move demos

regional_mom6/demos/premade_run_directories/README.md

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+## Premade Run Directories
+
+These directories are used for the demo notebooks, and can be used as templates for setting up a new experiment. The [documentation](https://regional-mom6.readthedocs.io/en/latest/mom6-file-structure-primer.html) explains what all the files are for.
+
+The `common_files` folder contains all of the required files for a regional MOM6 run, including a `data_table` with constant surface forcing as a placeholder. The other two directories offer different choices for the surface forcing, affecting the `data_table`.

regional_mom6/demos/premade_run_directories/common_files/MOM_layout

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+! === module MOM_domains ===
+REENTRANT_X = False             !   [Boolean] default = True
+                                ! If true, the domain is zonally reentrant.
+NIGLOBAL = 3040                  !
+                                ! The total number of thickness grid points in the x-direction in the physical
+                                ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
+NJGLOBAL = 3180                  !
+                                ! The total number of thickness grid points in the y-direction in the physical
+                                ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
+MASKTABLE = "mask_table.766.80x80" ! 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
+LAYOUT = 80, 80                 !
+                                ! The processor layout that was actually used.
+IO_LAYOUT = 1, 1                ! default = 1
+                                ! The processor layout to be used, or 0,0 to automatically set the io_layout to
+                                ! be the same as the layout.

regional_mom6/demos/premade_run_directories/common_files/MOM_override

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+## Add override files here
+
+#override DT=50
+#override DT_THERM=300

regional_mom6/demos/premade_run_directories/common_files/SIS_input

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+CGRID_ICE_DYNAMICS = True
+DT_ICE_DYNAMICS = 180.0
+! fixed bulk salinity of sea ice
+ICE_BULK_SALINITY = 0.0
+! salinity of sea ice as fraction of salinity
+! of sea water from which it formed
+ICE_RELATIVE_SALINITY = 0.1
+! cosine of solar zenith angle for first radiation step
+CONSTANT_COSZEN_IC = 0.0
+! don't call iceberg module
+DO_ICEBERGS = False
+! time between writes of global ice diags and conservation
+ICE_STATS_INTERVAL = 0.25
+
+GRID_CONFIG = "mosaic"
+GRID_FILE = "hgrid.nc"
+INPUTDIR = "INPUT"
+
+TOPO_FILE = "bathymetry.nc"
+
+MAXIMUM_DEPTH = 6000.0
+
+WRITE_GEOM = 0
+
+! rotation rate of earth
+OMEGA = 7.292E-05
+
+! tuning params for radiative properties
+ICE_DELTA_EDD_R_ICE = 1.0
+ICE_DELTA_EDD_R_SNOW = 1.0
+ICE_DELTA_EDD_R_POND = 1.0
+
+CP_ICE = 2100.0
+CP_SEAWATER = 3992.0
+CP_BRINE = 3992.0
+
+! subcycling timestep for rheology
+DT_RHEOLOGY = 50.0
+
+U_TRUNC_FILE = "SIS_U_truncations"
+V_TRUNC_FILE = "SIS_V_truncations"
+
+SIS_THICKNESS_ADVECTION_SCHEME = "PCM"
+SIS_CONTINUITY_SCHEME = "PCM"
+
+! use previous calculations of ice-top surface
+! skin temp for tsurf
+EULERIAN_TSURF = True
+! redistribute after advection
+RECATEGORIZE_ICE = True
+
+SIS_TRACER_ADVECTION_SCHEME = "PPM:H3"
+
+MAXTRUNC = 200
+DOCUMENT_FILE = "SIS_parameter_doc"
+
+REPORT_UNUSED_PARAMS = True
+FATAL_UNUSED_PARAMS = True
+
+! from overrides:
+ADD_DIURNAL_SW = False

regional_mom6/demos/premade_run_directories/common_files/config.yaml

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+project: x77
+queue: normal
+walltime: 05:00:00
+jobname: jobname
+ncpus: 1234
+jobfs: 10GB
+shortpath: /scratch/nm03
+
+model: mom6
+input:
+    - path_to_input_files
+
+## Executable that Ashley uses on nci. If you're an NCI user hopefully you can access this
+exe: /g/data/v45/ab8992/mom_executables/jan2024-latest-everything
+
+collate: false
+#runlog: true
+storage:
+  gdata:
+    - ua8
+    - x77
+    - ik11
+
+mpi:
+  module: openmpi/4.1.2
+

regional_mom6/demos/premade_run_directories/common_files/data_table

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+
+"ATM", "p_surf", "", "", "bilinear", 100410.25
+"ATM", "p_bot",  "", "", "bilinear", 100410.25
+"ATM", "t_bot",  "", "", "bilinear", 289.9
+"ATM", "sphum_bot", "", "", "bilinear", 0.0083
+"ATM", "u_bot", "", "", "bicubic", 0.0
+"ATM", "v_bot", "", "", "bicubic", 0.0
+"ATM", "z_bot", "", "", "bilinear", 10.0
+"ATM", "gust", "", "", "bilinear", 1.0e-4
+"ICE", "lw_flux_dn", "", "", "bilinear", 1.0
+"ICE", "sw_flux_vis_dir_dn", "", "", "bilinear", 0.0
+"ICE", "sw_flux_vis_dif_dn", "", "", "bilinear", 0.0
+"ICE", "sw_flux_nir_dir_dn", "", "", "bilinear", 0.0
+"ICE", "sw_flux_nir_dif_dn", "", "", "bilinear", 0.0
+"ICE", "lprec", "", "", "bilinear", 0.0
+"ICE", "fprec", "", "", "bilinear", 0.0
+"ICE", "runoff", "", "", "none", 0.0
+"ICE", "dhdt", "", "", "none", 80.0
+"ICE", "dedt", "", "", "none", 2.0e-6
+"ICE", "drdt", "", "", "none", 10.0
+"LND", "rough_mom", "", "", "none", 0.01
+"LND", "rough_heat", "", "", "none", 0.1

