Otter

Getting started

  • Installation
    • Requirements
    • Poetry installation
    • Install Otter
    • Run the tests
    • Build the documentation
  • Quick start
    • Google Colab
    • Single-species aluminium
    • Mixtures
    • Runtime output
    • Access and export results
    • Runtime and cached electronic structure
    • Consistent PNG and PDF figures
  • User guide
    • Complete Al 1 eV workflow
    • Aluminium KS-DFT versus Thomas–Fermi
      • Example and execution modes
      • What is plotted
      • Temperature sequence
      • Numerical record
    • Exchange-correlation functionals
      • Installation
      • Citation and provenance
      • Selecting a model
      • GGA potential
      • Finite GGA core regularization
      • Current scope
    • Aluminium static Rayleigh weight
    • Carbon local-field-correction sensitivity
      • Why similar responses can give different potentials
      • Run the example
    • Workflow results and portable NPZ files
      • In-memory access
      • Save and load
      • Species and pair axes
      • Native average-atom arrays
      • Bound levels and orbital densities
      • Metadata and discovery
      • API
    • Use Otter pair potentials in LAMMPS
      • Which Otter potential is used?
      • Complete mixture example from an Otter NPZ
      • Why charge_e=zbar is specified
      • In-memory and single-species inputs
      • Generated LAMMPS files
      • How \(g_{ab}(r)\) and \(S_{ab}(k)\) are obtained
      • Numerical checks before accepting a run
  • Example gallery
    • Al: complete electronic-to-ionic workflow
      • Electronic structure
      • Pseudoatom to ion structure
    • Experimental IS/SC feedback for aluminium
      • User controls
      • Ion structure
      • KS-DFT level shifts
      • Runtime and SC convergence
    • Aluminium KS-DFT and Thomas–Fermi comparison
    • Al: elastic Rayleigh weight versus density
    • Carbon ionization and pressure-ionization levels
    • Carbon: local-field-correction sensitivity
    • CH1.36: multicomponent electronic-to-ionic workflow
      • Pair structure and pseudoatom inputs

Physics and validation

  • Scientific benchmarks
  • Experimental models
    • Self-consistent ion-structure feedback
      • Implemented single-component coupling
      • Minimal diagnostic use
      • Scope and limitations
      • API
        • otter.experimental.SCFeedbackConfig
        • otter.experimental.solve_sc_feedback_workflow
        • otter.experimental.mixture_ionic_background_profiles
        • otter.experimental.estimate_mixture_correlation_potentials

Reference

  • API reference
    • Stable high-level interface
      • otter.PlasmaWorkflowConfig
        • PlasmaWorkflowConfig
        • otter.PlasmaWorkflowConfig.__init__
        • otter.PlasmaWorkflowConfig.citation
        • otter.PlasmaWorkflowConfig.solve
      • otter.solve_plasma_workflow
        • solve_plasma_workflow()
        • Examples using solve_plasma_workflow
      • otter.continue_plasma_workflow_from_electronic_result
        • continue_plasma_workflow_from_electronic_result()
        • Examples using continue_plasma_workflow_from_electronic_result
      • otter.PreparedMulticomponentIonStructure
        • PreparedMulticomponentIonStructure
        • otter.PreparedMulticomponentIonStructure.__init__
      • otter.prepare_multicomponent_ion_structure_from_electronic_result
        • prepare_multicomponent_ion_structure_from_electronic_result()
      • otter.run_formula_workflow
        • run_formula_workflow()
      • otter.parse_formula_composition
        • parse_formula_composition()
      • otter.resolve_plasma_composition
        • resolve_plasma_composition()
      • otter.StateExportOptions
        • StateExportOptions
        • otter.StateExportOptions.__init__
      • otter.save_plasma_state
        • save_plasma_state()
      • otter.load_plasma_state
        • load_plasma_state()
    • Workflow results and state files
      • otter.io.state.build_state_arrays
        • build_state_arrays()
      • otter.io.state.validate_state_arrays
        • validate_state_arrays()
    • Scientific plotting
      • otter.plotting.set_style
        • set_style()
        • Examples using set_style
      • otter.plotting.style_context
        • style_context()
        • Examples using style_context
      • otter.plotting.style_rcparams
        • style_rcparams()
      • otter.plotting.grid_figsize
        • grid_figsize()
        • Examples using grid_figsize
      • otter.plotting.add_panel_label
        • add_panel_label()
      • otter.plotting.save_figure
        • save_figure()
        • Examples using save_figure
    • Internal modules
    • API stability
  • Development
    • Contribution principles
    • Documentation workflow
    • Third-party software provenance
    • Benchmark workflow
      • Development roadmap
        • Pseudoatom molecular dynamics
        • Equation of state
  • Citing Otter
    • Runtime citation API
      • CitationMixin
        • CitationMixin.citation()
      • bibliography_entries()
      • write_citations_markdown()
    • Reference rules for contributors
  • Bibliography
Otter
  • Scientific benchmark gallery
  • View page source

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 example gallery. They test documented scientific configurations; they are not templates for silently changing a benchmark state.

Carbon structure factors: Otter PA-HNC and DFT-MD

Carbon structure factors: Otter PA-HNC and DFT-MD

Bethkenhagen et al. carbon-ionization comparison

Bethkenhagen et al. carbon-ionization comparison

Polypropylene (PP/CH2): HNC versus same-potential MD

Polypropylene (PP/CH2): HNC versus same-potential MD

Ion-structure literature library

Ion-structure literature library

Two-temperature aluminium: Johnson et al. (2025)

Two-temperature aluminium: Johnson et al. (2025)

Equilibrium aluminium structure factors: Schörner et al. (2022)

Equilibrium aluminium structure factors: Schörner et al. (2022)

Starrett et al. CH1.36 mixture pair distributions

Starrett et al. CH1.36 mixture pair distributions

Starrett–Saumon electronic levels and ionization

Starrett--Saumon electronic levels and ionization

Single-species Starrett–Saumon ion-structure benchmarks

Single-species Starrett--Saumon ion-structure benchmarks

Download all examples in Python source code: gen_benchmarks_python.zip

Download all examples in Jupyter notebooks: gen_benchmarks_jupyter.zip

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