Otter

Getting started

  • Installation
    • Requirements
    • Install the released package
    • Reproducible source installation
    • Install Otter
    • Run the tests
    • Build the documentation
    • Unlocked pip fallback
  • 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
      • Confirming QM SCF convergence
      • SCF history regularization
      • Continuum energy cutoff
      • Checking for missing shallow levels
      • WS boundary and numerical geometry
    • 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
      • Electronic structure
        • Compatibility
      • QOZ/HNC results
        • Migration from 0.3.1
      • Portable access
        • Mean-ionization definitions
        • Ion-orbital profiles and wavefunctions
        • Saving and reading orbital NPZ data
      • Export profiles
      • Save and load
      • Portable species and pair axes
      • Native average-atom arrays
      • Bound levels and orbital densities
      • Metadata and discovery
      • API
    • Parameter grids for interpolation
      • Install and run
      • Composition and numerical settings
      • Solver and output grids
      • Electron–ion potentials
      • HDF5 layout
      • Check completion before interpolation
      • Earlier HDF5 files
      • Python interface
    • Use Otter pair potentials in LAMMPS
      • Which Otter potential is used?
      • Complete mixture example from physical inputs
      • 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
        • Why particle coordinates are sufficient
      • Timestep and physical duration
      • Inspecting the active LAMMPS potential
      • Numerical checks before accepting a run
    • Reproducing examples and benchmarks
      • Run the included Python script
      • The three download buttons
      • Batch recalculation
      • MD and other optional dependencies
      • Recorded website results
  • Example gallery
    • Al: complete electronic-to-ionic workflow
      • Reproduction
      • Recorded results
        • Recorded terminal output
      • Orbital access and NPZ export
    • Experimental IS/SC feedback for aluminium
      • Reproduction
      • Recorded results
        • Recorded terminal output
      • User controls
    • Aluminium KS-DFT and Thomas–Fermi comparison
      • Reproduction
      • Recorded results
        • Recorded terminal output
    • Al: elastic Rayleigh weight versus density
      • Reproduction
      • Recorded results
        • Recorded terminal output
    • Carbon ionization at 100 eV
      • Reproduction
      • Recorded result
    • Carbon: local-field-correction sensitivity
      • Reproduction
      • Recorded results
        • Recorded terminal output
    • CH1.36: multicomponent electronic-to-ionic workflow
      • Electronic data access
      • Reproduction
      • Recorded results
        • Recorded terminal output

Physics and validation

  • Scientific benchmarks
  • Experimental models
    • Self-consistent ion-structure feedback
      • Implemented single-component coupling
      • Minimal diagnostic use
      • Numerical convergence and inner accuracy
      • Scope and limitations
      • API
        • otter.experimental.SCFeedbackConfig
        • otter.experimental.SCFeedbackConvergenceError
        • otter.experimental.solve_sc_feedback_workflow
        • otter.experimental.mixture_ionic_background_profiles
        • otter.experimental.estimate_mixture_correlation_potentials
    • Free-channel continuum completion
      • Usage
      • Spectral density
      • Scope

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.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()
        • Examples using save_plasma_state
      • otter.load_plasma_state
        • load_plasma_state()
        • Examples using load_plasma_state
      • otter.bound_wavefunctions
        • bound_wavefunctions()
      • otter.ion_orbital_form_factors
        • ion_orbital_form_factors()
    • Workflow results and state files
      • otter.io.state.build_state_arrays
        • build_state_arrays()
      • otter.io.state.validate_state_arrays
        • validate_state_arrays()
    • Parameter-grid calculations
      • otter.grid.GridConfig
        • GridConfig
        • otter.grid.GridConfig.__init__
        • otter.grid.GridConfig.composition
        • otter.grid.GridConfig.configuration
      • otter.grid.run_grid
        • run_grid()
    • 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
  • Citing Otter
    • Runtime citation API
      • CitationMixin
        • CitationMixin.citation()
      • bibliography_entries()
      • write_citations_markdown()
    • Reference rules for contributors
  • Bibliography
Otter
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