Merge pull request NOAA-EMC#18 from NOAA-GFDL/dev/gfdl

Merge in latest dev/gfdl updates

.gitlab-ci.yml

@@ -116,8 +116,8 @@ run:
     - time tar zxf $CACHE_DIR/build-intel-repro-$CI_PIPELINE_ID.tgz
     - time tar zxf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz
     # time tar zxf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz
-    - echo "make -f MRS/Makefile.tests all -B" > job.sh
-    - msub -l partition=c4,nodes=29,walltime=00:31:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_regression -K job.sh
+    - (echo '#!/bin/tcsh';echo 'make -f MRS/Makefile.tests all -B') > job.sh
+    - sbatch --clusters=c3,c4 --nodes=29 --time=0:34:00 --account=gfdl_o --qos=debug --job-name=mom6_regressions --output=log.$CI_PIPELINE_ID --wait job.sh
     - cat log.$CI_PIPELINE_ID
     - test -f restart_results_gnu.tar.gz
     - time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz

config_src/coupled_driver/MOM_surface_forcing.F90

@@ -1203,7 +1203,7 @@ subroutine surface_forcing_init(Time, G, US, param_file, diag, CS)
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "RESTORE_TEMPERATURE", CS%restore_temp, &
                  "If true, the coupled driver will add a  \n"//&
-                 "heat flux that drives sea-surface temperauture \n"//&
+                 "heat flux that drives sea-surface temperature \n"//&
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "ADJUST_NET_SRESTORE_TO_ZERO", &
                  CS%adjust_net_srestore_to_zero, &

config_src/mct_driver/MOM_ocean_model.F90

@@ -313,7 +313,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "RESTORE_TEMPERATURE",OS%restore_temp, &
                  "If true, the coupled driver will add a  \n"//&
-                 "heat flux that drives sea-surface temperauture \n"//&
+                 "heat flux that drives sea-surface temperature \n"//&
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "RHO_0", Rho0, &
                  "The mean ocean density used with BOUSSINESQ true to \n"//&

config_src/nuopc_driver/MOM_ocean_model.F90

@@ -334,7 +334,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "RESTORE_TEMPERATURE",OS%restore_temp, &
                  "If true, the coupled driver will add a  \n"//&
-                 "heat flux that drives sea-surface temperauture \n"//&
+                 "heat flux that drives sea-surface temperature \n"//&
                  "toward specified values.", default=.false.)
   call get_param(param_file, mdl, "RHO_0", Rho0, &
                  "The mean ocean density used with BOUSSINESQ true to \n"//&

src/ALE/MOM_ALE.F90

@@ -177,7 +177,7 @@ subroutine ALE_init( param_file, GV, US, max_depth, CS)
                  trim(remappingSchemesDoc), default=remappingDefaultScheme)
   call get_param(param_file, mdl, "FATAL_CHECK_RECONSTRUCTIONS", check_reconstruction, &
                  "If true, cell-by-cell reconstructions are checked for\n"//&
-                 "consistency and if non-monotonicty or an inconsistency is\n"//&
+                 "consistency and if non-monotonicity or an inconsistency is\n"//&
                  "detected then a FATAL error is issued.", default=.false.)
   call get_param(param_file, mdl, "FATAL_CHECK_REMAPPING", check_remapping, &
                  "If true, the results of remapping are checked for\n"//&
@@ -215,7 +215,7 @@ subroutine ALE_init( param_file, GV, US, max_depth, CS)
   call get_param(param_file, mdl, "REGRID_FILTER_DEEP_DEPTH", filter_deep_depth, &
                  "The depth below which full time-filtering is applied with time-scale\n"//&
                  "REGRID_TIME_SCALE. Between depths REGRID_FILTER_SHALLOW_DEPTH and\n"//&
-                 "REGRID_FILTER_SHALLOW_DEPTH the filter wieghts adopt a cubic profile.", &
+                 "REGRID_FILTER_SHALLOW_DEPTH the filter weights adopt a cubic profile.", &
                  units="m", default=0., scale=GV%m_to_H)
   call set_regrid_params(CS%regridCS, depth_of_time_filter_shallow=filter_shallow_depth, &
                                       depth_of_time_filter_deep=filter_deep_depth)

