Merge branch 'master' into darwin

darwinproject · Jun 6, 2024 · 1e57208 · 1e57208
2 parents d775ee3 + 976081d
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diff --git a/doc/phys_pkgs/shelfice.rst b/doc/phys_pkgs/shelfice.rst
@@ -110,6 +110,8 @@ that is different from :math:`\rho_c`, the anomaly is zero.
    +----------------------------------------+--------------------------------------------+---------------------------------------------------------------------------------------------------------+
    | :varlink:`rhoShelfIce`                 | 917.0E+00                                  | (constant) mean density of ice shelf (kg/m\ :sup:`3`)                                                   |
    +----------------------------------------+--------------------------------------------+---------------------------------------------------------------------------------------------------------+
+   | :varlink:`SHELFICEsalinity`            | 0.0E+00                                    | (constant) salinity of ice shelf                                                                        |
+   +----------------------------------------+--------------------------------------------+---------------------------------------------------------------------------------------------------------+
    | :varlink:`SHELFICEheatTransCoeff`      | 1.0E-04                                    | transfer coefficient (exchange velocity) for temperature (m/s)                                          |
    +----------------------------------------+--------------------------------------------+---------------------------------------------------------------------------------------------------------+
    | :varlink:`SHELFICEsaltTransCoeff`      | :varlink:`SHELFICEsaltToHeatRatio` *       | transfer coefficient (exchange velocity) for salinity (m/s)                                             |
@@ -473,19 +475,30 @@ to be substituted into :eq:`hellmersaltbalance`:
    \Leftrightarrow 0 &= a_{0}\,(\epsilon_{1} + \epsilon_{3})\,S_{b}^{2}
    + \{ \epsilon_{q}  - \epsilon_{2}
      - a_{0}\,(\epsilon_{1} + \epsilon_{3})\,S_{I} \}\,S_{b}
-     + \epsilon_{2}\,S - \epsilon_{q}\,S_{I}
+     + \epsilon_{2}\,S - \epsilon_{q}\,S_{I} \\
+   \Leftrightarrow 0 &= A\,S_{b}^{2} + B\,S_{b} + C \\
+   \Rightarrow S_{b} &= \frac{-B \pm \sqrt{ B^{2} - 4AC }}{2A}
+   \end{aligned}
+
+with the abbrevations
+
+.. math::
+   \begin{aligned}
+   \epsilon_{1} &= c_{p} \, \rho_c \, \gamma_{T}, \quad
+   \epsilon_{2} = \rho_c L \, \gamma_{S}, \quad
+   \epsilon_{3} = \frac{\rho_{I} \, c_{p,I} \, \kappa}{h}, \quad
+   \epsilon_{4} = b_{0}p + c_{0}, \\
+   \epsilon_{q} &= \epsilon_{1}\,(\epsilon_{4} - T)
+                  + \epsilon_{3}\,(\epsilon_{4} - T_{S}), \\
+   A &= a_{0}\,(\epsilon_{1} + \epsilon_{3}), \quad
+   B = \epsilon_{q} - \epsilon_{2} - a_{0}\,(\epsilon_{1} +
+   \epsilon_{3})\,S_{I}, \quad
+   C = \epsilon_{2}\,S -\epsilon_{q}\,S_{I}.
    \end{aligned}
 
-where the abbrevations
-:math:`\epsilon_{1} = c_{p} \, \rho_c \, \gamma_{T}`,
-:math:`\epsilon_{2} = \rho_c L \, \gamma_{S}`, :math:`\epsilon_{3} =
-\frac{\rho_{I} \, c_{p,I} \, \kappa}{h}`,
-:math:`\epsilon_{4}=b_{0}p + c_{0}`,
-:math:`\epsilon_{q} = \epsilon_{1}\,(\epsilon_{4} - T) +
-\epsilon_{3}\,(\epsilon_{4} - T_{S})` have been introduced. The
-quadratic equation in :math:`S_{b}` is solved and the smaller
-non-negative root is used. In the MITgcm code, the ice shelf salinity
-:math:`S_{I}` is always zero and the quadratic equation simplifies to
+The smaller non-negative root of the quadratic equation in :math:`S_{b}` is
+used. By default, the ice shelf salinity :math:`S_{I}` is zero and the
+quadratic equation simplifies to
 
 .. math::
    \begin{aligned}
@@ -497,9 +510,8 @@ non-negative root is used. In the MITgcm code, the ice shelf salinity
      {2\,a_{0}\,(\epsilon_{1} + \epsilon_{3})}
    \end{aligned}
 
-With :math:`S_b`, the boundary layer temperature :math:`T_b` and the
-melt rate :math:`q` are known through :eq:`hellmerfreeze` and
-:eq:`solvedmeltrate`.
+With :math:`S_b`, the boundary layer temperature :math:`T_b` and the melt rate
+:math:`q` are known through :eq:`hellmerfreeze` and :eq:`solvedmeltrate`.
 
