:orphan:

Scientific benchmark gallery
============================

This gallery contains fixed-state validation studies and comparisons with
published data.  Each script verifies the provenance and checksums of its
precomputed numerical inputs before plotting them.  Expensive electronic and
ionic calculations remain explicit, opt-in regeneration steps.

These pages are separate from the capability-oriented :doc:`example gallery
</gen_examples/index>`.  They test documented scientific configurations;
they are not templates for silently changing a benchmark state.


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark calculates carbon static ion structure factors with Otter&#x27;s average-atom -&gt; pseudoatom -&gt; QOZ/HNC workflow and compares them with unpublished DFT-MD data provided by Dr. Argha Roy (private communication).">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_argha_roy_carbon_sii_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_argha_roy_carbon_sii`

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      <div class="sphx-glr-thumbnail-title">Carbon structure factors: Otter PA-HNC and DFT-MD</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares Otter&#x27;s carbon ionization diagnostics at T_e=100 eV with the model-dependent Z^{\rm free} curves in Figure 3(a) of :citeBethkenhagenEtAl2020.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_bethkenhagen_et_al_2020_carbon_ionization_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_bethkenhagen_et_al_2020_carbon_ionization`

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      <div class="sphx-glr-thumbnail-title">Bethkenhagen et al. carbon-ionization comparison</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="   &lt;video controls loop muted playsinline preload=&quot;metadata&quot;           poster=&quot;../../_static/benchmarks/ch2_hnc_md/ch2_md.png&quot;           style=&quot;display:block; width:min(100%,760px); margin:0 auto;&quot;&gt;      &lt;source src=&quot;../../_static/benchmarks/ch2_hnc_md/ch2_md.mp4&quot;              type=&quot;video/mp4&quot;&gt;      Your browser does not support embedded MP4 video.    &lt;/video&gt;">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_ch2_hnc_md_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_ch2_hnc_md`

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      <div class="sphx-glr-thumbnail-title">Polypropylene (PP/CH2): HNC versus same-potential MD</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares Otter ion-structure results with literature curves for aluminium, beryllium, and carbon.  USE_PRECOMPUTED_DATA = True verifies and loads checksummed Otter NPZ files.  With False, this file constructs otter.PlasmaWorkflowConfig, evaluates every average atom and ion structure, saves new NPZ files below benchmarks/outputs/ion_structure_library/gallery_recomputed, and plots those results.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_ion_structure_library_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_ion_structure_library`

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      <div class="sphx-glr-thumbnail-title">Ion-structure literature library</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares Otter IS-QOZ g_{ii}(r) obtained with ordinary HNC and Rosenfeld--Ashcroft VMHNC closures with the three reference curve families in Fig. 2(a)--2(d) of :citeJohnsonEtAl2025. The states are aluminium at \rho=2.7 g cm\ -3, T_i=1 eV, and T_e=1,3,10,30 eV.  The paper labels the reference methods as 2TTCP HNC+bridge, DFT-MD, and YOCP HNC+bridge.  In every panel, the two Otter integral-equation curves reuse exactly the same ion- sphere (IS) electronic result and effective ion--ion potential; only the ionic closure changes.  Classical LAMMPS MD :citeThompsonEtAl2022 with that same potential is also shown, so closure error can be separated from pseudoatom pair-potential error.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_johnson_et_al_2025_two_temperature_al_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_johnson_et_al_2025_two_temperature_al`

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      <div class="sphx-glr-thumbnail-title">Two-temperature aluminium: Johnson et al. (2025)</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares Otter S_{ii}(k) with two curves digitized from Figure 2 of :citeSchornerEtAl2022. Each state is calculated with LDA-PW92 and PBE.  For each XC model, ordinary HNC and Rosenfeld--Ashcroft VMHNC reuse exactly the same IS electronic state and QOZ pair potential.  A classical LAMMPS MD calculation with that same potential is also shown.  Both states have T_e=T_i: 1 eV at \rho=4.712 g cm\ -3 and 5 eV at \rho=8.1 g cm\ -3.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_schorner_et_al_2022_al_sii_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_schorner_et_al_2022_al_sii`

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      <div class="sphx-glr-thumbnail-title">Equilibrium aluminium structure factors: Schörner et al. (2022)</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark covers the nine thermodynamic states in Figure 3 of :citeStarrettEtAl2014.  USE_PRECOMPUTED_DATA = True verifies and loads the bundled numerical arrays.  With False, this file creates otter.PlasmaWorkflowConfig, calls otter.solve_plasma_workflow for all nine C--H states, saves new NPZ files below benchmarks/outputs/starrett_et_al_2014_mixtures_fig3/gallery_recomputed, and plots those results.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_starrett_et_al_2014_mixtures_fig3_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_starrett_et_al_2014_mixtures_fig3`

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      <div class="sphx-glr-thumbnail-title">Starrett et al. CH1.36 mixture pair distributions</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares current Otter ion-sphere (IS) and experimental self-consistent (SC) diagnostics with Tables I--III of :citeStarrettSaumon2013 (doi: 10.1103/PhysRevE.87.013104).  It was added specifically to make pressure ionization auditable before interpreting the \bar Z difference in Johnson et al. (2025).">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_starrett_saumon_2013_electronic_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_starrett_saumon_2013_electronic`

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      <div class="sphx-glr-thumbnail-title">Starrett--Saumon electronic levels and ionization</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This benchmark compares Otter IS-QOZ/HNC pair-distribution functions with Starrett TF numerical extractions from :citeStarrettSaumon2014 (doi: 10.1016/j.hedp.2013.12.001).  Published data are shown only as open circles.  Otter KS-DFT (QM) calculations are requested for every thermodynamic state; the tungsten panels additionally request Thomas--Fermi (TF), matching the source comparison.  Curves are shown only when they pass the electronic, HNC, and transform-closure gates.">

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  .. image:: /benchmarks/gen_benchmarks/images/thumb/sphx_glr_plot_starrett_single_species_2013_2014_thumb.png
    :alt:

  :doc:`/benchmarks/gen_benchmarks/plot_starrett_single_species_2013_2014`

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      <div class="sphx-glr-thumbnail-title">Single-species Starrett--Saumon ion-structure benchmarks</div>
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.. toctree::
   :hidden:

   /benchmarks/gen_benchmarks/plot_argha_roy_carbon_sii
   /benchmarks/gen_benchmarks/plot_bethkenhagen_et_al_2020_carbon_ionization
   /benchmarks/gen_benchmarks/plot_ch2_hnc_md
   /benchmarks/gen_benchmarks/plot_ion_structure_library
   /benchmarks/gen_benchmarks/plot_johnson_et_al_2025_two_temperature_al
   /benchmarks/gen_benchmarks/plot_schorner_et_al_2022_al_sii
   /benchmarks/gen_benchmarks/plot_starrett_et_al_2014_mixtures_fig3
   /benchmarks/gen_benchmarks/plot_starrett_saumon_2013_electronic
   /benchmarks/gen_benchmarks/plot_starrett_single_species_2013_2014


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  .. container:: sphx-glr-footer sphx-glr-footer-gallery

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: gen_benchmarks_python.zip </benchmarks/gen_benchmarks/gen_benchmarks_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: gen_benchmarks_jupyter.zip </benchmarks/gen_benchmarks/gen_benchmarks_jupyter.zip>`


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 .. rst-class:: sphx-glr-signature

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