Adamselv Hydrodynamic Model Setup – Documentation & User Guide

Project Structure Overview

Case/
├── 01_build_grid/
├── 02_build_rivers/
├── 03_atm_forcing/
├── 04_add_fabm_tracer/
├── 05_qc/

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1. Grid Generation (01_build_grid/)

Purpose:

This step builds the model grid from .2DM that we get from SMS and bathymetric data (EMODNET).

Key Scripts:

• 2dm_to_grid_fvtools.py: Converts SMS 2DM files into grid.
• boundary_prepro.py: Processes open boundaries.
• make_grd_adamselv.py: Main driver script for assembling the grid and domain configuration.

Inputs:

• .2dm files (e.g., adamselv_v01.2dm)
• Bathymetry data (bathy_hybrid_adamselv_v01.npy)
• Depth file (adamselv_dep_NEW.dat)

Outputs:

• Grid files and initial configuration .nc and .npy files.

⚠️ Important: After the grid is built, a restart file must be generated on the server. This restart is crucial to initialize the model with the built grid and prepare it for simulation.

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2. River Forcing (02_build_rivers/)

Purpose:

Add river inflows and process their grid representation.

Key Scripts:

• build_rivers.py: Builds river inflow boundary files.
• convert_to_node.py: Converts river input locations to grid nodes.

Inputs:

• River discharge/temperature data (e.g., Finnmark_temperatures.npy)

Outputs:

• NetCDF or text-based boundary condition inputs for rivers.

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3. Atmospheric Forcing (03_atm_forcing/)

Purpose:

Processes and fixes atmospheric data (e.g., evaporation and precipitation) used to force the model.

Key Scripts:

• fix_evaporation.py: Cleans and adjusts evaporation data.
• check_MEPS_evap.py: Quality checks MEPS model evaporation outputs.
• run_effie.py: Wrapper or main driver to process meteorological forcing.

Outputs:

• Processed atmospheric data in output/
• Logs such as log_effie.txt

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4. FABM Tracer & Restart Files (04_add_fabm_tracer/)

Purpose:

This step integrates the FABM biogeochemical model and tracer data into the hydrodynamic model.

Key Components:

• add_fabm_river.ipynb: Jupyter notebook to add FABM-related fields and inputs.
• make_input.py, make_all_water_col.py: Python scripts to build water column inputs.

Outputs:

• Restart and tracer-ready NetCDF files
• FABM-compatible river files

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5. Quality Control (05_qc/)

Purpose:

Run quality checks on grid and atmospheric data to ensure consistency before simulation.

Scripts:

• qc_output.py: Validates output files.
• qc_atm_forcing.py: Checks integrity of atmospheric data.

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Running the Model (Simplified Workflow)

1. Build the Grid

   python make_grd_adamselv.py

2. Build Rivers

   python build_rivers.py
   python convert_to_node.py

3. Process Atmospheric Forcing

   python fix_evaporation.py
   python check_MEPS_evap.py
   python run_effie.py

4. ⚠️ Generate Restart on Server

   • This step is not fully scripted here and must be done after grid generation.
   • Upload or move generated grid to the server.
   • Use model engine (e.g., FVCOM or similar) to generate a restart file based on the initial grid.

5. Add FABM Tracers

   • Use Jupyter notebook add_fabm_river.ipynb to configure and add tracers.
   • Run supporting scripts to finalize input.

6. Run Quality Checks

   python qc_output.py
   python qc_atm_forcing.py

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Notes

• Make sure dependencies such as NumPy, netCDF4, and any custom grid libraries (like FVTools) are installed.
• Always verify file paths and environment variables, especially when running on a cluster or server.