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
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