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Use scientific notation for the loss #199

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Closed

Use scientific notation for the loss #199

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Commits on Nov 20, 2023

  1. Initial commit

    @frostedoyster
    frostedoyster authored Nov 20, 2023
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  2. Update README.md

    @frostedoyster
    frostedoyster authored Nov 20, 2023
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  3. Make the package installable

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  4. Set up CI, linters and tests (#1)

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Commits on Nov 21, 2023

  1. Add scaffold of all types of model (#2)

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Commits on Nov 29, 2023

  1. Remove setup.py-dependent build test

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  2. Debug CI

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  3. Allow ls for debugging

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  4. Retrieve sdist to build wheels from it

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  5. Debug again?

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  6. This works

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  7. Little cleanup for new purpose of the repo

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    PicoCentauri committed Nov 29, 2023
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  8. Replace matplotlib dependency

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  9. Merge pull request #3 from lab-cosmo/skeleton

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Commits on Nov 30, 2023

  1. Add basic cli interface to scripts (#5)

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  2. Fix ci job syntax error (#9)

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  3. Add xyz structure and target reader (#8)

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Commits on Dec 1, 2023

  1. Temporarily disable failing Windows tests (#12)

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  2. Implement a temporary dataset class (#10)

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Commits on Dec 5, 2023

  1. Add documentation structure (#13) 

    Co-authored-by: Philip Loche <[email protected]>
    @frostedoyster @PicoCentauri
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Commits on Dec 6, 2023

  1. Add SOAP-BPNN (#7)

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  2. Rename to metatensor-models (#15) 

    * Rename package to `metatensor-models`

* Rename module to `metatensor.models`
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Commits on Dec 7, 2023

  1. Extract species list from dataset (#17)

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Commits on Dec 8, 2023

  1. Add hydra parsing (#18)

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Commits on Dec 11, 2023

  1. Implement saving and loading of models (#19) 

    Co-authored-by: Philip Loche <[email protected]>
    @frostedoyster @PicoCentauri
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Commits on Dec 13, 2023

  1. Update cli interface (#21) 

    * Write train output to hydra's output directory

* Added evaluation function

* Add usage example for cli interface

* update train cli

* Disable MacOS tests

* Add cli skeleton for exporter

---------

Co-authored-by: frostedoyster <[email protected]>
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Commits on Jan 3, 2024

  1. Change CLI API (#24)

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  2. Make train function self-contained (#25)

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Commits on Jan 11, 2024

  1. Integrate with metatensor.torch.atomistic (#28)

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Commits on Jan 13, 2024

  1. Add gradient calculators (#26) 

    * Add gradient calculator
* Temporary losses
* Forces and stresses
* Support multiple model outputs in SOAP-BPNN
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Commits on Jan 19, 2024

  1. Add parser and update readers for new options.yaml (#30)

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Commits on Jan 20, 2024

  1. Add tutorial how to override arch params (#32)

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Commits on Jan 24, 2024

  1. Finalize training procedure (#31) 

    Co-authored-by: Philip Loche <[email protected]>
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  2. Add length_unit + cleanup (#35)

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  3. Compile slice and join (#36)

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Commits on Jan 25, 2024

  1. Fix wrong shapes in ase stress parsers (#38)

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Commits on Jan 26, 2024

  1. Provide better logging (#37)

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  2. Reactivate MacOS tests (#41)

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  3. Display metatensor-torch torchscript classes correctly in docs (#40) 

    * Display torchscript classes correctly in docs
* Disable compiled functions when building docs
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Commits on Jan 31, 2024

  1. Fix wrong name assignment in parser (#42) 

    Co-authored-by: Philip Loche <[email protected]>
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Commits on Feb 1, 2024

  1. Fix BPNN training issues (#44)

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Commits on Feb 2, 2024

  1. Export models (#34) 

    ---------

Co-authored-by: Philip Loche <[email protected]>
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  2. Add ASE tutorial (#43) 

    ---------

Co-authored-by: Philip Loche <[email protected]>
    @frostedoyster @PicoCentauri
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Commits on Feb 5, 2024

