Merge branch 'master' into addFluid+implDiv2DFlow

doc/getting_started/getting_started.rst

@@ -1495,14 +1495,6 @@ somewhat obscure, so newer users of the MITgcm are encouraged to jump to
    +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
    | :varlink:`SOLVE_DIAGONAL_KINNER`              | #undef  | choice for implicit solver routines solve_*diagonal.F suitable for AD                                                |
    +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
-   | :varlink:`COSINEMETH_III`                     | #define | selects implementation form of :math:`\cos{\varphi}` scaling of bi-harmonic term for viscosity                       |
-   |                                               |         | (note, CPP option for tracer diffusivity set independently in                                                        |
-   |                                               |         | :filelink:`GAD_OPTIONS.h <pkg/generic_advdiff/GAD_OPTIONS.h>`)                                                       |
-   +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
-   | :varlink:`ISOTROPIC_COS_SCALING`              | #undef  | selects isotropic scaling of harmonic and bi-harmonic viscous terms when using the :math:`\cos{\varphi}` scaling     |
-   |                                               |         | (note, CPP option for tracer diffusivity set independently in                                                        |
-   |                                               |         | :filelink:`GAD_OPTIONS.h <pkg/generic_advdiff/GAD_OPTIONS.h>`)                                                       |
-   +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 
 .. _default_pkg_list:
 

doc/phys_pkgs/generic_advdiff.rst

@@ -3,7 +3,6 @@
 Generic Advection/Diffusion
 ---------------------------
 
-
 The generic_advdiff package contains high-level subroutines to solve
 the advection-diffusion equation of any tracer, either active (potential
 temperature, salinity or water vapor) or passive (see :ref:`pkg/ptracer <sub_phys_pkg_ptracers>`).
@@ -38,20 +37,14 @@ There are two high-level routines:
    non-linear schemes and can not be used in conjuction with
    Adams–Bashforth time stepping.
 
-
 .. tabularcolumns:: |\Y{.4}|L|L|
 
-
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 | CPP Flag Name                                 | Default | Description                                                                                                          |
 +===============================================+=========+======================================================================================================================+
-| :varlink:`COSINEMETH_III`                     | #define | sets the implementation form of :math:`\cos{\varphi}` scaling of bi-harmonic terms for tracer diffusivity            |
-|                                               |         | (note, in :filelink:`pkg/generic_advdiff` routines the definition set here overrides whether this is defined in      |
-|                                               |         | :filelink:`model/inc/CPP_OPTIONS.h`, where the setting affects viscous term calculations)                            |
+| :varlink:`COSINEMETH_III`                     | #define | sets the form of :math:`\cos{\varphi}` scaling of horizontal bi-harmonic terms for tracer diffusivity                |
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
-| :varlink:`ISOTROPIC_COS_SCALING`              | #undef  | selects isotropic scaling of harmonic and bi-harmonic terms when using the :math:`\cos{\varphi}` scaling             |
-|                                               |         | (note, in :filelink:`pkg/generic_advdiff` routines the definition set here overrides whether this is defined in      |
-|                                               |         | :filelink:`model/inc/CPP_OPTIONS.h`, where the setting affects viscous term calculations)                            |
+| :varlink:`ISOTROPIC_COS_SCALING`              | #undef  | selects isotropic scaling of horizontal harmonic and bi-harmonic terms when using the :math:`\cos{\varphi}` scaling  |
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 | :varlink:`DISABLE_MULTIDIM_ADVECTION`         | #undef  | disables compilation of multi-dim. advection code                                                                    |
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
@@ -65,18 +58,15 @@ There are two high-level routines:
 |                                               |         | (for ptracers, except temp and salinity)                                                                             |
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 
-
-
 .. _gad_diagnostics:
 
 GAD Diagnostics
 +++++++++++++++
 
 ::
 
-
     ------------------------------------------------------------------------
-    <-Name->|Levs|<-parsing code->|<--  Units   -->|<- Tile (max=80c) 
+    <-Name->|Levs|<-parsing code->|<--  Units   -->|<- Tile (max=80c)
     ------------------------------------------------------------------------
     ADVr_TH | 15 |WM      LR      |degC.m^3/s      |Vertical   Advective Flux of Pot.Temperature
     ADVx_TH | 15 |UU   087MR      |degC.m^3/s      |Zonal      Advective Flux of Pot.Temperature
@@ -102,4 +92,3 @@ Experiments and tutorials that use GAD
 -  Tracer Sensitivity tutorial, in :filelink:`tutorial\_tracer\_adjsens <verification/tutorial_tracer_adjsens>`
    verification directory.
 
