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Switch to AEV based models #26

Merged
merged 139 commits into from
Oct 10, 2024
Merged

Switch to AEV based models #26

merged 139 commits into from
Oct 10, 2024

Commits on Jun 20, 2024

  1. Add emle_features argument to EMLECalculator

    @kzinovjev
    kzinovjev committed Jun 20, 2024
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  2. Create and store aev_computer from ANI-2x when AEV features are used

    @kzinovjev
    kzinovjev committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. Proof of concept replacing SOAP with AEV

    @kzinovjev
    kzinovjev committed Jun 21, 2024
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Commits on Jun 22, 2024

  1. Write 'emle-features' value to emle_settings.yaml

    @kzinovjev
    kzinovjev committed Jun 22, 2024
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  2. Keep SOAP features as default for now

    @kzinovjev
    kzinovjev committed Jun 22, 2024
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Commits on Jun 24, 2024

  1. Merge remote-tracking branch 'kzinovjev/soap-to-aev' into feature_aev

    @lohedges
    lohedges committed Jun 24, 2024
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  2. Blacken.

    @lohedges
    lohedges committed Jun 24, 2024
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  3. Valiate 'features' kwarg and apply minor formatting tweaks.

    @lohedges
    lohedges committed Jun 24, 2024
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  4. Expose 'features' in CLI and environment variable.

    @lohedges
    lohedges committed Jun 24, 2024
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  5. Update kwarg in error message.

    @lohedges
    lohedges committed Jun 24, 2024
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  6. Handle NoneType feature kwarg from emle-server.

    @lohedges
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  7. Formatting tweaks. [ci skip]

    @lohedges
    lohedges committed Jun 24, 2024
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  8. Add support for NNPOps and re-use existing AEVComputer.

    @lohedges
    lohedges committed Jun 24, 2024
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Commits on Jun 26, 2024

  1. Switch to using autograd.grad directly.

    @lohedges
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  2. Generalise feature naming.

    @lohedges
    lohedges committed Jun 26, 2024
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  3. Fix gradient tensor use with MM embedding.

    @lohedges
    lohedges committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Refactor features validation. [ci skip]

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  2. Extract AEVs from tuple by name. [ci skip]

    @lohedges
    lohedges committed Jun 27, 2024
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  3. Generalise GPRCalculator docstring.

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Commits on Jun 28, 2024

  1. Full AEV implementation with features computed in energy function. 

    This fixes the autograd backpropagation by moving the calculation
of the features and derived properties (s, chi) into the energy
function. There is now no need to manually compute feature derivatives
and apply their contribution to the QM gradient via the chain rule.
[ci skip]
    @lohedges
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  2. AEVCalculator doesn't need device argument. [ci skip]

    @lohedges
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  3. Remove comment about pt_main_thread issue. [ci skip]

    @lohedges
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  4. Remove redundant global. [ci skip]

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  5. Docstring tweaks. [ci skip]

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  6. Add initial AEV based EMLE torch.nn.Module model. [ci skip]

    @lohedges
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  7. Call base class constructor to ensure all attributes are initialised. 

    [ci skip]
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  8. Add combined ANI2x-EMLE model. [ci skip]

    @lohedges
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Commits on Jun 29, 2024

  1. Rename models module. [ci skip]

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Commits on Jun 30, 2024

  1. Handle situations where there are no point charges.

    @lohedges
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  2. Use same unit system as ANI2x, i.e. Angstrom and Hartree.

    @lohedges
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  3. Formatting tweak in license header. [ci skip]

    @lohedges
    lohedges committed Jun 30, 2024
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  4. Clarification in comment. [ci skip]

    @lohedges
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  5. Add an optimised Sire callback. [ci skip]

    @lohedges
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  6. Allow use of NNPOps with ANI2xEMLE model. [ci skip]

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Commits on Jul 1, 2024

  1. Allow model to be moved and used with existing ANI2x model. [ci skip]

    @lohedges
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  2. Named tuple isn't available for OptimizedTorchANI. [ci skip]

    @lohedges
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  3. Make module torch scriptable. [ci skip]

    @lohedges
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  4. Add support for masked AEV model and torch.compile. [ci skip]

    @lohedges
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  5. Conditionally apply NNPOps optimisations. [ci skip]

    @lohedges
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  6. Use torch.empty to create empty list of tensors. [ci skip]

    @lohedges
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Commits on Jul 2, 2024

  1. Make model dtype agnostic and support all model conversion methods. 

    [ci skip]
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  2. Fix .to() for self._aev_mask. [ci skip]

    @lohedges
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  3. Simplify calculation of species indices. [ci skip]

    @lohedges
    lohedges committed Jul 2, 2024
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  4. Make sure all model parameters are converted to tensors. [ci skip]

