##---Constant Parameter Arrays for Model---##
#I have commented out parameters that I am assuming are variable (for the time being)
s_c = np.linspace(0.019 - 0.0005, 0.019 + 0.0005,
2) #specific leaf area (m2 C/g C)
ra = np.zeros(shape=2) + 20.7 #specific rubisco activity (umol CO2/g Rub s)
nm_c = ((s_c * (100.0**2)) * 0.077 + 20.25) / 1000.0 #leaf nitrogen (g N/ g C)
flnr = np.zeros(
shape=2) + 0.65 #fraction of leaf nitrogen in rubisco (g N Rub/g N leaf)
frnr = np.zeros(
shape=2
) + 6.25 #weight fraction of nitrogen in rubisco molecule (g Rub/g N Rub)
ea_str = pa_con_atmfrac(611 * np.exp(
17.27 * t /
(t + 273.3))) #saturation vapor pressure of air (Pa-->umol h20.mol air)
rh = np.zeros(shape=2) + 0.55 #relative humidity (kPa/kPa)
ea = rh * ea_str #vapor pressure deficit (umol h2O/mol air)
ca = np.zeros(shape=2) + 410 #ambient carbon dioxide (umol CO2/mol air)
tau25 = np.zeros(
shape=2) + 2904.12 #specifity coefficient of tau at 25 C (unitless)
ko25 = np.zeros(
shape=2
) + 296100 #Michaelis-Menten kinetic coefficient for oxygen at 25 C(umol/mol)
kc25 = np.zeros(
shape=2
) + 296 #Michaelis-Menten kinetic coefficient for carbon dioxide at 25 C (umol/mol)
o = np.zeros(shape=2) + 210000 #concentration of ambient oxygen (umol/mol)
#lamb=np.zeros(shape=3)+0.0074 #marginal WUE (umol CO2/umol H2O)
b = np.zeros(
for iii in range(len(na[0])):
b_i = biotic_index[iii]
#correct for microclimate abiotic conditions
t_dm = t[0]
#correct for volumetric moisture content
vwc_dm = vwc[0]
#------calculate vapor pressure-----#
pa_v = 611 * np.exp(
(17.27 * t_dm) /
(t_dm + 237.3)) #saturation vapor pressure of air (Pa)
ea_str = pa_con_atmfrac(
pa_v, 3528
) #saturation vapor pressure of air (Pa-->umol h20/mol air)
ea = rh * ea_str #vapor pressure (umol h2O/mol air)
#correct for leaf temperatures using leaf height
t_diff = 18 - 0.4 * ht[0][iii]
tl = t_dm + t_diff
#---------------Photosynthesis Function---------------#
#alter this line of code for when implementing different photosynthesis functions
wue, nue, A, E, cs, ci, gsw, gs, gbw, gb, gm, cc, dd = photo(
tk_25, ekc, eko, etau, ev, ej, toptv, toptj, na[0][iii], qeff,
PAR, tl, ea, chl[0][iii], ij, kc25, ko25, o, ca, rh, m, a,
##---Constant Parameter Arrays for Model---##
#I have commented out parameters that I am assuming are variable (for the time being)
s_c = np.linspace(0.019 - 0.0005, 0.019 + 0.0005,
2) #specific leaf area (m2 C/g C)
ra = np.zeros(shape=2) + 20.7 #specific rubisco activity (umol CO2/g Rub s)
nm_c = ((s_c * (100.0**2)) * 0.077 + 20.25) / 1000.0 #leaf nitrogen (g N/ g C)
flnr = np.zeros(
shape=2) + 0.65 #fraction of leaf nitrogen in rubisco (g N Rub/g N leaf)
frnr = np.zeros(
shape=2
) + 6.25 #weight fraction of nitrogen in rubisco molecule (g Rub/g N Rub)
ea_str = pa_con_atmfrac(611 * np.exp(
17.27 * t /
(t + 273.3))) #saturation vapor pressure of air (Pa-->umol h20.mol air)
rh = np.zeros(shape=2) + 0.55 #relative humidity (kPa/kPa)
ea = rh * ea_str #vapor pressure deficit (umol h2O/mol air)
ca = np.zeros(shape=2) + 410 #ambient carbon dioxide (umol CO2/mol air)
tau25 = np.zeros(
shape=2) + 2904.12 #specifity coefficient of tau at 25 C (unitless)
ko25 = np.zeros(
shape=2
) + 296100 #Michaelis-Menten kinetic coefficient for oxygen at 25 C(umol/mol)
kc25 = np.zeros(
shape=2
) + 296 #Michaelis-Menten kinetic coefficient for carbon dioxide at 25 C (umol/mol)
o = np.zeros(shape=2) + 210000 #concentration of ambient oxygen (umol/mol)
#lamb=np.zeros(shape=3)+0.0074 #marginal WUE (umol CO2/umol H2O)
b = np.zeros(