BROM transport

About BROM-transport

BROM-transport is a one-dimensional model for water-sediment columns, resolving both vertically with an integrated approach. It applies the same set of FABM modules across both water and sediment (i.e., a single fabm.yaml file is used for both), allowing one to use the same building blocks (e.g., redox and carbonate chemistry, bacteria) in both.

BROM-transport is not a hydrodynamic model - it accept forcing in the form of water column turbulent diffusivity, temperature and salinity, which are then used to drive FABM and the transport (mixing and sinking/floating) of biogeochemical tracers. The forcing variables are typically derived from simulation with a 1D or 3D hydrodynamic model.

BROM-transport currently must be compiled with Intel Visual Studio on Windows, as it uses the libraries provided by this compiler to visualize results. BROM-transport is currently also hardcoded to use the BROM biogeochemical modules provided with FABM (under src/models/niva/brom).

Obtaining the code and compiling

BROM-transport is available at GitHub. You can obtain the source code by cloning its git repository. On Windows, you can use TortoiseGit for this purpose: right-click in a location in Windows explorer where you want the BROM-transport directory, choose "Git clone...", enter https://github.com/e-yakushev/BROM-transport.git as URL, and click "OK".

On Linux the same is achieved with

git clone https://github.com/e-yakushev/BROM-transport.git

but note that BROM-transport currently must be compiled with Intel Visual Studio on Windows.

BROM-transport uses CMake for its build system. In CMake, the relevant source directory is the Ver. 1.0/data directory within the directory you checked out using git. You will also need to set the FABM_BASE variable to the directory with FABM source code. Detailed instructions for using cmake on different platforms can be found here.

Using BROM-transport

BROM-transport must be compiled with Intel Visual Studio on Windows. After opening the Visual Studio created by cmake, yo can run BROM-transport by right-clicking the brom project and choosing "Set as startup project". After that, press F5 to start the program.

BROM-transport currently does not provide any configuration capabilities. It is hard-coded to use gotm_tke_l.dat (file created by GOTM v. 4.1.0) as source of temperature, salinity and turbulence diffusivity data and start8.dat (file created by previous runs of BROM-transport to get stable conditions of state variables like DIC, alkalinity and etc.) as source of initial data. It also requires 2 files with .rgb extension for plotting purposes and a fabm.yaml file with settings for the BROM biogeochemistry modules that are part of FABM. All necessary files can be found in Ver. 1.0/data folder that is part of the source code checked out with git. This directory should be chosen as working directory in Visual Studio (right-click the brom project, choose "Properties", "Debugging", and enter the path under "Working Directory").