Configuration

The transportation and biogeochemical configuration file is a JSON file made up of the following components:

Principal Key 1: BIOGEOCHEMISTRY_CONFIGURATION

<Compt_Name> -> CYCLING_FRAMEWORK	List of cycling frameworks As defined in Modules — Biogeochemistry Format: [<s#>, <s#>, ...] Example: ["N_org", "N_inorg", "P_org", "P_inorg"]
<Compt_Name> -> INITIAL_CONDITIONS -> DATA_FORMAT	Format of IC input. Options: "JSON" or "HDF5"

ADDITIONAL KEYS:

-> If DATA_FORMAT: "JSON"

Then IC data in DATA is provided in the following format: <Chem_Name>: {"(i#)": [ix,iy,iz,conc/load, units]}. If no information is provided for a particular compartment and/or chemical species, the initial conditions (concentrations and masss) will be assumed ZERO.

<i#>	Input numbering; as many entries as needed.
<ix>	Input ix index: "(i#)" or "all"
<iy>	Input iy index: "(i#)" or "all"
<iz>	Input iz index: "(i#)" or "all"
<conc/load>	Input load: "(f#)" (concentration or mass; units specified below)
<units>	Units of the previous field, e.g., "mg/l", `kg

-> If DATA_FORMAT: "HDF5"

Then IC data is provided using H5 files with the format as exported when running the model. The following additional json-keys need be included.

FOLDERPATH	Folder that contains the *.h5 files containing the IC data.
TIMESTAMP	Timestamp to be extracted. Format: YYYYMMMDD-HH:MM:SS Example: "1950Apr01-12:00:00"
UNITS	Units of the input data, which will be used to located the IC h5 files. Example: "mg", "mg/l"

The JSON file supports C/C++ syntax for comments: single-line comment (//) or comment blocks (/* and */).

The symbol <Compt_Name> refers to compartment names as defined by the host model. We can add as many of such compartment json-key blocks as desired (see example below). The compartment names should match those defined in the hostmodel.

The symbol <Chem_Name> refers to chemical species names as defined in Modules — Biogeochemistry.

The symbol (i#) refers to a integer number sequence.. The symbol (s#) refers to a string input. The symbol <f#> refers to a float input value.

Example:

{
    "BIOGEOCHEMISTRY_CONFIGURATION":{
        "RUNOFF":{
            "CYCLING_FRAMEWORK": ["N_inorg","P_inorg"],
            "INITIAL_CONDITIONS":{
              "species_A": {
                  "1": ["all","all","all",2,"mg/l"],
                  "2": [1,5,1,2,"mg/l"]
              },
              "species_B": {
                  "1": ["all","all","all",5,"kg"]
              }
            }
        },
        "SOIL_RECHR":{
            "CYCLING_FRAMEWORK": ["N_inorg","P_inorg","N_soil_org","P_soil_org"],
            "INITIAL_CONDITIONS":{
                  "DATA_FORMAT": "HDF5",
                  "FOLDERPATH": "openwq_ic_h5",
                  "TIMESTAMP": "1950Apr01-12:00:00",
                  "UNITS": "mg"
            }
        }
    }
}