Added OM4p25 COBALTv3 example

exps/OM4p25.COBALT/COBALT_parameter_doc.debugging

@@ -0,0 +1,3 @@
+! This file was written by the model and records the debugging parameters used at run-time.
+
+! === module COBALT ===

exps/OM4p25.COBALT/COBALT_parameter_doc.layout

@@ -0,0 +1 @@
+! This file was written by the model and records the layout parameters used at run-time.

exps/OM4p25.COBALT/COBALT_parameter_doc.short

@@ -0,0 +1,13 @@
+! This file was written by the model and records the non-default parameters used at run-time.
+
+! === module COBALT ===
+ca_2_n_arag = 0.035             !   [mol cadet_arag mol org. C-1] default = 0.055
+                                ! ratio of aragonite detritus prod. to org. C detritus prod. by aragonite shell
+                                ! formers
+ca_2_n_calc = 0.025             !   [mol cadet_calc mol org. C-1] default = 0.05
+                                ! ratio of calcite detritus prod. to org. C detritus prod. by calcite shell
+                                ! formers
+z_burial = 50.0                 !   [m] default = 10.0
+                                ! depth scale for ramping up particulate organic burial
+scale_burial = 1.0              !   [none] default = 0.0
+                                ! scaling factor for particulate organic burial

exps/OM4p25.COBALT/INPUT/All_edits.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/All_edits.nc

exps/OM4p25.COBALT/INPUT/COBALT_input

@@ -0,0 +1,5 @@
+! Put the contents of your COBALT_input file here
+ca_2_n_arag = 0.035
+ca_2_n_calc = 0.025
+z_burial = 50.0
+scale_burial = 1.0		      

exps/OM4p25.COBALT/INPUT/COBALT_override

@@ -0,0 +1,5 @@
+! Put the contents of your COBALT_override file here.
+! For parameters which are not specified in the COBALT_input file, just set the new value, ex:  
+! do_case2_mod = True
+! For parameters which are specified in the COBALT_input file, specify an override, ex:
+!#override do_case2_mod = True

exps/OM4p25.COBALT/INPUT/GLODAPv2.2016b.oi-filled.20180322.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/GLODAPv2.2016b.oi-filled.20180322.nc

exps/OM4p25.COBALT/INPUT/JRA_huss.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_huss.nc

exps/OM4p25.COBALT/INPUT/JRA_prra.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_prra.nc

exps/OM4p25.COBALT/INPUT/JRA_prsn.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_prsn.nc

exps/OM4p25.COBALT/INPUT/JRA_psl.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_psl.nc

exps/OM4p25.COBALT/INPUT/JRA_rlds.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_rlds.nc

exps/OM4p25.COBALT/INPUT/JRA_rsds.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_rsds.nc

exps/OM4p25.COBALT/INPUT/JRA_tas.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_tas.nc

exps/OM4p25.COBALT/INPUT/JRA_uas.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_uas.nc

exps/OM4p25.COBALT/INPUT/JRA_vas.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/JRA_vas.nc

exps/OM4p25.COBALT/INPUT/MOM_GENERICS.res.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/MOM_GENERICS.res.nc

exps/OM4p25.COBALT/INPUT/MOM_channels_global_025

@@ -0,0 +1,9 @@
+! This file specifies restricted channel widths in MOM.  The order is:
+!  [U|V]_width, min_longitude, max_longitude, min_latitude, max_latitude, width
+
+U_width,  -5.9,  -5.4, 35.8, 36.2,  12000.0  ! Gibraltar
+U_width,  26.4,  26.8, 40.4, 40.6,   5000.0  ! Dardanelles
+
+V_width,  28.8,  29.4, 41.1, 41.2,   2500.0  ! Bosporus - should be 1km wide.
+V_width,  43.25, 43.5, 12.6, 12.8,  10000.0  ! Red Sea, Bab-el-Mendeb
+V_width, 141.5, 141.7, 52.0,  52.15, 2500.0  ! Between Sakhalin & Russia

