The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry (Longo et al. 2019;Medvigy et al., 2009). Like its predecessor, ED (Moorcroft et al., 2001), ED2 uses a set of size- and age-structured partial differential equations that track the changing structure and composition of the plant canopy. With the ED2 model, in contrast to conventional biosphere models in which ecosystems with climatological grid cells are represented in a highly aggregated manner, the state of the aboveground ecosystem is described by the density of trees of different sizes and how this varies across horizontal space for a series of plant functional types. This more detailed description of ecosystem composition and structure enables the ED2 model to make realistic projections of both the fast-timescale exchanges of carbon, water and energy between the land and atmosphere, and long-term vegetation dynamics incorporating effects of ecosystem heterogeneity, including disturbance history and recovery.
Copies of the ED2 repository should contain the following directories:
The primary data structure in ED, which can be found in ed_state_vars.F90, is a named, nested array of arrays. Each level of the heirarchy contains many fields of depth one, but the key large scale structure is as follows:
Note: height and age, being continuous variables, are "binned". "Identical" in this context means sufficiently similar to be placed in the same bin. These bins are dynamically defined, based on the number of classes sought by the user and the similarity along the age and height axes.
If you plan to develop the code, please refer to the Wiki entries on code organization and design philosophy, to ensure your code developments are consistent with the existing model. Also, make sure that the code is thoroughly tested, and successfully passes the internal GitHub tests.
We strongly encourage that code developments are properly documented. Please refer to the Doxygen instructions, and especially the Doxygen and Git commits section, so additional documentation can be automatically generated from the source code comments.
To use ED2 with Docker use either the Dockerfile.gnu for the GNU compiler (works with both x86 and arm64) or Dockerfile.intel which compiled ED2 using the intel compiler (x86 only). For example the following command builds the GNU version (run this in the root of the ED2 source code):
docker build -t edmodel/ed2:gnu -f Dockerfile.gnu .
Once you have build ED2 model you can run it using:
docker run -ti --rm --ulimit stack=-1 --volume ${PWD}:/data edmodel/ed2:gnu
-ti : tells docker to use an interactive shell session --rm : will remove the container after it finishes running, make sure outputs are written to /data or current folder --ulimit stack=-1 : set the stack to be unlimited in size, this is needed otherwise ED2 will coredump --volume ${PWD}:/data : mounts the current folder to the /data folder. This is where the container starts
If no arguments are given it will run ed2 in the /data folder. Otherwise you can pass in any arguments, for example you can use ed2 -f Templates/ED2IN-tonzi.harvest to run ed2 with the input file Templates/ED2IN-tonzi.harvest.
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