-

doc/phys_pkgs/mom_packages.rst

@@ -6,6 +6,10 @@ Momentum Packages
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 | CPP Flag Name                                 | Default | Description                                                                                                          |
 +===============================================+=========+======================================================================================================================+
+| :varlink:`COSINEMETH_III`                     | #define | sets the form of :math:`\cos{\varphi}` scaling of horizontal bi-harmonic terms for viscosity                         |
++-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
+| :varlink:`ISOTROPIC_COS_SCALING`              | #undef  | selects isotropic scaling of horiz. harmonic and bi-harmonic viscosity when using the :math:`\cos{\varphi}` scaling  |
++-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 | :varlink:`ALLOW_SMAG_3D`                      | #undef  | allow isotropic 3D Smagorinsky viscosity (:filelink:`MOM_COMMON_OPTIONS.h <pkg/mom_common/MOM_COMMON_OPTIONS.h>`)    |
 +-----------------------------------------------+---------+----------------------------------------------------------------------------------------------------------------------+
 | :varlink:`ALLOW_3D_VISCAH`                    | #undef  | allow full 3D specification of horizontal Laplacian viscosity                                                        |

doc/tag-index

@@ -1,6 +1,14 @@
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/mom_common,fluxform,vecinv:
+  - remove ISOTROPIC_COS_SCALING code from pkg/mom_vecinv/mom_vi_hdissip.F (was
+    not right); add warning (or stop if side-drag) if used with pkg/mom_vecinv.
+  - move 2 Cos-Scaling CPP options from CPP_OPTIONS.h to MOM_COMMON_OPTIONS.h
+    to be used in horizontal viscosity formulation; more consistent use of
+    GAD_OPTIONS.h where these 2 CPP options are used for horizontal diffusion.
+  - update all verification exp. customized version of CPP_OPTIONS.h,
+    GAD_OPTIONS.h and MOM_COMMON_OPTIONS.h.
 o verification/atm_gray:
   - gray atmosphere test exp moved from "verification_other".
 o model/src:

model/inc/CPP_OPTIONS.h

@@ -17,8 +17,7 @@ C CPP flags controlling particular source code features
 
 C-- Forcing code options:
 
-C o Shortwave heating as extra term in external_forcing.F
-C Note: this should be a run-time option
+C o Shortwave heating as extra term in APPLY_FORCING_T (apply_forcing.F)
 #undef SHORTWAVE_HEATING
 
 C o Include/exclude Geothermal Heat Flux at the bottom of the ocean
@@ -141,28 +140,9 @@ C   Implementation alternative (might be faster on some platforms ?)
 
 C-- Retired code options:
 
-C o ALLOW isotropic scaling of harmonic and bi-harmonic terms when
-C   using an locally isotropic spherical grid with (dlambda) x (dphi*cos(phi))
-C *only for use on a lat-lon grid*
-C   Setting this flag here affects both momentum and tracer equation unless
-C   it is set/unset again in other header fields (e.g., GAD_OPTIONS.h).
-C   The definition of the flag is commented to avoid interference with
-C   such other header files.
-C   The preferred method is specifying a value for viscAhGrid or viscA4Grid
-C   in data which is then automatically scaled by the grid size;
-C   the old method of specifying viscAh/viscA4 and this flag is provided
-C   for completeness only (and for use with the adjoint).
-c#define ISOTROPIC_COS_SCALING
-
-C o This flag selects the form of COSINE(lat) scaling of bi-harmonic term.
-C *only for use on a lat-lon grid*
-C   Has no effect if ISOTROPIC_COS_SCALING is undefined.
-C   Has no effect on vector invariant momentum equations.
-C   Setting this flag here affects both momentum and tracer equation unless
-C   it is set/unset again in other header fields (e.g., GAD_OPTIONS.h).
-C   The definition of the flag is commented to avoid interference with
-C   such other header files.
-c#define COSINEMETH_III
+C-  These 2 flags: ISOTROPIC_COS_SCALING & COSINEMETH_III have no effect
+C   here as they are reset in GAD_OPTIONS.h and in MOM_COMMON_OPTIONS.h
+C   for tracer diffusivity and momentum viscosity respectively
 