 .. _shelfice_isomip:
 

diff --git a/doc/tag-index b/doc/tag-index
@@ -1,6 +1,56 @@
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint68y (2024/06/05)
+o pkg/bling:
+  - fix bigR setting when option CARBONCHEM_TOTALPHSCALE is defined.
+o pkg/steep_icecavity + shelfice:
+  - new package to be used together with pkg/shelfice to also account for
+    melting at the vertical faces of a steep ice-shelf interface ;
+  - allows to use non-zero (but constant) ice-shelf salinity ;
+  - new FWD and (TAF) AD secondary test exp. (in isomip) using new pkg.
+o pkg/bling:
+  - fix/improve initialization of biomass for the 3 phytoplankton groups ;
+  - add 2D diagnostics of optically integrated chlorophyll concentration
+    within local-time window to be compared with satellite observation ;
+  - improve TAF store directives (reduce recomputations).
+o pkg/obcs (tides):
+  - more efficient implementation of OB barotropic tidal velocity components,
+    with both Cos & Sin of phase times Amplitude stored in common block ;
+  - more flexible specification of OB tidal-components (only read-in components
+    with non-zero tidal period) ;
+  - allows to specify tangential component of barotropic tidal velocity at OB ;
+  - rename all OBC tidal component input parameter (period, amplitude and
+    phase of each OB barotropic tidal velocity component input files) ;
+  - upgrade OB tidal example (in seaice_obcs/input.tides) with fewer tidal
+    components (only 4) but including few tangential components.
+o verification:
+  - changing domain decomposition (more tiles) in global_with_exf experiment
+    (both FWD & AD) and update ref. output ;
+  - use correct CD-Scheme time-stepping in FWD exp. global_ocean_ebm and update
+    ref. output ;
+  - simplify global_ocean.90x40x15/code_ad (undef ALLOW_GENTIM2D_CONTROL,
+    ALLOW_DIFFKR_CONTROL & ALLOW_3D_DIFFKR); remove kpp from global_oce_latlon
+    (from both TAF & Tapenade code) ;
+  - after adjusting new host experiment code, merge forward test:
+      flt_example            --> exp4.with_flt
+      global_with_exf        --> global_ocean_ebm.w_exf
+      global_with_exf.yearly --> global_ocean_ebm.yearly
+      natl_box               --> lab_sea.natl_box
+      natl_box.longstep      --> lab_sea.longstep
+    and TAF & Tapenade tests:
+      global_with_exf        --> global_oce_latlon.w_exf
+    For now, keep original set-up in place and add symbolic links into new
+    host exp. for input dir and ref. output to run these as secondary test.
+o pkg/obcs:
+  - fix unusual division by zero in all 4 (N,S,E,W) orlanski main S/R.
+o pkg/diagnostics:
+  - new header file "DIAGNOSTICS_P2SHARE.h" (for now, just for useDiag4AdjOutp),
+    and remove DIAGNOSTICS.h in any src code outside pkg/diagnostics;
+  - new params "diag_dBugLevel" (default = main model "debugLevel");
+  - add new arg "seqFlag" to DIAGNOSTICS_SWITCH_ONOFF and DIAGNOSTICS_SUMMARY
+    and prevent "diagnostics_status" to be overwritten when using ADJ-diags.
+
 checkpoint68x (2024/04/30)
 o model/src:
   - more precise specific-volume anomaly expression for Ocean in P-coord;

diff --git a/model/inc/PARAMS.h b/model/inc/PARAMS.h
@@ -1069,6 +1069,7 @@ C-- Logical flags for selecting packages
       LOGICAL useSEAICE
       LOGICAL useSALT_PLUME
       LOGICAL useShelfIce
+      LOGICAL useSTIC
       LOGICAL useStreamIce
       LOGICAL useICEFRONT
       LOGICAL useThSIce
@@ -1093,7 +1094,7 @@ C-- Logical flags for selecting packages
      &        useGrdchk, useSMOOTH, usePROFILES, useECCO, useCTRL,
      &        useSBO, useFLT, useAUTODIFF, useRADTRANS,
      &        usePTRACERS, useGCHEM, useRBCS, useOffLine, useMATRIX,
-     &        useFRAZIL, useSEAICE, useSALT_PLUME, useShelfIce,
+     &        useFRAZIL, useSEAICE, useSALT_PLUME, useShelfIce, useSTIC,
      &        useStreamIce, useICEFRONT, useThSIce, useLand,
      &        useATM2d, useAIM, useAtm_Phys, useFizhi, useGridAlt,
      &        useDiagnostics, useREGRID, useLayers, useMNC,

