Merge pull request #52 from NOAA-GFDL/dev/gfdl

Merge in latest dev/gfdl updates

.gitlab-ci.yml

@@ -63,6 +63,7 @@ gnu:ocean-only-nolibs:
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
     - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{solo_driver,dynamic_symmetric} ../../../src ../../MOM6-examples/src/FMS
+    - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
 
@@ -75,6 +76,7 @@ gnu:ice-ocean-nolibs:
     - make -f MRS/Makefile.build build/gnu/env && cd build/gnu
     # mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
     - ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
+    - sed -i '/FMS\/.*\/test_/d' path_names
     - ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
     - time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
 

config_src/solo_driver/MOM_surface_forcing.F90

@@ -207,7 +207,7 @@ module MOM_surface_forcing
   type(Neverland_surface_forcing_CS), pointer :: Neverland_forcing_CSp => NULL()
   type(idealized_hurricane_CS), pointer :: idealized_hurricane_CSp => NULL()
   type(SCM_CVmix_tests_CS),      pointer :: SCM_CVmix_tests_CSp => NULL()
-  !!@}
+  !>@}
 
 end type surface_forcing_CS
 

src/ALE/regrid_interp.F90

@@ -54,7 +54,7 @@ module regrid_interp
 !>@{ Interpolant degrees
 integer, parameter :: DEGREE_1 = 1, DEGREE_2 = 2, DEGREE_3 = 3, DEGREE_4 = 4
 integer, public, parameter :: DEGREE_MAX = 5
-!!@}
+!>@}
 
 !> When the N-R algorithm produces an estimate that lies outside [0,1], the
 !! estimate is set to be equal to the boundary location, 0 or 1, plus or minus

src/core/MOM.F90

@@ -143,7 +143,8 @@ module MOM
 !> A structure with diagnostic IDs of the state variables
 type MOM_diag_IDs
   !>@{ 3-d state field diagnostic IDs
-  integer :: id_u  = -1, id_v  = -1, id_h  = -1  !!@}
+  integer :: id_u  = -1, id_v  = -1, id_h  = -1
+  !>@}
   !> 2-d state field diagnotic ID
   integer :: id_ssh_inst = -1
 end type MOM_diag_IDs
@@ -389,7 +390,7 @@ module MOM
 integer :: id_clock_ALE
 integer :: id_clock_other
 integer :: id_clock_offline_tracer
-!!@}
+!>@}
 
 contains
 

src/core/MOM_CoriolisAdv.F90

@@ -73,7 +73,8 @@ module MOM_CoriolisAdv
   type(diag_ctrl), pointer :: diag !< A structure that is used to regulate the timing of diagnostic output.
   !>@{ Diagnostic IDs
   integer :: id_rv = -1, id_PV = -1, id_gKEu = -1, id_gKEv = -1
-  integer :: id_rvxu = -1, id_rvxv = -1   !!@}
+  integer :: id_rvxu = -1, id_rvxv = -1
+  !>@}
 end type CoriolisAdv_CS
 
 !>@{ Enumeration values for Coriolis_Scheme
@@ -89,21 +90,21 @@ module MOM_CoriolisAdv
 character*(20), parameter :: SADOURNY75_ENSTRO_STRING = "SADOURNY75_ENSTRO"
 character*(20), parameter :: ARAKAWA_LAMB_STRING = "ARAKAWA_LAMB81"
 character*(20), parameter :: AL_BLEND_STRING = "ARAKAWA_LAMB_BLEND"
-!!@}
+!>@}
 !>@{ Enumeration values for KE_Scheme
 integer, parameter :: KE_ARAKAWA        = 10
 integer, parameter :: KE_SIMPLE_GUDONOV = 11
 integer, parameter :: KE_GUDONOV        = 12
 character*(20), parameter :: KE_ARAKAWA_STRING = "KE_ARAKAWA"
 character*(20), parameter :: KE_SIMPLE_GUDONOV_STRING = "KE_SIMPLE_GUDONOV"
 character*(20), parameter :: KE_GUDONOV_STRING = "KE_GUDONOV"
-!!@}
+!>@}
 !>@{ Enumeration values for PV_Adv_Scheme
 integer, parameter :: PV_ADV_CENTERED   = 21
 integer, parameter :: PV_ADV_UPWIND1    = 22
 character*(20), parameter :: PV_ADV_CENTERED_STRING = "PV_ADV_CENTERED"
 character*(20), parameter :: PV_ADV_UPWIND1_STRING = "PV_ADV_UPWIND1"
-!!@}
+!>@}
 