exps/OM4p25.COBALT/INPUT/MOM_override

@@ -0,0 +1,20 @@
+# Turn on generic tracers
+USE_generic_tracer = True
+#override CHL_FROM_FILE = False
+GENERIC_TRACER_IC_FILE = "MOM_GENERICS.res.nc"
+#override NUM_DIAG_COORDS = 2
+#override MAX_FIELDS=500
+#override DIAG_COORDS = "z 01 ZSTAR,zsfc 02 ZSTAR"
+#override DIAG_COORD_DEF_01 = "WOA09"
+#override DIAG_COORD_DEF_02 = "UNIFORM:50,250."
+# Use bug fixes not in old OM4 runs. 
+#override DEFAULT_ANSWER_DATE = 99991231
+#override FLUXCONST = 0.0834
+# New WOA18 temp and salinity initial conditions
+#override TEMP_Z_INIT_FILE = "woa18_decav_ptemp_monthly_fulldepth_01.nc"
+#override SALT_Z_INIT_FILE = "woa18_decav_s_monthly_fulldepth_01.nc" 
+#override Z_INIT_REMAP_OLD_ALG = False
+#override PHA_MLD_CALC = True
+#override PHA_MLD_USE_DELTA_RHO = True
+#override PHA_MLD_HREF = 10.0
+#override PHA_MLD_DRHO = 0.03

exps/OM4p25.COBALT/INPUT/MOM_saltrestore

@@ -0,0 +1,26 @@
+! These parameters are used in CORE mode but should not be used in
+! the coupled model (CM4).
+RESTORE_SALINITY = True         !   [Boolean] default = False
+                                ! If true, the coupled driver will add a globally-balanced
+                                ! fresh-water flux that drives sea-surface salinity
+                                ! toward specified values.
+FLUXCONST = 0.1667              !   [m day-1]
+                                ! The constant that relates the restoring surface fluxes
+                                ! to the relative surface anomalies (akin to a piston
+                                ! velocity).  Note the non-MKS units.
+SALT_RESTORE_FILE = "salt_restore_JRA.1440x1080.v20190706.nc" ! default = "salt_restore.nc"
+                                ! A file in which to find the surface salinity to use for restoring.
+SALT_RESTORE_VARIABLE = "sos"   ! default = "salt"
+                                ! The name of the surface salinity variable to read from SALT_RESTORE_FILE for
+                                ! restoring salinity.
+SRESTORE_AS_SFLUX = True        !   [Boolean] default = False
+                                ! If true, the restoring of salinity is applied as a salt
+                                ! flux instead of as a freshwater flux.
+MAX_DELTA_SRESTORE = 5.0        !   [PSU or g kg-1] default = 999.0
+                                ! The maximum salinity difference used in restoring terms.
+ADJUST_NET_FRESH_WATER_TO_ZERO = True !   [Boolean] default = False
+                                ! If true, adjusts the net fresh-water forcing seen
+                                ! by the ocean (including restoring) to zero.
+USE_NET_FW_ADJUSTMENT_SIGN_BUG = False !   [Boolean] default = True
+                                ! If true, use the wrong sign for the adjustment to
+                                ! the net fresh-water.

exps/OM4p25.COBALT/INPUT/Mineral_Flux_AM4.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/Mineral_Flux_AM4.nc

