photosynthesis: Simulate C3 photosynthesis

In photosynthesis: Tools for Plant Ecophysiology & Modeling

Simulate C3 photosynthesis

Description

photosynthesis: simulate C3 photosynthesis over multiple parameter sets

photo: simulate C3 photosynthesis over a single parameter set

Usage

photosynthesis(
  leaf_par,
  enviro_par,
  bake_par,
  constants,
  use_tealeaves,
  progress = TRUE,
  quiet = FALSE,
  assert_units = TRUE,
  check = TRUE,
  parallel = FALSE,
  use_legacy_version = FALSE
)

photo(
  leaf_par,
  enviro_par,
  bake_par,
  constants,
  use_tealeaves,
  quiet = FALSE,
  assert_units = TRUE,
  check = TRUE,
  prepare_for_tleaf = use_tealeaves,
  use_legacy_version = FALSE
)

Arguments

leaf_par	A list of leaf parameters inheriting class leaf_par. This can be generated using the make_leafpar function.
enviro_par	A list of environmental parameters inheriting class enviro_par. This can be generated using the make_enviropar function.
bake_par	A list of temperature response parameters inheriting class bake_par. This can be generated using the make_bakepar function.
constants	A list of physical constants inheriting class constants. This can be generated using the make_constants function.
use_tealeaves	Logical. Should leaf energy balance be used to calculate leaf temperature (T_leaf)? If TRUE, tleaf() calculates T_leaf. If FALSE, user-defined T_leaf is used. Additional parameters and constants are required, see make_parameters().
progress	Logical. Should a progress bar be displayed?
quiet	Logical. Should messages be displayed?
assert_units	Logical. Should parameter units be checked? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.
check	Logical. Should arguments checks be done? This is intended to be disabled when photo() is called from photosynthesis() Default is TRUE.
parallel	Logical. Should parallel processing be used via furrr::future_map()?
use_legacy_version	Logical. Should legacy model (<2.1.0) be used? See NEWS for further information. Default is FALSE.
prepare_for_tleaf	Logical. Should arguments additional calculations for tleaf()? This is intended to be disabled when photo() is called from photosynthesis(). Default is use_tealeaves.

Details

photo: This function takes simulates photosynthetic rate using the Farquhar-von Caemmerer-Berry (FvCB()) model of C3 photosynthesis for single combined set of leaf parameters (leaf_par()), environmental parameters (enviro_par()), and physical constants (constants()). Leaf parameters are provided at reference temperature (25 °C) and then "baked" to the appropriate leaf temperature using temperature response functions (see bake()).

photosynthesis: This function uses photo to simulate photosynthesis over multiple parameter sets that are generated using cross_df().

Value

A data.frame with the following units columns

Inputs:

