Bay-Delta SCHISM User Guide

The following topical guides take you through what it takes to set up a basic model run using the Bay-Delta SCHISM toolchain. You won’t have action items on all the topics for every run, but the Bay-Delta SCHISM Essentials section will get you started on a basic hindcast and the Topical Guides describe numerous common modeling tasks and where the gotchas are.

Bay-Delta SCHISM Setup

• Getting the Tools and Setting Up
  • Overview
  • SCHISM Code or Binaries
    • Downloading
    • Compile Settings
  • Git
  • Bay-Delta Package
  • Required Python Packages
  • Bathymetry
  • Complete Sample Inputs
  • VisIt SCHISM Plug-in
  • Links to tools
• Running a Preprepared Setup

---

Bay-Delta SCHISM Essentials

• Overview of a Bay-Delta SCHISM Run
  • Grid and Spatial Data
  • Time-dependent data
  • Files that Change with Both Mesh and Dates
  • Driver Files (param.tropic.nml, param.clinic.nml)
  • Other Nomenclature and Concepts
  • Organizing the Launch Directory
• Required Files, Directory Structure and Recommended Study Practices
  • Required files and structure
  • Study layout
• Grid, Spatial Data and Preprocessor
  • Do I need it? Copy existing run vs preprocess from template?
  • Running the preprocessor
  • Configuring the input (yaml)
  • Where to? Required files and directory structure
• Prepare Ocean Boundary (elev2D.th.nc)
• Inflow/Outflow Boundaries
  • Where are the data?
  • Clipping to run dates and conversion to elapsed time
  • What if I have to add or move a boundary?
  • Adding Data From Other Sources (e.g. Forecasts, other models)
• Atmospheric setup
  • Basic introduction and requirements
  • Where are the data?
  • Pointing to the data with make_links_full.py
• Ocean Boundary Stabilization: Barotropic Warmup
  • Introduction
  • Workflow
• Key Run Parameters and Gotchas
  • Runtime settings
  • Hotstart settings
  • Nudging settings
  • Output requests
  • Settings that have historically gone awry
  • What happens when SCHISM versions get advanced?
• Run Initialization and Restart (Hotstart)
  • When do you need an initial condition or hotstart?
  • What is the difference between a cold and hot start?
  • Combining hotstarts
  • Choosing a good start time
  • Creating a Hotstart for Hydro/Salt/Temp with schism_hotstart
• Nudging Files
  • Introduction: What is nudging?
  • Do I need nudging?
  • Prepping the data
  • Sequencing your run
• Output
  • Flavors of output
  • What you should plan in advance
  • Request station output
  • Request dense output:
  • Working with staout_ files
  • Working with flux.out files
  • Visualizing dense (.nc) output in VisIt
  • SCHISM’s extraction utilities
  • Quick validation plots
  • Where do we keep specialized postprocessing materials?
• Vegetation
  • Aquatic Vegetation in SCHISM
  • Approximations and preprocessor
  • Effective Stem Density
  • Height
• Vignette: Hindcast Bay Delta SCHISM at Delta Modeling Section with Preprocessor
  • Windows
  • Linux
• Checklists
  • Running a Processed Setup
  • Simple Hindcast Runs
• Test Suite for Prechecking Runs
  • Using the Tests
  • Writing Run Tests

---

Advanced Tasks and Concepts

• Horizontal Mesh
  • Meshing
    • Meshing considerations for SCHISM
    • Getting to know SMS
    • Building the Bay-Delta mesh the standard way
    • Presentation: Meshing consideration for marshes and restoration
    • Merging/Stitching SMS mesh/maps (new work, flooded islands, etc)
  • Vertical mesh setup
  • Checklist for after you change the mesh
• Common Problems and Diagnosis
  • Where does SCHISM write error messages?
  • My run says “segfault”
  • The runs seems very slow compared to normal
  • Dry boundary
• Simulating water age
  • Compile with age
  • Parameters in param.nml
  • Additional *.ic files
  • Hotstart considerations
  • Typical output processing
• Sea Level Rise
• Sources, Sinks, Delta Channel Depletions
  • Identifying source locations and names in preprocessor
  • Delta and Suisun channel depletions
  • Making sure you includ the th files for sources/sinks
  • Tracer concentrations
• Hydraulic Structures
  • Where is the documentation?
  • Setting up the mesh to make structures easy
  • Preventing dry boundary messages
  • Important Bay-Delta examples
• Utilities and Scripts
  • GIS Conversion
    • Mesh to shapefile
    • Polygons to/from shapefile
    • Polylines to/from shapefile
  • Hotstart Inventory: Convert iteration numbers to dates
  • model_time and multi_clip