rsofun BiomeE driver data (Leuning photosynthesis model)

Example driver to run the BiomeE-model at the CH-LAE site using the Leuning photosynthesis specification (and half-hourly time step) It can also be used together with leaf trait data from CH-LAE (biomee_validation) to optimize model parameters.

biomee_gs_leuning_drivers

Format

A tibble of driver data.

sitename

Site name

params_siml

Simulation parameters as a data.frame, including the following data:

spinup

Flag indicating whether this simulation does spin-up (deprecated).

spinupyears

Number of spin-up years. Set to 0 for no spinup.

recycle

Number of first N years of forcing data.frame that are recycled for spin-up.

firstyeartrend

Year of first transient year (AD) (optional). Is only used to set years in output data frames. Defaults to 0 if not provided.

nyeartrend

Number of transient years (optional). Determines the length of simulation output after spin-up. Defaults to number of years contained in the forcing data. (If longer than forcing data, last year of forcing is repeated until the end (spin-down).)

steps_per_day

Time resolution of the forcing (day-1).

do_U_shaped_mortality

Flag indicating whether U-shaped mortality is used.

do_closedN_run

Flag indicating whether doing N closed runs to recover N balance enforcing 0.2 kg N m-2 in the inorganic N pool.

method_photosynth

String specifying the method of photosynthesis used in the model, either "pmodel" or "gs_leuning".document()

method_mortality

String indicating the type of mortality in the model. One of the following: "dbh" is size-dependent mortality, "const_selfthin" is constant self thinning (in development), "cstarvation" is carbon starvation, and "growthrate" is growth rate dependent mortality.

do_daily_diagnostics

Whether to output daily diagnostics ('output_daily_tile'). Default: True.

site_info

Site meta info in a data.frame. This data structure can be freely used for documenting the dataset, but must include at least the following data:

lon

Longitude of the site location in degrees east.

lat

Latitude of the site location in degrees north.

elv

Elevation of the site location, in meters above sea level.

forcing

Forcing data.frame used as input

ppfd

Photosynthetic photon flux density (mol s-1 m-2)

tair

Air temperature (deg C)

vpd

Vapor pressure deficit (Pa)

rain

Precipitation (kgH2O m-2 s-1 == mm s-1)

wind

Wind velocity (m s-1)

pair

Atmospheric pressure (pa)

co2

CO2 atmospheric concentration (ppm)

params_tile

Tile-level model parameters, into a single row data.frame, including the following data:

soiltype

Integer indicating the type of soil: Sand = 1, LoamySand = 2, SandyLoam = 3, SiltLoam = 4, FrittedClay = 5, Loam = 6, Clay = 7.

FLDCAP

Field capacity (vol/vol). Water remaining in a soil after it has been thoroughly saturated and allowed to drain freely.

WILTPT

Wilting point (vol/vol). Water content of a soil at which plants wilt and fail to recover.

K1

Fast soil C decomposition rate (yr\(^{-1}\)).

K2

Slow soil C decomposition rate (yr\(^{-1}\)).

K_nitrogen

Mineral Nitrogen turnover rate (yr\(^{-1}\)).

MLmixRatio

Ratio of C and N returned to litters from microbes.

etaN

N loss rate through runoff (organic and mineral) (yr\(^{-1}\)).

LMAmin

Minimum LMA, leaf mass per unit area, kg C m\(^{-2}\).

fsc_fine

Fraction of fast turnover carbon in fine biomass.

fsc_wood

Fraction of fast turnover carbon in wood biomass.

GR_factor

Growth respiration factor.

l_fract

Fraction of the carbon retained after leaf drop.

retransN

Retranslocation coefficient of nitrogen.

f_initialBSW

Coefficient for setting up initial sapwood.

f_N_add

Re-fill of N for sapwood.

tf_base

Calibratable scalar for respiration, used to increase LUE levels.

par_mort

Canopy mortality parameter.

par_mort_under

Parameter for understory mortality.

params_species

A data.frame containing species-specific model parameters, with one species per row, including the following data:

The following columns pertaining to the plant type:

lifeform

Integer set to 0 for grasses and 1 for trees.

phenotype

Integer set to 0 for deciduous and 1 for evergreen.

pt

Integer indicating the type of plant according to photosynthesis: 0 for C3; 1 for C4

The following columns pertaining to the root parameters:

alpha_FR

Fine root turnover rate (yr\(^{-1}\)).

rho_FR

Material density of fine roots (kg C m\(^{-3}\)).

root_r

Radius of the fine roots, in m.

root_zeta

e-folding parameter of root vertical distribution, in m.

Kw_root

Fine root water conductivity (mol m\(^{-2}\) s\(^{-1}\) MPa\(^{-1}\)).

leaf_size

Characteristic leaf size.

The following columns pertaining to the photosynthesis parameters:

Vmax

Max RuBisCo rate, in mol m\(^{-2}\) s\(^{-1}\).

Vannual

Annual productivity per unit area at full sun (kg C m\(^{-2}\) year\(^{-2}\)).

wet_leaf_dreg

Wet leaf photosynthesis down-regulation.

m_cond

Factor of stomatal conductance.

alpha_phot

Photosynthesis efficiency.

gamma_L

Leaf respiration coefficient, in yr\(^{-1}\).

gamma_LN

Leaf respiration coefficient per unit N.

gamma_SW

Sapwood respiration rate, in kg C m\(^{-2}\) yr\(^{-1}\).

gamma_FR

Fine root respiration rate, kg C kg C\(^{-1}\) yr\(^{-1}\).

tk_crit

Critical temperature triggerng offset of phenology, in Kelvin.

tk_crit_on

Critical temperature triggerng onset of phenology, in Kelvin.

gdd_crit

Critical value of GDD5 for turning ON growth season.

betaON

Critical soil moisture for phenology onset.

betaOFF

Critical soil moisture for phenology offset.