  1. Clean up logging (#45)

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  2. added check_units for dataset_options with test (#50)

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Commits on Feb 6, 2024

  1. Fix typo

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  2. Improvements to hydra handling (#54)

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  3. Add option to continue training from checkpoint (#49) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
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Commits on Feb 7, 2024

  1. Setting global random seeds based on user input (#60)

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  2. Test training logging (#61) 

    ---------

Co-authored-by: Philip Loche <[email protected]>
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Commits on Feb 8, 2024

  1. Make SOAP-BPNN run on GPU (#58)

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  2. More Pythonic API for train and export (#67)

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  3. Add docs on what metatensor-models is (#64) 

    ---------

Co-authored-by: Guillaume Fraux <[email protected]>
Co-authored-by: frostedoyster <[email protected]>
Co-authored-by: Philip Loche <[email protected]>
    @DavideTisi @Luthaf
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Commits on Feb 9, 2024

  1. Change how eval function works (#65) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
    @PicoCentauri @frostedoyster
    PicoCentauri and frostedoyster authored Feb 9, 2024
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  2. Apply new naming conventions (#63)

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  3. Use metatensor-learn's Dataset, DataLoader, and collate fns in … 

    …`metatensor-models` (#52)

---------

Co-authored-by: Philip Loche <[email protected]>
Co-authored-by: frostedoyster <[email protected]>
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  4. Allow SOAP-BPNN to predict on a subset of atoms (#69)

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Commits on Feb 10, 2024

  1. Change reader output to follow new dataset design (#70)

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  2. Remove metatensor hotfix (#71)

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Commits on Feb 12, 2024

  1. Minor proofread to getting started docs

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  2. CI infrastructure work

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Commits on Feb 14, 2024

  1. Fix metatensor-torch-related docs (#74)

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Commits on Feb 16, 2024

  1. Add explicit dtype argument to readers (#77)

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  2. Add PR templates

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  3. Update .github/PULL_REQUEST_TEMPLATE/pull_request_new-model.md 

    Co-authored-by: Filippo Bigi <[email protected]>
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  4. Split architectures in stable/experimental/deprecated (#79) 

    ---------

Co-authored-by: Filippo Bigi <[email protected]>
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Commits on Feb 19, 2024

  1. Document hyperparameters for SOAP-BPNN (#72) 

    * Document SOAP-BPNN hypers

* Update saved model

* Add bibtex module for proper citations

* read bpnn-model


---------

Co-authored-by: Philip Loche <[email protected]>
    @frostedoyster @PicoCentauri
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  2. Fix Contributor images

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  3. Add ".extxyz" file suffix

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  4. Enforce new export rules (#83)

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Commits on Feb 20, 2024

  1. Implement the Alchemical Model from torch_alchemical repo (#66) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
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  2. Add debug flag and architecture error message (#80)

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Commits on Feb 21, 2024

  1. Better comment for sphericart-torch import

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  2. Test the metatensor.models.utils.export module

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  3. Added tests for model loading (#98)

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  4. Rename symmetry labels (#81)

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  5. Update the alchemical model docs (#94) 

    * Updated the alchemical model docs

* Removed unnecessary code

* Minor fix of the docs

* Minor fix of the docs

* Removed unused model name from the .yaml file

* Linting fix

* Removed unused hypers and reordered the Alchemical Model docs

* Update docs/src/architectures/alchemical-model.rst

Co-authored-by: Guillaume Fraux <[email protected]>

---------

Co-authored-by: Guillaume Fraux <[email protected]>
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Commits on Feb 22, 2024

  1. Update docs (#104)

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Commits on Feb 23, 2024

  1. Remove SOAP-BPNN bug

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  2. Add test

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  3. Actually do the test

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  4. Lint

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Commits on Feb 26, 2024

  1. Remove stray default dtype (#109)

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  2. Add shell completion

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  3. Allow list of datasets as input for training (#106) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
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  4. Rename "structures" -> "systems" (#110)

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Commits on Feb 27, 2024

  1. implement training on per atom energies by modifying loss modules (#105) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
    @SanggyuChong @frostedoyster
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Commits on Feb 28, 2024