src/ALE/MOM_regridding.F90

@@ -140,8 +140,8 @@ module MOM_regridding
 !> Documentation for coordinate options
 character(len=*), parameter, public :: regriddingCoordinateModeDoc = &
                  " LAYER - Isopycnal or stacked shallow water layers\n"//&
-                 " ZSTAR, Z* - stetched geopotential z*\n"//&
-                 " SIGMA_SHELF_ZSTAR - stetched geopotential z* ignoring shelf\n"//&
+                 " ZSTAR, Z* - stretched geopotential z*\n"//&
+                 " SIGMA_SHELF_ZSTAR - stretched geopotential z* ignoring shelf\n"//&
                  " SIGMA - terrain following coordinates\n"//&
                  " RHO   - continuous isopycnal\n"//&
                  " HYCOM1 - HyCOM-like hybrid coordinate\n"//&
@@ -230,8 +230,7 @@ subroutine initialize_regridding(CS, GV, US, max_depth, param_file, mdl, coord_m
   if (main_parameters) then
     ! Read coordinate units parameter (main model = REGRIDDING_COORDINATE_UNITS)
     call get_param(param_file, mdl, "REGRIDDING_COORDINATE_UNITS", coord_units, &
-                 "Units of the regridding coordinuate.",& !### Spelling error "coordinuate"
-                 default=coordinateUnits(coord_mode))
+                 "Units of the regridding coordinate.", default=coordinateUnits(coord_mode))
   else
     coord_units=coordinateUnits(coord_mode)
   endif
@@ -420,7 +419,7 @@ subroutine initialize_regridding(CS, GV, US, max_depth, param_file, mdl, coord_m
       call log_param(param_file, mdl, "!"//coord_res_param, dz, &
                trim(message), units=coordinateUnits(coord_mode))
       call log_param(param_file, mdl, "!TARGET_DENSITIES", rho_target, &
-               'HYBRID target densities for itnerfaces', units=coordinateUnits(coord_mode))
+               'HYBRID target densities for interfaces', units=coordinateUnits(coord_mode))
     endif
   elseif (index(trim(string),'WOA09')==1) then
     if (len_trim(string)==5) then
@@ -503,7 +502,7 @@ subroutine initialize_regridding(CS, GV, US, max_depth, param_file, mdl, coord_m
   if (main_parameters .and. coord_is_state_dependent) then
     call get_param(param_file, mdl, "REGRID_COMPRESSIBILITY_FRACTION", tmpReal, &
                  "When interpolating potential density profiles we can add\n"//&
-                 "some artificial compressibility solely to make homogenous\n"//&
+                 "some artificial compressibility solely to make homogeneous\n"//&
                  "regions appear stratified.", default=0.)
     call set_regrid_params(CS, compress_fraction=tmpReal)
   endif

src/ALE/coord_rho.F90

@@ -286,15 +286,15 @@ subroutine build_rho_column_iteratively(CS, remapCS, nz, depth, h, T, S, eqn_of_
     zInterface(1) = 0.
     do k = 1,nz
       zInterface(k+1) = zInterface(k) - h1(k)
-      ! Adjust interface position to accomodate inflating layers
+      ! Adjust interface position to accommodate inflating layers
       ! without disturbing the interface above
     enddo
   else
     ! The rest of the model defines grids integrating up from the bottom
     zInterface(nz+1) = -depth
     do k = nz,1,-1
       zInterface(k) = zInterface(k+1) + h1(k)
-      ! Adjust interface position to accomodate inflating layers
+      ! Adjust interface position to accommodate inflating layers
       ! without disturbing the interface above
     enddo
   endif

src/ALE/coord_sigma.F90

@@ -72,7 +72,7 @@ subroutine build_sigma_column(CS, depth, totalThickness, zInterface)
   zInterface(CS%nk+1) = -depth
   do k = CS%nk,1,-1
     zInterface(k) = zInterface(k+1) + (totalThickness * CS%coordinateResolution(k))
-    ! Adjust interface position to accomodate inflating layers
+    ! Adjust interface position to accommodate inflating layers
     ! without disturbing the interface above
     if (zInterface(k) < (zInterface(k+1) + CS%min_thickness)) then
       zInterface(k) = zInterface(k+1) + CS%min_thickness

