MOM6: Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl

- Last commit closes mom-ocean#135. NOAA-GFDL/MOM6@249e9f6 Merge branch 'Hallberg-NOAA-dev/gfdl' into dev/gfdl NOAA-GFDL/MOM6@74bcc77 Merge branch 'dev/gfdl' of https://github.com/Hallberg-NOAA/MOM6 into Hallberg-NOAA-dev/gfdl NOAA-GFDL/MOM6@83f606a Merge pull request mom-ocean#536 from adcroft/fix-gnu-openmp-490 NOAA-GFDL/MOM6@5f0fec7 Removed trailing white space NOAA-GFDL/MOM6@530fea2 +Made OS argument to ocean_model_flux_init optional NOAA-GFDL/MOM6@e6b7df2 +Always call initialization routines to get_params NOAA-GFDL/MOM6@9c3ff33 Merge pull request mom-ocean#535 from adcroft/fix-hor-visc-openmp NOAA-GFDL/MOM6@76bd4d4 Renames "mod" variable to avoid using imod() fn NOAA-GFDL/MOM6@d69ca55 Fixes openmp directives for Leith mods NOAA-GFDL/MOM6@0c4f909 Merge pull request mom-ocean#534 from adcroft/correct-horizontal-indexing-schematics NOAA-GFDL/MOM6@97c8f81 Corrects schematic of symmetric arrays NOAA-GFDL/MOM6@8d8ad81 Merge pull request mom-ocean#533 from CarolineCardinale/dev/gfdl NOAA-GFDL/MOM6@2cccc6a Merge pull request mom-ocean#530 from adcroft/document-fox-kemper NOAA-GFDL/MOM6@86786a5 Added Doxygen comments to subroutines NOAA-GFDL/MOM6@b616fbd Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into dev/gfdl NOAA-GFDL/MOM6@40a7aed Added Doxygen comments to subroutines NOAA-GFDL/MOM6@d2e6771 Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into dev/gfdl NOAA-GFDL/MOM6@0b961d1 Added doxumentation for the Fox-Kemper scheme NOAA-GFDL/MOM6@86972b5 Added doxygen comments to subroutines NOAA-GFDL/MOM6@0d5399f Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into dev/gfdl NOAA-GFDL/MOM6@26ed48b Added doxygen comments to MOM_wave_structure.F90 NOAA-GFDL/MOM6@154877e Added doxygen comments to MOM_sum_output.F90 NOAA-GFDL/MOM6@c8cdb04 Added doxygen comments to MOM_PointAccel.F90 NOAA-GFDL/MOM6@3fdcb86 Added doxygen comments to MOM_diagnostics.F90 NOAA-GFDL/MOM6@e9b0a48 Added doxygen comments to MOM_diag_to_Z.F90 NOAA-GFDL/MOM6@0356c63 Added doxygen comments to MOM_domains.F90 NOAA-GFDL/MOM6@9aa01c9 Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into dev/gfdl NOAA-GFDL/MOM6@5c49c2d Added doxygen comments to MOM_OCMIP_CFC.F90 NOAA-GFDL/MOM6@64b35c3 Added doxygen comments to MOM_legacy_barotropic.F90
nikizadehgfdl · Jun 29, 2017 · 92e1e7d · 92e1e7d
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diff --git a/ocean_only/adjustment2d/layer/MOM_parameter_doc.all b/ocean_only/adjustment2d/layer/MOM_parameter_doc.all
@@ -425,6 +425,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 MIN_THICKNESS = 1.0E-04         !   [m] default = 0.001
                                 ! Minimum layer thickness
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]

diff --git a/ocean_only/adjustment2d/layer/MOM_parameter_doc.short b/ocean_only/adjustment2d/layer/MOM_parameter_doc.short
@@ -197,6 +197,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 MIN_THICKNESS = 1.0E-04         !   [m] default = 0.001
                                 ! Minimum layer thickness
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]

diff --git a/ocean_only/adjustment2d/rho/MOM_parameter_doc.all b/ocean_only/adjustment2d/rho/MOM_parameter_doc.all
@@ -566,6 +566,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]
                                 ! Width of frontal zone
 DELTA_S_STRAT = 0.0             !   [1e-3]

diff --git a/ocean_only/adjustment2d/rho/MOM_parameter_doc.short b/ocean_only/adjustment2d/rho/MOM_parameter_doc.short
@@ -247,6 +247,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]
                                 ! Width of frontal zone
 DELTA_S_STRAT = 0.0             !   [1e-3]

