\(J_{max}\) limitation

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import matplotlib.pyplot as plt
import numpy as np
from pyrealm.pmodel.pmodel import PModel
from pyrealm.pmodel import PModelEnvironment

%matplotlib inline

# Set the resolution of examples
n_pts = 201

# Create a range of representative values for key inputs.
tc_1d = np.linspace(-25, 50, n_pts)

Environmental conditions can also lead to limitation of both the electron transfer rate (\(J_{max}\)) and the carboxylation capacity (\(V_{cmax}\)) of leaves. The jmax_limitation module implements three alternative approaches to the calculation of \(J_{max}\) and \(V_{cmax}\) and these are specified when fitting a P Model using the argument method_jmaxlim.

These options implement alternative calculations of two factor (\(f_j\) and \(f_v\)) which are applied to the calculation of \(J_{max}\) and \(V_{cmax}\). The options for this setting are:

• none: This approach implements \(f_j = f_v = 1\) and hence no limitation.

• wang17: This is the default setting for method_jmaxlim and applies the calculations describe in Wang et al. (2017). The calculation details can be seen in the JmaxLimitationWang17 method.

• smith19: This is an alternate calculation for optimal values of \(J_{max}\) and \(V_{cmax}\) described in Smith et al. (2019). The calculation details can be seen in the JmaxLimitationSmith19 method.

The plot below shows the effects of each method on the light use efficienct across a temperature gradient. The other forcing variables are fixed (\(P=101325.0 , \ce{CO2}= 400 \text{ppm}, \text{VPD}=820\)) and \(\phi_0\) is also fixed (\(\phi_0=0.08\)).

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# Calculate variation in m_jlim with temperature - no estimation of GPP needed
# so set fapar and ppfd to unity
env = PModelEnvironment(tc=tc_1d, patm=101325, vpd=820, co2=400, fapar=1, ppfd=1)

model_jmax_simple = PModel(
    env, method_jmaxlim="none", method_kphio="fixed", reference_kphio=0.08
)
model_jmax_wang17 = PModel(
    env, method_jmaxlim="wang17", method_kphio="fixed", reference_kphio=0.08
)
model_jmax_smith19 = PModel(
    env, method_jmaxlim="smith19", method_kphio="fixed", reference_kphio=0.08
)

# Create a line plot of the resulting values of m_j
plt.plot(tc_1d, model_jmax_simple.lue, label="simple")
plt.plot(tc_1d, model_jmax_wang17.lue, label="wang17")
plt.plot(tc_1d, model_jmax_smith19.lue, label="smith19")

plt.title("Effects of J_max limitation")
plt.xlabel("Temperature °C")
plt.ylabel("Light Use Efficiency (g C mol-1)")
plt.legend()
plt.show()

/home/docs/checkouts/readthedocs.org/user_builds/pyrealm/checkouts/latest/pyrealm/pmodel/pmodel.py:481: UserWarning: 
    Pyrealm 2.0.0 uses a new default for the quantum yield of photosynthesis (phi0=1/8).
    You may need to change settings to duplicate results from pyrealm 1.0.0.
            
  warn(