src/core/MOM.F90

@@ -1516,7 +1516,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
                           count_calls, tracer_flow_CSp)
   type(time_type), target,   intent(inout) :: Time        !< model time, set in this routine
   type(time_type),           intent(in)    :: Time_init   !< The start time for the coupled model's calendar
-  type(param_file_type),     intent(out)   :: param_file  !< structure indicating paramater file to parse
+  type(param_file_type),     intent(out)   :: param_file  !< structure indicating parameter file to parse
   type(directories),         intent(out)   :: dirs        !< structure with directory paths
   type(MOM_control_struct),  pointer       :: CS          !< pointer set in this routine to MOM control structure
   type(MOM_restart_CS),      pointer       :: restart_CSp !< pointer set in this routine to the
@@ -1830,6 +1830,10 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
                  "If true, limit salinity to being positive. (The sea-ice \n"//&
                  "model may ask for more salt than is available and \n"//&
                  "drive the salinity negative otherwise.)", default=.false.)
+    call get_param(param_file, "MOM", "MIN_SALINITY", CS%tv%min_salinity, &
+                 "The minimum value of salinity when BOUND_SALINITY=True. \n"//&
+                 "The default is 0.01 for backward compatibility but ideally \n"//&
+                 "should be 0.", units="PPT", default=0.01, do_not_log=.not.bound_salinity)
     call get_param(param_file, "MOM", "C_P", CS%tv%C_p, &
                  "The heat capacity of sea water, approximated as a \n"//&
                  "constant. This is only used if ENABLE_THERMODYNAMICS is \n"//&
@@ -3410,7 +3414,7 @@ end subroutine MOM_end
 !!  * src/tracer:
 !!    These files handle the lateral transport and diffusion of
 !!    tracers, or are the code to implement various passive tracer
-!!    packages.  Additional tracer packages are readily accomodated.
+!!    packages.  Additional tracer packages are readily accommodated.
 !!
 !!  * src/user:
 !!    These are either stub routines that a user could use to change

src/core/MOM_PressureForce_analytic_FV.F90

@@ -831,8 +831,8 @@ subroutine PressureForce_AFV_init(Time, G, GV, US, param_file, diag, CS, tides_C
                  "The default is set by USE_REGRIDDING.", &
                  default=use_ALE )
   call get_param(param_file, mdl, "PRESSURE_RECONSTRUCTION_SCHEME", CS%Recon_Scheme, &
-                 "Order of vertical reconstruction of T/S to use in the\n"//&
-                 "integrals within the FV pressure gradient calculation."//&
+                 "Order of vertical reconstruction of T/S to use in the \n"//&
+                 "integrals within the FV pressure gradient calculation.\n"//&
                  " 0: PCM or no reconstruction.\n"//&
                  " 1: PLM reconstruction.\n"//&
                  " 2: PPM reconstruction.", default=1)

src/core/MOM_PressureForce_blocked_AFV.F90

@@ -823,8 +823,8 @@ subroutine PressureForce_blk_AFV_init(Time, G, GV, US, param_file, diag, CS, tid
                  "The default is set by USE_REGRIDDING.", &
                  default=use_ALE )
   call get_param(param_file, mdl, "PRESSURE_RECONSTRUCTION_SCHEME", CS%Recon_Scheme, &
-                 "Order of vertical reconstruction of T/S to use in the\n"//&
-                 "integrals within the FV pressure gradient calculation."//&
+                 "Order of vertical reconstruction of T/S to use in the \n"//&
+                 "integrals within the FV pressure gradient calculation.\n"//&
                  " 0: PCM or no reconstruction.\n"//&
                  " 1: PLM reconstruction.\n"//&
                  " 2: PPM reconstruction.", default=1)

