Merge branch 'master' into darwin

doc/examples/global_oce_optim/global_oce_optim.rst

@@ -150,9 +150,6 @@ variable in :filelink:`pkg/ctrl` by modifying the following subroutines:
 -  :filelink:`pkg/ctrl/ctrl_map_forcing.F` in which the updated adjustment is added to the
    first guess :math:`Q_\mathrm{netm}`.
 
-Note also some minor changes in :filelink:`pkg/ctrl/ctrl.h`, :filelink:`pkg/ctrl/ctrl_readparms.F`, and
-:filelink:`pkg/ctrl/ctrl_dummy.h` (:varlink:`xx_hfluxm_file`, :varlink:`fname_hfluxm`, :varlink:`xx_hfluxm_dummy`).
-
 Cost functions
 ~~~~~~~~~~~~~~
 

doc/outp_pkgs/outp_pkgs.rst

@@ -450,8 +450,8 @@ Currently, the available adjoint state variables are:
    114 |ADJsalt | 15 |       |SMRA    MR|dJ/(g/kg)       |dJ/dSalt: Sensitivity to salinity
    115 |ADJtaux |  1 |   116 |UU A    U1|dJ/(N/m^2)      |dJ/dTaux: Senstivity to zonal surface wind stress
    116 |ADJtauy |  1 |   115 |VV A    U1|dJ/(N/m^2)      |dJ/dTauy: Sensitivity to merid. surface wind stress
-   117 |ADJempmr|  1 |       |SM A    U1|dJ/(kg/m^2/s)   |dJ/dEmPmR: Sensitivity to net surface Fresh-Water flux into the ocean
-   118 |ADJqnet |  1 |       |SM A    U1|dJ/(W/m^2)      |dJ/dQnet: Sensitivity to net surface heat fluxinto the ocean
+   117 |ADJempmr|  1 |       |SM A    U1|dJ/(kg/m^2/s)   |dJ/dEmPmR: Sensitivity to net surface freshwater flux
+   118 |ADJqnet |  1 |       |SM A    U1|dJ/(W/m^2)      |dJ/dQnet: Sensitivity to net surface heat flux
    119 |ADJqsw  |  1 |       |SM A    U1|dJ/(W/m^2)      |dJ/dQsw: Sensitivitiy to net Short-Wave radiation
    120 |ADJsst  |  1 |       |SM A    M1|dJ/K            |dJ/dSST: Sensitivity to Sea Surface Temperature
    121 |ADJsss  |  1 |       |SM A    M1|dJ/(g/kg)       |dJ/dSSS: Sensitivity to Sea Surface Salinity

doc/tag-index

@@ -1,6 +1,53 @@
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint68t (2023/10/28)
+o pkg/dic:
+  - improve carbonate dissolution options (new params: selectCalciteDissolution)
+    and fix a minor bug in dissolution rates according to Keir et al (1980);
+  - change exp. so_box_biogeo secondary tests caSat0/3 to test option 2 & 3.
+o pkg/gmredi:
+  - fix setting of GM_ExtraDiag that was not (always) turned on with 3D Kappa
+    read from file, with Bates-K3d or QG-Leith, therefore missing 2 terms in
+    isopycnal diffusion tensor; update ref. output of MLAdjust.QGLthGM test ;
+  - add more check and stop for the case #undef GM_NON_UNITY_DIAGONAL ;
+  - add runtime parameter GM_isoFac_calcK to allow to scale dynamically computed
+    Kappa contribution in the Redi-tensor (default = 1.).
+o pkg/autodiff:
+  - adjust call to S/R DIAGNOSTICS_SWITCH_ONOFF in autodiff_inadmode_set_ad.F
+    so that snap-shot Adjoint diagnostics are filled within the same time-step
+    as they are written to output file.
+o pkg/ctrl:
+  - rename ctrl_dummy.h to CTRL_DUMMY.h, remove unused variables & common blocks
+  - retire CPP-flag ALLOW_HFACC/HFACC3D_CONTROL and remove related code.
+o pkg/ctrl:
+  - rename header file "ctrl.h" to "CTRL.h".
+o utils/matlab/cs_grid:
+  - update some basic matlab-scripts for CS-grid (split_*_cub.m,
+    rotate_uv2uvEN.m, mk_psiLine_CS.m & use_psiLine.m) to a) also work with
+    compact-format input; and (b) always assume "long-vector" are stored one
+    face after the other (compact-format compatible);
+  - new script to generate broken-lines (for computing meridional transport
+    stream-function), simpler than the previous version in cs_grid/bk_line/;
+  - update RGB-dims in 2 latloncap/ scripts to match pkg/exch2 convention.
