Delta Modeling Office’s Instructions for running Bay Delta SCHISM¶

The process for starting a Bay Delta SCHISM run from scratch involves some pre-processing work on a Windows machine using the schimpy library (https://github.com/CADWRDeltaModeling/schimpy).

You’ll want to have a conda environment which has the latest version of schimpy in it. For this example that environment is called ‘schism’.

Windows¶

Clone the Bay Delta Schism repository to your Windows machine (ex: D:/schism/bdsch_scratch)
- git clone https://github.com/CADWRDeltaModeling/BayDeltaSCHISM.git (creates a BayDeltaSCHISM folder within bdsch_scratch)
Move some data
- Copy the “./BayDeltaSCHISM/templates/bay_delta” folder into your base folder and rename (ex: baydeltainputs)
- You’ll need a .2dm file for the pre-processor, copy this into the baydeltainputs folder
- Copy “./BayDeltaSCHISM/data/time_history/*.th” files into baydeltainputs folder
- Copy “./BayDeltaSCHISM/data/flow_station_xsects.yaml” into baydeltainputs folder
Edit input files
- main_bay_delta.yaml
  - change mesh_inputfile: parameter to match the .2dm file you copied into the project folder
  - check that the vgrid: section contains a vgrid_version: variable set to the SCHISM version being used (5.8 or 5.10)
- dem_4.2_cc.yaml
  - check the Dutch Slough DEM location, if unknown then comment output
- sav_density.yaml
  - change “W:/sav” to “//nasbdo/Modeling_Data/sav” for all cases where “W:/sav” is found

Run pre-processor

in a conda terminal run:

conda activate schimpy
prepare_schism main_bay_delta

Create Hotstart and Nudging datasets
- This can be done in a seperate folder from the repository cloned, and seperate from the model inputs, since you only need a few of the resulting files to copy into the final model folder. (ex: bdsch_scratch/model_hotstart/)
- Hotstart and Nudging input datasets:
  - Use hotstart_nudging_data.py to create the *.csv files necessary for the next step which creates the *.nc files which SCHISM uses
    
    Warning
    
    In order to use this utility you’ll need to have dms_datastore in your environment. I created a schism-dms environment which uses this environment.yml file LINK
    
    You’ll need to specify the length of time you’re nudging the data (ex: 7 days)
    
    nudgelen = days(7)
    
    Also specify the start date that the model will run from (es: May 1, 2009)
    
    t0 = pd.Timestamp(2009,5,1)
    
    Run hotstart_nudging_data.py in your ‘model_hotstart’ folder to produce ‘hotstart_data_temperature.csv’, ‘hotstart_data_salinity.csv’, ‘nudging_data_temperature.csv’, ‘nudging_data_salinity.csv’
  - Download polars .csv data here
    
    go to the year of your start date, select “All” from the drop-down, export csv and save to “model_hotstartUSGS_{year}_saltemp.csv”
  - Review and QA/QC the downloaded data from the above two steps
    
    this step looks for negative temperatures/salinity and evaluates the data for any spikes or other anamolies
    
    SCRIPT HERE
- Creating Hotstart and Nudging *.nc Model inputs
This step relies on the schimpy package and uses two files (hotstart.yaml and nudging.yaml) along with a script “hotstart.py”
- hotstart.yaml
  for all data using ‘extrude_casts:’ replace ‘data:’ entry with the polaris csv file “USGS_{year}_saltemp.csv”
  
  for all data using ‘obs_points:’ replace ‘data:’ entry with “hotstart_data_{salinity/temperature}.csv” depending on the ‘variable:’
  
  set ‘vgrid_version:’ to 5.8 NOTE: this will be updated in schism_hotstart and schism_nudging so that you can put in the real vgrid_version
- nudging.yaml
  set ‘vgrid_version:’ to 5.8 NOTE: this will be updated in schism_hotstart and schism_nudging so that you can put in the real vgrid_version
  
  change the run days based on your previous number (ex: 7 days)
  
  rnday: 7
  
  change temperature and salinity ‘data:’ to point to “nudging_data_{temperature/salinity}.csv”
- This should have created hotstart.nc, SAL_nu_obsroms.nc, SAL_nu_roms.nc, TEM_nu_obsroms.nc, and TEM_nu_roms.nc so copy these files into the model inputs folder “baydeltainputs”
  - rename the hotstart.nc file to something relevant like “hotstart.20090501.nc” or whatever your start date is

Linux¶

Create the folder where you will be running the model (ex: /scratch/dms/{username}/schism/bdsch_scratch_demo)
- from your Windows machine, copy “D:/schism/bdsch_scratch/BayDeltaSCHISM/templates/bay_delta/make_links.py” into your Linux model folder (bdsch_scratch_demo)
- in the model folder run these commands:
```
mkdir sflux
cd sflux
python make_links.py
cd ..
```
- copy the contents of your Windows model inputs folder (baydeltainputs) into the Linux model folder (bdsch_scratch_demo)
- link the following files:
```
ln -s bctides.in.3d bctides.in
ln -s param.nml.clinic param.nml
ln -s hotstart.20090501.nc hotstart.nc
```