scopeinpython.biochemical

Leaf-level Farquhar/Collatz photosynthesis + van der Tol et al. (2014) fluorescence yield, given an assumed leaf micro-environment. Direct port of SCOPEinR/R/biochemical.R (get.biochemical) and its helpers in Biochemical_functions.R. This is the piece SCOPE’s (unported) energy- balance iteration calls repeatedly to get eta at each candidate leaf temperature – it does not itself solve for temperature.

Warning

Type='C4' with temp_correction=False reproduces a real crash in the R source: Vcmax/Rd are never assigned in that branch combination of biochemical.R (only the tempcor==1 C4 branch and a separate C3-only block set them). Not worked around here.

Leaf biochemistry: Farquhar-von Caemmerer-Berry photosynthesis (Collatz C4 variant) coupled with a Ball-Berry/Leuning stomatal-conductance model and the van der Tol et al. (2014) fluorescence yield model.

Direct port of SCOPEinR/R/biochemical.R (get.biochemical) and its helpers in SCOPEinR/R/Biochemical_functions.R. This is the leaf-level photosynthesis+fluorescence solver called inside SCOPE’s energy-balance iteration (ebal.R, not ported) to get A/rcw/eta at a given leaf temperature – it does not itself iterate on temperature, so it can be called and verified standalone given an assumed leaf micro-environment (matching how the R function itself works: data.meteo$Temp is an input, not something this function solves for).

Only the tempcor=1 (temperature-corrected) C3 path and the BallBerry0 != 0 (iterative Ci) path are ported in full generality here; the BallBerry0 == 0 closed-form Ci path and the C4/no-temperature- correction paths are ported too but exercised less by the reference tests – see python/README.md.

class scopeinpython.biochemical.LeafBio(Type, stressfactor, Vcmax25, BallBerry0, BallBerrySlope, Rdparam, Kn0, Knalpha, Knbeta, g_m=None, TDP=<factory>)[source]

Bases: object

Leaf biochemical parameters (data.leafbio in R).

Parameters:

  • Type (str)

  • stressfactor (float)

  • Vcmax25 (float)

  • BallBerry0 (float)

  • BallBerrySlope (float)

  • Rdparam (float)

  • Kn0 (float)

  • Knalpha (float)

  • Knbeta (float)

  • g_m (float | None)

  • TDP (dict)

Type: str
stressfactor: float
Vcmax25: float
BallBerry0: float
BallBerrySlope: float
Rdparam: float
Kn0: float
Knalpha: float
Knbeta: float
g_m: float | None = None
TDP: dict
class scopeinpython.biochemical.MeteoLeaf(Q, Cs, Temp, eb, Oa, p)[source]

Bases: object

Leaf micro-environment (data.meteo in R).

Parameters:

  • Q (float)

  • Cs (float)

  • Temp (float)

  • eb (float)

  • Oa (float)

  • p (float)

Q: float
Cs: float
Temp: float
eb: float
Oa: float
p: float
class scopeinpython.biochemical.BiochemResult(A: 'np.ndarray', Ci: 'np.ndarray', Cc: 'np.ndarray | None', rcw: 'np.ndarray', gs: 'np.ndarray', RH: 'np.ndarray', Vcmax: 'np.ndarray', Rd: 'np.ndarray', Ja: 'np.ndarray', ps: 'np.ndarray', ps_rel: 'np.ndarray', Kd: 'np.ndarray', Kn: 'np.ndarray', NPQ: 'np.ndarray', Kf: 'float', Kp0: 'float', Kp: 'np.ndarray', eta: 'np.ndarray', qE: 'np.ndarray', fs: 'np.ndarray', SIF: 'np.ndarray', fo0: 'np.ndarray', fm0: 'np.ndarray', fo: 'np.ndarray', fm: 'np.ndarray', qQ: 'np.ndarray', Phi_N: 'np.ndarray')[source]

