mkdocs.yml

site_name: SCHISM
use_directory_urls: false
theme:
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  icon:
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plugins:
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markdown_extensions:
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  - footnotes
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  - pymdownx.inlinehilite
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extra:
  version:
    provider: mike
    default: stable

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

repo_url: https://github.com/schism-dev/schism

# Page tree
nav:
  - Home: index.md
  - Changelog: changelog.md
  - Getting started:
    - Overview: schism/overview.md
    - Getting the source code: getting-started/getting-sourcecode.md
    - Compilation: getting-started/compilation.md
    - Test suite:  getting-started/test_suite.md
    - Typical workflow (a cheat sheet): getting-started/typical-workflow.md
    - Mesh generation: getting-started/grid-generation.md
    - Preprocessing: getting-started/pre-processing.md
    - Preprocessing with PySCHISM:
      - Overview: getting-started/pre-processing-with-pyschism/overview.md
      - Installation: getting-started/pre-processing-with-pyschism/installation.md
      - Boundary Conditions: getting-started/pre-processing-with-pyschism/boundary.md
      - Atmospheric forcing: getting-started/pre-processing-with-pyschism/atmos.md
      - Souce and Sink: getting-started/pre-processing-with-pyschism/nwm.md
    - Running the model: getting-started/running-model.md
    - Visualization: getting-started/visualization.md
    - Postprocessing: getting-started/post-processing.md
  - Model formulation:
    - Physical formulation: schism/physical-formulation.md
    - Numerical formulation:
      - Geometry and discretization: schism/geometry-discretization.md
      - Barotropic solver: schism/barotropic-solver.md
      - Eulerian-Lagrangian Method: schism/eulerian-lagrangian-method.md
      - Momentum equation: schism/momentum-equation.md
      - Vertical velocity: schism/vertical-velocity.md
      - Turbulence closure: schism/turbulence-closure.md
      - Transport equation: schism/transport-equation.md
      - Updating the levels/Inundation: schism/updating-levels.md
      - Spherical coordinates: schism/spherical-coordinates.md
  - Input/Output: 
    - Overview: input-output/overview.md
    - Horizontal grid (hgrid.gr3): input-output/hgrid.md
    - Vertical grid (vgrid.in): input-output/vgrid.md
    - Model parameters (param.nml): input-output/param.md
    - Boundary conditions (bctides.in): input-output/bctides.md
    - Bottom friction: input-output/friction.md
    - Atmospheric flux (/sflux): input-output/sflux.md
    - Optional inputs: input-output/optional-inputs.md
    - Outputs: input-output/outputs.md
  - Mesh generation - advanced topics:
    - Overview: mesh-generation/overview.md
    - Meshing for cross-scale regimes: mesh-generation/cross_regime.md
    - Meshing for compound floods:
      - Overview: mesh-generation/meshing-for-compound-floods/overview.md
      - Extract thalwegs: mesh-generation/meshing-for-compound-floods/extract-thalweg.md
      - Generate river map: mesh-generation/meshing-for-compound-floods/generate-river-map.md
      - Meshing in SMS: mesh-generation/meshing-for-compound-floods/meshing-in-SMS.md
  - Modules:
    - Overview: modules/overview.md
    - Generic tracer module: modules/generic-tracer.md
    - AGE: modules/age.md
    - 2D Sediment model: modules/sed2d.md
    - 3D Sediment model: modules/sed3d.md
    - ICM: modules/icm.md
    - CoSiNe: modules/cosine.md
    - DVD: modules/dvd.md
    - Marsh migration: modules/marsh-migration.md
    - Analysis mode: modules/analysis-mode.md
    - Hydraulics: modules/hydraulics.md
    - Particle tracking: modules/particle-tracking.md
    - WWM: modules/wwm.md
    - FABM: modules/fabm.md
    - PaHM: modules/pahm.md
    - Single-class ice module: modules/single-class-ice.md
  - Code structure: code-contribution.md
  - Case studies: case-study.md
  - SCHISM external coupling:
    - Earth System Modeling Framework: coupling/esmf.md
    - National Unified Operational Prediction Capability: coupling/nuopc.md
    - NOAA's CoastalApp: coupling/coastalapp.md
    - Modular System for Shelves and Coasts: coupling/mossco.md
    - NCAR's Community Earth System Model: coupling/cesm.md
  - Frequently Asked Questions: faq.md
  - Known issues: known_issues.md
  - Contribute to this online manual: contribute-to-this-online-manual.md