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  • 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
    • Essentials for Running the Model
      • Running a Preprepared Setup
      • 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
      • 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
        • Input/Output Units
          • File Units
          • Coordinate System
      • Vignette: Hindcast Bay Delta SCHISM at Delta Modeling Section with Preprocessor
        • Windows
        • Linux
        • Barotropic Simulation
        • Baroclinic
    • Model Inputs & Generation
      • Overview of Model Inputs
      • Spatial Inputs and the Preprocessor
        • Mesh Input File
          • 2dms
          • hgrid.gr3
        • Preprocesing Spatial Data
          • When to use the preprocessor
          • Running the preprocessor
            • Applying the template
            • Partial preprocessing for modification
            • Configuring the input (yaml)
          • Where to? Required files and directory structure
          • Volumetric Refinement and Smoothing, Depth Enforcement
            • Overview
            • Mathematical Formulation
            • Depth Enforcement
            • Shoreline Discovery Seeds
            • Preprocessor Integration
            • Inline Parameters (Annotated)
            • Examples
        • Hydraulic Structures
          • Where is the documentation?
          • Setting up the mesh to make structures easy
          • Preventing dry boundary messages
          • Important Bay-Delta examples
        • Vegetation
          • Aquatic Vegetation in SCHISM
          • Approximations and preprocessor
          • Effective Stem Density
          • Height
      • Boundaries and Sources: Time-Varying Inputs
        • Bay Delta Boundaries
        • Prepare Ocean Boundary (elev2D.th.nc)
        • Ocean Boundary Stabilization: Barotropic Warmup (uv3D.th.nc)
          • Introduction
          • Workflow
            • bctides.in
            • param.nml
            • vgrid.in
        • Inflow/Outflow Boundaries (flux.th)
          • Where are the data?
          • Clipping to run dates and conversion to elapsed time
          • What if I have to add or move a boundary?
          • Porting Boundaries from Other Sources
            • File Descriptions
            • Configuring the port_boundary yaml file
            • Use
            • Configuring the mapping file
          • Parsing Consumptive Use
            • Configuring the parse_cu yaml file
          • Plotting Input Boundaries
            • Use
        • Atmospheric setup (sflux_*.nc)
          • Basic introduction and requirements
          • Where are the data?
          • Pointing to the data with make_links_full.py
        • 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 Nudging: Spatio-Temporal Inputs
        • Nudging Files
          • Introduction: What is nudging?
          • Do I need nudging?
          • Generating nudging files
          • Preparing for nudging with observed data
          • Nudging Example
          • Nudging Suffix Standards and Procedure
            • SCHISM Conventions
            • BayDeltaSCHISM Conventions
            • Using the set_nudge Utility
          • Sequencing your run
          • References
        • Run Initialization and Restart (Hotstart)
          • When do you need an initial condition or hotstart?
          • What is the difference between a cold and hot start?
          • Choosing a good start time
          • Creating a Hotstart for Hydro/Salt/Temp with schism_hotstart
            • Acquiring the data
          • Combining Hotstarts and Managing Restart Files
          • Hotstart Inventory Utility (schimpy.hotstart_inventory)
          • Automated Hotstart Combining (bdschism.combine_hotstart)
          • Why This Matters
    • Inspection of Model Setup
      • Test Suite for Prechecking Runs
        • Using the Tests
        • Writing Run Tests
          • Basics of testing
          • Test Fixtures
          • Markers
          • What to test
      • 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
        • Sea level rise (SLR) runs
          • SLR-specific items
          • Workflow for setting up a SLR run where bathymetry and hydrology come from two separate, existing runs
    • Output
      • Flavors of output
      • What you should plan in advance
        • Request station output
          • station.in
          • flow_station_xsects.yaml and fluxflag.prop
        • Request dense output (netCDF/*.nc files)
      • Working with output files
        • staout_ files
        • flux.out files
        • Visualizing dense (.nc) output in VisIt
          • SCHISM VisIT Plug-in Manual
      • 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
          • Register with Azure
            • Set Console Variables
            • Create Azure Accounts
            • Removing a Resource Group
          • Download azure_dms_batch
        • Upload Applications
          • SCHISM
          • Python Packages
        • File Transfer Commands
          • azcopy commands
            • Generating SAS Links
          • azcopy options
        • Ensure Batch Quota
        • References
      • Step-by-step: HelloSCHISM on Azure
        • Initial Setup
        • Uploading Model Input Files
        • Set up Model Run Config
          • Spot Pricing Config
        • Run Simulation!
