Plants model configuration#

Configuration for the plants model includes four sections:

A path to a CSV file defining the plant functional types to be used in the model ([plants.pft_definitions_path])
A path to another CSV file defining the size-structured communities of plant functional types found in each cell ([plants.cohort_data_path]).
Configuration details for the export of plant community data at each time step ([plants.community_data_export]).
A set of constants values used within the model ([plants.constants]) that need to be specified in the configuration if you want to change them from the default values.

Plant functional types#

The plants.pft_definitions_path configuration setting must point to a CSV defining the plant functional types to be used in a simulation. Each row in the CSV must provide a unique PFT name and then a set of plant functional trait values for that PFT. The file in the example data is a good template to use for preparing this file. The required trait fields are:

“name”, “a_hd”, “ca_ratio”, “h_max”, “rho_s”, “lai”, “sla”, “tau_f”, “tau_rt”, “tau_r”, “par_ext”, “yld”, “zeta”, “resp_r”, “resp_rt”, “resp_s”, “resp_f”, “m”, “n”, “f_g”, “p_foliage_for_reproductive_tissue”, “gpp_topslice”, “deadwood_c_n_ratio”, “deadwood_c_p_ratio”, “leaf_turnover_c_n_ratio”, “leaf_turnover_c_p_ratio”, “plant_reproductive_tissue_turnover_c_n_ratio”, “plant_reproductive_tissue_turnover_c_p_ratio”, “root_turnover_c_p_ratio”, “root_turnover_c_n_ratio”, “foliage_c_n_ratio”, “foliage_c_p_ratio”, “c_mass_fruit_flesh”, “c_mass_per_fruit_seed”, “seeds_per_fruit”.

Plant cohort data#

The plants.cohort_data_path configuration setting must point to a CSV file defining the cohorts in each cell. Again, the file in the example data is a good template but the basic structure is that each row must provide size-structured cohort data as:

the name of a PFT,
a cell ID value,
the size of the individuals in the cohort as diameter at breast height, and
the number of individuals in the cohort.

Plants community data export#

The plants model holds a large amount of detailed data on the plant communities growing in each cell, on the community-wide canopy structure within each cell and the canopy properties of individual stems within each cohort. This data is not required by other science models and so is not shared through the central data store. If you want to look at plant community data within a simulation, you will need to configure export of plant community data using the following configuration settings.

[plants.community_data_export]
required_data = []
cohort_attributes = []
community_canopy_attributes = []
stem_canopy_attributes = []
float_format = "%0.5f"

plants.community_data_export.required_data: A list of the strings giving the required plant data types to be exported. The accepted values are “cohorts”, “community_canopy” and “stem_canopy”. Default = ()
plants.community_data_export.cohort_attributes: A list of the cohort attributes that should be exported. Default = ()
plants.community_data_export.community_canopy_attributes: The community canopy attributes that should be exported. Default = ()
plants.community_data_export.stem_canopy_attributes: The stem canopy attributes that should be exported. Default = ()
plants.community_data_export.float_format: A float format string to control data precision in export files. Default = %0.5f

There are three possible data files that can be exported - you select one or more by including them in [plants.community_data_export.required] and can then select which attributes you want exported using the appropriate attributes configuration option.

The choices are:

If cohorts is included in required_data then the file plants_cohorts_data.csv will be exported for each time step. The available attributes for plant cohort data are: “biomass_fruit_n_actual_element_mass”, “biomass_foliage_n_actual_element_mass”, “biomass_root_carbon_mass”, “biomass_root_p_actual_element_mass”, “reproductive_tissue_respiration”, “biomass_stem_carbon_mass”, “delta_foliage_mass”, “sapwood_mass”, “biomass_fruit_carbon_mass”, “n_individuals”, “foliage_mass”, “stem_height”, “crown_r0”, “reproductive_tissue_turnover”, “sapwood_respiration”, “crown_z_max”, “biomass_seed_carbon_mass”, “whole_crown_gpp”, “delta_stem_mass”, “biomass_foliage_p_actual_element_mass”, “delta_dbh”, “biomass_stem_n_actual_element_mass”, “crown_area”, “fine_root_respiration”, “dbh_values”, “time”, “biomass_seed_p_actual_element_mass”, “biomass_seed_n_actual_element_mass”, “reproductive_tissue_mass”, “stem_mass”, “biomass_root_n_actual_element_mass”, “biomass_fruit_p_actual_element_mass”, “fine_root_turnover”, “biomass_stem_p_actual_element_mass”, “cell_id”, “crown_fraction”, “foliar_respiration”, “biomass_foliage_carbon_mass”, “npp”, “pft_names”, “cohort_id”, “dbh”, “foliage_turnover”.
If community_canopy is included in required_data then the file plants_community_canopy_data.csv will be exported for each time step. The available attributes for plant cohort data are: “average_layer_lai”, “cell_id”, “time”, “transmission_profile”, “average_layer_absorption”, “average_layer_fapar”, “canopy_layer_index”, “heights”.
If stem_canopy is included in required_data then the file plants_stem_canopy_data.csv will be exported for each time step. The available attributes for plant cohort data are: “fapar”, “cell_id”, “stem_leaf_area”, “time”, “cohort_id”, “canopy_layer_index”.