exps/OM4p25.COBALT/INPUT/SIS_input

@@ -0,0 +1,173 @@
+! This input file provides the adjustable run-time parameters for version 2 of the Sea Ice Simulator (SIS2).
+! Where appropriate, parameters use usually given in MKS units.
+
+! This particular file is for the example in ice_ocean_SIS2/OM4_025.JRA.
+
+! This SIS_input file typically contains only the non-default values that are needed to reproduce this example.
+! A full list of parameters for this example can be found in the corresponding SIS_parameter_doc.all file
+! which is generated by the model at run-time.
+
+! === module ice_model ===
+CGRID_ICE_DYNAMICS = True       !   [Boolean] default = False
+                                ! If true, use a C-grid discretization of the sea-ice dynamics; if false use a
+                                ! B-grid discretization.
+CONSTANT_COSZEN_IC = 0.0        !   [nondim] default = -1.0
+                                ! A constant value to use to initialize the cosine of the solar zenith angle for
+                                ! the first radiation step, or a negative number to use the current time and
+                                ! astronomy.
+DO_ICEBERGS = True              !   [Boolean] default = False
+                                ! If true, call the iceberg module.
+! ADD_DIURNAL_SW should only be true if the model is forced with a product that does not include SW forcing!
+ADD_DIURNAL_SW = False          !   [Boolean] default = False
+                                ! If true, add a synthetic diurnal cycle to the shortwave radiation.
+
+! === module MOM_domains ===
+TRIPOLAR_N = True               !   [Boolean] default = False
+                                ! Use tripolar connectivity at the northern edge of the domain.  With
+                                ! TRIPOLAR_N, NIGLOBAL must be even.
+NIGLOBAL = 1440                 !
+                                ! The total number of thickness grid points in the x-direction in the physical
+                                ! domain. With STATIC_MEMORY_ this is set in SIS2_memory.h at compile time.
+NJGLOBAL = 1080                 !
+                                ! The total number of thickness grid points in the y-direction in the physical
+                                ! domain. With STATIC_MEMORY_ this is set in SIS2_memory.h at compile time.
+NIHALO = 4                      ! default = 4
+                                ! The number of halo points on each side in the x-direction.  With
+                                ! STATIC_MEMORY_ this is set as NIHALO_ in SIS2_memory.h at compile time;
+                                ! without STATIC_MEMORY_ the default is NIHALO_ in SIS2_memory.h (if defined) or
+                                ! 2.
+NJHALO = 4                      ! default = 4
+                                ! The number of halo points on each side in the y-direction.  With
+                                ! STATIC_MEMORY_ this is set as NJHALO_ in SIS2_memory.h at compile time;
+                                ! without STATIC_MEMORY_ the default is NJHALO_ in SIS2_memory.h (if defined) or
+                                ! 2.
+
+! === module MOM_hor_index ===
+! Sets the horizontal array index types.
+
+! === module SIS_initialize_fixed ===
+INPUTDIR = "INPUT"              ! default = "."
+                                ! The directory in which input files are found.
+
+! === module MOM_grid_init ===
+GRID_CONFIG = "mosaic"          !
+                                ! A character string that determines the method for defining the horizontal
+                                ! grid.  Current options are:
+                                !     mosaic - read the grid from a mosaic (supergrid)
+                                !              file set by GRID_FILE.
+                                !     cartesian - use a (flat) Cartesian grid.
+                                !     spherical - use a simple spherical grid.
+                                !     mercator - use a Mercator spherical grid.
+GRID_FILE = "ocean_hgrid.nc"    !
+                                ! Name of the file from which to read horizontal grid data.
+USE_TRIPOLAR_GEOLONB_BUG = True !   [Boolean] default = False
+                                ! If true, use older code that incorrectly sets the longitude in some points
+                                ! along the tripolar fold to be off by 360 degrees.
+!MAXIMUM_DEPTH = 9682.232421875 !   [m]
+                                ! The (diagnosed) maximum depth of the ocean.
+OMEGA = 7.292E-05               !   [s-1] default = 7.2921E-05
+                                ! The rotation rate of the earth.
+GRID_ROTATION_ANGLE_BUGS = True !   [Boolean] default = False
+                                ! If true, use an older algorithm to calculate the sine and cosines needed
+                                ! rotate between grid-oriented directions and true north and east.  Differences
+                                ! arise at the tripolar fold.
+
+! === module hor_grid ===
+! Parameters providing information about the lateral grid.
+
+! === module MOM_hor_index ===
+! Sets the horizontal array index types.
+
+! === module SIS2_ice_thm (thermo) ===
+! This sub-module calculates ice thermodynamic quantities.
+CP_SEAWATER = 3992.0            !   [J kg-1 K-1] default = 4200.0
+                                ! The heat capacity of sea water, approximated as a constant.
+
+! === module SIS_tracer_registry ===
+
+! === module SIS_tracer_flow_control ===
+
+! === module SIS_slow_thermo ===
+! This module calculates the slow evolution of the ice mass, heat, and salt budgets.