diff --git a/ocean_only/adjustment2d/z/MOM_parameter_doc.all b/ocean_only/adjustment2d/z/MOM_parameter_doc.all
@@ -520,6 +520,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]
                                 ! Width of frontal zone
 DELTA_S_STRAT = 0.0             !   [1e-3]

diff --git a/ocean_only/adjustment2d/z/MOM_parameter_doc.short b/ocean_only/adjustment2d/z/MOM_parameter_doc.short
@@ -223,6 +223,8 @@ THICKNESS_CONFIG = "adjustment2d" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module adjustment_initialization ===
 ADJUSTMENT_WIDTH = 0.01         !   [same as x,y]
                                 ! Width of frontal zone
 DELTA_S_STRAT = 0.0             !   [1e-3]

diff --git a/ocean_only/circle_obcs/MOM_parameter_doc.all b/ocean_only/circle_obcs/MOM_parameter_doc.all
@@ -409,7 +409,7 @@ THICKNESS_CONFIG = "circle_obcs" !
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
 
-! === module circle_obcs_initialize_thickness ===
+! === module circle_obcs_initialization ===
 DISK_RADIUS = 24.0              !   [kilometers]
                                 ! The radius of the initially elevated disk in the
                                 ! circle_obcs test case.

diff --git a/ocean_only/circle_obcs/MOM_parameter_doc.short b/ocean_only/circle_obcs/MOM_parameter_doc.short
@@ -194,7 +194,7 @@ THICKNESS_CONFIG = "circle_obcs" !
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
 
-! === module circle_obcs_initialize_thickness ===
+! === module circle_obcs_initialization ===
 DISK_RADIUS = 24.0              !   [kilometers]
                                 ! The radius of the initially elevated disk in the
                                 ! circle_obcs test case.

diff --git a/ocean_only/external_gwave/MOM_parameter_doc.all b/ocean_only/external_gwave/MOM_parameter_doc.all
@@ -423,6 +423,8 @@ THICKNESS_CONFIG = "external_gwave" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module external_gwave_initialize_thickness ===
 SSH_ANOMALY_HEIGHT = 1.0        !   [m]
                                 ! The vertical displacement of the SSH anomaly.
 SSH_ANOMALY_WIDTH = 5.0         !   [coordinate]

diff --git a/ocean_only/external_gwave/MOM_parameter_doc.short b/ocean_only/external_gwave/MOM_parameter_doc.short
@@ -191,6 +191,8 @@ THICKNESS_CONFIG = "external_gwave" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module external_gwave_initialize_thickness ===
 SSH_ANOMALY_HEIGHT = 1.0        !   [m]
                                 ! The vertical displacement of the SSH anomaly.
 SSH_ANOMALY_WIDTH = 5.0         !   [coordinate]

diff --git a/ocean_only/flow_downslope/layer/MOM_parameter_doc.all b/ocean_only/flow_downslope/layer/MOM_parameter_doc.all
@@ -326,6 +326,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 DOME2D_SHELF_WIDTH = 0.1        !   [nondim] default = 0.1
                                 ! Width of shelf, as fraction of domain, in 2d DOME configuration.
 DOME2D_BASIN_WIDTH = 0.3        !   [nondim] default = 0.3

diff --git a/ocean_only/flow_downslope/layer/MOM_parameter_doc.short b/ocean_only/flow_downslope/layer/MOM_parameter_doc.short
@@ -122,6 +122,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 MAXIMUM_DEPTH = 4000.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 1.0             !   [m] default = 0.0

diff --git a/ocean_only/flow_downslope/rho/MOM_parameter_doc.all b/ocean_only/flow_downslope/rho/MOM_parameter_doc.all
@@ -326,6 +326,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 DOME2D_SHELF_WIDTH = 0.1        !   [nondim] default = 0.1
                                 ! Width of shelf, as fraction of domain, in 2d DOME configuration.
 DOME2D_BASIN_WIDTH = 0.3        !   [nondim] default = 0.3

diff --git a/ocean_only/flow_downslope/rho/MOM_parameter_doc.short b/ocean_only/flow_downslope/rho/MOM_parameter_doc.short
@@ -118,6 +118,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 MAXIMUM_DEPTH = 4000.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 1.0             !   [m] default = 0.0