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  5. No need to store model params as a class attribute. [ci skip]

    @lohedges
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  6. Remove all redundant module attributes. [ci skip]

    @lohedges
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  7. Remove self from model in error message. [ci skip]

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  8. Add missing n_z tensor attribute. [ci skip]

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  9. Remove redundant attribure. [ci skip]

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  10. Apply species map updates to ANI2xEMLE forward method. [ci skip]

    @lohedges
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  11. Call base class methods in overloads. [ci skip]

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Commits on Jul 3, 2024

  1. Standardise type names in docstrings. [ci skip]

    @lohedges
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  2. Use -1 to specify unsupported species. [ci skip]

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  3. Work around TorchANI's broken .to(torch.float32) and .float() operators. 

    [ci skip]
    @lohedges
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  4. Don't use forward_hook until it can work with TorchScript. [ci skip]

    @lohedges
    lohedges committed Jul 3, 2024
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  5. Convert model to TorchScript in optimised callback. [ci skip]

    @lohedges
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  6. Add note regarding running without optimised execution. [ci skip]

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Commits on Jul 4, 2024

  1. Add note about forward hook and leave commented implementation. 

    [ci skip]
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  2. Allow user to specify the ANI2x model index. [ci skip]

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    lohedges committed Jul 4, 2024
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Commits on Jul 8, 2024

  1. Monkey-patch torchani so AEVComputer forward hook works with TorchScript 

    [ci skip]
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  2. Monkey-patch NNPOps.OptimizedTorchANI too. [ci skip]

    @lohedges
    lohedges committed Jul 8, 2024
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  3. Rename TorchANI monkey-patch module. [ci skip]

    @lohedges
    lohedges committed Jul 8, 2024
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  4. Move OptimizedTorchANI model to device. [ci skip]

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Commits on Jul 15, 2024

  1. Use register_buffer for constant model parameters. [ci skip]

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Commits on Jul 16, 2024

  1. Remove librascal and dependencies from environment file. [ci skip]

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Commits on Jul 17, 2024

  1. Guard patched NNPOps class against import error. [ci skip]

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  2. Add flag to specify whether NNPOps is available. [ci skip]

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Commits on Jul 29, 2024

  1. Energy needs to be an array/tensor. [ci skip]

    @lohedges
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  2. Detach tensors and convert to NumPy arrays. [ci skip]

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Commits on Jul 30, 2024

  1. Rename ref_soap param to ref_aev

    @kzinovjev
    kzinovjev committed Jul 30, 2024
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  2. Implement 'reference' mode for polarizabilities calculation

    @kzinovjev
    kzinovjev committed Jul 30, 2024
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  3. Remove old SOAP-based model file

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Commits on Jul 31, 2024

  1. Merge branch 'chemle:feature_aev' into feature_aev

    @kzinovjev
    kzinovjev authored Jul 31, 2024
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  2. Merge pull request #22 from kzinovjev/feature_aev 

    Add support for choosing method for atomic polarizabilities. [ci skip]
    @lohedges
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  3. Validate the alpha_mode type.

    @lohedges
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  4. Add alpha_mode environment variable and command-line option.

    @lohedges
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  5. Blacken.

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  6. Choose default model based on the specified alpha mode.

    @lohedges
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  7. Update requirements.

    @lohedges
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  8. Add alpha_model option to modules and decouple model files from repo.

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  9. Fix mixing of NumPy arrays and Torch Tensors.

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  10. Mask the AEV features.

    @lohedges
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  11. Blacken.

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  12. Add license block for vendored pygit2 example code. [ci skip]

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  13. Handle vacuum simulations in optimised callback. [ci skip]

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  14. Only compute induced dipoles when needed. [ci skip]

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  15. Remove redundant E_ind in module too. [ci skip]

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  16. Validate required keys are in model file.

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Commits on Aug 1, 2024

  1. Remove redundant MANIFEST.in file. [ci skip]

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  2. Add environment file for using rascal for delta learning. [ci skip]

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  3. Use os.path.join to create resource directory path.

