mkdocs.yml

site_name: PROTEUS
site_url: https://proteus-framework.org/PROTEUS/
repo_url: https://github.com/FormingWorlds/PROTEUS
repo_name: GitHub

copyright: '© 2023-2026 <a href="https://formingworlds.space">Forming Worlds Lab</a>'

nav:
  - Home: index.md

  - Get started: getting_started.md

  - How-to guides:
      - Install PROTEUS:
          - Quick installation: How-to/installation.md
          - Manual installation: How-to/manual_installation.md
          - Install with pixi (experimental): How-to/pixi.md
          - Optional modules: How-to/optionalmodules_installation.md
          - Run on a local machine: How-to/local_machine_guide.md
      - Getting started:
          - Diagnose and update: How-to/doctor.md
          - Configure PROTEUS: How-to/config.md
          - Usage:
              - Overview: How-to/usage.md
              - Running and output: How-to/usage_running.md
              - Initial thermal conditions: How-to/usage_initial_conditions.md
              - Core evolution: How-to/usage_core_evolution.md
              - Parameter grids: How-to/usage_grids.md
              - Postprocessing and chemistry: How-to/usage_postprocessing.md
              - Choose stellar spectrum: How-to/switch_spectrum.md
          - Stabilise simulations: How-to/stabilise_run.md
          - Troubleshooting: How-to/troubleshooting.md
      - Advanced usage:
          - Bayesian inference: How-to/inference.md
      - Cluster guides:
          - Run on Kapteyn: How-to/kapteyn_cluster_guide.md
          - Run on Snellius: How-to/snellius_cluster_guide.md
          - Run on Habrok: How-to/habrok_cluster_guide.md
          - Run on Cambridge IoA: How-to/ioa_cluster_guide.md
      - Development:
          - Testing: How-to/testing.md
          - Development standards: How-to/development_standards.md
          - Updating module pins: How-to/update_module_pins.md
          - Developing documentation: How-to/documentation.md

  - Tutorials:
      - Quick start (all-dummy): Tutorials/quick_start_dummy.md
      - Earth analogue: Tutorials/earth_analogue.md
      - Parameter grid sweep: Tutorials/parameter_grid.md
      - Solar System CHILI intercomparison: Tutorials/chili_intercomparison.md
      - Orbit and tidal evolution: Tutorials/orbit_tides.md
      - Giant impacts with a partial re-melt: Tutorials/giant_impact_remelt.md

  - Explanations:
      - Scientific background:
          - Model description: Explanations/model.md
          - Orbital dynamics and tides: Explanations/orbit.md
          - Outgassing, rock vapour and volatile trapping: Explanations/outgas.md
      - Software design:
          - Code architecture: Explanations/code_architecture.md
          - Coupling loop: Explanations/coupling_loop.md
          - Dummy modules: Explanations/dummy_modules.md
          - Test framework: Explanations/test_framework.md

  - Validation:
      - Overview: Validation/index.md
      - Accretion:
          - Analytical accretion (dummy.py): Validation/accretion/dummy.md
          - Impact atmosphere-loss dispatch (wrapper.py): Validation/accretion/wrapper.md
      - Atmosphere climate:
          - Transparent black-body limit (agni.py): Validation/atmos_clim/agni.md
      - Interior energetics:
          - Partial giant-impact re-melt (remelt.py): Validation/interior_energetics/remelt.md
      - Interior structure:
          - Liquidus-super IC anchor (zalmoxis.py): Validation/interior_struct/zalmoxis.md
      - Orbit:
          - Orbital evolution (orbit.py): Validation/orbit/orbit.md
          - Satellite angular momentum (satellite.py): Validation/orbit/satellite.md
          - Orbit module wrapper (wrapper.py): Validation/orbit/wrapper.md
          - Tidal Love-number lookup (obliqua.py): Validation/orbit/obliqua.md
          - Prescribed migration laws (parameterized.py): Validation/orbit/parameterized.md
      - Outgas:
          - Species-to-element mass split (atmodeller.py): Validation/outgas/atmodeller.md
          - H2-MgSiO3 binodal (binodal.py): Validation/outgas/binodal.md
          - Rock-vapour molar masses (lavatmos.py): Validation/outgas/lavatmos.md
          - Melt drainage across the freezing front (compaction.py): Validation/outgas/compaction.md
          - Burial ledger for remelting (burial_ledger.py): Validation/outgas/burial_ledger.md
          - Solid-phase volatile trapping (trapping.py): Validation/outgas/trapping.md
      - Star:
          - Stellar luminosity and instellation (dummy.py): Validation/star/dummy.md
          - Stellar wrapper dispatch (wrapper.py): Validation/star/wrapper.md