+o pkg/ctrl:
+  - simplify file name handling in ctrl_map_ini_gentim2d.F to please TAF (fixes
+    hs94.1x64x5 TL test) without upsetting Tapenade & OpenAD.
+o pkg/autodiff + ecco:
+  - fix a typo in AD-var output file name (addummy_in_stepping.F);
+  - fix and improve weight output in pkg/ecco/cost_generic.F
+o pkg/streamice:
+  - implementation of parameterized depth-dependent ice-shelf melt rate ;
+  - new subroutines added to accumulate misfit cost based on time-dependent
+    surface elevation and velocity observations (+ calls in pkg/cost) ;
+  - fix generic ctrl (ctrl_map_ini_{genarr,gentim2d}.F) for OpenAD and
+    add mapping of STREAMICE arrays to generic controls ;
+  - update exp. halfpipe_streamice OAD & Tap setup (remove customized *.F)
+    and switch on new CPP option ALLOW_COST_STREAMICE (+adjust params files).
+o pkg/autodiff:
+  - fix a bug in ALLOW_AUTODIFF_WHTAPEIO code with ALLOW_DIVIDED_ADJOINT ;
+  - refine grad-check + update output for AD test "lab_sea.noseaicedyn".
+
 checkpoint68s (2023/09/11)
 o verification:
   - change default ALLOW_IB_CORR (in pkg/ecco/ECCO_OPTIONS.h) to "#undef" and

model/src/diags_sound_speed.F

@@ -10,7 +10,7 @@ SUBROUTINE DIAGS_SOUND_SPEED(
 C     *==========================================================*
 C     | S/R DIAGS_SOUND_SPEED
 C     | o Diagnose speed of sound in seawater
-C     |   from the algorithm by Del Grasso (1974).
+C     |   from the algorithm by Del Grosso (1974).
 C     |   This is NOT the sound-speed that can be derived from
 C     |   the equation of state (EOS). It is independent of
 C     |   the model setup specific EOS.
@@ -97,7 +97,7 @@ SUBROUTINE DIAGS_SOUND_SPEED(
              temp = SW_TEMP( SALT(i,j,k,bi,bj),
      &                 THETA(i,j,k,bi,bj), pres, zeroRL )
              sal  = SALT(i,j,k,bi,bj)
-C convert pressure to kg/cm^2 for Del Grasso algorithm
+C convert pressure to kg/cm^2 for Del Grosso algorithm
              pres = pres/gravity
              ct   = ( 5.01109398873 _d 0 - ( 0.550946843172 _d -1
      &              - 0.221535969240 _d -3 * temp ) * temp ) * temp

model/src/do_oceanic_phys.F

@@ -169,7 +169,7 @@ SUBROUTINE DO_OCEANIC_PHYS(myTime, myIter, myThid)
 # endif
 # ifdef ALLOW_EXF
 #  ifdef ALLOW_CTRL
-#   include "ctrl.h"
+#   include "CTRL.h"
 #  endif
 #  include "EXF_FIELDS.h"
 #  ifdef ALLOW_BULKFORMULAE

model/src/forward_step.F

@@ -265,8 +265,8 @@ SUBROUTINE FORWARD_STEP( iloop, myTime, myIter, myThid )
 # endif
 # ifdef ALLOW_CTRL
 #  include "CTRL_SIZE.h"
-#  include "ctrl.h"
-#  include "ctrl_dummy.h"
+#  include "CTRL.h"
+#  include "CTRL_DUMMY.h"
 #  include "CTRL_GENARR.h"
 #  include "CTRL_OBCS.h"
 # endif

model/src/initialise_varia.F

@@ -119,9 +119,9 @@ SUBROUTINE INITIALISE_VARIA( myThid )
 # ifdef ALLOW_CTRL
 #  include "CTRL_SIZE.h"
 #  include "optim.h"
-#  include "ctrl.h"
+#  include "CTRL.h"
 #  include "CTRL_GENARR.h"
-#  include "ctrl_dummy.h"
+#  include "CTRL_DUMMY.h"
 # endif
 # ifdef ALLOW_CD_CODE
 #  include "CD_CODE_VARS.h"

model/src/load_fields_driver.F

@@ -59,9 +59,9 @@ SUBROUTINE LOAD_FIELDS_DRIVER( myTime, myIter, myThid )
 # endif
 # ifdef ALLOW_CTRL
 #  include "CTRL_SIZE.h"
-#  include "ctrl.h"
+#  include "CTRL.h"
 #  include "CTRL_GENARR.h"
-#  include "ctrl_dummy.h"