+ICE_BULK_SALINITY = 0.0         !   [g/kg] default = 4.0
+                                ! The fixed bulk salinity of sea ice.
+ICE_RELATIVE_SALINITY = 0.1     !   [nondim] default = 0.0
+                                ! The initial salinity of sea ice as a fraction of the salinity of the seawater
+                                ! from which it formed.
+
+! === module SIS2_ice_thm (updates) ===
+! This sub-module does updates of the sea-ice due to thermodynamic changes.
+
+! === module SIS_dyn_trans ===
+! This module updates the ice momentum and does ice transport.
+DT_ICE_DYNAMICS = 1200.0        !   [seconds] default = -1.0
+                                ! The time step used for the slow ice dynamics, including stepping the
+                                ! continuity equation and interactions between the ice mass field and
+                                ! velocities.  If 0 or negative the coupling time step will be used.
+ICE_STATS_INTERVAL = 0.25       !   [days] default = 1.0
+                                ! The interval in units of TIMEUNIT between writes of the globally summed ice
+                                ! statistics and conservation checks.
+DT_RHEOLOGY = 50.0              !   [seconds] default = -1.0
+                                ! The sub-cycling time step for iterating the rheology and ice momentum
+                                ! equations. If DT_RHEOLOGY is negative, the time step is set via NSTEPS_DYN.
+SIS_THICKNESS_ADVECTION_SCHEME = "PCM" ! default = "UPWIND_2D"
+                                ! The horizontal transport scheme for thickness:
+                                !   UPWIND_2D - Non-directionally split upwind
+                                !   PCM    - Directionally split piecewise constant
+                                !   PLM    - Piecewise Linear Method
+                                !   PPM:H3 - Piecewise Parabolic Method (Huyhn 3rd order)
+INCONSISTENT_COVER_BUG = True   !   [Boolean] default = True
+                                ! If true, omit a recalculation of the fractional ice-free areal coverage after
+                                ! the adjustment of the ice categories.
+SIS_CONTINUITY_SCHEME = "PCM"   ! default = "UPWIND_2D"
+                                ! The horizontal transport scheme used in continuity:
+                                !   UPWIND_2D - Non-directionally split upwind
+                                !   PCM       - Directionally split piecewise constant
+                                !   PPM:C2PD  - Positive definite PPM with 2nd order edge values
+                                !   PPM:C2MO  - Monotonic PPM with 2nd order edge values
+
+! === module SIS_tracer_advect ===
+SIS_TRACER_ADVECTION_SCHEME = "PPM:H3" ! default = "UPWIND_2D"
+                                ! The horizontal transport scheme for tracers:
+                                !   UPWIND_2D - Non-directionally split upwind
+                                !   PCM    - Directionally split piecewise constant
+                                !   PLM    - Piecewise Linear Method
+                                !   PPM:H3 - Piecewise Parabolic Method (Huyhn 3rd order)
+CFL_MASS_NEGLECT_BUG = True     !   [Boolean] default = True
+                                ! If true use a globally constant negligible volume in the denominator of the
+                                ! tracer advection CFL calculation, reproducing an older incorrect expression,
+                                ! rather than using a proper scaling of this negligible mass with cell area.
+
+! === module SIS_sum_output ===
+MAXTRUNC = 200                  !   [truncations save_interval-1] default = 0
+                                ! The run will be stopped, and the day set to a very large value if the velocity
+                                ! is truncated more than MAXTRUNC times between  writing ice statistics. Set
+                                ! MAXTRUNC to 0 to stop if there is any truncation of sea ice velocities.
+
+! === module SIS_ice_diagnostics ===
+! This module handles sea-ice state diagnostics.
+
+! === module SIS_fast_thermo ===
+! This module applies rapidly varying heat fluxes to the ice and does an implicit surface temperature
+! calculation.
+
+! === module SIS2_ice_thm (updates) ===
+! This sub-module does updates of the sea-ice due to thermodynamic changes.
+
+! === module SIS_optics ===
+! This module calculates the albedo and absorption profiles for shortwave radiation.
+ICE_DELTA_EDD_R_ICE = 1.0       !   [nondimensional] default = 0.0
+                                ! A dreadfully documented tuning parameter for the radiative propeties of sea
+                                ! ice with the delta-Eddington radiative transfer calculation.
+ICE_DELTA_EDD_R_SNOW = 1.0      !   [nondimensional] default = 0.0
+                                ! A dreadfully documented tuning parameter for the radiative propeties of snow
+                                ! on sea ice with the delta-Eddington radiative transfer calculation.
+ICE_DELTA_EDD_R_POND = 1.0      !   [nondimensional] default = 0.0
+                                ! A dreadfully documented tuning parameter for the radiative propeties of
+                                ! meltwater ponds on sea ice with the delta-Eddington radiative transfer
+                                ! calculation.
+
+! === module MOM_file_parser ===
+DOCUMENT_FILE = "SIS_parameter_doc" ! default = "MOM_parameter_doc"
+                                ! The basename for files where run-time parameters, their settings, units and
+                                ! defaults are documented. Blank will disable all parameter documentation.