The following columns pertaining to the allometry parameters:

alphaHT

Coefficient for allometry (height = alphaHT * DBH_m ** thetaHT), in m m\(^{-thetaHT}\).

thetaHT

Coefficient for allometry (height = alphaHT * DBH_m ** thetaHT), in m m\(^{-thetaHT}\).

alphaCA

Coefficient for allometry (projected crown area = pi * (alphaCA * DBH_m) ** thetaCA), in m\(^{2/thetaCA-1}\).

thetaCA

Coefficient for allometry (projected crown area = pi * (alphaCA * DBH_m) ** thetaCA), unitless. Dybzinski (eq. G1) showed that thetaCA = theatBM - 1.

alphaBM

Coefficient for allometry (biomass = alphaBM * DBH ** thetaBM), in kg C m\(^{-thetaBM}\).

thetaBM

Coefficient for allometry (biomass = alphaBM * DBH ** thetaBM), unitless. Dybzinski (eq. G1) showed that thetaCA = theatBM - 1.

The following columns pertaining to the reproduction parameters:

seedlingsize

Initial size of seedlings, in kg C per individual.

maturalage

Age at which trees can reproduce (years).

v_seed

Fraction of G_SF to G_F.

The following columns pertaining to the mortality parameters:

mortrate_d_c

Canopy tree mortality rate (yr\(^{-1}\)).

mortrate_d_u

Understory tree mortality rate (yr\(^{-1}\)).

The following columns pertaining to the leaf parameters:

LMA

Leaf mass per unit area (kg C m\(^{-2}\)).

leafLS

TODO

LNbase

Basal leaf N per unit area, in kg N m\(^{-2}\).

CNleafsupport

TODO

rho_wood

Wood density (kg C m\(^{-3}\)).

taperfactor

TODO

lAImax

Maximum crown LAI (leaf area index).

tauNSC

TODO

fNSmax

Multiplier for NSNmax as sum of potential bl and br.

phiCSA

Ratio of sapwood area to leaf area.

The following columns pertaining to the C/N ratios for plant pools:

CNleaf0

TODO

CNsw0

TODO

CNwood0

TODO

CNroot0

TODO

CNseed0

TODO

Nfixrate0

Reference N fixation rate (kg N kg C\(^{-1}\) root).

NfixCost0

Carbon cost of N fixation (kg C kg N\(^{-1}\)).

internal_gap_frac

TODO

The following columns pertaining to the calibratable parameters:

kphio

Quantum yield efficiency \(\varphi_0\), in mol mol\(^{-1}\).

phiRL

Ratio of fine root to leaf area.

LAI_light

Maximum LAI limited by light.

init_cohort

A data.frame of initial cohort specifications, including the following data:

init_cohort_species

Index of a species described in param_species.

init_cohort_nindivs

Initial individual density, in individuals per m\(^{2}\).

init_cohort_bl

Initial biomass of leaf, in kg C per individual.

init_cohort_br

Initial biomass of fine root, in kg C per individual.

init_cohort_bsw

Initial biomass of sapwood, in kg C per individual.

init_cohort_bHW

Initial biomass of heartwood, in kg C per individual.

init_cohort_seedC

Initial biomass of seed, in kg C per individual.

init_cohort_nsc

Initial non-structural biomass, in kg C per individual.

lu_index

Land use type this cohorts belongs to (given as index in init_lu aray). Default: 0 (attach to all LU types except thoses which do not accept vegetation – cf init_lu.vegetated).

init_soil

A data.frame of initial soil pools, including the following data:

init_fast_soil_C

Initial fast soil carbon, in kg C m\(^{-2}\).

init_slow_soil_C

Initial slow soil carbon, in kg C m\(^{-2}\).

init_Nmineral

Mineral nitrogen pool, in kg N m\(^{-2}\).

N_input

Annual nitrogen input to soil N pool, in kg N m\(^{-2}\) yr\(^{-1}\).

init_lu

A data.frame of initial land unit (LU) specifications, including the following data:

fraction

Initial grid cell fraction occupied by this LU, dimensionless (0 to 1) or m\(^{-2}\) LU area per m\(^{-2}\) grid cell area. The sum of all fractions is typically equal to 1, but may be less in which case the difference is the fraction of the grid cell occupied by ice/water.

preset

Predefined land use type (optional). One of: 'unmanaged', 'urban', 'cropland', 'pasture'. See below for meaning of these presets. Leave empty to not use any preset.

vegetated

Whether this LU accepts vegetation. Default for preset 'urban': False, default for other presets: True.

extra_N_input

Additional inorg N supply (to account for N fertiliser application), in kg m-2 yr-1. Default for preset 'cropland': 0.01, default other presets: 0.

extra_turnover_rate

Additional soil turnover rate (to account for soil management such as tillage), dimensionless. Default for preset 'cropland': 0.2, default for other presets: 0.

oxidized_litter_fraction

Fraction of above-ground turnover that is directly oxidized (crop and grass harvest), dimensionless. Default for preset 'cropland': 0.9, default for preset 'pasture': 0.4, default for other presets: 0.

luc_forcing

Array of land use change (LUC) used during transient phase. During spinup, the initial land unit fractions are used (i.e. no transition). If there are more transient years than provided LUC data, the last state is maintained until the end of the transient phase (i.e. no transition). The array is a nxn square matrix, where n is the number of LU (i.e. dimension of init_lu). Each entry f(i, j) expresses the grid cell fraction of LU i (row) being transfered to LU j (column). I.e. same units as init_lu$fraction. Self transitions are allowed, meaning that a part of the land unit is clear cut, but the area remains in the same land use.