  1. Setup codecov (#111) 

    ---------

Co-authored-by: Luthaf <[email protected]>
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  2. Cleanup of omegconf and export functions (#112)

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Commits on Feb 29, 2024

  1. Fix codecov badge (#116)

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  2. Move normalize.py to utils of alchemical_model (#115)

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  3. Add an interface to PET (#68) 

    ---------

Co-authored-by: frostedoyster <[email protected]>
Co-authored-by: Filippo Bigi <[email protected]>
Co-authored-by: Arslan Mazitov <[email protected]>
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Commits on Mar 1, 2024

  1. Improve docs for BPNN and alchemical model (#130)

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Commits on Mar 5, 2024

  1. Add tests that .to() works on exported models (#125)

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  2. Remove matrix for actions that don't need it (#124) 

    * Remove matrix for actions that don't need it
* Remove codecov at the end of architecture tests
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Commits on Mar 7, 2024

  1. Pin rascaline version, limit metatensor version (#133) 

    Co-authored-by: SanggyuChong <[email protected]>
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    PicoCentauri and SanggyuChong authored Mar 7, 2024
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Commits on Mar 11, 2024

  1. Update the Alchemical Model for consistency with the torch-alchemical… 

    … repo (#118)
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Commits on Mar 12, 2024

  1. Update to new metatensor and rascaline (#135)

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  2. Remove rascaline as a dependency of the main package (#139) 

    ---------

Co-authored-by: Philip Loche <[email protected]>
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    frostedoyster and PicoCentauri authored Mar 12, 2024
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  3. Use extra field for installing (#142)

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    PicoCentauri authored Mar 12, 2024
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Commits on Mar 13, 2024

  1. Fixing composition weights defined by the user (#131)

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  2. Rework model io utilities (#144)

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Commits on Mar 14, 2024

  1. Fix tests (#146)

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Commits on Mar 15, 2024

  1. Do not disable rascaline's logger (#147)

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  2. Record authors and maintainers for each architecture (#145)

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Commits on Mar 18, 2024

  1. Test model evaluation on different dtypes and devices (#151)

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Commits on Mar 19, 2024

  1. Pass dataset information to the trainers instead of `ModelCapabilitie… 

    …s` (#143)
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  2. Account for empty validation and test sets (#152)

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  3. Slightly re-design dataset checks (#156)

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  4. Pass a list of torch.devices to the train functions of the architec… 

    …tures (#126)

---------

Co-authored-by: Guillaume Fraux <[email protected]>
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    frostedoyster and Luthaf authored Mar 19, 2024
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Commits on Mar 21, 2024

  1. Implementing schedulers for SOAP-BPNN and alchemical models (#134) 

    implement `ReduceLROnPlateau` as a default scheduler of learning rate, and also introduce `early_stopping_patience` as a training parameter for both SOAP-BPNN and alchemical models
    @SanggyuChong
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Commits on Mar 26, 2024

  1. Remove global dtypes (#155)

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    PicoCentauri authored Mar 26, 2024
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Commits on Mar 27, 2024

  1. Improve eval (#150)

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Commits on Apr 1, 2024

  1. Add domain decomposition support for PET (#137) 

    * Added selected atoms and per-atom properties support for PET

* A bit of cleanup

* Updated interaction between per_atom and selected_atoms

* Working prototype of LAMMPS-PET interface

* Linting fix

* Fixed naming convention

* Fixed tests

* Added suggested changes

* Fixed missing fixture

* Fixed the case of zero neighbors in building batch dict

* Fixed zero neighbors case

* Fixed a bug with zero neighbors

* Added test for model compatibility with original PET

* Linting fix

* Resolved an issue with isolated atoms with domain decomposition

* Empty NL fix

* Linting fix

* Updated torch_alchemical version

* Fixed pet compatibility test description

* Updated PET dependency for SelfContributionsWrapper
    @abmazitov
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Commits on Apr 2, 2024

  1. Fix SOAP feature count and sparsity in SOAP-BPNN (#164) 

    * Fix SOAP feature count and sparsity in SOAP-BPNN

* Fix SOAP-BPNN regression tests

co-authored by @SanggyuChong
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    frostedoyster authored Apr 2, 2024
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Commits on Apr 3, 2024

