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953c875
Add displacements and momenta outputs
frostedoyster 1c1cb29
Change displacements to positions
frostedoyster 2eb2c17
Point to correct file in TOC
johannes-spies f57e79e
Fix typos
johannes-spies e1ef4d2
Properly propagate renaming
johannes-spies cef5ed2
Make class name uppercase
johannes-spies 5249f50
Use different baseline unit with conversion
johannes-spies 355ef7c
Update output illustrations
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.. _displacements-output: | ||
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Displacements | ||
^^^^^^^^^^^^^ | ||
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Displacements are differences between atomic positions at two different times. | ||
They can be used to predict the next configuration in molecular dynamics | ||
(see, e.g., https://arxiv.org/pdf/2505.19350). | ||
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In metatomic models, they are associated with the ``"displacements"`` | ||
key in the model outputs, and must adhere to the following metadata schema: | ||
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.. list-table:: Metadata for displacements | ||
:widths: 2 3 7 | ||
:header-rows: 1 | ||
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* - Metadata | ||
- Names | ||
- Description | ||
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* - keys | ||
- ``"_"`` | ||
- the keys must have a single dimension named ``"_"``, with a single | ||
entry set to ``0``. Displacements are always a | ||
:py:class:`metatensor.torch.TensorMap` with a single block. | ||
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* - samples | ||
- ``["system", "atom"]`` | ||
- the samples must be named ``["system", "atom"]``, since | ||
displacements are always per-atom. | ||
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``"system"`` must range from 0 to the number of systems given as an input | ||
to the model. ``"atom"`` must range between 0 and the number of | ||
atoms/particles in the corresponding system. If ``selected_atoms`` is | ||
provided, then only the selected atoms for each system should be part of | ||
the samples. | ||
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* - components | ||
- ``"xyz"`` | ||
- displacements must have a single component dimension named | ||
``"xyz"``, with three entries set to ``0``, ``1``, and ``2``. The | ||
displacements are always 3D vectors, and the order of the | ||
components is x, y, z. | ||
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* - properties | ||
- ``"displacements"`` | ||
- displacements must have a single property dimension named | ||
``"displacements"``, with a single entry set to ``0``. | ||
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At the moment, displacements are not integrated into any simulation engines. | ||
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.. _momenta-output: | ||
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Momenta | ||
^^^^^^^ | ||
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The momentum of a particle is a vector defined as its mass times its velocity. | ||
Predictions of momenta can be used, for example, to predict a future step in molecular | ||
dynamics (see, e.g., https://arxiv.org/pdf/2505.19350). | ||
|
||
In metatomic models, they are associated with the ``"momenta"`` | ||
key in the model outputs, and must adhere to the following metadata schema: | ||
|
||
.. list-table:: Metadata for momenta | ||
:widths: 2 3 7 | ||
:header-rows: 1 | ||
|
||
* - Metadata | ||
- Names | ||
- Description | ||
|
||
* - keys | ||
- ``"_"`` | ||
- the keys must have a single dimension named ``"_"``, with a single | ||
entry set to ``0``. Momenta are always a | ||
:py:class:`metatensor.torch.TensorMap` with a single block. | ||
|
||
* - samples | ||
- ``["system", "atom"]`` | ||
- the samples must be named ``["system", "atom"]``, since | ||
momenta are always per-atom. | ||
|
||
``"system"`` must range from 0 to the number of systems given as an input | ||
to the model. ``"atom"`` must range between 0 and the number of | ||
atoms/particles in the corresponding system. If ``selected_atoms`` is | ||
provided, then only the selected atoms for each system should be part of | ||
the samples. | ||
|
||
* - components | ||
- ``"xyz"`` | ||
- momenta must have a single component dimension named | ||
``"xyz"``, with three entries set to ``0``, ``1``, and ``2``. The | ||
momenta are always 3D vectors, and the order of the | ||
components is x, y, z. | ||
|
||
* - properties | ||
- ``"momenta"`` | ||
- momenta must have a single property dimension named | ||
``"momenta"``, with a single entry set to ``0``. | ||
|
||
At the moment, momenta are not integrated into any simulation engines. |
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