Bases: object

Parameters:
A: ndarray
Ci: ndarray
Cc: ndarray | None
rcw: ndarray
gs: ndarray
RH: ndarray
Vcmax: ndarray
Rd: ndarray
Ja: ndarray
ps: ndarray
ps_rel: ndarray
Kd: ndarray
Kn: ndarray
NPQ: ndarray
Kf: float
Kp0: float
Kp: ndarray
eta: ndarray
qE: ndarray
fs: ndarray
SIF: ndarray
fo0: ndarray
fm0: ndarray
fo: ndarray
fm: ndarray
qQ: ndarray
Phi_N: ndarray
scopeinpython.biochemical.sel_root(a, b, c, dsign)[source]

Root of least magnitude of a*x^2 + b*x + c = 0. Direct port of SCOPEinR::sel_root. dsign: -1/0 picks the smaller root, +1 the larger (per quadratic-formula sign convention on the discriminant).

scopeinpython.biochemical.get_gs_fun(Cs, RH, A, BallBerrySlope, BallBerry0)[source]

Ball-Berry stomatal conductance. Direct port of SCOPEinR::get.gsFun.

scopeinpython.biochemical.get_ball_berry(Cs, RH, A, BallBerrySlope, BallBerry0, minCi, Ci_input=None)[source]

Ball-Berry/Leuning Ci and (optionally) gs. Direct port of SCOPEinR::get.BallBerry. Returns (gs, Ci) (gs is None when not computable, matching R’s NULL).

scopeinpython.biochemical.get_temperature_function_c3(Tref, R, Temp, deltaHa)[source]

Arrhenius temperature correction factor. Direct port of SCOPEinR::get.temperature.functionC3.

scopeinpython.biochemical.get_high_temp_inhibtion_c3(Tref, R, T, deltaS, deltaHd)[source]

High-temperature inhibition factor. Direct port of SCOPEinR::get.high.temp.inhibtionC3.

scopeinpython.biochemical.get_fluorescence_model(ps, x, Kp, Kf, Kd, Knparams)[source]

van der Tol et al. (2014) fluorescence-yield model. Direct port of SCOPEinR::get.Fluorescence.model. Returns a dict with eta, qE, qQ, fs, fo, fm, fo0, fm0, Kn.

scopeinpython.biochemical.get_ci_next(Ci_in, Cs, RH, minCi, BallBerrySlope, BallBerry0, A_fun, ppm2bar)[source]

Ci fixed-point residual (Ball-Berry Ci minus guessed Ci_in), used as the objective for the Brent root-finder in get_biochemical(). Direct port of SCOPEinR::get.Ci.next.

scopeinpython.biochemical.get_compute_a(Ci, Type, g_m, Vs_C3, MM_consts, Rd, Vcmax, Gamma_star, Je, effcon, atheta, kpepcase)[source]

Farquhar (C3) / Collatz (C4) net CO2 assimilation. Direct port of SCOPEinR::get.computeA. Returns a dict with A, Ag, Vc, Vs, Ve, CO2_per_electron (fcount – a debug iteration counter via R’s <<- – is not reproduced; it has no effect on the physics).

scopeinpython.biochemical.get_biochemical(leafbio, meteo, temp_correction, fV=1.0)[source]

Leaf-level photosynthesis (Farquhar/Collatz) + fluorescence yield (van der Tol et al. 2014). Direct port of SCOPEinR::get.biochemical.

Parameters:

  • leafbio (LeafBio)

  • meteo (MeteoLeaf)

  • temp_correction (bool) – Whether to apply temperature correction to Vcmax/Rd/Kc/Ko/Gamma_star (matches R’s data.opts row-7 tempcor flag). If True, leafbio.TDP must contain the relevant temperature-dependence parameters (C3: delHaV/delSV/delHdV/delHaR/delSR/ delHdR/delHaKc/delHaKo/delHaT; C4: Q10/s1-s6).

  • fV (float, default 1.0) – Scaling factor on Vcmax25 (e.g. a canopy N/Vcmax profile factor).

Return type:

BiochemResult