Include example of diagnostics in scalar (conservative temperature) coordinates

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers_diagscalarhistogram/MOM_override

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+! Blank file in which we can put "overrides" for parameters
+NUM_DIAG_COORDS = 2
+DIAG_COORDS = "z Z ZSTAR", "scalar SCALAR SCALAR"
+DIAG_COORD_P_REF_SCALAR = 0.0
+DIAG_COORD_DEF_SCALAR = "FILE:targetlayers_scalar.nc,interfaces=interfaces"
+DIAG_COORD_HISTOGRAM_EXTENSIVE_DIAGS_SCALAR = True

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers_diagscalarhistogram/MOM_override_offline

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+! Blank file in which we can put "overrides" for parameters
+#override USE_REGRIDDING = True
+#override BULKMIXEDLAYER = False
+#override COORD_FILE = "Layer_coord50.nc"
+#override DIABATIC_FIRST = False
+#override PEN_SW_NBANDS = 0
+#override REGRID_TIME_SCALE = 0.0
+
+! Related to offline tracer transport
+OFFLINE_TRACER_MODE = True
+OFFLINEDIR = "ONLINE/"
+OFF_SUM_FILE = "00010101.off_sum_1day.nc"
+OFF_SNAP_FILE = "00010101.off_snap_1day.nc"
+OFF_SURF_FILE = "00010101.off_sum_1day.nc"
+OFF_MEAN_FILE = "00010101.off_avg_1day.nc"
+START_INDEX = 1
+DT_OFFLINE = 86400.0
+DT_OFFLINE_VERTICAL = 86400.0
+NUM_OFF_ITER = 30
+NUMTIME = 5

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers_diagscalarhistogram/MOM_override_online

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+! Blank file in which we can put "overrides" for parameters
+NK = 50
+#override USE_REGRIDDING = True
+#override BULKMIXEDLAYER = False
+#override COORD_FILE = "Layer_coord50.nc"
+#override DIABATIC_FIRST = False
+#override REGRID_TIME_SCALE = 0.0
+
+ALE_COORDINATE_CONFIG = "FILE:vgrid.nc,dz"
+
+USE_ADVECTION_TEST_TRACER = True
+ADVECTION_TEST_X_ORIGIN = 19.5
+ADVECTION_TEST_Y_ORIGIN = 60.5
+ADVECTION_TEST_X_WIDTH = 1.0
+ADVECTION_TEST_Y_WIDTH = 1.0
+
+

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers_diagscalarhistogram/MOM_parameter_doc.debugging

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+! This file was written by the model and records the debugging parameters used at run-time.
+
+! === module MOM_unit_scaling ===
+! Parameters for doing unit scaling of variables.
+Z_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! depths and heights.  Valid values range from -300 to 300.
+L_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! lateral distances.  Valid values range from -300 to 300.
+T_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! time.  Valid values range from -300 to 300.
+R_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! density.  Valid values range from -300 to 300.
+Q_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! heat content.  Valid values range from -300 to 300.
+C_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! temperature.  Valid values range from -300 to 300.
+S_RESCALE_POWER = 0             ! default = 0
+                                ! An integer power of 2 that is used to rescale the model's internal units of
+                                ! salinity.  Valid values range from -300 to 300.
+
+! === module MOM ===
+VERBOSITY = 2                   ! default = 2
+                                ! Integer controlling level of messaging
+                                !   0 = Only FATAL messages
+                                !   2 = Only FATAL, WARNING, NOTE [default]
+                                !   9 = All)
+DO_UNIT_TESTS = False           !   [Boolean] default = False
+                                ! If True, exercises unit tests at model start up.
+DEBUG = False                   !   [Boolean] default = False
+                                ! If true, write out verbose debugging data.
+DEBUG_TRUNCATIONS = False       !   [Boolean] default = False
+                                ! If true, calculate all diagnostics that are useful for debugging truncations.
+ROTATE_INDEX = False            !   [Boolean] default = False
+                                ! Enable rotation of the horizontal indices.
+DEBUG_CHKSUMS = False           !   [Boolean] default = False
+                                ! If true, checksums are performed on arrays in the various vec_chksum routines.
+DEBUG_REDUNDANT = False         !   [Boolean] default = False
+                                ! If true, debug redundant data points during calls to the various vec_chksum
+                                ! routines.
+
+! === module MOM_verticalGrid ===
+! Parameters providing information about the vertical grid.
+H_RESCALE_POWER = 0             !   [nondim] default = 0
+                                ! An integer power of 2 that is used to rescale the model's intenal units of
+                                ! thickness.  Valid values range from -300 to 300.
+
+! === module MOM_vert_friction ===
+U_TRUNC_FILE = "U_velocity_truncations" ! default = ""
+                                ! The absolute path to a file into which the accelerations leading to zonal
+                                ! velocity truncations are written. Undefine this for efficiency if this
+                                ! diagnostic is not needed.
+V_TRUNC_FILE = "V_velocity_truncations" ! default = ""
+                                ! The absolute path to a file into which the accelerations leading to meridional
+                                ! velocity truncations are written. Undefine this for efficiency if this
+                                ! diagnostic is not needed.
+
+! === module MOM_PointAccel ===
+MAX_TRUNC_FILE_SIZE_PER_PE = 50 ! default = 50
+                                ! The maximum number of columns of truncations that any PE will write out during
+                                ! a run.
+DEBUG_FULL_COLUMN = False       !   [Boolean] default = False
+                                ! If true, write out the accelerations in all massive layers; otherwise just
+                                ! document the ones with large velocities.
+
+! === module MOM_barotropic ===
+DEBUG_BT = False                !   [Boolean] default = False
+                                ! If true, write out verbose debugging data within the barotropic time-stepping
+                                ! loop. The data volume can be quite large if this is true.
+
+! === module MOM_diabatic_driver ===
+! The following parameters are used for diabatic processes.
+DEBUG_CONSERVATION = False      !   [Boolean] default = False
+                                ! If true, monitor conservation and extrema.
+
+! === module MOM_kappa_shear ===
+! Parameterization of shear-driven turbulence following Jackson, Hallberg and Legg, JPO 2008
+WRITE_TRACER_MIN_MAX = False    !   [Boolean] default = False
+                                ! If true, write the maximum and minimum values of temperature, salinity and
+                                ! some tracer concentrations to stdout when the energy files are written.
+
+! === module MOM_surface_forcing ===
+CHECK_NO_LAND_FLUXES = False    !   [Boolean] default = False
+                                ! If true, checks that values from IOB fluxes are zero above land points (i.e.
+                                ! G%mask2dT = 0).
+
+! === module MOM_file_parser ===
+REPORT_UNUSED_PARAMS = True     !   [Boolean] default = True
+                                ! If true, report any parameter lines that are not used in the run.
+FATAL_UNUSED_PARAMS = False     !   [Boolean] default = False
+                                ! If true, kill the run if there are any unused parameters.

