BioRT-HBV is a reactive transport module that works with the semi-distributed rainfall-runoff model HBV Light. BioRT-HBV takes HBV Light simulated hydrologic states and fluxes to drive reactive transport processes. The reaction processes are the same as in BioRT-Flux-PIHM.
BioRT-HBV is open source software licensed under the MIT License. All bug reports and feature requests should be submitted using the Issues page.
The following guide applies to UNIX (include MacOS) systems.
After downloading the BioRT-HBV source code, go into the BioRT-HBV directory.
Use the command
make allto install CVODE library (required by BioRT-HBV) and compile BioRT-HBV executable.
If you already have CVODE v2.9.0 installed, you can edit the Makefile and point CVODE_PATH to your CVODE directory, and use
make biortto compile BioRT-HBV.
When installation succeeds, you should see a biort executable in your BioRT-HBV directory.
To compile BioRT-HBV for Windows using Cygwin, ensure that you have installed CMake and Make through Cygwin. Then, in a Cygwin terminal in the source directory, run the following commands in the source code directory to build using CMake:
mkdir build
cd build
cmake ..
cmake --build . -j4If compilation was successful, the file biort.exe should be in the BioRT-HBV directory, and the model is then ready to use.
To build BioRT-HBV for Windows, ensure that you have a C compiler and CMake installed on your local machine through Visual Studio. Then in a Powershell terminal, run:
mkdir build
cd build
cmake ..
cmake --build . --config ReleaseIf successfully compiled, the executable biort.exe should be in the BioRT-HBV directory.
To directly run the BioRT-HBV model on your system, unzip "Biort_HBV_v1_windows_exe.zip". There will be "biort.exe" file and "input" folder inside "Biort_HBV_v1_windows_exe" folder. Navigate to the folder "Biort_HBV_v1_windows_exe" on your command prompt and you can run the model using the command "biort xxx", where xxx is a subfolder of "input" folder containing the input files for the study site user wants to model.
The BioRT-HBV model requires six input files, including HBV Light model input and output files.
Before running the BioRT-HBV model, users should first run the HBV Light model for their watersheds of interest.
The parameters used for the HBV Light simulation should be saved.
After HBV Light simulations, create a sub-directory in the BioRT-HBV input directory.
White spaces should be avoided when naming the sub-directory.
Then put the saved parameter file and Results.txt to the created sub-directory.
The parameter file should be renamed to Parameter.xml.
Four additional files, cdbs.txt, chem.txt, cini.txt, and soil.txt are required for the BioRT-HBV model.
The chemical database, cdbs.txt, has the exactly same format as CrunchFlow and BioRT-Flux-PIHM database files.
For a complete description on the CrunchFlow's database file, please refer to CrunchFlow user's manual.
The chemical model control file, chem.txt, follows the reactive transport code CrunchFlow input file structure.
The first block provides parameters to control the reactive transport module:
RECYCLE:
Number of times to recycle HBV Light results as forcing for spin-up.
The model will run RECYCLE + 1 times.
ACTIVITY:
Set to 0 to disable activity model.
Set to 1 to use the Debye-Huckel equation.
RELMIN:
Mineral volume fraction mode.
Set to 0 if you input absolute volume fraction.
Set to 1 if you input relative fraction (to total mineral volume fraction).
TRANSPORT_ONLY:
Transport only mode switch.
Set to 0 to turn on reactions.
Set to 1 to run transport only mode with reactions skipped.
CEMENTATION:
Cementation factor.
TEMPERATURE:
Field temperature in degree celsius.
SW_THRESHOLD and SW_EXP:
Threshold and exponent parameters in soil moisture control function.
Set SW_THRESHOLD to 1 to use increase behavior.
Q10:
Q10 parameter for reactions.
The PRIMARY_SPECIES block lists all primary species to be simulated.
The SECONDARY_SPECIES block lists all secondary species the users would like to track.
The MINERAL_KINETICS block lists all kinetic mineral reactions.
This block follows a similar format as the corresponding block in CrunchFlow input file.
The chemical initial condition file (cini.txt) provides precipitation concentrations (PRECIPITATION) and the initial concentrations in the upper (UZ) and lower (LZ) zones.
The total concentrations of all primary species should be provided in the cini.txt file.
The default unit for aqueous concentrations is mol L−1,
for volume fractions is m3 m−3,
for specific surface area is m2 g−1,
for surface site density is eq g−1.
The soil parameter file (soil.txt) adds necessary soil parameters to BioRT simulations.
POROSITY_UZ and POROSITY_LZ:
Porosity of upper and lower zones (m3 m-3);
RES_UZ and RES_LZ:
Residual water storages in upper and lower zones (mm).
This storage is the lowest allowed storages in BioRT-HBV simulations.
The residual storages are added to simulated storages at every time step.
D_UZ and D_LZ:
Depths of upper and lower zones (mm).
The depths are used for the model to calculate degrees of saturation.
Now you can run BioRT-HBV models using:
$ ./biort [-vV] <input directory>where <input directory> is the input directory name of your choice,
and [-v] is an optional parameter to turn on verbose mode.
The -V parameter will display model version.
Note that model will quit after displaying the version information.
No simulation will be performed when using the -V parameter.
After running the simulation, an output file containing the concentrations of all species and reaction rates of minerals at each time step is generated in your BioRT-HBV/output directory named <input directory>_results_<simulation_time>.txt.
The header line shows the names of all species, followed by a suffix indicating locations (and rates).
_inf:
Infiltration concentrations (mol L-1).
_UZ:
Upper zone concentrations (mol L-1).
_LZ:
Lower zone concentrations (mol L-1).
_riv:
Stream concentrations (mol L-1).
_rate_UZ:
Upper zone mineral reaction rates (mol m-2 day-1)
_rate_LZ:
Lower zone mineral reaction rates (mol m-2 day-1)