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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
      • 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)
      • 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
            • Run interpolate_variables to get uv3D.th.nc
            • Move the outputs directory aside
      • 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
            • Nudging.create_nudging()
        • Preparing for nudging with observed data
        • Nudging Example
        • Nudging Suffix Standards and Procedure
          • SCHISM Conventions
          • BayDeltaSCHISM Conventions
          • Using the set_nudge Utility
            • bds set_nudge
        • 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
        • Upload Applications
          • SCHISM
          • Python Packages
        • File Transfer Commands
          • azcopy commands
            • Generating SAS Links
          • azcopy options
        • References
      • Step-by-step: HelloSCHISM on Azure
        • Initial Setup
        • Uploading Model Input Files
        • Set up Model Run Config
          • Spot Pricing Config
        • Ensure Batch Quota
        • 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?
        • 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
        • 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
  • Calibration Report and References
    • Calibration
  • Training
  • Support
  • References
  • bdschism package
    • Subpackages
      • bdschism.config package
        • Module contents
    • Submodules
    • bdschism.analyze_dt module
      • load_data()
      • plot_summarized_bad_actors()
      • summarize_elements()
    • bdschism.calc_ndoi module
      • calc_indoi()
    • bdschism.ccf_gate_height module
      • ccf_gate()
      • create_priority_series()
      • draw_down_regression()
      • export_lookup()
      • flow_to_max_gate()
      • flow_to_priority()
      • gen_gate_height()
      • gen_prio_for_varying_exports()
      • get_export_ts()
      • get_tidal_hh_lh()
      • get_tidal_ll_hl()
      • make_3_prio()
      • predict_oh4_level()
      • process_height()
      • radial_gate_flow()
      • raidal_gate_flow_ts()
      • remove_continuous_duplicates()
      • save_prio_ts()
      • sffpx_level()
      • simple_mass_balance()
      • tlmax()
      • tlmin()
    • bdschism.create_sflux_links module
    • bdschism.diff_gr3 module
      • diff_congruent_gr3()
    • bdschism.generate_realtime_elev2d module
      • main()
      • stitch_station()
    • bdschism.hotstart_date module
      • set_hotstart_date()
    • bdschism.hotstart_from_hotstart module
      • hotstart_newgrid()
      • str_or_path()
    • bdschism.hotstart_nudging_data module
      • hotstart_nudge_data()
    • 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.run_sequence module
    • bdschism.set_nudging module
      • get_nudge_list()
      • parse_var_map()
      • set_nudging()
    • bdschism.settings module
      • create_link()
      • get_settings()
    • bdschism.three_point_linear_norm module
      • ThreePointLinearNorm
        • ThreePointLinearNorm.autoscale()
        • ThreePointLinearNorm.autoscale_None()
        • ThreePointLinearNorm.inverse()
        • ThreePointLinearNorm.scaled()
    • bdschism.uv3d module
      • interpolate_uv3d()
    • bdschism.x2_buildpoints module
      • create_arg_parser()
      • main()
      • main_fixed()
      • x2_route2_bp()
    • bdschism.x2_time_series module
      • create_arg_parser()
      • default_outname()
      • find_x2()
      • get_start_date_from_param()
      • main()
      • main_hardwire()
      • process_x2()
    • 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

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