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Examples Gallery
================

This gallery contains examples demonstrating the capabilities of ALCHEMI Toolkit-Ops.
Each example is a fully executable Python script that showcases different features
of the library, from basic neighbor list construction to advanced dispersion corrections.

All examples are designed to run on both CPU and GPU, automatically detecting available
hardware. The code can be downloaded as Python scripts or Jupyter notebooks.



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Interactions
============

Examples demonstrating GPU-accelerated computation of atomic interactions,
including DFT-D3 dispersion corrections with environment-dependent C6 coefficients.

These examples show how to:

* Compute dispersion energies and forces for molecules
* Process batches of crystal structures
* Integrate with PyTorch for differentiable workflows



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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to compute the DFT-D3 dispersion energy and forces for a single molecular system using GPU-accelerated kernels.">

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  .. image:: /examples/interactions/images/thumb/sphx_glr_01_dftd3_molecule_thumb.png
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  :doc:`/examples/interactions/01_dftd3_molecule`

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      <div class="sphx-glr-thumbnail-title">DFT-D3 Dispersion Correction for a Molecule</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates GPU-accelerated DFT-D3 calculations for batches of periodic crystal structures. Batch processing is essential for high-throughput computational materials screening and allows efficient parallelization across multiple structures simultaneously.">

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  .. image:: /examples/interactions/images/thumb/sphx_glr_02_dftd3_batch_crystals_thumb.png
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  :doc:`/examples/interactions/02_dftd3_batch_crystals`

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      <div class="sphx-glr-thumbnail-title">DFT-D3 Dispersion Correction for Batched Crystals</div>
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Neighbor Lists
==============

Examples demonstrating efficient O(N) neighbor list construction using GPU-accelerated
cell list algorithms.

These examples show how to:

* Build neighbor lists for single and batched systems
* Use dense or sparse COO output formats
* Detect when neighbor lists need rebuilding
* Optimize performance with ``torch.compile``
* Integrate with molecular dynamics workflows



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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the basic neighbor list functions in nvalchemiops on random systems. We&#x27;ll cover:">

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  .. image:: /examples/neighborlist/images/thumb/sphx_glr_01_simple_neighbor_list_thumb.png
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  :doc:`/examples/neighborlist/01_simple_neighbor_list`

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      <div class="sphx-glr-thumbnail-title">Simple Neighbor List Example</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the batch neighbor list functions in nvalchemiops with multiple molecular and crystalline systems. We&#x27;ll cover:">

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  .. image:: /examples/neighborlist/images/thumb/sphx_glr_02_batch_neighbor_list_thumb.png
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  :doc:`/examples/neighborlist/02_batch_neighbor_list`

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      <div class="sphx-glr-thumbnail-title">Batch Neighbor List Example</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use rebuild detection functions in nvalchemiops to efficiently determine when neighbor lists need to be reconstructed during molecular dynamics simulations. We&#x27;ll cover:">

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  .. image:: /examples/neighborlist/images/thumb/sphx_glr_03_rebuild_neighborlist_detection_thumb.png
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  :doc:`/examples/neighborlist/03_rebuild_neighborlist_detection`

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      <div class="sphx-glr-thumbnail-title">Neighbor List Rebuild Detection Example</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the significant performance benefits of using torch.compile with nvalchemiops neighbor list routines in a realistic molecular dynamics simulation. We&#x27;ll cover:">

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  .. image:: /examples/neighborlist/images/thumb/sphx_glr_04_neighbors_list_torch_compile_performance_thumb.png
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  :doc:`/examples/neighborlist/04_neighbors_list_torch_compile_performance`

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      <div class="sphx-glr-thumbnail-title">Torch.compile Performance Benefits Example</div>
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   /examples/interactions/index.rst
   /examples/neighborlist/index.rst


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      :download:`Download all examples in Python source code: examples_python.zip </examples/examples_python.zip>`

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      :download:`Download all examples in Jupyter notebooks: examples_jupyter.zip </examples/examples_jupyter.zip>`


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    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_