 contains
 

src/core/MOM_PressureForce_Montgomery.F90

@@ -46,7 +46,7 @@ module MOM_PressureForce_Mont
                             !! deriving from density gradients within layers [L T-2 ~> m s-2].
   !>@{ Diagnostic IDs
   integer :: id_PFu_bc = -1, id_PFv_bc = -1, id_e_tidal = -1
-  !!@}
+  !>@}
   type(tidal_forcing_CS), pointer :: tides_CSp => NULL() !< The tidal forcing control structure
 end type PressureForce_Mont_CS
 

src/core/MOM_barotropic.F90

@@ -86,7 +86,7 @@ module MOM_barotropic
   !>@{ Index ranges for the open boundary conditions
   integer :: is_u_obc, ie_u_obc, js_u_obc, je_u_obc
   integer :: is_v_obc, ie_v_obc, js_v_obc, je_v_obc
-  !!@}
+  !>@}
   logical :: is_alloced = .false. !< True if BT_OBC is in use and has been allocated
 
   type(group_pass_type) :: pass_uv   !< Structure for group halo pass
@@ -273,10 +273,10 @@ module MOM_barotropic
   type(time_type), pointer :: Time  => NULL() !< A pointer to the ocean models clock.
   type(diag_ctrl), pointer :: diag => NULL()  !< A structure that is used to regulate
                              !! the timing of diagnostic output.
-  type(MOM_domain_type), pointer :: BT_Domain => NULL()
+  type(MOM_domain_type), pointer :: BT_Domain => NULL()  !< Barotropic MOM domain
   type(hor_index_type), pointer :: debug_BT_HI => NULL() !< debugging copy of horizontal index_type
-  type(tidal_forcing_CS), pointer :: tides_CSp => NULL()
-  logical :: module_is_initialized = .false.
+  type(tidal_forcing_CS), pointer :: tides_CSp => NULL() !< Control structure for tides
+  logical :: module_is_initialized = .false.  !< If true, module has been initialized
 
   integer :: isdw !< The lower i-memory limit for the wide halo arrays.
   integer :: iedw !< The upper i-memory limit for the wide halo arrays.
@@ -312,7 +312,7 @@ module MOM_barotropic
   integer :: id_BTC_FA_v_NN = -1, id_BTC_FA_v_N0 = -1, id_BTC_FA_v_S0 = -1, id_BTC_FA_v_SS = -1
   integer :: id_BTC_vbt_NN = -1, id_BTC_vbt_SS = -1
   integer :: id_uhbt0 = -1, id_vhbt0 = -1
-  !!@}
+  !>@}
 
 end type barotropic_CS
 
@@ -360,14 +360,14 @@ module MOM_barotropic
 type, private :: memory_size_type
   !>@{ Currently active memory limits
   integer :: isdw, iedw, jsdw, jedw ! The memory limits of the wide halo arrays.
-  !!@}
+  !>@}
 end type memory_size_type
 
 !>@{ CPU time clock IDs
 integer :: id_clock_sync=-1, id_clock_calc=-1
 integer :: id_clock_calc_pre=-1, id_clock_calc_post=-1
 integer :: id_clock_pass_step=-1, id_clock_pass_pre=-1, id_clock_pass_post=-1
-!!@}
+!>@}
 