diff --git a/ocean_only/flow_downslope/sigma/MOM_parameter_doc.all b/ocean_only/flow_downslope/sigma/MOM_parameter_doc.all
@@ -326,6 +326,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 DOME2D_SHELF_WIDTH = 0.1        !   [nondim] default = 0.1
                                 ! Width of shelf, as fraction of domain, in 2d DOME configuration.
 DOME2D_BASIN_WIDTH = 0.3        !   [nondim] default = 0.3

diff --git a/ocean_only/flow_downslope/sigma/MOM_parameter_doc.short b/ocean_only/flow_downslope/sigma/MOM_parameter_doc.short
@@ -118,6 +118,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 MAXIMUM_DEPTH = 4000.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 1.0             !   [m] default = 0.0

diff --git a/ocean_only/flow_downslope/z/MOM_parameter_doc.all b/ocean_only/flow_downslope/z/MOM_parameter_doc.all
@@ -326,6 +326,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 DOME2D_SHELF_WIDTH = 0.1        !   [nondim] default = 0.1
                                 ! Width of shelf, as fraction of domain, in 2d DOME configuration.
 DOME2D_BASIN_WIDTH = 0.3        !   [nondim] default = 0.3

diff --git a/ocean_only/flow_downslope/z/MOM_parameter_doc.short b/ocean_only/flow_downslope/z/MOM_parameter_doc.short
@@ -118,6 +118,8 @@ TOPO_CONFIG = "DOME2D"          !
                                 !     Phillips - ACC-like idealized topography used in the Phillips config.
                                 !     dense - Denmark Strait-like dense water formation and overflow.
                                 !     USER - call a user modified routine.
+
+! === module DOME2D_initialization ===
 MAXIMUM_DEPTH = 4000.0          !   [m]
                                 ! The maximum depth of the ocean.
 MINIMUM_DEPTH = 1.0             !   [m] default = 0.0

diff --git a/ocean_only/lock_exchange/MOM_parameter_doc.all b/ocean_only/lock_exchange/MOM_parameter_doc.all
@@ -423,6 +423,8 @@ THICKNESS_CONFIG = "lock_exchange" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module lock_exchange_initialize_thickness ===
 FRONT_DISPLACEMENT = 20.0       !   [m]
                                 ! The vertical displacement of interfaces across the front.
                                 ! A value larger in magnitude that MAX_DEPTH is truncated,

diff --git a/ocean_only/lock_exchange/MOM_parameter_doc.short b/ocean_only/lock_exchange/MOM_parameter_doc.short
@@ -184,6 +184,8 @@ THICKNESS_CONFIG = "lock_exchange" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module lock_exchange_initialize_thickness ===
 FRONT_DISPLACEMENT = 20.0       !   [m]
                                 ! The vertical displacement of interfaces across the front.
                                 ! A value larger in magnitude that MAX_DEPTH is truncated,

diff --git a/ocean_only/mixed_layer_restrat_2d/MOM_parameter_doc.all b/ocean_only/mixed_layer_restrat_2d/MOM_parameter_doc.all
@@ -520,6 +520,8 @@ THICKNESS_CONFIG = "rossby_front" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module Rossby_front_2d_initialization ===
 T_RANGE = 5.0                   !   [C] default = 0.0
                                 ! Initial temperature range
 TS_CONFIG = "rossby_front"      !

diff --git a/ocean_only/mixed_layer_restrat_2d/MOM_parameter_doc.short b/ocean_only/mixed_layer_restrat_2d/MOM_parameter_doc.short
@@ -195,6 +195,8 @@ THICKNESS_CONFIG = "rossby_front" !
                                 !     soliton - Equatorial Rossby soliton.
                                 !     rossby_front - a mixed layer front in thermal wind balance.
                                 !     USER - call a user modified routine.
+
+! === module Rossby_front_2d_initialization ===
 T_RANGE = 5.0                   !   [C] default = 0.0
                                 ! Initial temperature range
 TS_CONFIG = "rossby_front"      !

diff --git a/ocean_only/tracer_mixing/rho/MOM_parameter_doc.all b/ocean_only/tracer_mixing/rho/MOM_parameter_doc.all
@@ -588,7 +588,7 @@ TS_CONFIG = "baroclinic_zone"   !
                                 !     USER - call a user modified routine.
 
 ! === module baroclinic_zone_initialization ===
-! Initialization of an analytic baroclninic zone
+! Initialization of an analytic baroclinic zone
 BCZIC%
 S_REF = 34.75                   !   [ppt] default = 35.0
                                 ! Reference salinity

diff --git a/ocean_only/tracer_mixing/rho/MOM_parameter_doc.short b/ocean_only/tracer_mixing/rho/MOM_parameter_doc.short
@@ -265,7 +265,7 @@ TS_CONFIG = "baroclinic_zone"   !
                                 !     USER - call a user modified routine.
 
