Simulate C3 photosynthesis — photosynthesis • photosynthesis

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.

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` (\(\mu\)mol CO2 / m\(^2\) / s)	`C_chl`
chloroplastic CO2 concentration where `A_supply` intersects `A_demand` (\(mu\)mol / mol)	`C_i`
intercellular CO2 concentration where `A_supply` intersects `A_demand` (\(mu\)mol / mol)	`g_tc`
total conductance to CO2 at `T_leaf` (mol / m\(^2\) / s))	`value`
`A_supply` - `A_demand` (\(\mu\)mol / (m\(^2\) s)) at `C_chl`	`convergence`

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().

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
)
#> 
#>             
#>   As of version 2.1.0, the CO2 conductance model changed slightly. 
#>   To implement legacy version, use:
#>   
#>   `> photosynthesis(..., use_legacy_version = TRUE)`.
#> 
#> Solving for C_chl ...
#>  done
#>                 C_chl         value convergence                  g_tc
#> 1 258.1218 [umol/mol] -1.363227e-06           0 0.1726157 [mol/m^2/s]
#>                       A            J_max          J_max25              K_C
#> 1 27.94273 [umol/m^2/s] 200 [umol/m^2/s] 200 [umol/m^2/s] 268.3 [umol/mol]
#>              K_C25                 K_O               K_O25            R_d
#> 1 268.3 [umol/mol] 165084.2 [umol/mol] 165084.2 [umol/mol] 2 [umol/m^2/s]
#>            R_d25     T_leaf           V_cmax         V_cmax25            V_tpu
#> 1 2 [umol/m^2/s] 298.15 [K] 150 [umol/m^2/s] 150 [umol/m^2/s] 200 [umol/m^2/s]
#>            V_tpu25            g_mc          g_mc25            g_sc
#> 1 200 [umol/m^2/s] 0.4 [mol/m^2/s] 0.4 [mol/m^2/s] 0.4 [mol/m^2/s]
#>               g_uc         gamma_star       gamma_star25  k_mc  k_sc  k_uc
#> 1 0.01 [mol/m^2/s] 37.9258 [umol/mol] 37.9258 [umol/mol] 1 [1] 1 [1] 1 [1]
#>   leafsize     phi_J   theta_J          C_air              O              P
#> 1  0.1 [m] 0.331 [1] 0.825 [1] 420 [umol/mol] 0.21 [mol/mol] 101.3246 [kPa]
#>                PPFD      RH    wind          Ds_Jmax           Ds_gmc
#> 1 1500 [umol/m^2/s] 0.5 [1] 2 [m/s] 388.04 [J/K/mol] 487.29 [J/K/mol]
#>            Ea_Jmax            Ea_KC            Ea_KO            Ea_Rd
#> 1 56095.18 [J/mol] 80989.78 [J/mol] 23719.97 [J/mol] 40446.75 [J/mol]
#>           Ea_Vcmax          Ea_Vtpu     Ea_gammastar           Ea_gmc
#> 1 52245.78 [J/mol] 52245.78 [J/mol] 24459.97 [J/mol] 68901.56 [J/mol]
#>            Ed_Jmax           Ed_gmc             D_c0            D_h0
#> 1 121244.8 [J/mol] 148788.6 [J/mol] 1.29e-05 [m^2/s] 1.9e-05 [m^2/s]
#>               D_m0             D_w0           G                 R       eT
#> 1 1.33e-05 [m^2/s] 2.12e-05 [m^2/s] 9.8 [m/s^2] 8.31446 [J/K/mol] 1.75 [1]
#>     epsilon                sigma                 C_i
#> 1 0.622 [1] 5.67e-08 [W/K^4/m^2] 350.1432 [umol/mol]

