Logo
  • Bay-Delta SCHISM Project
  • Installation And Getting Started
    • Overview
    • SCHISM Software Code/Binaries
      • Downloading
      • Compile Settings
    • Bay-Delta SCHISM Python Package
      • Downloading
      • Contents
      • Bathymetry
      • Complete Sample Inputs
      • Other Required Python Packages
    • Configuration System
      • Overview
      • Configuration File Locations and Priorities
      • Usage
      • Example Configuration File
    • VisIt SCHISM Plug-in
    • Links to tools
  • Bay-Delta SCHISM User Guide
    • Setup
      • Running a Preprepared Setup
    • Model Essentials
      • Overview
        • Overview of a Bay-Delta SCHISM Run
          • Grid and Spatial Data
            • Templates
            • Preprocessor
          • 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
        • Vignette: Hindcast Bay Delta SCHISM at Delta Modeling Section with Preprocessor
          • Windows
          • Linux
            • Barotropic
            • Baroclinic
        • Required Files, Directory Structure and Recommended Study Practices
          • Required files and structure
            • SCHISM launch directory structure
            • Launch directory
            • Output directory
            • Atmospheric (sflux) directory
          • Study layout
        • Grid, Spatial Data and Preprocessor
          • Do I need it? Copy existing run vs preprocess from template?
          • Running the preprocessor
            • Applying the template
            • Partial preprocessing for modification
          • Configuring the input (yaml)
          • Where to? Required files and directory structure
      • Boundaries & Input Files
        • 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)
            • read_csv()
        • 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
            • bctides.in
            • param.nml
            • vgrid.in
        • 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
            • Acquiring the data
            • Configuring the Hotstart request (yaml)
            • Running the hotstart generator
        • Nudging Files
          • Introduction: What is nudging?
          • Do I need nudging?
          • Generating nudging files
            • Nudging
          • Preparing for nudging with observed data
          • Nudging Example
          • Sequencing your run
          • References
        • Vegetation
          • Aquatic Vegetation in SCHISM
          • Approximations and preprocessor
          • Effective Stem Density
          • Height
      • Inspection of Model Setup
        • Checklists
          • Running a Processed Setup
          • Simple Hindcast Runs
            • ☐ Choose run dates
            • ☐ Apply template to existing mesh
            • ☐ Collect time series inputs
            • ☐ Hotstart (can be concurrent with barotropic)
            • ☐ Nudging (can be concurrent with barotropic)
            • ☐ Barotropic warmup
            • ☐ Baroclinic simulation
        • Test Suite for Prechecking Runs
          • Using the Tests
          • Writing Run Tests
            • Basics of testing
            • Test Fixtures
            • Markers
            • What to test
      • Output Files
        • Output
          • Flavors of output
          • What you should plan in advance
          • Request station output
            • station.in
            • flow_xsects.yaml and fluxflags.out
          • 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?
    • Computing Resources
      • Intro to Clusters and High Performance Computing
        • Anatomy of a Cluster
        • Figure: Cluster Components
        • Compilation
        • Job Submission
        • Compute Nodes and Message Passing
        • Input/Output and Scribes
        • Example Slurm Launch File
        • Example Shell Script to Run SCHISM
        • Intro to Batch Cloud Cluster
        • Figure: Azure Batch Cluster Components
      • Running on Azure Batch
        • Setup Azure
          • Download Azure Utilities
          • Login
          • Create a Resource Group
          • Download azure_dms_batch
        • References
      • Step-by-step: Bay-Delta SCHISM on Azure
        • Initial Setup
        • Upload Applications
          • SCHISM
          • Python Packages
        • Uploading Model Input Files
          • azcopy commands
          • azcopy options
        • Running Model Simulation
          • Simple Run Config
          • Spot Pricing Config
    • Advanced Tasks and Concepts
      • 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
      • Gridding the Horizontal Mesh
        • Meshing
          • Meshing considerations for SCHISM
            • Video (Joseph Zhang, SCHISM summit)
            • Recap/checklist
          • Getting to know SMS
            • Sample Data
            • Recap checklist
            • Presentation: clip_dems and efficient use of DEMS
          • 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)
            • Video
            • Recap/checklist
        • Vertical mesh setup
        • Checklist for after you change the mesh
        • Performance Tuning
          • The analyze_dt Utility
      • 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
  • Learning Resources for Bay-Delta SCHISM
    • General Resources and Tools
      • Bay-Delta SCHSIM Tutorials
      • Linux Hints for SCHISM
        • Using Linux from Windows
          • Basic connection
          • Copying files
          • XWindow Emulation
          • All-in-one: MobaXTerm
        • Copying a Run Safely
          • Special Case: Remote Computer Using RSA Keys
        • Symbolic links
        • Archives and Tarballs
        • Essential commands in a SCHISM context
    • Manuals
    • Getting Help
    • VIMS and Other External Resources
  • Contributing to the Documentation
    • Introduction
    • Getting Started
      • Windows
      • Linux
    • How it works
      • Local html pages
      • GitHub Pages
    • Examples and Concepts
      • Sphinx Documentation Principles
        • Headings order
        • BayDeltaSCHISM Specifics
      • Sphinx examples
        • Math
        • Figures
        • Diagrams
          • Sphinx Mermaid Directive
          • Embedding Charts with SVG
        • Embedding Videos
      • Mermaid Chart Principles
        • BayDeltaSCHISM Standards
          • Symbols
          • Style
        • VS Code plugin
        • Cool stuff
          • Clickables
          • Icons in an Element
      • Click Documentation Principles
  • Calibration Report and References
    • Calibration
  • Training
  • Support
  • References
Bay-Delta SCHISM

Index

Symbols | B | C | N | R

Symbols

  • --dest_dir
    • bds-hot_nudge_data command line option
  • --help
    • bds-hot_nudge_data command line option
  • --nudge_len
    • bds-hot_nudge_data command line option
  • --repo_dir
    • bds-hot_nudge_data command line option
  • --start_date
    • bds-hot_nudge_data command line option
  • -h
    • bds-hot_nudge_data command line option

B

  • bds-hot_nudge_data command line option
    • --dest_dir
    • --help
    • --nudge_len
    • --repo_dir
    • --start_date
    • -h

C

  • create_nudging() (schimpy.nudging.Nudging method)

N

  • Nudging (class in schimpy.nudging)

R

  • read_csv() (in module port_boundary)

© Copyright 2014,2020 California Department of Water Resources.

Built with Sphinx using a theme provided by Read the Docs.