To show the configuration of the exporter in use, the TOML data below configures the exporter to write out trait data in all three data files:

[plants.community_data_export]
required_data = [
    "cohorts",
    "community_canopy",
    "stem_canopy",
]
cohort_attributes = [
    "cell_id",
    "cohort_id",
    "dbh",
    "delta_dbh",
    "stem_height",
]
community_canopy_attributes = [
    "cell_id",
    "canopy_layer_index",
    "heights",
]
stem_canopy_attributes = [
    "cell_id",
    "cohort_id",
    "canopy_layer_index",
    "fapar",
]
float_format = "%0.5f"

Plants constants#

[plants.constants]
per_stem_annual_mortality_probability = 0.1
per_propagule_annual_recruitment_probability = 0.2
dsr_to_ppfd = 2.04
stem_lignin = 0.545
senesced_leaf_lignin = 0.05
plant_reproductive_tissue_lignin = 0.01
root_lignin = 0.2
subcanopy_extinction_coef = 0.5
subcanopy_specific_leaf_area = 14.0
subcanopy_respiration_fraction = 0.1
subcanopy_yield = 0.6
subcanopy_reproductive_allocation = 0.1
subcanopy_sprout_rate = 0.1
subcanopy_sprout_yield = 0.5
subcanopy_vegetation_turnover = 1.0
subcanopy_seedbank_turnover = 0.25
subcanopy_seedbank_c_n_ratio = 20.0
subcanopy_seedbank_c_p_ratio = 50.0
subcanopy_vegetation_c_n_ratio = 20.0
subcanopy_vegetation_c_p_ratio = 50.0
subcanopy_vegetation_lignin = 0.2
subcanopy_seedbank_lignin = 0.2
root_exudates = 0.5
propagule_mass_portion = 0.5
carbon_mass_per_propagule = 1.0

plants.constants.per_stem_annual_mortality_probability

Basic annual mortality rate for plants. Default = 0.1

plants.constants.per_propagule_annual_recruitment_probability

Basic annual recruitment rate from plant propagules. Default = 0.2

plants.constants.dsr_to_ppfd

Convert from downward shortwave radiation to photosynthetic photon flux density.

Converting DSR in W m-2 to PPFD in µmol m-2 s-1. 1 W m-2 of sunlight is roughly 4.57 µmol m-2 s-1 of full spectrum sunlight, of which about 4.57 * 46% = 2.04 µmol m-2 s-1 is PPFD. Default = 2.04

plants.constants.stem_lignin

Fraction of stem biomass that is lignin. Default = 0.545

plants.constants.senesced_leaf_lignin

Fraction of senesced leaf biomass that is lignin. Default = 0.05

plants.constants.plant_reproductive_tissue_lignin

Fraction of plant reproductive tissue biomass that is lignin. Default = 0.01

plants.constants.root_lignin

Fraction of root biomass that is lignin. Default = 0.2

plants.constants.subcanopy_extinction_coef

The extinction coefficient of subcanopy vegetation (unitless). Default = 0.5

plants.constants.subcanopy_specific_leaf_area

The specific leaf area of subcanopy vegetation (m2 kg-1). Default = 14

plants.constants.subcanopy_respiration_fraction

The fraction of gross primary productivity used in respiration (unitless). Default = 0.1

plants.constants.subcanopy_yield

The yield fraction of net primary productivity in subcanopy vegetation (unitless). Default = 0.6

plants.constants.subcanopy_reproductive_allocation

The fraction of subcanopy net primary productivity that is allocated to subcanopy seedbank mass (unitless). Default = 0.1

plants.constants.subcanopy_sprout_rate

The rate at which new subcanopy biomass sprouts from the subcanopy seedbank mass (kg kg-1 m-2 y-1). Default = 0.1

plants.constants.subcanopy_sprout_yield

The fraction of subcanopy seedbank mass that is realised as subcanopy vegetation mass (kg kg-1). Default = 0.5

plants.constants.subcanopy_vegetation_turnover

The annual fraaction of subcanopy vegetative biomass turnover (kg kg-1 m-2 y-1). Default = 1.0

plants.constants.subcanopy_seedbank_turnover

The annual fraction of subcanopy seedbank biomass turnover (kg kg-1 m-2 y-1). Default = 0.25

plants.constants.subcanopy_seedbank_c_n_ratio

The ideal mass ratio of nitrogen in subcanopy seedbank biomass (-). Default = 20

plants.constants.subcanopy_seedbank_c_p_ratio

The ideal mass ratio of phosphorous in subcanopy seedbank biomass (-). Default = 50

plants.constants.subcanopy_vegetation_c_n_ratio

The ideal mass ratio of nitrogen in subcanopy vegetation biomass (-). Default = 20

plants.constants.subcanopy_vegetation_c_p_ratio

The ideal mass ratio of phosphorous in subcanopy vegetation biomass (-). Default = 50

plants.constants.subcanopy_vegetation_lignin

The proportion of lignin in subcanopy vegetation. Default = 0.2

plants.constants.subcanopy_seedbank_lignin

The proportion of lignin in subcanopy seedbank. Default = 0.2

plants.constants.root_exudates

Fraction of GPP topslice allocated to root exudates. Default = 0.5

plants.constants.propagule_mass_portion

Fraction of reprodutive tissue allocated to propagules. Default = 0.5

plants.constants.carbon_mass_per_propagule

Mass of carbon per propagule in g. Default = 1