+#  include "CTRL_DUMMY.h"
 # endif
 # ifdef ALLOW_COST
 #  include "cost.h"

model/src/main_do_loop.F

@@ -85,8 +85,8 @@ SUBROUTINE MAIN_DO_LOOP( iloop, myTime, myIter, myThid )
 
 # ifdef ALLOW_CTRL
 #  include "CTRL_SIZE.h"
-#  include "ctrl.h"
-#  include "ctrl_dummy.h"
+#  include "CTRL.h"
+#  include "CTRL_DUMMY.h"
 #  include "CTRL_GENARR.h"
 #  include "CTRL_OBCS.h"
 # endif

model/src/packages_init_variables.F

@@ -135,9 +135,9 @@ SUBROUTINE PACKAGES_INIT_VARIABLES( myThid )
 # ifdef ALLOW_CTRL
 #  include "CTRL_SIZE.h"
 #  include "optim.h"
-#  include "ctrl.h"
+#  include "CTRL.h"
 #  include "CTRL_GENARR.h"
-#  include "ctrl_dummy.h"
+#  include "CTRL_DUMMY.h"
 # endif
 # ifdef ALLOW_PTRACERS
 #  include "PTRACERS_SIZE.h"

model/src/the_main_loop.F

@@ -204,8 +204,8 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 
 # ifdef ALLOW_CTRL
 # include "CTRL_SIZE.h"
-# include "ctrl.h"
-# include "ctrl_dummy.h"
+# include "CTRL.h"
+# include "CTRL_DUMMY.h"
 # include "CTRL_GENARR.h"
 # include "CTRL_OBCS.h"
 # endif
@@ -290,7 +290,7 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 c--   Initialize storage for the cost function evaluation.
 c---------------------------------------------------------
 c--   Initialize storage for the initialisation phase.
-# ifdef ALLOW_AUTODIFF_WHTAPEIO
+# if ( defined ALLOW_AUTODIFF_WHTAPEIO && !defined ALLOW_DIVIDED_ADJOINT )
 CADJ INIT tapelev_init       = COMMON, 1
 # else
 CADJ INIT tapelev_init       = USER
@@ -299,7 +299,11 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 cCADJ INIT tapelev_ini_bibj   = USER
 # ifdef INCLUDE_CONVECT_INI_CALL
 c--   currently only used in convective_adjustement_ini.F
+#  if ( defined ALLOW_AUTODIFF_WHTAPEIO && !defined ALLOW_DIVIDED_ADJOINT )
 CADJ INIT tapelev_ini_bibj_k = COMMON, nSx*nSy*Nr
+#  else
+CADJ INIT tapelev_ini_bibj_k = USER
+#  endif
 # endif
 # ifdef ALLOW_GENTIM2D_CONTROL
 c--   exclusive tape for variables with suffix "_dummy"
@@ -327,15 +331,25 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 
 #ifdef ALLOW_AUTODIFF_TAMC
       ikey_dynamics = 1
+# if ( defined ALLOW_AUTODIFF_WHTAPEIO && defined ALLOW_DIVIDED_ADJOINT )
+C     this needs to happen before any store directive to taplev_init
+      CALL AUTODIFF_WHTAPEIO_SYNC( 1 , 0, myThid )
+# endif
 # ifdef ALLOW_GENTIM2D_CONTROL
 CADJ STORE xx_gentim2d_dummy = dummytape, key = 1 , kind = isbyte
 # endif
 # ifdef ALLOW_SHELFICE
 CADJ STORE shelficeLoadAnomaly = tapelev_init, key=1, kind=isbyte
 # endif
 # ifdef ALLOW_STREAMICE
-CADJ STORE H_streamice = tapelev_init, key=1
-CADJ STORE B_glen      = tapelev_init, key=1
+CADJ STORE H_streamice              = tapelev_init, key=1
+CADJ STORE B_glen                   = tapelev_init, key=1
+CADJ STORE bdot_streamice           = tapelev_init, key=1
+CADJ STORE c_basal_friction         = tapelev_init, key=1
+CADJ STORE streamice_bdot_maxmelt_v = tapelev_init, key=1
+#  ifdef USE_ALT_RLOW
+CADJ STORE r_low_si                 = tapelev_init, key=1
+#  endif
 # endif
 # ifdef ALLOW_DIC
 CADJ STORE co2atmos = tapelev_init, key = 1
@@ -344,12 +358,6 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
 #endif
 
 #ifdef ALLOW_OPENAD
-# ifdef ALLOW_DIFFKR_CONTROL
-c$openad INDEPENDENT(xx_diffkr_dummy)
