make_parameters: Make lists of parameters for 'photosynthesis'

In cdmuir/photosynthesis: Tools for Plant Ecophysiology & Modeling

Make lists of parameters for photosynthesis

Description

Make lists of parameters for photosynthesis

make_leafpar

make_enviropar

make_bakepar

make_constants

Usage

make_leafpar(replace = NULL, use_tealeaves)

make_enviropar(replace = NULL, use_tealeaves)

make_bakepar(replace = NULL)

make_constants(replace = NULL, use_tealeaves)

Arguments

replace	A named list of parameters to replace defaults. If NULL, defaults will be used.
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().

Details

Constants:

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

Baking (i.e. temperature response) parameters:

Symbol	R	Description	Units	Default
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

Environment parameters:

Symbol	R	Description	Units	Default
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

Leaf parameters:

Symbol	R	Description	Units	Default
d	leafsize	leaf characteristic dimension	m	0.1
\Gamma*	gamma_star	chloroplastic CO2 compensation point (T_leaf)	umol/mol	NA
\Gamma*_{25}	gamma_star25	chloroplastic CO2 compensation point (25 °C)	umol/mol	37.9
g_\mathrm{mc}	g_mc	mesophyll conductance to CO2 (T_leaf)	mol / m^2 / s	NA
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
J_\mathrm{max}	J_max	potential electron transport (T_leaf)	umol / m^2 / s	NA
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{C}	K_C	Michaelis constant for carboxylation (T_leaf)	umol / mol	NA
K_\mathrm{O,25}	K_O25	Michaelis constant for oxygenation (25 °C)	umol / mol	165000
K_\mathrm{O}	K_O	Michaelis constant for oxygenation (T_leaf)	umol / mol	NA
\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
R_\mathrm{d}	R_d	nonphotorespiratory CO2 release (T_leaf)	umol / m^2 / s	NA
\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{c,max}	V_cmax	maximum rate of carboxylation (T_leaf)	umol / m^2 / s	NA
V_\mathrm{tpu,25}	V_tpu25	rate of triose phosphate utilization (25 °C)	umol / m^2 / s	200
V_\mathrm{tpu}	V_tpu	rate of triose phosphate utilisation (T_leaf)	umol / m^2 / s	NA

If use_tealeaves = TRUE, additional parameters are:

Constants:

Symbol	R	Description	Units	Default
c_p	c_p	heat capacity of air	J / g / K	1.01
R_\mathrm{air}	R_air	specific gas constant for dry air	J / kg / K	287

Baking (i.e. temperature response) parameters:

Symbol	R	Description	Units	Default

Environment parameters:

Symbol	R	Description	Units	Default
E_q	E_q	energy per mole quanta	kJ / mol	220
f_\mathrm{PAR}	f_par	fraction of incoming shortwave radiation that is photosynthetically active radiation (PAR)	none	0.5
r	r	reflectance for shortwave irradiance (albedo)	none	0.2
T_\mathrm{air}	T_air	air temperature	K	298
T_\mathrm{sky}	T_sky	sky temperature	K	NA

Leaf parameters:

Symbol	R	Description	Units	Default
\alpha_\mathrm{l}	abs_l	absorbtivity of longwave radiation (4 - 80 um)	none	0.97
\alpha_\mathrm{s}	abs_s	absorbtivity of shortwave radiation (0.3 - 4 um)	none	0.5
g_\mathrm{sw}	g_sw	stomatal conductance to H2O	mol / m^2 / s	NA
g_\mathrm{uw}	g_uw	cuticular conductance to H2O	mol / m^2 / s	NA
\mathrm{logit}(sr)	logit_sr	stomatal ratio (logit transformed)	none	NA

Optional leaf parameters:

Symbol	R	Description	Units	Default
\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
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

Value

make_leafpar: An object inheriting from class leaf_par()
make_enviropar: An object inheriting from class enviro_par()
make_bakepar: An object inheriting from class bake_par()
make_constants: An object inheriting from class constants()

References

Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.

Examples

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

leaf_par = make_leafpar(
  replace = list(
    g_sc = set_units(0.3, mol / m^2 / s),
    V_cmax25 = set_units(100, umol / m^2 / s)
  ), use_tealeaves = FALSE
)

cdmuir/photosynthesis documentation built on April 11, 2025, 3:28 p.m.