--- MITgcm_contrib/darwin2/pkg/monod/MONOD.h	2011/04/13 18:56:25	1.1
+++ MITgcm_contrib/darwin2/pkg/monod/MONOD.h	2012/05/31 21:08:25	1.5
@@ -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 1.5 2012/05/31 21:08:25 stephd 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
@@ -43,6 +44,7 @@
      &          zooTempCoeff, zooTempExp, zooTempOptimum, kinhib,
      &          diatomgraz, coccograz, olargegraz,
      &          mortphy, ExportFracP,
+     &          mortzoo2,
      &          Smallgrow, Biggrow, Smallmort, Bigmort,
      &          Smallgrowrange, Biggrowrange, Smallmortrange, 
      &          Bigmortrange,
@@ -72,8 +74,10 @@
      &          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,
@@ -88,6 +92,11 @@
 #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)
@@ -99,6 +108,7 @@
          _RL ksatFeT(npmax)
          _RL ksatPAR(npmax)
          _RL mortzoo(nzmax)
+         _RL mortzoo2(nzmax)
          _RL wsink(npmax)
          _RL R_NP(npmax)
          _RL R_FeP(npmax)
@@ -163,8 +173,10 @@
          _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
          _RL ngrowfac,ilight
@@ -180,7 +192,11 @@
 #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 +230,11 @@
          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