 !>@{ Enumeration values for various schemes
 integer, parameter :: HARMONIC        = 1
@@ -379,7 +379,7 @@ module MOM_barotropic
 character*(20), parameter :: HARMONIC_STRING = "HARMONIC"
 character*(20), parameter :: ARITHMETIC_STRING = "ARITHMETIC"
 character*(20), parameter :: BT_CONT_STRING = "FROM_BT_CONT"
-!!@}
+!>@}
 
 contains
 

src/core/MOM_boundary_update.F90

@@ -46,7 +46,7 @@ module MOM_boundary_update
   type(tidal_bay_OBC_CS), pointer :: tidal_bay_OBC_CSp => NULL()
   type(shelfwave_OBC_CS), pointer :: shelfwave_OBC_CSp => NULL()
   type(dyed_channel_OBC_CS), pointer :: dyed_channel_OBC_CSp => NULL()
-  !!@}
+  !>@}
 end type update_OBC_CS
 
 integer :: id_clock_pass !< A CPU time clock ID

src/core/MOM_continuity_PPM.F90

@@ -22,7 +22,7 @@ module MOM_continuity_PPM
 
 !>@{ CPU time clock IDs
 integer :: id_clock_update, id_clock_correct
-!!@}
+!>@}
 
 !> Control structure for mom_continuity_ppm
 type, public :: continuity_PPM_CS ; private
@@ -66,7 +66,7 @@ module MOM_continuity_PPM
 type :: loop_bounds_type ; private
   !>@{ Loop bounds
   integer :: ish, ieh, jsh, jeh
-  !!@}
+  !>@}
 end type loop_bounds_type
 
 contains

src/core/MOM_dynamics_split_RK2.F90

@@ -163,7 +163,7 @@ module MOM_dynamics_split_RK2
   ! Split scheme only.
   integer :: id_uav        = -1, id_vav        = -1
   integer :: id_u_BT_accel = -1, id_v_BT_accel = -1
-  !!@}
+  !>@}
 
   type(diag_ctrl), pointer       :: diag !< A structure that is used to regulate the
                                          !! timing of diagnostic output.
@@ -227,7 +227,7 @@ module MOM_dynamics_split_RK2
 integer :: id_clock_continuity, id_clock_thick_diff
 integer :: id_clock_btstep, id_clock_btcalc, id_clock_btforce
 integer :: id_clock_pass, id_clock_pass_init
-!!@}
+!>@}
 
 contains
 

src/core/MOM_dynamics_unsplit.F90

@@ -127,7 +127,7 @@ module MOM_dynamics_unsplit
   !>@{ Diagnostic IDs
   integer :: id_uh = -1, id_vh = -1
   integer :: id_PFu = -1, id_PFv = -1, id_CAu = -1, id_CAv = -1
-  !!@}
+  !>@}
 
   type(diag_ctrl), pointer :: diag => NULL() !< A structure that is used to
                                    !! regulate the timing of diagnostic output.
@@ -174,7 +174,7 @@ module MOM_dynamics_unsplit
 integer :: id_clock_Cor, id_clock_pres, id_clock_vertvisc
 integer :: id_clock_continuity, id_clock_horvisc, id_clock_mom_update
 integer :: id_clock_pass, id_clock_pass_init
-!!@}
+!>@}
 
 contains
 

src/core/MOM_dynamics_unsplit_RK2.F90

@@ -130,7 +130,7 @@ module MOM_dynamics_unsplit_RK2
   !>@{ Diagnostic IDs
   integer :: id_uh = -1, id_vh = -1
   integer :: id_PFu = -1, id_PFv = -1, id_CAu = -1, id_CAv = -1
-  !!@}
+  !>@}
 
   type(diag_ctrl), pointer :: diag => NULL() !< A structure that is used to
                                    !! regulate the timing of diagnostic output.
@@ -178,7 +178,7 @@ module MOM_dynamics_unsplit_RK2
 integer :: id_clock_Cor, id_clock_pres, id_clock_vertvisc
 integer :: id_clock_horvisc, id_clock_continuity, id_clock_mom_update
 integer :: id_clock_pass, id_clock_pass_init
-!!@}
+!>@}
 
