References
==========

Adversarial methods
-------------------

.. _method-ref-fgsm:

* `FGSM: Explaining and Harnessing Adversarial Examples
  <https://arxiv.org/abs/1412.6572>`_

.. _method-ref-ifgsm:

* `I-FGSM: Adversarial Examples in the Physical World
  <https://arxiv.org/abs/1607.02533>`_

.. _method-ref-pgd:

* `PGD: Towards Deep Learning Models Resistant to Adversarial Attacks
  <https://arxiv.org/abs/1706.06083>`_

Machine learning force fields
-----------------------------

.. _method-ref-mace:

* `MACE architecture paper <https://arxiv.org/abs/2206.07697>`_

.. _method-ref-mace-mh:

* `MACE-MH paper <https://arxiv.org/abs/2510.25380>`_
* `MACE-MH model documentation
  <https://huggingface.co/mace-foundations/mace-mh-1/blob/main/README.md>`_

.. _method-ref-uma:

* `UMA paper <https://arxiv.org/abs/2506.23971>`_
* `UMA model documentation <https://huggingface.co/facebook/UMA>`_

.. _method-ref-chgnet:

* `CHGNet documentation <https://chgnet.lbl.gov/>`_

.. _method-ref-mtp:

* `LiCOHPF database with pre-trained MACE + MTP
  <https://github.com/gitliwq/LiCOHPF_database_1>`_

Validation and failure analysis
-------------------------------

.. _method-ref-validation:

* `How to validate machine-learned interatomic potentials
  <https://pubs.aip.org/aip/jcp/article/158/12/121501/2881528/How-to-validate-machine-learned-interatomic>`_
* `MLFF error evaluation
  <https://www.nature.com/articles/s41524-023-01123-3>`_
* `MLFFs for modelling deformation
  <https://pmc.ncbi.nlm.nih.gov/articles/PMC12451742/>`_
* `MLFFs for material properties
  <https://arxiv.org/html/2412.10516v4>`_
* `Correct energies does not guarantee the correct trajectory
  <https://arxiv.org/abs/2401.00096>`_
* `Fine-tuning machine-learned interatomic potentials
  <https://arxiv.org/html/2606.12704v1>`_
* `Variance in machine learning force fields
  <https://arxiv.org/pdf/2103.03098>`_

Structural metrics
------------------

.. _method-ref-numpy-norm:

* `NumPy vector-norm documentation
  <https://numpy.org/doc/stable/reference/generated/numpy.linalg.norm.html>`_

.. _method-ref-jaccard:

* `Jaccard-distance reference
  <https://arxiv.org/pdf/1010.0725>`_
* `A Note on the Triangle Inequality for the Jaccard Distance
  <https://arxiv.org/abs/1612.02696>`_
* `SciPy Jaccard-distance documentation
  <https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.jaccard.html>`_

.. _method-ref-rdf:

* `Radial distribution functions
  <https://arxiv.org/pdf/2011.00616>`_
* `ASE RDF implementation
  <https://docs.ase-lib.org/ase/geometry/analysis.html>`_

.. _method-ref-coordination:

* `Coordination-number analysis
  <https://arxiv.org/pdf/1911.01358>`_
* `ASE neighbour-list documentation
  <https://docs.ase-lib.org/ase/neighborlist.html>`_

.. _method-ref-symmetry:

* `Pymatgen symmetry-analysis documentation
  <https://pymatgen.org/pymatgen.symmetry.html>`_
* `Spglib documentation
  <https://spglib.readthedocs.io/en/stable/>`_

.. _method-ref-numpy-quantile:

* `NumPy quantile documentation
  <https://numpy.org/doc/stable/reference/generated/numpy.quantile.html>`_

.. _method-ref-r2:

* `Scikit-learn coefficient-of-determination documentation
  <https://scikit-learn.org/stable/modules/generated/sklearn.metrics.r2_score.html>`_

Simulation and structure tools
------------------------------

.. _method-ref-mlff-attack:

* `MLFF Attack source repository
  <https://github.com/TRustworthy-AI-Tools-for-Science/mlff_attack>`_

.. _method-ref-ase:

* `Atomic Simulation Environment documentation
  <https://docs.ase-lib.org/>`_

.. _method-ref-ase-optimize:

* `ASE geometry-optimization documentation
  <https://docs.ase-lib.org/ase/optimize.html>`_

.. _method-ref-ase-neighbor:

* `ASE neighbour-list, natural-cutoff, and connectivity documentation
  <https://docs.ase-lib.org/ase/neighborlist.html>`_

.. _method-ref-supercell:

* `ASE supercell implementation
  <https://docs.ase-lib.org/ase/build/supercells.html>`_

Contour exploration
-------------------

.. _method-ref-contour:

* `ASE contour exploration documentation
  <https://ase-lib.org/ase/md.html#module-ase.md.contour_exploration>`_
* `Contour exploration method
  <https://arxiv.org/abs/2103.08054>`_