exps/OM4p25.COBALT/INPUT/SIS_override

@@ -0,0 +1,5 @@
+#override U_TRUNC_FILE = "SIS_U_truncations"
+#override V_TRUNC_FILE = "SIS_V_truncations"
+#override MIN_OCN_INTERTIAL_H = 2.
+#override ADD_DIURNAL_SW = False 
+#override ICE_STATS_INTERVAL = 30

exps/OM4p25.COBALT/INPUT/Soluble_Fe_Flux_AM4.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/Soluble_Fe_Flux_AM4.nc

exps/OM4p25.COBALT/INPUT/analysis_vgrid_lev35.v1.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/analysis_vgrid_lev35.v1.nc

exps/OM4p25.COBALT/INPUT/atmos_mosaic_tile1Xland_mosaic_tile1.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/atmos_mosaic_tile1Xland_mosaic_tile1.nc

exps/OM4p25.COBALT/INPUT/atmos_mosaic_tile1Xocean_mosaic_tile1.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/atmos_mosaic_tile1Xocean_mosaic_tile1.nc

exps/OM4p25.COBALT/INPUT/basin_codes.v20140629.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/basin_codes.v20140629.nc

exps/OM4p25.COBALT/INPUT/esm4_drynh4_climo_1993-2014.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/esm4_drynh4_climo_1993-2014.nc

exps/OM4p25.COBALT/INPUT/esm4_drynoy_climo_1993-2014.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/esm4_drynoy_climo_1993-2014.nc

exps/OM4p25.COBALT/INPUT/esm4_wetnh4_climo_1993-2014.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/esm4_wetnh4_climo_1993-2014.nc

exps/OM4p25.COBALT/INPUT/esm4_wetnoy_climo_1993-2014.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/esm4_wetnoy_climo_1993-2014.nc

exps/OM4p25.COBALT/INPUT/geothermal_davies2013_v1.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/geothermal_davies2013_v1.nc

exps/OM4p25.COBALT/INPUT/grid_spec.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/grid_spec.nc

exps/OM4p25.COBALT/INPUT/hycom1_75_800m.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/hycom1_75_800m.nc

exps/OM4p25.COBALT/INPUT/init_ocean_cobalt.res.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/init_ocean_cobalt.res.nc

exps/OM4p25.COBALT/INPUT/init_ocean_cobalt_nh3.res.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/init_ocean_cobalt_nh3.res.nc

exps/OM4p25.COBALT/INPUT/land_mask.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/land_mask.nc

exps/OM4p25.COBALT/INPUT/land_mosaic_tile1Xocean_mosaic_tile1.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/land_mosaic_tile1Xocean_mosaic_tile1.nc

exps/OM4p25.COBALT/INPUT/layer_coord.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/layer_coord.nc

exps/OM4p25.COBALT/INPUT/mole_fraction_of_co2_extended_ssp245.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/mole_fraction_of_co2_extended_ssp245.nc

exps/OM4p25.COBALT/INPUT/news_nutrients.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/news_nutrients.nc

exps/OM4p25.COBALT/INPUT/ocean_hgrid.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/ocean_hgrid.nc

exps/OM4p25.COBALT/INPUT/ocean_mask.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/ocean_mask.nc

exps/OM4p25.COBALT/INPUT/ocean_mosaic.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/ocean_mosaic.nc

exps/OM4p25.COBALT/INPUT/ocean_topog.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/ocean_topog.nc

exps/OM4p25.COBALT/INPUT/runoff.daitren.clim.1440x1080.v20180328.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/runoff.daitren.clim.1440x1080.v20180328.nc

exps/OM4p25.COBALT/INPUT/salt_restore_JRA.1440x1080.v20190706.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/salt_restore_JRA.1440x1080.v20190706.nc

exps/OM4p25.COBALT/INPUT/tidal_amplitude.v20140616.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/tidal_amplitude.v20140616.nc

exps/OM4p25.COBALT/INPUT/topog.nc

@@ -0,0 +1 @@
+ocean_topog.nc

exps/OM4p25.COBALT/INPUT/vgrid_75_2m.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/vgrid_75_2m.nc

exps/OM4p25.COBALT/INPUT/woa18_all_i00_01.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/woa18_all_i00_01.nc

exps/OM4p25.COBALT/INPUT/woa18_all_n00_01.nc

@@ -0,0 +1 @@
+../../datasets/OM4_025.JRA/woa18_all_n00_01.nc