diff --git a/model/src/do_oceanic_phys.F b/model/src/do_oceanic_phys.F
@@ -65,6 +65,7 @@ SUBROUTINE DO_OCEANIC_PHYS(myTime, myIter, myThid)
 C       |
 C       |-- OCN_EXPORT_DATA
 C       |
+C       |-- STIC_THERMODYNAMICS
 C       |-- SHELFICE_THERMODYNAMICS
 C       |
 C       |-- ICEFRONT_THERMODYNAMICS
@@ -450,20 +451,34 @@ SUBROUTINE DO_OCEANIC_PHYS(myTime, myIter, myThid)
 
 #ifdef ALLOW_SHELFICE
       IF ( useShelfIce .AND. fluidIsWater ) THEN
-#ifdef ALLOW_DEBUG
-       IF (debugMode) CALL DEBUG_CALL('SHELFICE_THERMODYNAMICS',myThid)
-#endif
 #ifdef ALLOW_AUTODIFF_TAMC
 CADJ STORE salt, theta       = comlev1, key=ikey_dynamics, kind=isbyte
 CADJ STORE uvel, vvel        = comlev1, key=ikey_dynamics, kind=isbyte
 #endif
+#ifdef ALLOW_STEEP_ICECAVITY
+       IF ( useSTIC ) THEN
+# ifdef ALLOW_DEBUG
+        IF (debugMode) CALL DEBUG_CALL('STIC_THERMODYNAMICS',myThid)
+# endif
+C     use stic_thermodynamics that includes icefront melt processes
+        CALL TIMER_START('STIC_THERMODYNAMICS [DO_OCEANIC_PHYS]',myThid)
+        CALL STIC_THERMODYNAMICS( myTime, myIter, myThid )
+        CALL TIMER_STOP ('STIC_THERMODYNAMICS [DO_OCEANIC_PHYS]',myThid)
+       ELSE
+#else
+       IF ( .TRUE. ) THEN
+#endif
+#ifdef ALLOW_DEBUG
+        IF (debugMode) CALL DEBUG_CALL('SHELFICE_THERMODYNAMICS',myThid)
+#endif
 C     compute temperature and (virtual) salt flux at the
 C     shelf-ice ocean interface
-       CALL TIMER_START('SHELFICE_THERMODYNAMICS [DO_OCEANIC_PHYS]',
+        CALL TIMER_START('SHELFICE_THERMODYNAMICS [DO_OCEANIC_PHYS]',
      &       myThid)
-       CALL SHELFICE_THERMODYNAMICS( myTime, myIter, myThid )
-       CALL TIMER_STOP( 'SHELFICE_THERMODYNAMICS [DO_OCEANIC_PHYS]',
-     &      myThid)
+        CALL SHELFICE_THERMODYNAMICS( myTime, myIter, myThid )
+        CALL TIMER_STOP ('SHELFICE_THERMODYNAMICS [DO_OCEANIC_PHYS]',
+     &       myThid)
+       ENDIF
       ENDIF
 #endif /* ALLOW_SHELFICE */
 

diff --git a/model/src/forward_step.F b/model/src/forward_step.F
@@ -507,7 +507,7 @@ SUBROUTINE FORWARD_STEP( iloop, myTime, myIter, myThid )
 C--   Switch on/off diagnostics for snap-shot output:
 #ifdef ALLOW_DIAGNOSTICS
       IF ( useDiagnostics ) THEN
-        CALL DIAGNOSTICS_SWITCH_ONOFF( myTime, myIter, myThid )
+        CALL DIAGNOSTICS_SWITCH_ONOFF( 1, myTime, myIter, myThid )
 C--   State-variables diagnostics
         CALL TIMER_START('DO_STATEVARS_DIAGS  [FORWARD_STEP]',myThid)
         CALL DO_STATEVARS_DIAGS( myTime, 0, myIter, myThid )

diff --git a/model/src/ini_masks_etc.F b/model/src/ini_masks_etc.F
@@ -58,6 +58,9 @@ SUBROUTINE INI_MASKS_ETC( myThid )
      I               myThid )
       ENDIF
 #endif /* ALLOW_SHELFICE */
+#ifdef ALLOW_STEEP_ICECAVITY
+      IF ( useSTIC ) CALL STIC_INIT_DEPTHS( myThid )
+#endif /* ALLOW_STEEP_ICECAVITY */
 
