--- MITgcm_contrib/darwin2/pkg/monod/MONOD.h	2011/04/13 18:56:25	1.1
+++ MITgcm_contrib/darwin2/pkg/monod/MONOD.h	2014/05/01 16:19:32	1.7
@@ -1,4 +1,4 @@
-C $Header: /home/ubuntu/mnt/e9_copy/MITgcm_contrib/darwin2/pkg/monod/MONOD.h,v 1.1 2011/04/13 18:56:25 jahn Exp $
+C $Header: /home/ubuntu/mnt/e9_copy/MITgcm_contrib/darwin2/pkg/monod/MONOD.h,v 1.7 2014/05/01 16:19:32 jahn Exp $
 C $Name:  $
 
 c MONOD.h
@@ -17,6 +17,7 @@
 c ksatlight = half sat coeff wrt light, phyto specific 
 c graze = grazing rate, phyto specific for each zooplankton
 c mortzoo = mortality rate for each zooplankton
+c mortzoo2 = quadratic mortality rate for each zooplankton
 c wsink = sinking speed, phyto specific
 c R_XY = stoichiometric ratios of nutrients in phytoplankton
 c        specific to each functional group, relative to Phos
@@ -35,6 +36,9 @@
          COMMON/darwin_ecoparam/mu,ksatPO4,ksatNO3,ksatNO2,ksatNH4,
      &          ksatSi,ksatFeT,ksatPAR,
      &          mortzoo,wsink,R_NP,R_FeP,R_SiP,R_PC,R_PICPOC, physize,
+#ifdef FIX_ZOO_QUOTAS
+     &          R_NP_zoo,R_FeP_zoo,R_SiP_zoo,R_PC_zoo,
+#endif
      &          diacoc,diazotroph,zoosize,ExportFracZ,
      &          Kpremin_P, Kpremin_N, Kpremin_Fe, Kpremin_Si,
      &          sig1,sig2,sig3,
@@ -43,6 +47,7 @@
      &          zooTempCoeff, zooTempExp, zooTempOptimum, kinhib,
      &          diatomgraz, coccograz, olargegraz,
      &          mortphy, ExportFracP,
+     &          mortzoo2,
      &          Smallgrow, Biggrow, Smallmort, Bigmort,
      &          Smallgrowrange, Biggrowrange, Smallmortrange, 
      &          Bigmortrange,
@@ -58,7 +63,7 @@
      &          SmallPsatrange, BigPsatrange, ProcPsatrange,
      &          prochlPsat,
      &          UniDzPsat, UniDzPsatrange, 
-     &          depthdenit, o2crit, denit_np,
+     &          depthdenit, o2crit, denit_np, denit_no3, no3crit,
 #ifdef OLD_GRAZE
      &          graze,
      &          kgrazesat,
@@ -72,11 +77,16 @@
      &          phygrazmin,
      &          ExportFracGraz,
      &          ExGrazfracbig, ExGrazfracsmall,
+     &          hollexp,
 #endif
      &          ZoomortSmall, ZoomortBig, ZooexfacSmall, ZooexfacBig,
+     &          ZoomortSmall2, ZoomortBig2,
      &          val_R_SiP_diatom, val_R_NP_diaz, val_RFeP_diaz,
      &          val_R_NP, val_RFeP, val_R_PC,
      &          val_R_PICPOC,
+#ifdef FIX_ZOO_QUOTAS
+     &          val_R_NP_zoo, val_RFeP_zoo, val_R_SiP_zoo, val_R_PC_zoo,
+#endif
      &          ksatNH4fac, ksatNO2fac, val_ksatsi,
      &          ngrowfac, ilight,
      &          phymin, PAR0, diaz_growfac,
@@ -88,6 +98,11 @@
 #ifdef PART_SCAV
      &         ,scav_rat, scav_inter, scav_exp
 #endif
+#ifdef ALLOW_CDOM
+     &         , fraccdom, cdomdegrd, cdombleach, PARcdom
+     &         , rnp_cdom, rfep_cdom, rcp_cdom
+     &         , cdomcoeff
+#endif
      &         ,nsource,ngroups
     
          _RL mu(npmax)
@@ -99,12 +114,19 @@
          _RL ksatFeT(npmax)
          _RL ksatPAR(npmax)
          _RL mortzoo(nzmax)
+         _RL mortzoo2(nzmax)
          _RL wsink(npmax)
          _RL R_NP(npmax)
          _RL R_FeP(npmax)
          _RL R_SiP(npmax)
          _RL R_PC(npmax)
          _RL R_PICPOC(npmax)
+#ifdef FIX_ZOO_QUOTAS
+         _RL R_NP_zoo(nzmax)
+         _RL R_FeP_zoo(nzmax)
+         _RL R_SiP_zoo(nzmax)
+         _RL R_PC_zoo(nzmax)
+#endif
          _RL physize(npmax)
          _RL diacoc(npmax)
          _RL diazotroph(npmax)
@@ -144,7 +166,8 @@
          _RL UniDzPsat, UniDzPsatrange
          _RL depthdenit
          _RL o2crit
-         _RL denit_np
+         _RL denit_np, denit_no3
+         _RL no3crit
          _RL ksatNH4fac, ksatNO2fac
          _RL sig1,sig2,sig3
          _RL val_ksatsi
@@ -163,10 +186,15 @@
          _RL phygrazmin
          _RL ExportFracGraz(nzmax)
          _RL ExGrazfracbig, ExGrazfracsmall
+         _RL hollexp
 #endif
          _RL ZoomortSmall, ZoomortBig, ZooexfacSmall, ZooexfacBig
+         _RL ZoomortSmall2, ZoomortBig2
          _RL val_R_SiP_diatom, val_R_NP_diaz, val_RFeP_diaz,
      &          val_R_NP, val_RFeP, val_R_PC, val_R_PICPOC
+#ifdef FIX_ZOO_QUOTAS
+         _RL val_R_SiP_zoo, val_R_NP_zoo, val_RFeP_zoo, val_R_PC_zoo
+#endif
          _RL ngrowfac,ilight
          _RL phymin
          _RL PAR0
@@ -180,7 +208,11 @@
 #ifdef PART_SCAV
          _RL scav_rat, scav_inter, scav_exp
 #endif
-
+#ifdef ALLOW_CDOM
+         _RL fraccdom, cdomdegrd, cdombleach, PARcdom
+         _RL rnp_cdom, rfep_cdom, rcp_cdom
+         _RL cdomcoeff
+#endif
          INTEGER nsource(npmax)
          INTEGER ngroups
 
@@ -214,11 +246,11 @@
          COMMON/darwin_diags_param/
      &          diver_thresh0, diver_thresh1,
      &          diver_thresh2, diver_thresh3,
-     &          diver_thresh4
+     &          diver_thresh4, shannon_thresh
 
          _RL diver_thresh0, diver_thresh1
          _RL diver_thresh2, diver_thresh3
-         _RL diver_thresh4
+         _RL diver_thresh4, shannon_thresh
 
 #ifdef GEIDER
 c ANNA geider by mQyield instead of alpha