14.6 LDNDC

Model Information
Home Page https://ldndc.imk-ifu.kit.edu/about/model.php
Source Code
Authors Prof. Dr. Klaus Butterbach-Bahl, Dr. Edwin Haas, …
PEcAn Integration Henri Kajasilta

14.6.1 Introduction

LandscapeDNDC is designed to simulate biosphere/hydrosphere processes of forest, arable and grassland ecosystems. The design of LDNDC allows different models/modules to be plugged in, allowing the simulations for different ecosystems. The most up-to-date information on LDNDC can be found here, as well as the authors, users guide and documentation of the model: https://ldndc.imk-ifu.kit.edu/index.php

Please note! The PEcAn setups here are written for the LDNDC version that has been downloaded on 2022-10-19. Some of the newer versions of LDNDC may have differences in the names of variables and parameters.

PEcAn configuration file additions

The following sections of the PEcAn XML are relevant or have influence at this development stage:

ensemble variable: LAI, GPP, NPP, NEE, Respirations (AutoResp, HeteroResp, TotalResp), biomass of harvesting (harvest_carbon_flux), AGB and BGB (below_ground_carbon_content).

model id: Corresponding the id of LDNDC in BETY.

run inputs start_date: Start date of the simulation end_date: End date of the simulation

Paths to meteorological drivers, events and initial conditions. Paths to airchemistry and groundwater files, may also be included, but are not required.

14.6.2 Model specific input files

LDNDC takes multiple input files, and can also generate multiple output files. These notes on input files are written from the PEcAn integration point of view, and detailed information on input files can be found in the user guide, which is available via the links above.

Input files:

Project — Contains essential information in order to set up the simulation run. For example, the file contains paths to other files that will be used in the simulations, as well as the time period in which the simulations will take place.

Setup — Defines which modules are used.

Climate — Met data that is used in simulations.

Speciesparameters — Species used in the simulations should be defined here and the file contains the parametrization for the species.

Siteparameters — Works similarly to speciesparameters, but from the point of view of site parametrization.

Event — Holds information about the events, which are essential in arable simulations.

Site — Specific information about the site (e.g. carbon and nitrogen contents, hydrological characteristics).

Airchemistry — Information about the air chemistry. Model configuration files

Due to the number of different input files, there are several templates that are used in the model configuration. The templates are located in models/ldndc/inst/. These templates wll be populated with parametrizations and initial conditions when configurations are written. The drivers and events on the other hand should be informed by giving a path to the driver/event file in pecan.xml.

Many configurations for the model are (less surprisingly) written in write.configs.LDNDC. This is the file that may need to be modified in order to make the model to run appropriately in terms of the simulated species. Currently, there are a few crop species that the workflow recognizes (triticale, barley and oat), a couple of grass species (timothy and meadow) and one forest species (pipy). However, if other species options are needed, it is relatively easy to modify the code in configurations and add them so that the workflow can handle them. Also, the path for running the model binary is created in write.configs.LDNDC and will likely need some changes depending on the location of the model binaries/configurations on the user’s server.

  • project.ldndc : The project file is populated in write.configs.LDNDC based on the input from the PEcAn settings. In addition to containing the correct names for the input files used in the simulation, the project file contains the start and end points for the simulation period. The file also specifies the path where the output files will be written. The other input files should be in the same directory as the project file when the model run is started. The output directory is created amongst the other outputs of the simulation. Simulations are run half-hourly by default and this is hard coded in the write.configs.LDNDC file.

  • template.job : Will be filled in with the information needed to run the model in PEcAn. For example, calls the model binary and executes the project.ldndc file.

  • speciesparameter_template.xml : Has a replaceable section. This section is filled in within write.configs.LDNDC. This file uses the given prior values for the species. Currently, there are a few species hard coded in write.configs.LDNDC. See the comment above.

  • siteparameters.xml : This file is populated by given site(parameter) prior values.

  • site.xml : This file is written based on the given initial condition file (netcdf). If no path is given in poolinitcond, then some default mineral clay soil settings will be written to this file. However, it is strongly recommended that some initial conditions based on the simulated site are provided. Variables that can be found from the initial conditions, but are not required:

    • For each layer
      • pH (-),
      • volume_fraction_of_water_in_soil_at_field_capacity (m3 m-3),
      • volume_fraction_of_condensed_water_in_soil_at_wilting_point (m3 m-3),
      • soil_nitrogen_content (kg kg-1),
      • soil_carbon_content (kg kg-1),
      • mass_fraction_of_clay_in_soil (kg kg-1),
      • mass_fraction_of_sand_in_soil (kg kg-1),
      • mass_fraction_of_silt_in_soil (kg kg-1),
      • soil_density (kg m-3),
      • soil_hydraulic_conductivity_at_saturation (m s-1),
      • stratum = (-) [number of how many stratums a soil layer has]
    • Single value
      • c2n_humus (ratio), [is written in siteparameter file]
      • AGB = (kg m-2), [is written in events file]
      • fractional_cover (%) [is written in events file]
    • Model specific
      • history (soil use history, e.g. arable)
      • soil_type (e.g. ORMA, SALO)
  • setup.xml : Contains information about which modules the model simulation is using. Default settings should be suitable for most of the purposes and are currently hard-coded. The setups differ for agricultural and forest sites.

14.6.3 Installation notes

In order to obtain the LDNDC model, the credentials are required. The user can request them from the developers of the model. With the credentials, the pre-compiled LDNDC program can be downloaded here: https://ldndc.imk-ifu.kit.edu/download/download-model.php

Once the necessary files have been obtained, the user should execute the installation script found in the ldndc-‘version-number’ directory. On linux, executing would happen with the command sh install.sh. A successful installation will create a .ldndc directory in the user’s home directory. (Note, that this .ldndc directory path will be used in write.configs.LDNDC.) Running the simulations is done by calling the ldndc executable (found in the /bin directory) and giving the path to the project file containing the specs of the simulation. Detailed instructions and how to play with these setups can be found in the user guide.