more work on photosynthesis; needs cleanup

src/CanopyFluxes.cc

@@ -16,6 +16,8 @@ ComputeFlux()
 #include "landtype.h"
 #include "frictionvelocity.h"
 #include "SoilMoistStress.hh"
+#include "photosynthesis.h"
+#include "vegproperties.h"
 
 
 class CanopyFluxes {
@@ -457,6 +459,17 @@ void StabilityIteration(
   const double& htop,
   const double t_soisno[nlevgrnd+nlevsno],
 
+  const VegProperties& veg,
+  const int& nrad,
+  const double& t10,
+  const double tlai_z[nlevcan],
+  const double& vcmaxcintsha,
+  const double& vcmaxcintsun,
+  const double parsha_z[nlevcan],
+  const double parsun_z[nlevcan],
+  const double laisha_z[nlevcan],
+  const double laisun_z[nlevcan],
+
 
 
   double& btran,
@@ -533,6 +546,8 @@ void StabilityIteration(
 
       // call photosynthesis
       // Photosynthesis(phase=sun); need to implement
+      Photosynthesis(veg, Land.vtype, nrad, forc_pbot, t_veg, t10, svpts, eah, o2, co2, rb, btran, 
+        dayl_factor, thm, tlai_z, vcmaxcintsun, parsun_z, laisun_z, rssun);
 
       if (Land.vtype == nsoybean || Land.vtype == nsoybeanirrig) { btran = std::min(1.0, btran * 1.25); }
 

src/photosynthesis.h

+#ifndef PHOTOSYNTHESIS_H_
+#define PHOTOSYNTHESIS_H_
+#include "clm_constants.h"
+#include "vegproperties.h"
+
+void Photosynthesis(const VegProperties& veg, const int& vtype, const int& nrad, const double& forc_pbot, 
+  const double& t_veg, const double& t10, const double& esat_tv, const double& eair, const double& oair, 
+  const double& cair, const double& rb, const double& btran, const double& dayl_factor, const double thm, 
+  const double tlai_z[nlevcan], const double& vcmaxcint, const double par_z[nlevcan], const double lai_z[nlevcan],
+  double& rs);
+
+#endif
\ No newline at end of file

src/vegproperties.h

+#ifndef VEGPROPERTIES_H_
+#define VEGPROPERTIES_H_
+#include "clm_constants.h"
+
+struct VegProperties {
+double fnr[numpft];  //      fraction of nitrogen in RuBisCO
+double act25[numpft];  //    (umol/mgRubisco/min) Rubisco activity at 25 C 
+double kcha[numpft];  //     Activation energy for kc
+double koha[numpft];  //     Activation energy for ko
+double cpha[numpft];  //     Activation energy for cp
+double vcmaxha[numpft];  //  Activation energy for vcmax
+double jmaxha[numpft];  //   Activation energy for jmax
+double tpuha[numpft];  //    Activation energy for tpu
+double lmrha[numpft];  //    Acitivation energy for lmr
+double vcmaxhd[numpft];  //  Deactivation energy for vcmax
+double jmaxhd[numpft];  //   Deactivation energy for jmax
+double tpuhd[numpft];  //    Deactivation energy for tpu
+double lmrhd[numpft];  //    Deacitivation energy for lmr
+double lmrse[numpft];  //    SE for lmr
+double qe[numpft];  //       Quantum efficiency
+double theta_cj[numpft];  // empirical curvature parameter for ac, aj photosynthesis co-limitation
+double bbbopt[numpft];  //   Ball-Berry stomatal conductance intercept
+double mbbopt[numpft];  //   Ball-Berry stomatal conductance slope
+double c3psn[numpft];  //    photosynthetic pathway: 0. = c4, 1. = c3
+double slatop[numpft];  //   specific leaf area at top of canopy, projected area basis [m^2/gC]
+double leafcn[numpft];  //   leaf C:N (gC/gN)
+double flnr[numpft];  //     fraction of leaf N in the Rubisco enzyme (gN Rubisco / gN leaf)
+double fnitr[numpft];  //    foliage nitrogen limitation factor (-)
+
+};
+
+#endif
\ No newline at end of file