-0213b8d1d8ee79dcb6e2ede545bc87f90bfa369294ad01fbc1e16fe4b9abc373> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_4.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-747badb4763d7c5dbf0760cab3df6b06e8851245744293fbb11162cdf8bb5fe2> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_5.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-5a61382482b38b0bc640657733edb95c13328a25cc6a0b5102df7f5541609879> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_6.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-1170cf6822f8188e04fd54ad4044491eaf93090d32cd14ec74476ef78be7f3b3> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_7.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-502f8cccaff95075f3d69199dd2e03e3bc2c503c96909343ee47d18fbe312fb4> (0) - *D* crescendo/extern/m3gnet/zoo/Ti-O/FEFF-XANES-Ti-v230926_materials-ensemble_8.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-3f3fa9edd81bc3ed981f0b47bdd4d44eadb1593b49217bfdb28eefa21daebf16> (0) - 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*R* crescendo/extern/m3gnet/zoo/XANES/FEFF/K-edge/Ti/v230925-oxides-materials_split.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-276ca77cb008be5dfba1017b9e9f49615c799638cc380dfb4a09de896312d639> (0) - *R* crescendo/extern/m3gnet/zoo/XANES/FEFF/K-edge/Ti/v230925-oxides-random_split.pt <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-cb68fda53f05e4d94aa69facadf8ab85922ccb37c751d97f02b3aaa23918c8f7> (0) - *M* pyproject.toml <https://github.com/matthewcarbone/Crescendo/pull/69/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711> (13) Patch Links: - https://github.com/matthewcarbone/Crescendo/pull/69.patch - https://github.com/matthewcarbone/Crescendo/pull/69.diff — Reply to this email directly, view it on GitHub <#69>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AP66N6JYZMFN764SZC6YNSLX6F7ENAVCNFSM6AAAAAA5XA36Q2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZTCNBRGA4DKNQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Owner Author

matthewcarbone commented Oct 8, 2023

@deyulu yes XAS_TYPE is XANES or EXAFS! I like your ordering and will make the changes. Let me know if you have any other suggestions.

matthewcarbone marked this pull request as draft

October 8, 2023 02:41

Collaborator

deyulu commented Oct 9, 2023 via email

@matthew Carbone ***@***.***> Sounds good.

On Sat, Oct 7, 2023 at 10:41 PM Matthew Carbone ***@***.***> wrote: @deyulu <https://github.com/deyulu> yes XAS_TYPE is XANES or EXAFS! I like your ordering and will make the changes. Let me know if you have any other suggestions. — Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AP66N6NZTKO6DWDSAWZOWU3X6IHHHAVCNFSM6AAAAAA5XA36Q2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRHA4TSNJYGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

matthewcarbone added 2 commits

October 9, 2023 16:22


          Update grids in m3gnet4py, modify zoo file paths

0c43bf7


          Debug _lightshow module

6bd26e5

matthewcarbone mentioned this pull request

Re-think path order for models #70

Open

matthewcarbone marked this pull request as ready for review

October 9, 2023 20:36


          Code style/security fixes

b44cc77

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