 C o Use "OLD" UV discretisation near boundaries (*not* recommended)
 C   Note - only works with pkg/mom_fluxform and "no_slip_sides=.FALSE."
@@ -182,14 +162,6 @@ C-- Other option files:
 C o Execution environment support options
 #include "CPP_EEOPTIONS.h"
 
-C o Include/exclude single header file containing multiple packages options
-C   (AUTODIFF, COST, CTRL, ECCO, EXF ...) instead of the standard way where
-C   each of the above pkg get its own options from its specific option file.
-C   Although this method, inherited from ECCO setup, has been traditionally
-C   used for all adjoint built, work is in progress to allow to use the
-C   standard method also for adjoint built.
-c#ifdef PACKAGES_CONFIG_H
-c# include "ECCO_CPPOPTIONS.h"
-c#endif
+C-  Place where multi-pkg header file ECCO_CPPOPTIONS.h used to be included
 
 #endif /* CPP_OPTIONS_H */

model/src/config_check.F

@@ -27,6 +27,9 @@ SUBROUTINE CONFIG_CHECK( myThid )
 #include "SIZE.h"
 #include "EEPARAMS.h"
 #include "PARAMS.h"
+#ifdef ALLOW_MOM_COMMON
+# include "MOM_VISC.h"
+#endif
 
 C     !INPUT/OUTPUT PARAMETERS:
 C     === Routine arguments ===
@@ -961,6 +964,37 @@ SUBROUTINE CONFIG_CHECK( myThid )
         errCount = errCount + 1
        ENDIF
       ENDIF
+#ifdef ALLOW_MOM_COMMON
+      IF ( vectorInvariantMomentum .AND. momViscosity .AND.
+     &     usingSphericalPolarGrid .AND. cosPower.NE.zeroRL ) THEN
+#ifdef ISOTROPIC_COS_SCALING
+       IF ( no_slip_sides ) THEN
+        WRITE(msgBuf,'(2A)') 'CONFIG_CHECK: inconsistent ',
+     &    'no_slip_sides & ISOTROPIC_COS_SCALING in mom_vecinv'
+        CALL PRINT_ERROR( msgBuf, myThid )
+        errCount = errCount + 1
+       ELSE
+        WRITE(msgBuf,'(2A)') '** WARNING ** CONFIG_CHECK: ',
+     &    'ISOTROPIC_COS_SCALING not implemented in mom_vecinv'
+        CALL PRINT_MESSAGE( msgBuf, errorMessageUnit,
+     &                      SQUEEZE_RIGHT, myThid )
+       ENDIF
+#endif /* ISOTROPIC_COS_SCALING */
+#ifdef COSINEMETH_III
+       IF ( useBiharmonicVisc .AND. no_slip_sides ) THEN
+        WRITE(msgBuf,'(2A)') 'CONFIG_CHECK: inconsistent ',
+     &    'no_slip_sides & COSINEMETH_III in mom_vecinv'
+        CALL PRINT_ERROR( msgBuf, myThid )
+        errCount = errCount + 1
+       ELSEIF ( useBiharmonicVisc ) THEN
+        WRITE(msgBuf,'(2A)') '** WARNING ** CONFIG_CHECK: ',
+     &    'COSINEMETH_III not implemented in mom_vecinv'
+        CALL PRINT_MESSAGE( msgBuf, errorMessageUnit,
+     &                      SQUEEZE_RIGHT, myThid )
+       ENDIF
+#endif /* COSINEMETH_III */
+      ENDIF
+#endif /* ALLOW_MOM_COMMON */
       IF ( .NOT.vectorInvariantMomentum .AND. momAdvection ) THEN
        IF ( usingCurvilinearGrid ) THEN
         WRITE(msgBuf,'(2A)') '** WARNING ** CONFIG_CHECK: ',

pkg/generic_advdiff/GAD_OPTIONS.h

@@ -19,18 +19,16 @@ C Use this file for selecting options within the GAD package
 #ifdef ALLOW_GENERIC_ADVDIFF
 C     Package-specific Options & Macros go here
 