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  4. Switch to using pip install. [ci skip]

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  5. Add note about Rascal specific environment. [ci skip]

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  6. Add section for new alpha mode option. [ci skip]

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  7. Add NNPOps to emle-sire environment file. [ci skip]

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Commits on Aug 2, 2024

  1. Add Emily Engine mascot. [ci skip]

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  2. Update OpenMM section. [ci skip]

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  3. Remove redundant gitattribute. [ci skip]

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Commits on Aug 3, 2024

  1. Link to original mascot image. [ci skip]

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Commits on Aug 6, 2024

  1. Document reason for create_aev_calculator kwarg. [ci skip]

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Commits on Aug 7, 2024

  1. Fix polarisability prediction. Need to square the result.

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Commits on Aug 8, 2024

  1. Added the MACExEMLE model

    @JMorado
    JMorado committed Aug 8, 2024
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  2. Fix typo

    @JMorado
    JMorado committed Aug 8, 2024
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  3. Updated MACExEMLE to optionally initialize the model without requirin… 

    …g atomic_numbers
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  4. Miscellaneous formatting

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Commits on Aug 9, 2024

  1. Addressed points raised by @lohedges

    @JMorado
    JMorado committed Aug 9, 2024
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  2. Merge pull request #25 from JMorado/feature_mace 

    Add the MACEEMLE Torch model
    @lohedges
    lohedges authored Aug 9, 2024
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  3. Refactor emle.models.

    @lohedges
    lohedges committed Aug 9, 2024
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  4. Rename patches module.

    @lohedges
    lohedges committed Aug 9, 2024
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  5. Move _get_neighbour_pairs to base class and make static.

    @lohedges
    lohedges committed Aug 9, 2024
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  6. Add support for custom models and species.

    @lohedges
    lohedges committed Aug 9, 2024
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  7. Formatting tweaks.

    @lohedges
    lohedges committed Aug 9, 2024
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  8. Fix forward docstrings. [ci skip]

    @lohedges
    lohedges committed Aug 9, 2024
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  9. Add support for custom species to EMLECalculator.

    @lohedges
    lohedges committed Aug 9, 2024
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Commits on Aug 10, 2024

  1. Blacken.

    @lohedges
    lohedges committed Aug 10, 2024
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Commits on Aug 12, 2024

  1. Refactor to remove code duplication. 

    Note that TorchScript doesn't support inheritance so we can't derive
from the base EMLE module and call its forward method. Intead, derived
models store instances of both the EMLE and in vacuo models as
attriburtes, then use these to perform the two parts of the calculation.
This avoids re-using the same EMLE logic in each modules forward method.
    @lohedges
    lohedges committed Aug 12, 2024
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  2. Clarify setting of AEVs. [ci skip]

    @lohedges
    lohedges committed Aug 12, 2024
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  3. Clarify pre-computed AEVs. [ci skip]

    @lohedges
    lohedges committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. Fix missing _has_nnpops variable.

    @lohedges
    lohedges committed Aug 13, 2024
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  2. Fix typo in passing device when loading custom MACE models.

    @lohedges
    lohedges committed Aug 13, 2024
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  3. Move _get_neigbor_pairs back to MACE module now inheritance removed.

    @lohedges
    lohedges committed Aug 13, 2024
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  4. Move _get_neigbor_pairs to utility module.

    @lohedges
    lohedges committed Aug 13, 2024
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  5. Formatting tweak. [ci skip]

    @lohedges
    lohedges committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. Formatting tweaks. [ci skip]

    @lohedges
    lohedges committed Aug 14, 2024
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  2. Validate the mace_model kwarg.

    @lohedges
    lohedges committed Aug 14, 2024
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  3. Miniforge now defaults to mamba. [ci skip]

    @lohedges
    lohedges committed Aug 14, 2024
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  4. Remove redundant import.

    @lohedges
    lohedges committed Aug 14, 2024
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  5. Add basic tests for model instantiation.

    @lohedges
    lohedges committed Aug 14, 2024
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  6. Test that each model can be converted to TorchScript.

    @lohedges
    lohedges committed Aug 14, 2024
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  7. Need to use pip to install test dependencies.

    @lohedges
    lohedges committed Aug 14, 2024
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  8. Need to install using conda and pip.

    @lohedges
    lohedges committed Aug 14, 2024
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  9. Test that models can calculate energies and gradients.

    @lohedges
    lohedges committed Aug 14, 2024
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  10. Update test docstrings. [ci skip]

    @lohedges
    lohedges committed Aug 14, 2024
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Commits on Aug 18, 2024

  1. Update environment files.

    @lohedges
    lohedges committed Aug 18, 2024
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Commits on Sep 2, 2024

  1. Pass user defined model through to ANI2xEMLE constructor.

    @lohedges
    lohedges committed Sep 2, 2024
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Commits on Oct 1, 2024

  1. Update default model names.

    @lohedges
    lohedges committed Oct 1, 2024
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Commits on Oct 10, 2024

  1. Merge branch 'main' into feature_aev

    @lohedges
    lohedges committed Oct 10, 2024
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  2. Update links for emle-sire tutorial.

    @lohedges
    lohedges committed Oct 10, 2024
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  3. Add section on emle.models module.

    @lohedges
    lohedges committed Oct 10, 2024
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