-# endif
-# ifdef ALLOW_KAPGM_CONTROL
-c$openad INDEPENDENT(xx_kapgm)
-# endif
 # ifdef ALLOW_GENARR2D_CONTROL
 cphc$openad INDEPENDENT(xx_genarr2d)
 c$openad INDEPENDENT(xx_genarr2d_dummy)
@@ -391,6 +399,11 @@ SUBROUTINE THE_MAIN_LOOP( myTime, myIter, myThid )
       CALL TIMER_STOP ('INIT_PDAF           [THE_MAIN_LOOP]', myThid)
 #endif
 
+#if ( defined ALLOW_AUTODIFF_WHTAPEIO && defined ALLOW_DIVIDED_ADJOINT )
+C     end of initialisation and use of tapelev_init: write buffer to disk
+      CALL AUTODIFF_WHTAPEIO_SYNC( 1 , 1, myThid )
+#endif
+
 c++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 #ifndef ALLOW_OPENAD
 # ifdef ALLOW_AUTODIFF

model/src/the_model_main.F

@@ -586,7 +586,7 @@ SUBROUTINE THE_MODEL_MAIN(myThid)
 # include "tamc.h"
 #endif
 #ifdef ALLOW_CTRL
-# include "ctrl.h"
+# include "CTRL.h"
 # include "optim.h"
 #endif
 

pkg/admtlm/admtlm_bypassad.F

@@ -12,8 +12,8 @@ subroutine admtlm_bypassad( myThid )
 #include "EEPARAMS.h"
 #include "PARAMS.h"
 #if (defined (ALLOW_ADMTLM) && defined (ALLOW_BYPASSAD))
-# include "ctrl.h"
-# include "ctrl_dummy.h"
+# include "CTRL.h"
+# include "CTRL_DUMMY.h"
 # include "optim.h"
 # include "adcost.h"
 # include "g_cost.h"

pkg/admtlm/admtlm_driver.F

@@ -27,7 +27,7 @@ SUBROUTINE ADMTLM_DRIVER( myThid )
 # ifdef ALLOW_AUTODIFF_TAMC
 #  include "tamc.h"
 # endif
-# include "ctrl.h"
+# include "CTRL.h"
 # include "optim.h"
 #endif
 

pkg/admtlm/admtlm_dsvd.F

@@ -143,7 +143,7 @@ subroutine admtlm_dsvd ( mythid )
 # ifdef ALLOW_AUTODIFF_TAMC
 #  include "tamc.h"
 # endif
-# include "ctrl.h"
+# include "CTRL.h"
 # include "optim.h"
 # include "cost.h"
 # include "adcost.h"

pkg/admtlm/admtlm_dsvd2model.F

@@ -25,7 +25,7 @@ subroutine admtlm_dsvd2model(
 #include "PARAMS.h"
 #include "GRID.h"
 
-#include "ctrl.h"
+#include "CTRL.h"
 #include "optim.h"
 
 #ifdef ALLOW_COST

pkg/admtlm/admtlm_init_fixed.F

@@ -12,7 +12,7 @@ subroutine admtlm_init_fixed( myThid )
 #include "EEPARAMS.h"
 #include "PARAMS.h"
 #ifdef ALLOW_ADMTLM
-# include "ctrl.h"
+# include "CTRL.h"
 # include "ctrl_weights.h"
 #endif
 

pkg/admtlm/admtlm_model2dsvd.F

@@ -26,7 +26,7 @@ subroutine admtlm_model2dsvd(
 #include "PARAMS.h"
 #include "GRID.h"
 
-#include "ctrl.h"
+#include "CTRL.h"
 #include "optim.h"
 
 #ifdef ALLOW_COST

pkg/autodiff/active_file_control.F

@@ -58,7 +58,7 @@ SUBROUTINE ACTIVE_READ_3D_RL(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -234,7 +234,7 @@ SUBROUTINE ACTIVE_READ_3D_RS(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -408,7 +408,7 @@ SUBROUTINE ACTIVE_READ_1D_RL(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -573,7 +573,7 @@ SUBROUTINE ACTIVE_READ_1D_RS(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -736,7 +736,7 @@ SUBROUTINE ACTIVE_WRITE_3D_RL(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -857,7 +857,7 @@ SUBROUTINE ACTIVE_WRITE_3D_RS(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -977,7 +977,7 @@ SUBROUTINE ACTIVE_WRITE_1D_RL(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename
@@ -1106,7 +1106,7 @@ SUBROUTINE ACTIVE_WRITE_1D_RS(
 #include "EEPARAMS.h"
 #include "SIZE.h"
 #include "PARAMS.h"
-#include "ctrl.h"
+#include "CTRL.h"
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     activeVar_file :: filename