src/core/MOM_barotropic.F90

@@ -199,7 +199,7 @@ module MOM_barotropic
                              !! update at the start of a call to btstep.  The
                              !! default is 1.
   logical :: BT_project_velocity !< If true, step the barotropic velocity first
-                             !! and project out the velocity tendancy by 1+BEBT
+                             !! and project out the velocity tendency by 1+BEBT
                              !! when calculating the transport.  The default
                              !! (false) is to use a predictor continuity step to
                              !! find the pressure field, and then do a corrector
@@ -3785,7 +3785,7 @@ subroutine barotropic_init(u, v, h, eta, Time, G, GV, US, param_file, diag, CS,
   call get_param(param_file, mdl, "BT_CONT_CORR_BOUNDS", CS%BT_cont_bounds, &
                  "If true, and BOUND_BT_CORRECTION is true, use the \n"//&
                  "BT_cont_type variables to set limits determined by \n"//&
-                 "MAXCFL_BT_CONT on the CFL number of the velocites \n"//&
+                 "MAXCFL_BT_CONT on the CFL number of the velocities \n"//&
                  "that are likely to be driven by the corrective mass fluxes.", &
                  default=.true.) !, do_not_log=.not.CS%bound_BT_corr)
   call get_param(param_file, mdl, "ADJUST_BT_CONT", CS%adjust_BT_cont, &
@@ -3846,7 +3846,7 @@ subroutine barotropic_init(u, v, h, eta, Time, G, GV, US, param_file, diag, CS,
                  units="nondim", default=1)
   call get_param(param_file, mdl, "BT_PROJECT_VELOCITY", CS%BT_project_velocity,&
                  "If true, step the barotropic velocity first and project \n"//&
-                 "out the velocity tendancy by 1+BEBT when calculating the \n"//&
+                 "out the velocity tendency by 1+BEBT when calculating the \n"//&
                  "transport.  The default (false) is to use a predictor \n"//&
                  "continuity step to find the pressure field, and then \n"//&
                  "to do a corrector continuity step using a weighted \n"//&
@@ -3917,7 +3917,7 @@ subroutine barotropic_init(u, v, h, eta, Time, G, GV, US, param_file, diag, CS,
                  "barotropic steps.", default=.false.)
   call get_param(param_file, mdl, "BT_LINEAR_WAVE_DRAG", CS%linear_wave_drag, &
                  "If true, apply a linear drag to the barotropic velocities, \n"//&
-                 "using rates set by lin_drag_u & _vdivided by the depth of \n"//&
+                 "using rates set by lin_drag_u & _v divided by the depth of \n"//&
                  "the ocean.  This was introduced to facilitate tide modeling.", &
                  default=.false.)
   call get_param(param_file, mdl, "BT_WAVE_DRAG_FILE", wave_drag_file, &

src/core/MOM_continuity_PPM.F90

@@ -2264,7 +2264,7 @@ subroutine continuity_PPM_init(Time, G, GV, param_file, diag, CS)
   call get_param(param_file, mdl, "SIMPLE_2ND_PPM_CONTINUITY", CS%simple_2nd, &
                  "If true, CONTINUITY_PPM uses a simple 2nd order \n"//&
                  "(arithmetic mean) interpolation of the edge values. \n"//&
-                 "This may give better PV conservation propterties. While \n"//&
+                 "This may give better PV conservation properties. While \n"//&
                  "it formally reduces the accuracy of the continuity \n"//&
                  "solver itself in the strongly advective limit, it does \n"//&
                  "not reduce the overall order of accuracy of the dynamic \n"//&

src/core/MOM_open_boundary.F90

@@ -305,8 +305,9 @@ subroutine open_boundary_config(G, US, param_file, OBC)
   real               :: Lscale_in, Lscale_out ! parameters controlling tracer values at the boundaries
   allocate(OBC)
 
