Usage

SPLASH

This setup simulates potential evapotranspiration (Priestly-Taylor equation) and the soil water balance (bucket model), given precipitation and cloud cover as inputs. The model is described in Davis et al. (2107). The photosyntetically active radiation calculated by SPLASH may be used to drive the P-model. Soil moisture calculated by SPLASH may be used for an empirical estimate of the reduction in light use efficiency in the P-model.

Compile and execute the model by

make splash
echo example_splash_sitescale | ./runsplash

An alternative implementation of the soil water balance follows the Simple Water Balance Model by Orth et al. (2013), where runoff is generated before 100% water holding capacity is reached. This version can be compiled and executed by

make swbm
echo example_swbm_sitescale | ./runswbm

P-model

This setup implements the P-model descrbed by Prentice et al. (2013) and Wang Han et al. (2017). See also P-model. In combination with prescribed rates of absorbed photosynthetically active radiation, the P-model can be applied as a light use efficiency model for simulating ecosystem-level gross primary productivity.

Compile and execute for site-scale simulations by

make pmodel
echo example_sitescale | ./runpmodel

Compile and execute for global simulations by

make gpmodel
echo example_global | ./rungpmodel

CN-model

This implements a fully integrated model for the cycling of carbon and nitrogen in a grassland (see here). Currently only implemented for site-scale simulations.

make cnmodel
echo example_sitescale | ./runcnmodel

C-model

This implements the same components as the CN-model, but assumes a fixed allocation (root-to-shoot ratio) and does not close the N budget. It mimics a C-only model.

make cmodel
echo example_sitescale | ./runcmodel

Overview of steps

Steps to run SOFUN are:

1. Get code
2. Get forcing data (see ‘Input’ XXX)
3. Get site and simulation parameter files
4. Link files and directories
5. Compile and run

1. Get code

The repository sofun contains all the model code (Fortran 90) that implements the P-model and additional levels of model integration (water balance only, closed C, closed C and N cycles, see also here).

Clone the SOFUN repository and switch to branch pnmodel (XXX) using command line:

cd your_chosen_home
git clone https://bitbucket.org/labprentice/sofun
cd sofun
git checkout pnmodel

2. Get forcing data (see ‘Input’ XXX)

3. Get site and simulation parameter files

P-model simulations are done for each FLUXNET 2015 Tier 1 site separately, covering years for which data is available. After having prepared all the model forcing data by the steps described above, we now prepare the simulation and site parameter files. Here, we’re conducting one simulation per site.

Two types of paramter files have to be created:

1. Site parameter files: Define the geographical location, elevation and soil parameters (or soil type) for each site.
2. Simulation parameter files: Define the simulation start, and end years, number of spinup years, forcing data types, output variables, etc.

Both are created by prepare_paramfils.R available from the repository getin. In the header adjust manually:

##--------------------------------------------------------------------
## MANUAL SETTINGS
##--------------------------------------------------------------------
myhome           = "/alphadata01/bstocker/"
simsuite         = "fluxnet2015"  
overwrite        = TRUE
##--------------------------------------------------------------------
## uncomment:
systr <- "''"    # for Mac
##--------------------------------------------------------------------

Then run in R:

setwd("your_chosen_home/getin")
source("prepare_paramfils.R")

5. Get, compile and run SOFUN

The repository sofun contains all the model code (Fortran 90) that implements the P-model and additional levels of model integration (water balance only, closed C, closed C and N cycles, see also here). Typically, a certain tag from a certain branch is desired. Let’s say you wish to checkout version 1.1.0, corresponding to the git tag v1.1.0 from the git branch pnmodel. For this, do the following in your shell:

cd your_chosen_home
git clone https://github.com/stineb/sofun.git
git remote set-url origin https://github.com/stineb/sofun.git
git fetch origin
git checkout tags/v1\.1\.0 -b pnmodel

You may avoid the backslashes above (\) - I had to write it, otherwise a bug prevented this code snippet to be displayed.

Then, create soft links to input and parameter file directories by executing the Python script linkdirs_sofun.py. Before executing, specify the simulation suite inside this script manually:

simsuite = 'fluxnet2015'

The following specification is required only for global simulations to link input fields (climate, fAPAR) to locations where data is read by SOFUN:

dataroot = 'your_chosen_home/data/'

Then

python linkdirs_sofun.py

5. Compile and run

Running the set of simulations for the suite fluxnet2015 is done be simply executing the Python script (after setting manually: simsuite = 'fluxnet2015'):

python submitjobs_sofun.py

This executes the following basic statements that compile and run SOFUN:

make pmodel
echo simulation_name | ./runpmodel

This setup compiles with the open-access GNU compiler for Fortran 90 gfortran and with the (non-open access) Portland Group Fortran Compiler.