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A new model representing the soil-root-vegetation-atmosphere continuum is presented. The vegetation canopy is represented using a dual big leaf, coupled energy balance, photosynthesis and stomatal conductance problem. The equations are taken from [(Wang and Leuning, 1998)](https://www.sciencedirect.com/science/article/pii/S0168192398000616) and [(Kowalczyk et al., 2006)](https://publications.csiro.au/rpr/pub?list=BRO&pid=procite:dfd74831-39c6-422a-896d-c0e71cdcc199). Hydraulic transport within the soil and the vegetation is represented by analogy to flow through a porous medium following [(Silva et al., 2022)](https://gmd.copernicus.org/articles/15/2619/2022/). Plant hydraulic and canopy processes are tightly coupled through stomatal conductance which is assumed to depend on leaf hydraulic pressure following [(Tuzet et al., 2003)](https://onlinelibrary.wiley.com/doi/10.1046/j.1365-3040.2003.01035.x)
## model presentation
### model structure
The model is contained into the following modules:
| name of the module| description |
|---|---|
| `mo_time.f90` | time management related tools |
| `mo_solver.f90` |numerical resolution utilities |
| `mo_grid.f90` | mesh utilities |
| `mo_forcing.f90` | forcing file management related tools |
| `mo_output.f90` | output file (netCDF) management related tools |
| `mo_constants.f90` | physical constants |
| `mo_photosynthesis.f90` | Farquhar's photosynthesis model |
| `mo_fluxes.f90` | canopy fluxes functions and conductance functions |
| `mo_radiation.f90` | big leaves radiation functions |
| `mo_bigleaf.f90` | complete bigleaves model |
| `mo_soil.f90` | soil parameters and retention curves |
| `mo_root.f90` | root parameters and utilities |
| `mo_stem.f90` | stem parameters and retention curves |
| `mo_pheno.f90` | phenology model |
Utility modules are not presented (nml management, files management, ...).
The simulation is directed by the `main.f90` file.
Two files are required: a forcing file with meteorological inputs and a parameter file with the numerical, optical, photosynthesis, soil, root, stem and mesh parameter values. The required forcing inputs are:
* DOS (Day of Simulation): the simulation day. Should start at 1
* SW_in (Incoming short wave radiation, W/m2)
* Ta (air temperature, °C)
* Ca (atmospheric CO2 concentration, ppmv = mu mol/mol)
* u (wind speed, m/s)
* SolAng (the zenith solar angle, rad)
* Pa (atmospheric pressure, hPa)
* rain (incoming rain, mm)
**The forcing file should be in csv format**
## how to use
* **step 0**: be sure that the LAPACK and the NETCDF fortran libraries are installed and that the paths to the librairies are correctly set in the `Makefile` (`src/` subdirectory)
* **step 1**: make sure the `output` folder is created in the `simu/` subdirectory
* **step 2**: in `simu/run_python.py`:
* in the `var_dic` object, turn the variables to be displayed in the final netCDF file to `True`. **Make sure that there is at least as much variables already activated in the `.nml` file as you wish to activate. If it is not the case, you should add empty variables (`''`) in the `.nml` file**
* in the `plot_dic` object, turn the name of the graphics to be produced to `True`. Each graphic is composed of two or more subgraphics. The required variables used to produce the graphic are indicated in the comments. **Make sure that you have the required variables activated to produce the graph**
* set the correct names for the parameter file and the forcing file
* set the desired simulation length (in days)
* set the output netCDF file name
* set the final pdf name containing the desired graphics
* set the starting simulation year, month, day, hour and minute
* save and exit
* **step 3**: run `./run.sh`. The script will compile the program, prepare the `.nml` file for the simulation, run the simulation, produce the desired graphs and plot them
## references
* Kowalczyk et al., 2006, The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model for use in climate models and as an offline model, CSIRO Marine and Atmospheric Research paper 013
* Wang and Leuning, 1998, A two-leaf model for canopy conductance, photosynthesis and partitioning of available energy I: Model description and comparison with a multi-layered model, Agricultural and Forest Meteorology 91
* Silva et al., 2022, Tree hydrodynamic modelling of the soil-plant-atmosphere continuum using FETCH3, Geosci. Model Dev., 15, 2619-2634
* Tuzet et al., 2003, A coupled model of stomatal conductance, photosynthesis and transpiration, Plant, Cell and Environment, 26, 1097-1116