  - Reference:
      - Configuration:
          - Execution and output: Reference/config/params.md
          - Planet and volatiles: Reference/config/planet.md
          - Star and orbit: Reference/config/star_orbit.md
          - Interior structure and energetics: Reference/config/interior.md
          - Atmosphere and chemistry: Reference/config/atmosphere.md
          - Escape and outgassing: Reference/config/escape_outgas.md
          - Accretion: Reference/config/accretion.md
          - Observations: Reference/config/observe.md
      - Melting curves: Reference/melting_curves.md
      - Module map: Reference/module_map.md
      - Module versions: Reference/module_versions.md
      - Output format: Reference/output.md
      - Reference data: Reference/data.md
      - Bibliography: Reference/bibliography.md
      - API:
          - Interior structure (Zalmoxis wrapper): Reference/api/interior_struct_zalmoxis.md
          - Interior structure config: Reference/api/config_struct.md
          - Interior energetics wrapper: Reference/api/interior_energetics_wrapper.md
          - Outgassing:
              - Wrapper: Reference/api/outgas_wrapper.md
              - Shared code: Reference/api/outgas_common.md
              - CALLIOPE driver: Reference/api/outgas_calliope.md
              - atmodeller driver: Reference/api/outgas_atmodeller.md
              - Dummy outgassing: Reference/api/outgas_dummy.md
              - H2-silicate binodal: Reference/api/outgas_binodal.md
              - LavAtmos rock vapour: Reference/api/outgas_lavatmos.md
              - Volatile trapping: Reference/api/outgas_trapping.md
              - Melt drainage: Reference/api/outgas_compaction.md
              - Burial ledger: Reference/api/outgas_burial_ledger.md

  - Community:
      - Contact: Community/contact.md
      - Contributing: Community/CONTRIBUTING.md
      - Code of Conduct: Community/CODE_OF_CONDUCT.md
      - Developers: https://proteus-framework.org/people
      - Issues: https://github.com/FormingWorlds/PROTEUS/issues

  - Funding: funding.md

  - Source code: https://github.com/FormingWorlds/PROTEUS

  - Submodules:
      - PROTEUS submodules: submodules.md
      - MORS: https://proteus-framework.org/MORS/
      - JANUS: https://proteus-framework.org/JANUS/
      - ZEPHYRUS: https://proteus-framework.org/ZEPHYRUS/
      - CALLIOPE: https://proteus-framework.org/CALLIOPE/
      - AGNI: https://www.h-nicholls.space/AGNI/
      - Obliqua: https://proteus-framework.org/Obliqua/
      - VULCAN: https://proteus-framework.org/VULCAN/
      - Zalmoxis: https://proteus-framework.org/Zalmoxis/
      - Morrigan: https://proteus-framework.org/Morrigan/
      - Aragog: https://proteus-framework.org/aragog/
      - SPIDER: https://proteus-framework.org/SPIDER/
      - Atmodeller: https://atmodeller.readthedocs.io/en/latest/
      - FastChem: https://newstrangeworlds.github.io/FastChem/
      - SOCRATES: https://github.com/FormingWorlds/SOCRATES/
      - PetitRADTRANS: https://petitradtrans.readthedocs.io/en/latest/

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