       IF ( selectSigmaCoord.EQ.0 ) THEN
 C---  r-coordinate with partial-cell or full cell mask

diff --git a/model/src/packages_boot.F b/model/src/packages_boot.F
@@ -80,6 +80,7 @@ SUBROUTINE PACKAGES_BOOT( myThid )
      &          useSEAICE,
      &          useSALT_PLUME,
      &          useShelfIce,
+     &          useSTIC,
      &          useStreamIce,
      &          useICEFRONT,
      &          useThSIce,
@@ -146,6 +147,7 @@ SUBROUTINE PACKAGES_BOOT( myThid )
       useSEAICE       =.FALSE.
       useSALT_PLUME   =.FALSE.
       useShelfIce     =.FALSE.
+      useSTIC         =.FALSE.
       useStreamIce    =.FALSE.
       useICEFRONT     =.FALSE.
       useThSIce       =.FALSE.
@@ -363,6 +365,9 @@ SUBROUTINE PACKAGES_BOOT( myThid )
 #ifdef ALLOW_SHELFICE
       CALL PACKAGES_PRINT_MSG( useShelfIce,   'ShelfIce',    ' ' )
 #endif
+#ifdef ALLOW_STEEP_ICECAVITY
+      CALL PACKAGES_PRINT_MSG( useSTIC,   'STEEP_ICECAVITY', ' ' )
+#endif
 #ifdef ALLOW_STREAMICE
       CALL PACKAGES_PRINT_MSG( useStreamIce,  'StreamIce',   ' ' )
 #endif

diff --git a/model/src/packages_check.F b/model/src/packages_check.F
@@ -53,6 +53,8 @@ SUBROUTINE PACKAGES_CHECK( myThid )
 C       |
 C       |-- SHELFICE_CHECK
 C       |
+C       |-- STIC_CHECK
+C       |
 C       |-- SMOOTH_CHECK
 C       |
 C       |-- STREAMICE_CHECK
@@ -360,6 +362,13 @@ SUBROUTINE PACKAGES_CHECK( myThid )
       IF (useShelfIce) CALL PACKAGES_ERROR_MSG('ShelfIce',' ',myThid)
 #endif
 
+#ifdef ALLOW_STEEP_ICECAVITY
+      IF (useSTIC) CALL STIC_CHECK( myThid )
+#else
+      IF (useSTIC) CALL PACKAGES_ERROR_MSG(
+     &                  'STEEP_ICECAVITY','useSTIC=.T.', myThid )
+#endif
+
 #ifdef ALLOW_SMOOTH
       IF (useSmooth) CALL SMOOTH_CHECK( myThid )
 #else

diff --git a/model/src/packages_init_fixed.F b/model/src/packages_init_fixed.F
@@ -86,6 +86,8 @@ SUBROUTINE PACKAGES_INIT_FIXED( myThid )
 C       |
 C       |-- SHELFICE_INIT_FIXED
 C       |
+C       |-- STIC_INIT_FIXED
+C       |
 C       |-- ICEFRONT_INIT_FIXED
 C       |
 C       |-- FRAZIL_INIT_FIXED
@@ -473,6 +475,15 @@ SUBROUTINE PACKAGES_INIT_FIXED( myThid )
       ENDIF
 #endif /* ALLOW_SHELFICE */
 
+#ifdef ALLOW_STEEP_ICECAVITY
+      IF (useSTIC) THEN
+# ifdef ALLOW_DEBUG
+        IF (debugMode) CALL DEBUG_CALL('STIC_INIT_FIXED',myThid)
+# endif
+        CALL STIC_INIT_FIXED( myThid )
+      ENDIF
+#endif /* ALLOW_STEEP_ICECAVITY */
+
 #ifdef ALLOW_SMOOTH
       IF (useSMOOTH) THEN
 # ifdef ALLOW_DEBUG

diff --git a/model/src/packages_init_variables.F b/model/src/packages_init_variables.F
@@ -84,6 +84,8 @@ SUBROUTINE PACKAGES_INIT_VARIABLES( myThid )
 C       |
 C       |-- SHELFICE_INIT_VARIA
 C       |
+C       |-- STIC_INIT_VARIA
+C       |
 C       |-- ICEFRONT_INIT_VARIA
 C       |
 C       |-- FRAZIL_INIT_VARIA
@@ -149,6 +151,9 @@ SUBROUTINE PACKAGES_INIT_VARIABLES( myThid )
 # ifdef ALLOW_SHELFICE
 #  include "SHELFICE.h"
 # endif
+# ifdef ALLOW_STEEP_ICECAVITY
+#  include "STIC.h"
+# endif
 # ifdef ALLOW_STREAMICE
 #  include "STREAMICE.h"
 # endif
@@ -404,6 +409,22 @@ SUBROUTINE PACKAGES_INIT_VARIABLES( myThid )
 # endif
 #endif /* ALLOW_SHELFICE */
 