-C This flag selects the form of COSINE(lat) scaling of bi-harmonic term.
-C *only for use on a lat-lon grid*
-C Setting this flag here only affects the bi-harmonic tracer terms; to
-C use COSINEMETH_III in the momentum equations set it CPP_OPTIONS.h
+C This flag selects the form of COSINE(lat) scaling of horizontal
+C bi-harmonic diffusivity -- only on lat-lon grid.
+C Setting this flag here only affects tracer diffusivity; to use it
+C in the momentum equations it needs to be set in MOM_COMMON_OPTIONS.h
 #define COSINEMETH_III
 
-C This selects isotropic scaling of harmonic and bi-harmonic term when
-C using the COSINE(lat) scaling.
-C Setting this flag here only affects the tracer diffusion terms; to
-C use ISOTROPIC_COS_SCALING of the horizontal viscosity terms in the
-C momentum equations set it CPP_OPTIONS.h; the following line
-C even overrides setting the flag in CPP_OPTIONS.h
+C This selects isotropic scaling of horizontal harmonic and bi-harmonic
+C diffusivity when using the COSINE(lat) scaling -- only on lat-lon grid.
+C Setting this flag here only affects tracer diffusivity; to use it
+C in the momentum equations it needs to be set in MOM_COMMON_OPTIONS.h
 #undef ISOTROPIC_COS_SCALING
 
 C As of checkpoint41, the inclusion of multi-dimensional advection

pkg/ggl90/ggl90_calc.F

@@ -1,4 +1,7 @@
 #include "GGL90_OPTIONS.h"
+#ifdef ALLOW_GENERIC_ADVDIFF
+# include "GAD_OPTIONS.h"
+#endif
 #ifdef ALLOW_AUTODIFF
 # include "AUTODIFF_OPTIONS.h"
 #endif

pkg/gmredi/gmredi_calc_geom.F

@@ -1,4 +1,7 @@
 #include "GMREDI_OPTIONS.h"
+#ifdef ALLOW_GENERIC_ADVDIFF
+# include "GAD_OPTIONS.h"
+#endif
 
 CBOP
 C !ROUTINE: GMREDI_CALC_GEOM

pkg/mom_common/MOM_COMMON_OPTIONS.h

@@ -9,6 +9,18 @@ C Use this file for selecting CPP options within the mom_common package
 #ifdef ALLOW_MOM_COMMON
 C     Package-specific options go here
 
+C This flag selects the form of COSINE(lat) scaling of horizontal
+C bi-harmonic viscosity -- only on lat-lon grid.
+C Setting this flag here only affects momentum viscosity; to use it
+C in the tracer equations it needs to be set in GAD_OPTIONS.h
+#define COSINEMETH_III
+
+C This selects isotropic scaling of horizontal harmonic and bi-harmonic
+C viscosity when using the COSINE(lat) scaling -- only on lat-lon grid.
+C Setting this flag here only affects momentum viscosity; to use it
+C in the tracer equations it needs to be set in GAD_OPTIONS.h
+#undef ISOTROPIC_COS_SCALING
+
 C allow LeithQG coefficient to be calculated
 #undef ALLOW_LEITH_QG
 

pkg/mom_fluxform/mom_u_del2u.F

@@ -1,4 +1,7 @@
 #include "MOM_FLUXFORM_OPTIONS.h"
+#ifdef ALLOW_MOM_COMMON
+# include "MOM_COMMON_OPTIONS.h"
+#endif
 
 CBOP
 C !ROUTINE: MOM_U_DEL2U
@@ -40,7 +43,7 @@ SUBROUTINE MOM_U_DEL2U(
 
 C !LOCAL VARIABLES: ====================================================
 C  i,j                  :: loop indices
-      INTEGER I,J
+      INTEGER i,j
       _RL fZon(1-OLx:sNx+OLx,1-OLy:sNy+OLy)
       _RL fMer(1-OLx:sNx+OLx,1-OLy:sNy+OLy)
       _RS hFacZClosedS, hFacZClosedN
@@ -54,7 +57,7 @@ SUBROUTINE MOM_U_DEL2U(
      &   *_recip_dxF(i,j,bi,bj)
      &   *(uFld(i+1,j)-uFld(i,j))
 #ifdef COSINEMETH_III
-     &   *sqCosFacU(J,bi,bj)
+     &   *sqCosFacU(j,bi,bj)
 #endif
 #ifdef ALLOW_OBCS
      &   *maskInC(i,j,bi,bj)
@@ -72,7 +75,7 @@ SUBROUTINE MOM_U_DEL2U(
      &   *_recip_dyU(i,j,bi,bj)
      &   *(uFld(i,j)-uFld(i,j-1))
 #if (defined (ISOTROPIC_COS_SCALING) && defined (COSINEMETH_III))
-     &   *sqCosFacV(J,bi,bj)
+     &   *sqCosFacV(j,bi,bj)
 #endif
 c    &   *deepFacC(k)        ! dxV scaling factor
 c    &   *recip_deepFacC(k)  ! recip_dyU scaling factor

