Parameter sets for the WOFOST cropping system model

This repository contains the parameter sets for 23 crops for the WOFOST cropping system model.

WOFOST versions and parameter files

Since the release of PCSE 6.0, there are several versions of WOFOST available (7.2, 7.3, 8.1 and the deprecated version 8.0-beta). The parameter files for the different model version reside on different branches within this repository. The parameter files that are currently on the master branch of this repository will remain available for backwards compatibility with PCSE 5.5 and are suitable for WOFOST versions 7.2 and 8.0-beta. However, they will probably be deleted at some point in the future in order to reduce the burden of maintaining the files.

Format and structure of the parameter files

The parameters are stored in a data serialization format called YAML. YAML is similar to XML or JSON but has a strong focus on human readability and therefore is much more suited to store parameter sets that often have to be edited manually. Moreover, YAML is language independent and YAML parsers are available for a variety of languages.

The parameter files are organized by crop type and within each file different crop ecotypes and crop varieties can be defined. To accommodate the definition of different crop varieties in one file, the parameter files have been organized in a clear structure. This can be most easily explained with an example (barley in this case):

Version: 1.0.0
Metadata:
    ## Meta data at the crop level goes here

CropParameters:
    GenericC3: &GenericC3

        ## All parameters for C3 crops go here

    GenericC4: &GenericC4

        ## All parameters for C4 crops go here

    EcoTypes:
        springbarley: &springbarley
            <<: *GenericC3           # Ecotype springbarley inherits from GenericC3

            ## All parameters specific for springbarley go here

    Varieties:
        Spring_barley_301:
            <<: *springbarley        # Variety Spring_barley_301 inherits from ecotype springbarley
            Metadata:
                <<: *meta
                ## Metadata at the variety level goes here
            TSUM1:
            -  800
            - temperature sum from emergence to anthesis
            - ['C.d']
            TSUM2:
            -  750
            - temperature sum from anthesis to maturity
            - ['C.d']

The parameter file starts with a version number that is used to identify the file structure and the metadata at the crop level. Next, the crop parameters are defined starting at the tag CropParameters. First all parameters that are generic for C3 and C4 crops are defined by the tags GenericC3 and GenericC4. These parameters mainly have to do with CO₂ response on assimilation and transpiration. Moreover they define two anchors &GenericC3 and &GenericC4 that can be used to refer to in later sections.

Second, the parameter file defines the EcoTypes. These can be regarded as distinct sets of crop parameters that define the properties of groups of varieties. The parameter definitions of EcoTypes have to be complete (all crop parameters have to be present) and they have to inherit from either GenericC3 or GenericC4 by providing a reference to the anchor. For example, the ecotype 'springbarley' refers to the anchor GenericC3 through the syntax <<: *GenericC3. Each ecotype defines an anchor to itself that can be used to refer to later on.

Finally, the parameter file defines the varieties for the given crop (often called cultivars). Varieties in the parameter file inherit all parameters from one of the defined EcoTypes and redefine one or more parameters that are specific for the given variety. In the example above, the variety 'Spring_barley_301' inherits its parameters from the EcoType 'springbarley' while it redefines the parameters TSUM1 and TSUM2 to values specific for this variety. Moreover, a variety also inherits its metadata from the main metadata at the crop level but in many cases specific metadata at the variety level is available.

Parameters themselves are defined by a tag that is the name of the parameter and a list of three items: 1) the value of the parameter, 2) a description of the parameter and 3) the units of the parameter. The units are defined in such way that they can be easily parsed and used by software that supports units during model definition and simulation.

The indenting and general structure of the parameter files are part of the YAML syntax and not only enhance readability of the file, but also are essential for YAML to parse it.

The repository contains one additional file (crops.yaml) which lists all the crops that are available in the repository. the crops.yaml file is used as an entrypoint for the YAMLCropDataProvider (see below) which uses it to fetch all parameter files. This approach ensures that the same data provider can be used for other repositories with parameter files, for example those for the LINGRA model.

How to use the parameter files

The crop parameter files have been designed to work with the Python Crop Simulation Environment (PCSE) which provides a DataProvider that can directly use the YAML crop parameter files. From PCSE 6.0 onward it is required to provide the WOFOST model object as input for the YAMLCropDataProvider. This way, the YAMLCropDataProvider can select the correct branch from the repository:

>>> from pcse.input import YAMLCropDataProvider
>>> from pcse.models import Wofost81_PP
>>> cropd = YAMLCropDataProvider(Wofost81_PP)
>>> cropd.print_crops_varieties()
crop 'mungbean', available varieties:
 - 'Mungbean_VanHeemst_1988'
crop 'millet', available varieties:
 - 'Millet_VanHeemst_1988'
crop 'chickpea', available varieties:
 - 'Chickpea_VanHeemst_1988'
crop 'soybean', available varieties:
 - 'Soybean_906'
 - 'Soybean_904'

.....

crop 'potato', available varieties:
 - 'Potato_701'
 - 'Potato_703'
 - 'Potato_702'
 - 'Potato_704'
crop 'sorghum', available varieties:
 - 'Sorghum_VanHeemst_1988'
>>> cropd.set_active_crop('soybean', 'Soybean_906')
>>> print(cropd)
Crop parameters loaded from: https://raw.githubusercontent.com/ajwdewit/WOFOST_crop_parameters/wofost81
YAMLCropDataProvider - current active crop 'soybean' with variety 'Soybean_906'
Available crop parameters:
 {'CO2EFFTB': [40.0, 0.0, 360.0, 1.0, 720.0, 1.11, 1000.0, 1.11, 2000.0, 1.11], 'CO2TRATB': [40.0, 0.0, 360.0, 1.0, 720.0,
...
'REALLOC_DVS': 3.0, 'REALLOC_STEM_FRACTION': 0.2, 'REALLOC_LEAF_FRACTION': 0.0, 'REALLOC_STEM_RATE': 0.0415,
 'REALLOC_LEAF_RATE': 0.0, 'REALLOC_EFFICIENCY': 0.95}

YAMLCropDataProvider - current active crop 'soybean' with variety 'Soybean_906'
Available crop parameters:
 {'DTSMTB': [0.0, 0.0, 7.0, 0.0, 30.0, 23.0, 45.0, 38.0], 'NLAI_NPK': 1.0, 'NRESIDLV': 0.0093, 'KCRIT_FR': 1.0,

 ....

 720.0, 0.9, 1000.0, 0.9, 2000.0, 0.9], 'TSUM2': 1300, 'TSUM1': 500, 'TSUMEM': 90}

For PCSE 5.X releases, the following code is still sufficient:

>>> from pcse.fileinput import YAMLCropDataProvider
>>> cropd = YAMLCropDataProvider()

Connecting crop parameters and agromanagement

the PCSE AgroManager is designed to work with the YAMLCropDataProvider and the parameters files by referring to the crop type (crop_name) and crop variety (variety_name) in its definition of the agromanagement:

Version: 1.0.0
AgroManagement:
- 1998-01-01:
    CropCalendar:
        crop_name: soybean
        variety_name: Soybean_906
        crop_start_date: 1998-05-15
        crop_start_type: sowing
        crop_end_date:
        crop_end_type: maturity
        max_duration: 150
    TimedEvents:
    StateEvents:
- 1999-01-01:

Within the agromanagement definition (also defined in YAML) the crop_name and variety_name tags within the CropCalendar definition directly refer to the name of the parameter file ('soybean') and the variety ('Soybean_906') that is defined in the crop parameter file.

Note that crop_name and variety_name in the agromanagement definition are case sensitive!