# 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
)
#> 
#>             
#>   As of version 2.1.0, the CO2 conductance model changed slightly. 
#>   To implement legacy version, use:
#>   
#>   `> photosynthesis(..., use_legacy_version = TRUE)`.
#> Solving for photosynthetic rate from 2 parameter sets ...
#>                 C_chl         value convergence                  g_tc
#> 1 269.8118 [umol/mol] -3.407982e-06           0 0.1498162 [mol/m^2/s]
#> 2 258.1218 [umol/mol] -1.363227e-06           0 0.1726157 [mol/m^2/s]
#>                       A                 J_max          J_max25
#> 1 22.50062 [umol/m^2/s] 143.6921 [umol/m^2/s] 200 [umol/m^2/s]
#> 2 27.94273 [umol/m^2/s] 200.0000 [umol/m^2/s] 200 [umol/m^2/s]
#>                  K_C            K_C25                 K_O               K_O25
#> 1 153.505 [umol/mol] 268.3 [umol/mol] 140179.2 [umol/mol] 165084.2 [umol/mol]
#> 2 268.300 [umol/mol] 268.3 [umol/mol] 165084.2 [umol/mol] 165084.2 [umol/mol]
#>                   R_d          R_d25     T_leaf                V_cmax
#> 1 1.5133 [umol/m^2/s] 2 [umol/m^2/s] 293.14 [K] 104.6304 [umol/m^2/s]
#> 2 2.0000 [umol/m^2/s] 2 [umol/m^2/s] 298.15 [K] 150.0000 [umol/m^2/s]
#>           V_cmax25                 V_tpu          V_tpu25                  g_mc
#> 1 150 [umol/m^2/s] 139.5072 [umol/m^2/s] 200 [umol/m^2/s] 0.2844658 [mol/m^2/s]
#> 2 150 [umol/m^2/s] 200.0000 [umol/m^2/s] 200 [umol/m^2/s] 0.4000000 [mol/m^2/s]
#>            g_mc25            g_sc             g_uc          gamma_star
#> 1 0.4 [mol/m^2/s] 0.4 [mol/m^2/s] 0.01 [mol/m^2/s] 32.04034 [umol/mol]
#> 2 0.4 [mol/m^2/s] 0.4 [mol/m^2/s] 0.01 [mol/m^2/s] 37.92580 [umol/mol]
#>         gamma_star25  k_mc  k_sc  k_uc leafsize     phi_J   theta_J
#> 1 37.9258 [umol/mol] 1 [1] 1 [1] 1 [1]  0.1 [m] 0.331 [1] 0.825 [1]
#> 2 37.9258 [umol/mol] 1 [1] 1 [1] 1 [1]  0.1 [m] 0.331 [1] 0.825 [1]
#>            C_air              O              P              PPFD      RH
#> 1 420 [umol/mol] 0.21 [mol/mol] 101.3246 [kPa] 1500 [umol/m^2/s] 0.5 [1]
#> 2 420 [umol/mol] 0.21 [mol/mol] 101.3246 [kPa] 1500 [umol/m^2/s] 0.5 [1]
#>      wind          Ds_Jmax           Ds_gmc          Ea_Jmax            Ea_KC
#> 1 2 [m/s] 388.04 [J/K/mol] 487.29 [J/K/mol] 56095.18 [J/mol] 80989.78 [J/mol]
#> 2 2 [m/s] 388.04 [J/K/mol] 487.29 [J/K/mol] 56095.18 [J/mol] 80989.78 [J/mol]
#>              Ea_KO            Ea_Rd         Ea_Vcmax          Ea_Vtpu
#> 1 23719.97 [J/mol] 40446.75 [J/mol] 52245.78 [J/mol] 52245.78 [J/mol]
#> 2 23719.97 [J/mol] 40446.75 [J/mol] 52245.78 [J/mol] 52245.78 [J/mol]
#>       Ea_gammastar           Ea_gmc          Ed_Jmax           Ed_gmc
#> 1 24459.97 [J/mol] 68901.56 [J/mol] 121244.8 [J/mol] 148788.6 [J/mol]
#> 2 24459.97 [J/mol] 68901.56 [J/mol] 121244.8 [J/mol] 148788.6 [J/mol]
#>               D_c0            D_h0             D_m0             D_w0
#> 1 1.29e-05 [m^2/s] 1.9e-05 [m^2/s] 1.33e-05 [m^2/s] 2.12e-05 [m^2/s]
#> 2 1.29e-05 [m^2/s] 1.9e-05 [m^2/s] 1.33e-05 [m^2/s] 2.12e-05 [m^2/s]
#>             G                 R       eT   epsilon                sigma
#> 1 9.8 [m/s^2] 8.31446 [J/K/mol] 1.75 [1] 0.622 [1] 5.67e-08 [W/K^4/m^2]
#> 2 9.8 [m/s^2] 8.31446 [J/K/mol] 1.75 [1] 0.622 [1] 5.67e-08 [W/K^4/m^2]
#>                   C_i
#> 1 363.7484 [umol/mol]
#> 2 350.1432 [umol/mol]