-  call log_version(param_file, mdl, version, "Controls where open boundaries are located, what "//&
-                 "kind of boundary condition to impose, and what data to apply, if any.")
+  call log_version(param_file, mdl, version, &
+                 "Controls where open boundaries are located, what kind of boundary condition \n"//&
+                 "to impose, and what data to apply, if any.")
   call get_param(param_file, mdl, "OBC_NUMBER_OF_SEGMENTS", OBC%number_of_segments, &
                  "The number of open boundary segments.", &
                  default=0)

src/core/MOM_variables.F90

@@ -80,7 +80,7 @@ module MOM_variables
 !> Pointers to an assortment of thermodynamic fields that may be available, including
 !! potential temperature, salinity, heat capacity, and the equation of state control structure.
 type, public :: thermo_var_ptrs
-!   If allocated, the following variables have nz layers.
+  ! If allocated, the following variables have nz layers.
   real, pointer :: T(:,:,:) => NULL() !< Potential temperature [degC].
   real, pointer :: S(:,:,:) => NULL() !< Salnity [PSU] or [gSalt/kg], generically [ppt].
   type(EOS_type), pointer :: eqn_of_state => NULL() !< Type that indicates the
@@ -95,14 +95,16 @@ module MOM_variables
                          !! actually the conservative temperature [degC].
   logical :: S_is_absS = .false. !< If true, the salinity variable tv%S is
                          !! actually the absolute salinity in units of [gSalt/kg].
-!  These arrays are accumulated fluxes for communication with other components.
+  real :: min_salinity = 0.01 !< The minimum value of salinity when BOUND_SALINITY=True [ppt].
+                         !! The default is 0.01 for backward compatibility but should be 0.
+  ! These arrays are accumulated fluxes for communication with other components.
   real, dimension(:,:), pointer :: frazil => NULL()
                          !< The energy needed to heat the ocean column to the
                          !! freezing point since calculate_surface_state was2
                          !! last called [J m-2].
   real, dimension(:,:), pointer :: salt_deficit => NULL()
                          !<   The salt needed to maintain the ocean column
-                         !! at a minumum salinity of 0.01 PSU since the last time
+                         !! at a minimum salinity of MIN_SALINITY since the last time
                          !! that calculate_surface_state was called, [gSalt m-2].
   real, dimension(:,:), pointer :: TempxPmE => NULL()
                          !<   The net inflow of water into the ocean times the
@@ -206,7 +208,8 @@ module MOM_variables
     ustar_BBL => NULL()      !< The turbulence velocity in the bottom boundary layer at h points [Z s-1 ~> m s-1].
   real, pointer, dimension(:,:) :: TKE_BBL => NULL()
                              !< A term related to the bottom boundary layer source of turbulent kinetic
-                             !! energy, currently in [m3 s-3], but will later be changed to [W m-2].
+                             !! energy, currently in [Z3 T-3 ~> m3 s-3], but may at some time be changed
+                             !! to [kg Z3 m-3 T-3 ~> W m-2].
   real, pointer, dimension(:,:) :: &
     taux_shelf => NULL(), &  !< The zonal stresses on the ocean under shelves [Pa].
     tauy_shelf => NULL()     !< The meridional stresses on the ocean under shelves [Pa].

src/core/MOM_verticalGrid.F90

@@ -50,7 +50,7 @@ module MOM_verticalGrid
     g_prime, &          !< The reduced gravity at each interface [m2 Z-1 s-2 ~> m s-2].
     Rlay                !< The target coordinate value (potential density) in each layer [kg m-3].
   integer :: nkml = 0   !< The number of layers at the top that should be treated
-                        !! as parts of a homogenous region.
+                        !! as parts of a homogeneous region.
   integer :: nk_rho_varies = 0 !< The number of layers at the top where the
                         !! density does not track any target density.
   real :: H_to_kg_m2    !< A constant that translates thicknesses from the units of thickness to kg m-2.
@@ -100,7 +100,7 @@ subroutine verticalGridInit( param_file, GV, US )
   call get_param(param_file, mdl, "BOUSSINESQ", GV%Boussinesq, &
                  "If true, make the Boussinesq approximation.", default=.true.)
   call get_param(param_file, mdl, "ANGSTROM", GV%Angstrom_m, &
-                 "The minumum layer thickness, usually one-Angstrom.", &
+                 "The minimum layer thickness, usually one-Angstrom.", &
                  units="m", default=1.0e-10)
   call get_param(param_file, mdl, "H_RESCALE_POWER", H_power, &
                  "An integer power of 2 that is used to rescale the model's \n"//&