 contains
 

src/core/MOM_forcing_type.F90

@@ -327,7 +327,7 @@ module MOM_forcing_type
   ! Iceberg + Ice shelf diagnostic handles
   integer :: id_ustar_ice_cover = -1
   integer :: id_frac_ice_cover = -1
-  !!@}
+  !>@}
 
   integer :: id_clock_forcing = -1 !< CPU clock id
 

src/diagnostics/MOM_diagnostics.F90

@@ -134,7 +134,8 @@ module MOM_diagnostics
   integer :: id_pbo            = -1
   integer :: id_thkcello       = -1, id_rhoinsitu      = -1
   integer :: id_rhopot0        = -1, id_rhopot2        = -1
-  integer :: id_h_pre_sync     = -1   !!@}
+  integer :: id_h_pre_sync     = -1
+  !>@}
   !> The control structure for calculating wave speed.
   type(wave_speed_CS), pointer :: wave_speed_CSp => NULL()
 
@@ -168,7 +169,7 @@ module MOM_diagnostics
   integer :: id_salt_deficit = -1
   integer :: id_Heat_PmE     = -1
   integer :: id_intern_heat  = -1
-  !!@}
+  !>@}
 end type surface_diag_IDs
 
 
@@ -177,7 +178,8 @@ module MOM_diagnostics
   !>@{  Diagnostics for tracer horizontal transport
   integer :: id_uhtr = -1, id_umo = -1, id_umo_2d = -1
   integer :: id_vhtr = -1, id_vmo = -1, id_vmo_2d = -1
-  integer :: id_dynamics_h = -1, id_dynamics_h_tendency = -1   !!@}
+  integer :: id_dynamics_h = -1, id_dynamics_h_tendency = -1
+  !>@}
 end type transport_diag_IDs
 
 

src/equation_of_state/MOM_EOS_NEMO.F90

@@ -169,7 +169,7 @@ module MOM_EOS_NEMO
 real, parameter :: BET102 = 6.2255521644e-02
 real, parameter :: BET012 = -2.6514181169e-03
 real, parameter :: BET003 = -2.3025968587e-04
-!!@}
+!>@}
 
 contains
 

src/equation_of_state/MOM_EOS_UNESCO.F90

@@ -49,7 +49,7 @@ module MOM_EOS_UNESCO
   Sp30 = 1.956415e-6, Sp01 = 6.704388e-3, Sp11 = -1.847318e-4, Sp21 = 2.059331e-7, &
   Sp032 = 1.480266e-4, SP000 = 2.102898e-4, SP010 = -1.202016e-5, SP020 = 1.394680e-7, &
   SP001 = -2.040237e-6, SP011 = 6.128773e-8, SP021 = 6.207323e-10
-!!@}
+!>@}
 
 contains
 

src/equation_of_state/MOM_EOS_Wright.F90

@@ -69,7 +69,7 @@ module MOM_EOS_Wright
 real, parameter :: b3 = 2.084372e2,  b4 = 5.944068e5,  b5 = -9.643486e3
 real, parameter :: c0 = 1.704853e5,  c1 = 7.904722e2,  c2 = -7.984422    ! c0/c1 ~= 216  ; c0/c4 ~= -740
 real, parameter :: c3 = 5.140652e-2, c4 = -2.302158e2, c5 = -3.079464
-!!@}
+!>@}
 
 contains
 

src/framework/MOM_diag_mediator.F90

@@ -216,7 +216,7 @@ module MOM_diag_mediator
   type(axes_grp)  :: axesB1, axesT1, axesCu1, axesCv1
   type(axes_grp), dimension(:), allocatable :: remap_axesTL, remap_axesBL, remap_axesCuL, remap_axesCvL
   type(axes_grp), dimension(:), allocatable :: remap_axesTi, remap_axesBi, remap_axesCui, remap_axesCvi
-  !!@}
+  !>@}
 
   real, dimension(:,:),   pointer :: mask2dT   => null() !< 2D mask array for cell-center points
   real, dimension(:,:),   pointer :: mask2dBu  => null() !< 2D mask array for cell-corner points
@@ -231,7 +231,7 @@ module MOM_diag_mediator
   real, dimension(:,:,:), pointer :: mask3dBi  => null()
   real, dimension(:,:,:), pointer :: mask3dCui => null()
   real, dimension(:,:,:), pointer :: mask3dCvi => null()
-  !!@}
+  !>@}
 end type diagcs_dsamp
 