      • Step-by-step: Bay-Delta SCHISM on Azure
        • Initial Setup
        • Uploading Model Input Files
        • Running Model Simulation
          • Simple Run Config
          • Spot Pricing Config
    • Advanced Tasks and Concepts
      • Common Problems and Diagnosis
        • Where does SCHISM write error messages?
        • Common Problems
          • SIGSEGV or segmentation fault
          • The runs seems very slow compared to normal
          • Dry boundary
        • SCHISM Errors & Solutions
        • SCHISM Utility Errors & Solutions
      • 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
      • 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
  • Calibration Report and References
    • Calibration
  • Contributing to the Documentation
    • Introduction
    • Getting Started
      • Windows
      • Linux
    • How it works
      • Local html pages
      • GitHub Pages
    • Examples and Concepts
      • Sphinx Documentation Principles
        • Code Auto-Documentation
        • 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
  • Training
  • Support
  • References
  • bdschism python package
    • Subpackages
      • bdschism.config package
        • Module contents
    • Submodules
    • bdschism.analyze_dt module
      • load_data()
      • plot_summarized_bad_actors()
      • summarize_elements()
      • write_bad_csv()
      • write_bad_shp()
    • bdschism.barrier_status module
    • bdschism.calc_ndoi module
    • bdschism.ccf_gate_height module
    • bdschism.combine_hotstart module
    • bdschism.combine_nc module
      • combine_nc()
      • combine_uv3d()
      • compare_dataarray_all_axes()
      • get_selected_files()
      • validate_time_step_consistency()
    • bdschism.config_cli module
    • bdschism.create_sflux_links module
    • bdschism.diff_gr3 module
      • diff_congruent_gr3()
    • bdschism.gen_elev2d module
    • bdschism.generate_realtime_elev2d module
    • bdschism.generate_visit_filelist module
      • visit_list()
    • bdschism.hotstart_date module
    • bdschism.hotstart_from_hotstart module
    • bdschism.hotstart_nudging_data module
    • bdschism.nc_metadata module
      • nc_metadata()
    • bdschism.parse_cu module
    • bdschism.plot_input_boundaries module
    • bdschism.port_boundary module
    • bdschism.profile_plot module
      • get_index_bounds()
      • nearest_neighbor_fill()
      • profile_plot()
      • set_index_bounds()
      • vertical_fill()
    • bdschism.read_dss module
    • bdschism.run_sequence module
    • bdschism.runtime_hotstart module
    • bdschism.set_mode module
    • bdschism.set_nudging module
    • bdschism.settings module
      • create_link()
      • get_output_from_interpolate_variables()
      • get_settings()
      • interpolate_variables()
    • bdschism.smscg_log_2_schism_th module
    • bdschism.synthetic_copy module
    • bdschism.synthetic_sflux module
    • bdschism.three_point_linear_norm module
      • ThreePointLinearNorm
        • ThreePointLinearNorm.autoscale()
        • ThreePointLinearNorm.autoscale_None()
        • ThreePointLinearNorm.inverse()
        • ThreePointLinearNorm.scaled()
    • bdschism.tide module
      • Node
        • Node.add_child()
        • Node.add_parent()
        • Node.get_ancestors()
        • Node.get_descendants()
        • Node.num_ancestors()
        • Node.num_descendants()
      • gen_constituents_tree()
      • get_astro_constituent_names()
      • get_constituents()
    • bdschism.uv3d module
    • bdschism.x2_buildpoints module
    • bdschism.x2_time_series module
    • bdschism.zone_utils module
      • face_aver()
      • face_aver_inst()
      • fill_ele_area()
      • fill_ele_area510()
      • gen_node_neibor_ele()
      • gen_node_wet_dry()
      • quad_area()
      • triangle_area()
    • Module contents
Bay-Delta SCHISM

Advanced Tasks and Concepts

  • Common Problems and Diagnosis
  • Simulating water age
  • Sea Level Rise
  • Sources, Sinks, Delta Channel Depletions
  • Gridding the Horizontal Mesh
  • Utilities and Scripts
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