 ! === module baroclinic_zone_initialization ===
-! Initialization of an analytic baroclninic zone
+! Initialization of an analytic baroclinic zone
 BCZIC%
 S_REF = 34.75                   !   [ppt] default = 35.0
                                 ! Reference salinity

diff --git a/ocean_only/tracer_mixing/z/MOM_parameter_doc.all b/ocean_only/tracer_mixing/z/MOM_parameter_doc.all
@@ -542,7 +542,7 @@ TS_CONFIG = "baroclinic_zone"   !
                                 !     USER - call a user modified routine.
 
 ! === module baroclinic_zone_initialization ===
-! Initialization of an analytic baroclninic zone
+! Initialization of an analytic baroclinic zone
 BCZIC%
 S_REF = 34.75                   !   [ppt] default = 35.0
                                 ! Reference salinity

diff --git a/ocean_only/tracer_mixing/z/MOM_parameter_doc.short b/ocean_only/tracer_mixing/z/MOM_parameter_doc.short
@@ -241,7 +241,7 @@ TS_CONFIG = "baroclinic_zone"   !
                                 !     USER - call a user modified routine.
 
 ! === module baroclinic_zone_initialization ===
-! Initialization of an analytic baroclninic zone
+! Initialization of an analytic baroclinic zone
 BCZIC%
 S_REF = 34.75                   !   [ppt] default = 35.0
                                 ! Reference salinity

diff --git a/src/MOM6 b/src/MOM6
+9 −6		config_src/coupled_driver/ocean_model_MOM.F90
+15 −15		config_src/solo_driver/MOM_driver.F90
+128 −0		docs/images/Horizontal indexing in MOM6.ipynb
+ −		docs/images/Horizontal_NE_indexing_nonsym.png
+342 −145		src/core/MOM_legacy_barotropic.F90
+73 −32		src/diagnostics/MOM_PointAccel.F90
+108 −62		src/diagnostics/MOM_diag_to_Z.F90
+123 −63		src/diagnostics/MOM_diagnostics.F90
+46 −22		src/diagnostics/MOM_sum_output.F90
+46 −18		src/diagnostics/MOM_wave_structure.F90
+47 −11		src/equation_of_state/MOM_EOS_UNESCO.F90
+127 −27		src/equation_of_state/MOM_EOS_Wright.F90
+153 −35		src/equation_of_state/MOM_EOS_linear.F90
+49 −15		src/equation_of_state/MOM_TFreeze.F90
+430 −133		src/framework/MOM_domains.F90
+511 −364		src/initialization/MOM_state_initialization.F90
+44 −17		src/parameterizations/lateral/MOM_hor_visc.F90
+212 −111		src/parameterizations/lateral/MOM_internal_tides.F90
+139 −100		src/parameterizations/lateral/MOM_mixed_layer_restrat.F90
+37 −13		src/parameterizations/lateral/MOM_tidal_forcing.F90
+402 −100		src/parameterizations/vertical/MOM_bulk_mixed_layer.F90
+38 −16		src/parameterizations/vertical/MOM_diapyc_energy_req.F90
+84 −38		src/tracer/MOM_OCMIP2_CFC.F90
+150 −63		src/tracer/MOM_tracer_flow_control.F90
+44 −17		src/user/DOME2d_initialization.F90
+17 −9		src/user/DOME_initialization.F90
+99 −72		src/user/ISOMIP_initialization.F90
+43 −38		src/user/Phillips_initialization.F90
+50 −17		src/user/Rossby_front_2d_initialization.F90
+17 −10		src/user/SCM_CVmix_tests.F90
+15 −6		src/user/SCM_idealized_hurricane.F90
+58 −30		src/user/adjustment_initialization.F90
+37 −13		src/user/baroclinic_zone_initialization.F90
+35 −21		src/user/benchmark_initialization.F90
+25 −16		src/user/circle_obcs_initialization.F90
+9 −2		src/user/dense_water_initialization.F90
+20 −9		src/user/external_gwave_initialization.F90
+27 −15		src/user/lock_exchange_initialization.F90
+43 −19		src/user/seamount_initialization.F90
+31 −13		src/user/sloshing_initialization.F90
+32 −32		src/user/user_initialization.F90