  1. Fix bug in RMSE accumulator (#162)

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    frostedoyster authored Apr 3, 2024
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Commits on Apr 4, 2024

  1. Fix validation RMSE calculation in SOAP-BPNN (#160)

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    frostedoyster authored Apr 4, 2024
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  2. Fix bug in scripted SOAP-BPNN without LayerNorm (#166) 

    ---------
Co-authored-by: Sanggyu Chong <[email protected]>
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    frostedoyster authored Apr 4, 2024
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  3. Fix combined dataloader bug (#163)

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    frostedoyster authored Apr 4, 2024
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Commits on Apr 11, 2024

  1. Use default device obtained from architecture (#165)

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    PicoCentauri authored Apr 11, 2024
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Commits on Apr 20, 2024

  1. github username update (#170) 

    * username update

* update in other places
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Commits on Apr 26, 2024

  1. Temporarily suppress sphinx cache warning (#173)

    @PicoCentauri
    PicoCentauri authored Apr 26, 2024
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  2. Add GPU support for PET-LAMMPS interface (#171)

    @abmazitov
    abmazitov authored Apr 26, 2024
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  3. Implement faster ASE neighbor list (#172) 

    ---------

Co-authored-by: Luthaf <[email protected]>
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    frostedoyster and Luthaf authored Apr 26, 2024
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Commits on May 13, 2024

  1. Correct typo in readme (#176) 

    Single letter spelling error.
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Commits on May 14, 2024

  1. Loss improvements (#177) 

    * Make it clear upon logging that errors are always virial errors (and not stress)
* Weight energies and virials by default, with an option to turn it off
* Add (per atom) in logs if quantities are returned per-atom
* Reduce code repetition
    @frostedoyster
    frostedoyster authored May 14, 2024
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  2. Remove hydra dependency (#175)

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    PicoCentauri authored May 14, 2024
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Commits on May 15, 2024

  1. Remove override_options from train command (#183)

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  2. Move default-hypers.yaml into architecture directories (#182)

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    PicoCentauri authored May 15, 2024
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Commits on May 16, 2024

  1. Remove milliseconds from logger (#184)

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    PicoCentauri authored May 16, 2024
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  2. Upgrade to metatensor-torch 0.5.1 (#181)

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    frostedoyster authored May 16, 2024
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  3. Allow models to output last-layer features (#158)

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    frostedoyster authored May 16, 2024
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  4. Reduce code redundancy of SOAP-BPNN by embedding metatensor-learn n… 

    …n modules (#55)

---------

Co-authored-by: frostedoyster <[email protected]>
Co-authored-by: Filippo Bigi <[email protected]>
    @agoscinski @frostedoyster
    3 people authored May 16, 2024
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  5. Ignore sphinx-linting the docs/src/examples folder (#187)

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    PicoCentauri authored May 16, 2024
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Commits on May 17, 2024

  1. Fix link to workflow page for test banner (#188)

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    PicoCentauri authored May 17, 2024
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Commits on May 22, 2024

  1. Split export into pure export and save function (#190)

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    PicoCentauri authored May 22, 2024
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  2. minor docs tweaks (#197) 

    Co-authored-by: Filippo Bigi <[email protected]>
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    PicoCentauri and frostedoyster authored May 22, 2024
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Commits on May 23, 2024

  1. Use scientific notation for the loss

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    frostedoyster committed May 23, 2024
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  2. Evaluate per-atom properties (#191) 

    ---------

Co-authored-by: Philip Loche <[email protected]>
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    frostedoyster and PicoCentauri authored May 23, 2024
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  3. Allow users to set weights for different loss terms from outside (#193)

    @frostedoyster
    frostedoyster authored May 23, 2024
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  4. Fix tests badge (#198)

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    frostedoyster authored May 23, 2024
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  5. Merge branch 'main' into scientific-notation-loss

    @frostedoyster
    frostedoyster authored May 23, 2024
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  6. Failed test

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    frostedoyster committed May 23, 2024
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