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers_diagscalarhistogram/MOM_parameter_doc.layout

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+! This file was written by the model and records the layout parameters used at run-time.
+
+! === module MOM ===
+GLOBAL_INDEXING = False         !   [Boolean] default = False
+                                ! If true, use a global lateral indexing convention, so that corresponding
+                                ! points on different processors have the same index. This does not work with
+                                ! static memory.
+
+! === module MOM_domains ===
+!SYMMETRIC_MEMORY_ = True       !   [Boolean]
+                                ! If defined, the velocity point data domain includes every face of the
+                                ! thickness points. In other words, some arrays are larger than others,
+                                ! depending on where they are on the staggered grid.  Also, the starting index
+                                ! of the velocity-point arrays is usually 0, not 1. This can only be set at
+                                ! compile time.
+NONBLOCKING_UPDATES = False     !   [Boolean] default = False
+                                ! If true, non-blocking halo updates may be used.
+THIN_HALO_UPDATES = True        !   [Boolean] default = True
+                                ! If true, optional arguments may be used to specify the width of the halos that
+                                ! are updated with each call.
+!STATIC_MEMORY_ = False         !   [Boolean]
+                                ! If STATIC_MEMORY_ is defined, the principle variables will have sizes that are
+                                ! statically determined at compile time.  Otherwise the sizes are not determined
+                                ! until run time. The STATIC option is substantially faster, but does not allow
+                                ! the PE count to be changed at run time.  This can only be set at compile time.
+AUTO_MASKTABLE = False          !   [Boolean] default = False
+                                ! Turn on automatic mask table generation to eliminate land blocks.
+MASKTABLE = "MOM_mask_table"    ! default = "MOM_mask_table"
+                                ! A text file to specify n_mask, layout and mask_list. This feature masks out
+                                ! processors that contain only land points. The first line of mask_table is the
+                                ! number of regions to be masked out. The second line is the layout of the model
+                                ! and must be consistent with the actual model layout. The following (n_mask)
+                                ! lines give the logical positions of the processors that are masked out. The
+                                ! mask_table can be created by tools like check_mask. The following example of
+                                ! mask_table masks out 2 processors, (1,2) and (3,6), out of the 24 in a 4x6
+                                ! layout:
+                                !  2
+                                !  4,6
+                                !  1,2
+                                !  3,6
+NIPROC = 4                      !
+                                ! The number of processors in the x-direction. With STATIC_MEMORY_ this is set
+                                ! in MOM_memory.h at compile time.
+NJPROC = 2                      !
+                                ! The number of processors in the y-direction. With STATIC_MEMORY_ this is set
+                                ! in MOM_memory.h at compile time.
+LAYOUT = 4, 2                   !
+                                ! The processor layout that was actually used.
+IO_LAYOUT = 1, 1                ! default = 1, 1
+                                ! The processor layout to be used, or 0,0 to automatically set the io_layout to
+                                ! be the same as the layout.
+
+! === module MOM_grid ===
+! Parameters providing information about the lateral grid.
+NIBLOCK = 1                     ! default = 1
+                                ! The number of blocks in the x-direction on each processor (for openmp).
+NJBLOCK = 1                     ! default = 1
+                                ! The number of blocks in the y-direction on each processor (for openmp).
+
+! === module MOM_barotropic ===
+BT_USE_WIDE_HALOS = True        !   [Boolean] default = True
+                                ! If true, use wide halos and march in during the barotropic time stepping for
+                                ! efficiency.
+BTHALO = 0                      ! default = 0
+                                ! The minimum halo size for the barotropic solver.
+!BT x-halo = 4                  !
+                                ! The barotropic x-halo size that is actually used.
+!BT y-halo = 4                  !
+                                ! The barotropic y-halo size that is actually used.