 !> The following data type a list of diagnostic fields an their variants,
@@ -264,7 +264,7 @@ module MOM_diag_mediator
   type(axes_grp) :: axesBL, axesTL, axesCuL, axesCvL
   type(axes_grp) :: axesBi, axesTi, axesCui, axesCvi
   type(axes_grp) :: axesB1, axesT1, axesCu1, axesCv1
-  !!@}
+  !>@}
   type(axes_grp) :: axesZi !< A 1-D z-space axis at interfaces
   type(axes_grp) :: axesZL !< A 1-D z-space axis at layer centers
   type(axes_grp) :: axesNull !< An axis group for scalars
@@ -285,7 +285,7 @@ module MOM_diag_mediator
 
   type(diagcs_dsamp), dimension(2:MAX_DSAMP_LEV) :: dsamp !< Downsample control container
 
-  !!@}
+  !>@}
 
 ! Space for diagnostics is dynamically allocated as it is needed.
 ! The chunk size is how much the array should grow on each new allocation.
@@ -306,10 +306,10 @@ module MOM_diag_mediator
   type(axes_grp), dimension(:), allocatable :: &
     remap_axesZL, &  !< The 1-D z-space cell-centered axis for remapping
     remap_axesZi     !< The 1-D z-space interface axis for remapping
-  !!@{
+  !>@{ Axes used for remapping
   type(axes_grp), dimension(:), allocatable :: remap_axesTL, remap_axesBL, remap_axesCuL, remap_axesCvL
   type(axes_grp), dimension(:), allocatable :: remap_axesTi, remap_axesBi, remap_axesCui, remap_axesCvi
-  !!@}
+  !>@}
 
   ! Pointer to H, G and T&S needed for remapping
   real, dimension(:,:,:), pointer :: h => null() !< The thicknesses needed for remapping
@@ -334,8 +334,9 @@ module MOM_diag_mediator
 
 end type diag_ctrl
 
-! CPU clocks
+!>@{ CPU clocks
 integer :: id_clock_diag_mediator, id_clock_diag_remap, id_clock_diag_grid_updates
+!>@}
 
 contains
 

src/framework/MOM_file_parser.F90

@@ -29,7 +29,7 @@ module MOM_file_parser
 logical, parameter :: log_to_stdout_default = .false.
 logical, parameter :: complete_doc_default = .true.
 logical, parameter :: minimal_doc_default = .true.
-!!@}
+!>@}
 
 !> The valid lines extracted from an input parameter file without comments
 type, private :: file_data_type ; private

src/framework/MOM_horizontal_regridding.F90

@@ -60,10 +60,10 @@ module MOM_horizontal_regridding
 subroutine myStats(array, missing, is, ie, js, je, k, mesg)
   real, dimension(:,:), intent(in) :: array !< input array (ND)
   real, intent(in) :: missing !< missing value (ND)
-  !!@{
-  !> Horizontal loop bounds to calculate statistics for
-  integer :: is,ie,js,je
-  !!@}
+  integer :: is   !< Start index in i
+  integer :: ie   !< End index in i
+  integer :: js   !< Start index in j
+  integer :: je   !< End index in j
   integer :: k !< Level to calculate statistics for
   character(len=*) :: mesg !< Label to use in message
   ! Local variables

src/framework/MOM_restart.F90

@@ -99,7 +99,7 @@ module MOM_restart
   type(p2d), pointer :: var_ptr2d(:) => NULL()
   type(p3d), pointer :: var_ptr3d(:) => NULL()
   type(p4d), pointer :: var_ptr4d(:) => NULL()
-  !!@}
+  !>@}
   integer :: max_fields !< The maximum number of restart fields
 end type MOM_restart_CS