pkg/mom_fluxform/mom_u_xviscflux.F

@@ -1,4 +1,7 @@
 #include "MOM_FLUXFORM_OPTIONS.h"
+#ifdef ALLOW_MOM_COMMON
+# include "MOM_COMMON_OPTIONS.h"
+#endif
 
 CBOP
 C !ROUTINE: MOM_U_XVISCFLUX
@@ -44,22 +47,22 @@ SUBROUTINE MOM_U_XVISCFLUX(
 
 C !LOCAL VARIABLES: ====================================================
 C  i,j                  :: loop indices
-      INTEGER I,J
+      INTEGER i,j
 CEOP
 
 C     - Laplacian  and bi-harmonic terms
-      DO j=1-Oly,sNy+Oly-1
-       DO i=1-Olx,sNx+Olx-1
+      DO j=1-OLy,sNy+OLy-1
+       DO i=1-OLx,sNx+OLx-1
         xViscFluxU(i,j) =
      &    _dyF(i,j,bi,bj)*drF(k)*_hFacC(i,j,k,bi,bj)
      &     *(
      &       -viscAh_D(i,j)*( uFld(i+1,j)-uFld(i,j) )
-     &       *cosFacU(J,bi,bj)
+     &       *cosFacU(j,bi,bj)
      &       +viscA4_D(i,j)*(del2u(i+1,j)-del2u(i,j))
 #ifdef COSINEMETH_III
-     &       *sqCosFacU(J,bi,bj)
+     &       *sqCosFacU(j,bi,bj)
 #else
-     &       *cosFacU(J,bi,bj)
+     &       *cosFacU(j,bi,bj)
 #endif
      &      )*_recip_dxF(i,j,bi,bj)
 c    &       *deepFacC(k)        ! dyF scaling factor

pkg/mom_fluxform/mom_u_yviscflux.F

@@ -1,4 +1,7 @@
 #include "MOM_FLUXFORM_OPTIONS.h"
+#ifdef ALLOW_MOM_COMMON
+# include "MOM_COMMON_OPTIONS.h"
+#endif
 
 CBOP
 C !ROUTINE: MOM_U_YVISCFLUX
@@ -45,25 +48,25 @@ SUBROUTINE MOM_U_YVISCFLUX(
 
 C !LOCAL VARIABLES: ====================================================
 C  i,j                  :: loop indices
-      INTEGER I,J
+      INTEGER i,j
 CEOP
 
 C     - Laplacian  and bi-harmonic terms
-      DO j=1-Oly+1,sNy+Oly
-       DO i=1-Olx,sNx+Olx
+      DO j=1-OLy+1,sNy+OLy
+       DO i=1-OLx,sNx+OLx
         yViscFluxU(i,j) =
      &    _dxV(i,j,bi,bj)*drF(k)*hFacZ(i,j)
      &     *(
      &       -viscAh_Z(i,j)*( uFld(i,j)-uFld(i,j-1) )
 #ifdef ISOTROPIC_COS_SCALING
-     &       *cosFacV(J,bi,bj)
+     &       *cosFacV(j,bi,bj)
 #endif
      &       +viscA4_Z(i,j)*(del2u(i,j)-del2u(i,j-1))
 #ifdef ISOTROPIC_COS_SCALING
 #ifdef COSINEMETH_III
-     &       *sqCosFacV(J,bi,bj)
+     &       *sqCosFacV(j,bi,bj)
 #else
-     &       *cosFacV(J,bi,bj)
+     &       *cosFacV(j,bi,bj)
 #endif
 #endif
      &      )*_recip_dyU(i,j,bi,bj)