Symbol	R	Description	Units	Default
D_{\mathrm{c},0}	D_c0	diffusion coefficient for CO2 in air at 0 °C	m^2 / s	1.29\times 10^{-5}
D_{\mathrm{h},0}	D_h0	diffusion coefficient for heat in air at 0 °C	m^2 / s	1.90\times 10^{-5}
D_{\mathrm{m},0}	D_m0	diffusion coefficient for momentum in air at 0 °C	m^2 / s	1.33\times 10^{-5}
D_{\mathrm{w},0}	D_w0	diffusion coefficient for water vapor in air at 0 °C	m^2 / s	2.12\times 10^{-5}
\epsilon	epsilon	ratio of water to air molar masses	none	0.622
G	G	gravitational acceleration	m / s^2	9.8
eT	eT	exponent for temperature dependence of diffusion	none	1.75
R	R	ideal gas constant	J / mol / K	8.31
\sigma	sigma	Stephan-Boltzmann constant	W / m^2 / K^4	5.67\times 10^{-8}
f_\mathrm{Sh}	f_sh	function to calculate constant(s) for Sherwood number	none	NA
f_\mathrm{Nu}	f_nu	function to calculate constant(s) for Nusselt number	none	NA
D_\mathrm{s,gmc}	Ds_gmc	empirical temperature response parameter	J / mol / K	487
D_\mathrm{s,Jmax}	Ds_Jmax	empirical temperature response parameter	J / mol / K	388
E_\mathrm{a,\Gamma *}	Ea_gammastar	empirical temperature response parameter	J / mol	24500
E_\mathrm{a,gmc}	Ea_gmc	empirical temperature response parameter	J / mol	68900
E_\mathrm{a,Jmax}	Ea_Jmax	empirical temperature response parameter	J / mol	56100
E_\mathrm{a,KC}	Ea_KC	empirical temperature response parameter	J / mol	81000
E_\mathrm{a,KO}	Ea_KO	empirical temperature response parameter	J / mol	23700
E_\mathrm{a,Rd}	Ea_Rd	empirical temperature response parameter	J / mol	40400
E_\mathrm{a,Vcmax}	Ea_Vcmax	empirical temperature response parameter	J / mol	52200
E_\mathrm{a,Vtpu}	Ea_Vtpu	empirical temperature response parameter	J / mol	52200
E_\mathrm{d,gmc}	Ed_gmc	empirical temperature response parameter	J / mol	149000
E_\mathrm{d,Jmax}	Ed_Jmax	empirical temperature response parameter	J / mol	121000
C_\mathrm{air}	C_air	atmospheric CO2 concentration	umol/mol	420
O	O	atmospheric O2 concentration	mol/mol	0.21
P	P	atmospheric pressure	kPa	101
\mathrm{PPFD}	PPFD	photosynthetic photon flux density	umol / m^2 / s	1500
\mathrm{RH}	RH	relative humidity	none	0.5
u	wind	windspeed	m / s	2
d	leafsize	leaf characteristic dimension	m	0.1
\Gamma*_{25}	gamma_star25	chloroplastic CO2 compensation point (25 °C)	umol/mol	37.9
g_\mathrm{mc,25}	g_mc25	mesophyll conductance to CO2 (25 °C)	mol / m^2 / s	0.4
g_\mathrm{sc}	g_sc	stomatal conductance to CO2	mol / m^2 / s	0.4
g_\mathrm{uc}	g_uc	cuticular conductance to CO2	mol / m^2 / s	0.01
J_\mathrm{max,25}	J_max25	potential electron transport (25 °C)	umol / m^2 / s	200
k_\mathrm{mc}	k_mc	partition of g_mc to lower mesophyll	none	1
k_\mathrm{sc}	k_sc	partition of g_sc to lower surface	none	1
k_\mathrm{uc}	k_uc	partition of g_uc to lower surface	none	1
K_\mathrm{C,25}	K_C25	Michaelis constant for carboxylation (25 °C)	umol / mol	268
K_\mathrm{O,25}	K_O25	Michaelis constant for oxygenation (25 °C)	umol / mol	165000
\phi_J	phi_J	initial slope of the response of J to PPFD	none	0.331
R_\mathrm{d,25}	R_d25	nonphotorespiratory CO2 release (25 °C)	umol / m^2 / s	2
\theta_J	theta_J	curvature factor for light-response curve	none	0.825
T_\mathrm{leaf}	T_leaf	leaf temperature	K	298
V_\mathrm{c,max,25}	V_cmax25	maximum rate of carboxylation (25 °C)	umol / m^2 / s	150
V_\mathrm{tpu,25}	V_tpu25	rate of triose phosphate utilization (25 °C)	umol / m^2 / s	200
\delta_\mathrm{ias,lower}	delta_ias_lower	effective distance through lower internal airspace	um	NA
\delta_\mathrm{ias,upper}	delta_ias_upper	effective distance through upper internal airspace	um	NA
A_\mathrm{mes} / A	A_mes_A	mesophyll surface area per unit leaf area	none	NA
g_\mathrm{liq,c,25}	g_liqc25	liquid-phase conductance to CO2 (25 °C)	mol / m^2 / s	NA
Baked Inputs:
Symbol	R	Description	Units	Default
:----------------------------	:-------------------	:-------------------------------------------------------------------	:--------------------	:-------
\Gamma*	gamma_star	chloroplastic CO2 compensation point (T_leaf)	umol/mol	NA
g_\mathrm{mc}	g_mc	mesophyll conductance to CO2 (T_leaf)	mol / m^2 / s	NA
J_\mathrm{max}	J_max	potential electron transport (T_leaf)	umol / m^2 / s	NA
K_\mathrm{C}	K_C	Michaelis constant for carboxylation (T_leaf)	umol / mol	NA
K_\mathrm{O}	K_O	Michaelis constant for oxygenation (T_leaf)	umol / mol	NA
R_\mathrm{d}	R_d	nonphotorespiratory CO2 release (T_leaf)	umol / m^2 / s	NA
V_\mathrm{c,max}	V_cmax	maximum rate of carboxylation (T_leaf)	umol / m^2 / s	NA
V_\mathrm{tpu}	V_tpu	rate of triose phosphate utilisation (T_leaf)	umol / m^2 / s	NA
g_\mathrm{liq,c}	g_liqc	liquid-phase conductance to CO2 (T_leaf)	mol / m^2 / s	NA
g_\mathrm{ias,c,lower}	g_iasc_lower	internal airspace conductance to CO2 in lower part of leaf (T_leaf)	mol / m^2 / s	NA
g_\mathrm{ias,c,upper}	g_iasc_upper	internal airspace conductance to CO2 in upper part of leaf (T_leaf)	mol / m^2 / s	NA

Output:
A	photosynthetic rate at C_chl (\mumol CO2 / m^2 / s)
C_chl	chloroplastic CO2 concentration where A_supply intersects A_demand (mumol / mol)
C_i	intercellular CO2 concentration where A_supply intersects A_demand (mumol / mol)
g_tc	total conductance to CO2 at T_leaf (mol / m^2 / s))
value	A_supply - A_demand (\mumol / (m^2 s)) at C_chl
convergence	convergence code (0 = converged)

Examples

# Single parameter set with 'photo'

bake_par = make_bakepar()
constants = make_constants(use_tealeaves = FALSE)
enviro_par = make_enviropar(use_tealeaves = FALSE)
leaf_par = make_leafpar(use_tealeaves = FALSE)
photo(leaf_par, enviro_par, bake_par, constants,
  use_tealeaves = FALSE
)

# Multiple parameter sets with 'photosynthesis'

leaf_par = make_leafpar(
  replace = list(
    T_leaf = set_units(c(293.14, 298.15), "K")
  ), use_tealeaves = FALSE
)
photosynthesis(leaf_par, enviro_par, bake_par, constants,
  use_tealeaves = FALSE
)

photosynthesis documentation built on Aug. 15, 2023, 9:08 a.m.