Steps for setting up an open bay hydro simulation:

1. create a folder for the run, e.g. runfolder

2. clone sfb_dfm from https://github.com/allietheking/sfb_dfm using a recursive clone to include the submodules, e.g. from the command line: cd runfolder git clone --recursive https://github.com/allietheking/sfb_dfm

3. clone stompy into the same folder: git clone https://github.com/rustychris/stompy

4. edit sfb_dfm.py inside the sfb_dfm package to specify run name, start time, and end time

5. using run_launcher_part_1.sh in the sfb_dfm package, call sfb_dfm.py to set up the vast majority of the model input files. The main input file is the *.mdu file, and this points to everything else. To execute from command line: ./run_launcher_part_1.sh may need to change permissions to execute: chmod 777 run_launcher_part_1.sh

6. use the SFEI_Wind and SFEI_Meteo packages on SFEI's Google Drive (both are in the 1_Nutrient_Share/2_Data_NUTRIENTS folder) to generate wind and meteorological forcing files. Make sure they are in the UTC time zone). Upload these files to the run folder (where the *.mdu file is located) and manually edit the FlowFMold_bnd.ext file, adding the following lines pointing to the wind and met forcing files: QUANTITY=windx FILENAME=wind_x_velocity_filename.amu FILETYPE=4 METHOD=1 OPERAND=O

    QUANTITY=windy
    FILENAME=wind_y_velocity_filename.amv
    FILETYPE=4
    METHOD=1
    OPERAND=O
    
    QUANTITY=humidity_airtemperature_cloudiness
    FILENAME=humidity_airtemp_cloud_filename.tem
    FILETYPE=6
    METHOD=3
    OPERAND=O
   

7. using run_launcher_part_2.sh, call dflowfm to launch the run To execute from command line: ./run_launcher_part_2.sh may need to change permissions to execute: chmod 777 run_launcher_part_2.sh

What does sfb_dfm.py script do?

• Adds freshwater flows to the model, making sure that the pour points are deep enough (-0.5m) to remain wet at all times.
• Adds POTW flows as point sources at the bed.
• Download tide and Delta outflow data, applying these as additional boundary conditions.
• Download a coarse wind field, add as boundary condition.
• Update settings in template.mdu to customize paths, time information, output selection.
• Partition the grid and scatter the MDUs.

Files

derived Data/files derived from other inputs, but not part of a specific run. Currently only used for shapefiles generated from the grid.

inputs-static Files which do not change across runs, are not derived, but are instead referenced directly from the MDU or other parts of the model setup.

nudged_features.pli A Delft-style polyline file defining locations of sources. This is created by exporting boundary condition features from Delta Shell.

write_grid_shp.py Short script which writes the shapefile for grid edges, used for loading grid representation into GIS.

runs Script-generated simulation setups are in subdirectories below here.

sample_run_dfm Not currently used. Reference for how to start multiprocessor runs.

sfbay_freshwater sfbay_potw Git submodules holding forcing data for rivers and wastewater discharges.

sfb_dfm.py Main script for generating new runs.

sfei_v19_net.nc Grid. This grid is modified slightly during the setup of each run based on freshwater inputs, and the modified grid is written into the run directory.

template.mdu Template model definition. Settings which needn't be set dynamically can be set here. Can be tweaked in sfb_dfm.py

update_alviso_bathy.py, plot_sources.py Temporary dev-related scripts for troubleshooting some issues. Probably will be removed down the road.