Merge branch 'master' into ihop

doc/tag-index

@@ -1,6 +1,16 @@
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/bling:
+  - size-dependent phytoplankton growth code cleaned up and related parameters
+    can now be specified in data.bling;
+  - clean up OPTIONS in pkg/bling code ( SIZE_NUT_LIM merged with SIZE_DEP_LIM,
+    MULT_NUT_LIM merged with MIN_NUT_LIM ) and switch USE_QSW to #undef ; this
+    fixes FWD exp. global_oce_biogeo_bling which a) use default BLING_OPTIONS.h
+    and b) since no short-wave is provided, light was zero with USE_QSW defined.
+o pkg/profiles:
+  - add option to write model-equivalent profiles in a netcdf file, thus
+    removing the need for post-processing tiled output files.
 o pkg/grdchk:
   - write either "grd_ratio_ad" or "grd_ratio_ftl" depending on type of run
     and remove limitation to "useSingleCpuIO=F" when writing 2D files ;

pkg/bling/BLING_OPTIONS.h

@@ -30,8 +30,8 @@ C nutrient limitations to calculate maximum phyto growth rate
 #define MIN_NUT_LIM
 
 C Allow different phytoplankton groups to have different growth rates and
-C nutrient/light limitations. Parameters implemented have yet to be tuned.
-#undef SIZE_NUT_LIM
+C nutrient/light limitations. Parameters implemented have yet to be tuned
+#undef SIZE_DEP_LIM
 
 C Assume that phytoplankton in the mixed layer experience
 C the average light over the mixed layer (as in original BLING model)
@@ -46,7 +46,8 @@ C MLD is calculated using the second derivative of rho(z)
 
 C Determine PAR from shortwave radiation Qsw;
 C otherwise determined from date and latitude
-#define USE_QSW
+C (Do not define if not using pkg/exf)
+#undef USE_QSW
 
 C Light absorption scheme from Manizza et al. (2005),
 C with self shading from phytoplankton
@@ -75,7 +76,7 @@ C For adjoint safe, do not call bling_dvm
 C ABIOTIC OPTIONS
 C Compile "Solvesaphe" package (Munhoven 2013) for pH/pCO2
 C  can still select Follows et al (2006) solver in data.bling,
-C  but will use solvesaphe dissociation coefficient options.
+C  but will use solvesaphe dissociation coefficient options
 #undef CARBONCHEM_SOLVESAPHE
 
 C In S/R CARBON_CHEM convert ak1 and ak2 to the total pH scale
@@ -87,13 +88,5 @@ C  coeffs are used).
 C When calculating the fraction of sinking organic matter, use model biomass diagnostics.
 #define NEW_FRAC_EXP
 
-C Assume different nutrient limitations for small and large phytoplankton.
-#define SIZE_DEP_LIM
-
-C-- Undocumented Options:
-#undef MULT_NUT_LIM
-#undef USE_ATMOSCO2
-#undef USE_EXFCO2
-
 #endif /* ALLOW_BLING */
 #endif /* BLING_OPTIONS_H */

pkg/bling/BLING_VARS.h

@@ -277,6 +277,12 @@ C          satellite-equivalent chlorophyll diagnostic (and cost)
      &                     gamma_DON,
      &                     k_Fe_diaz,
      &                     k_NO3,
+     &                     k_NO3_sm,
+     &                     k_NO3_lg,
+     &                     k_PO4_sm,
+     &                     k_PO4_lg,
+     &                     k_Fe_sm,
+     &                     k_Fe_lg,
      &                     k_PtoN,
      &                     k_FetoN,
      &                     PtoN_min,
@@ -379,6 +385,12 @@ C          satellite-equivalent chlorophyll diagnostic (and cost)
       _RL gamma_DON
       _RL k_Fe_diaz
       _RL k_NO3
+      _RL k_NO3_sm
+      _RL k_NO3_lg
+      _RL k_PO4_sm
+      _RL k_PO4_lg
+      _RL k_Fe_sm
+      _RL k_Fe_lg
       _RL k_PtoN
       _RL k_FetoN
       _RL PtoN_min

pkg/bling/bling_bio.F

@@ -433,12 +433,12 @@ SUBROUTINE BLING_BIO(
 c  the default Liebig limitation (the minimum of Michaelis-Menton
 c  PO4-limitation, or iron-limitation) by the product (safer for adjoint)
 
-#ifdef MULT_NUT_LIM
+#ifdef MIN_NUT_LIM
           Pc_m = Pc_0*expkT(i,j,k)
-     &           *PO4_lim(i,j,k)*Fe_lim(i,j,k)*maskC(i,j,k,bi,bj)
+     &           *min(PO4_lim(i,j,k), Fe_lim(i,j,k))*maskC(i,j,k,bi,bj)
 #else
           Pc_m = Pc_0*expkT(i,j,k)
-     &           *min(PO4_lim(i,j,k), Fe_lim(i,j,k))*maskC(i,j,k,bi,bj)
+     &           *PO4_lim(i,j,k)*Fe_lim(i,j,k)*maskC(i,j,k,bi,bj)
 #endif
 
 c ---------------------------------------------------------------------