+#ifdef ALLOW_STEEP_ICECAVITY
+# ifdef ALLOW_AUTODIFF
+C- Note: use same trick as for pkg/gmredi (call to GMREDI_INIT_VARIA) when
+C  compiling pkg/autodiff (with IF-statements inside stic_init_varia.F)
+# else
+      IF (useSTIC) THEN
+# endif
+# ifdef ALLOW_DEBUG
+       IF (debugMode) CALL DEBUG_CALL('STIC_INIT_VARIA',myThid)
+# endif
+       CALL STIC_INIT_VARIA( myThid )
+# ifndef ALLOW_AUTODIFF
+      ENDIF
+# endif
+#endif /* ALLOW_STEEP_ICECAVITY */
+
 #ifdef ALLOW_ICEFRONT
       IF (useICEFRONT) THEN
 # ifdef ALLOW_DEBUG

diff --git a/model/src/packages_readparms.F b/model/src/packages_readparms.F
@@ -82,6 +82,8 @@ SUBROUTINE PACKAGES_READPARMS(myThid)
 C       |
 C       |-- SHELFICE_READPARMS
 C       |
+C       |-- STIC_READPARMS
+C       |
 C       |-- ICEFRONT_READPARMS
 C       |
 C       |-- SEAICE_READPARMS
@@ -290,6 +292,11 @@ SUBROUTINE PACKAGES_READPARMS(myThid)
       CALL SHELFICE_READPARMS( myThid )
 #endif
 
+#ifdef ALLOW_STEEP_ICECAVITY
+C--   if useSTIC=T, set STEEP_ICECAVITY parameters; otherwise just return
+      CALL STIC_READPARMS( myThid )
+#endif
+
 #ifdef ALLOW_ICEFRONT
 C--   if useICEFRONT=T, set ICEFRONT parameters; otherwise just return
       CALL ICEFRONT_READPARMS( myThid )

diff --git a/model/src/the_main_loop.F b/model/src/the_main_loop.F
@@ -562,6 +562,11 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 #    endif
 #   endif /* ALLOW_THSICE */
 c--
+#   ifdef ALLOW_STEEP_ICECAVITY
+CADJ INIT comlev1_stic_bibj_ijk = COMMON,
+CADJ &    nchklev_1*nSx*nSy*Nr*(2*OLy+sNy)*(2*OLx+sNx)
+#   endif
+c--
 #   ifdef ALLOW_STREAMICE
 CADJ INIT comlev1_stream_nl    = COMMON,nchklev_1*streamice_max_nl
 CADJ INIT comlev1_stream_front = COMMON,nchklev_1*4

diff --git a/pkg/autodiff/adcommon.h b/pkg/autodiff/adcommon.h
@@ -221,11 +221,21 @@ C Special Care: more forward vars in FWD common block ; check TAF AD-code !
       _RL adshelficemass    (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
       _RL adshicdragfld     (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
       _RL adshidragquadfld  (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
+      COMMON /adSHELFICE_FIELDS_RL/ adshelficemass,
+     &  adshelficeforcingt, adshelficeforcings,
+     &  adshicdragfld, adshidragquadfld
+
+# ifdef ALLOW_SHITRANSCOEFF_3D
+      COMMON /adSHELFICE_GAMMA3D_RL/
+     &  adshitranscoefft3d, adshitranscoeffs3d
+      _RL adshitranscoeffs3d(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy)
+      _RL adshitranscoefft3d(1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy)
+# else
+      COMMON /adSHELFICE_GAMMA_RL/
+     &  adshitranscoefft, adshitranscoeffs
       _RL adshitranscoeffs  (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
       _RL adshitranscoefft  (1-OLx:sNx+OLx,1-OLy:sNy+OLy,nSx,nSy)
-      COMMON /adSHELFICE_FIELDS_RL/ adshelficemass,
-     &  adshelficeforcingt, adshelficeforcings, adshitranscoefft,
-     &  adshitranscoeffs, adshicdragfld, adshidragquadfld
+# endif
 #endif
 
 #endif /* ALLOW_AUTODIFF_MONITOR */