regional_mom6/demos/premade_run_directories/common_files/diag_table

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+mom6-regional
+2003 1 1 0 0 0
+
+"ocean_daily",            1, "days",   1, "days", "time"
+"ocean_static",          -1, "months", 1, "days", "time" # ocean_static is a protected name. Do not change this line.
+
+# Sea Surface Height
+"ocean_model",   "zos",          "zos",              "ocean_daily",         "all", "mean", "none",2
+# Sea Surface Temperature
+"ocean_model",   "tos",          "tos",              "ocean_daily",         "all", "mean", "none",2
+# Sea Surface Salinity
+"ocean_model",   "sos",          "sos",              "ocean_daily",         "all", "mean", "none",2
+# Sea Water Potential Temperature at Sea Floor
+"ocean_model",   "tob",          "tob",              "ocean_daily",        "all", "mean", "none",2
+# Sea Water Salinity at Sea Floor
+"ocean_model",   "sob",          "sob",              "ocean_daily",         "all", "mean", "none",2
+# Mixed layer depth (delta rho = 0.03)
+"ocean_model",   "mlotst",       "mlotst",           "ocean_daily",         "all", "mean", "none",2
+# Sea Surface Speed
+"ocean_model",   "speed",        "speed",            "ocean_daily",         "all", "mean", "none",2
+
+# Surface area of tracer (T) cells
+"ocean_model", "areacello",   "areacello",   "ocean_static", "all", "none", "none", 2
+# Depth of the ocean at tracer points
+"ocean_model", "deptho",      "deptho",      "ocean_static", "all", "none", "none", 2
+"ocean_model", "Coriolis",    "Coriolis",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolon",      "geolon",      "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolat",      "geolat",      "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolon_c",    "geolon_c",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolat_c",    "geolat_c",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolon_u",    "geolon_u",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolat_u",    "geolat_u",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolon_v",    "geolon_v",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "geolat_v",    "geolat_v",    "ocean_static", "all", "none", "none", 2
+"ocean_model", "wet",         "wet",         "ocean_static", "all", "none", "none", 2
+"ocean_model", "wet_c",       "wet_c",       "ocean_static", "all", "none", "none", 2
+"ocean_model", "wet_u",       "wet_u",       "ocean_static", "all", "none", "none", 2
+"ocean_model", "wet_v",       "wet_v",       "ocean_static", "all", "none", "none", 2
+"ocean_model", "dxt",         "dxt",         "ocean_static", "all", "none", "none", 2
+"ocean_model", "dyt",         "dyt",         "ocean_static", "all", "none", "none", 2
+"ocean_model", "dxCu",        "dxCu",        "ocean_static", "all", "none", "none", 2
+"ocean_model", "dyCu",        "dyCu",        "ocean_static", "all", "none", "none", 2
+"ocean_model", "dxCv",        "dxCv",        "ocean_static", "all", "none", "none", 2
+"ocean_model", "dyCv",        "dyCv",        "ocean_static", "all", "none", "none", 2
+"ocean_model", "areacello_cu","areacello_cu","ocean_static", "all", "none", "none", 2
+"ocean_model", "areacello_cv","areacello_cv","ocean_static", "all", "none", "none", 2
+"ocean_model", "areacello_bu","areacello_bu","ocean_static", "all", "none", "none", 2
+
+

regional_mom6/demos/premade_run_directories/common_files/field_table

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+"TRACER", "atmos_mod", "sphum" /
+"TRACER", "land_mod", "sphum" /

regional_mom6/demos/premade_run_directories/common_files/input.nml

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+&MOM_input_nml
+	output_directory = '.',
+	input_filename = 'n',
+	restart_input_dir = 'INPUT',
+	restart_output_dir = 'RESTART',
+	parameter_filename = 'MOM_input', 'MOM_layout', 'MOM_override'
+/
+
+&SIS_input_nml
+	output_directory = '.',
+	input_filename = 'n',
+	restart_input_dir = 'INPUT',
+	restart_output_dir = 'RESTART',
+	parameter_filename = 'SIS_input','MOM_layout'
+/
+
+&fms_nml
+	domains_stack_size = 1600000,
+	stack_size = 0,
+	clock_grain = 'LOOP'
+/
+
+&fms2_io_nml
+        netcdf_default_format = "netcdf4"
+	shuffle = .true.,
+	deflate = 5
+/
+
+&coupler_nml
+	months = 0,
+	days = 1,
+	hours = 0,
+	current_date = 2015,1,1,0,0,0,
+	calendar = 'JULIAN',
+	dt_cpld = 3600,
+	dt_atmos = 3600,
+	do_atmos = .false.,
+	do_land = .false.,
+	do_ice = .true.,
+	do_ocean = .true.,
+	do_flux = .true.,
+	atmos_npes = 0,
+	concurrent = .false.,
+	use_lag_fluxes = .false.,
+	check_stocks = 0
+/
+
+&flux_exchange_nml
+	debug_stocks = .false.,
+	divert_stocks_report = .true.,
+	do_area_weighted_flux = .false.
+/
+
+&ice_albedo_nml
+	t_range = 10.
+/
+
+&monin_obukhov_nml
+	neutral = .true.
+/
+
+&ocean_albedo_nml
+	ocean_albedo_option = 2
+/
+
+&ocean_rough_nml
+	rough_scheme = 'beljaars'
+/
+
+&sat_vapor_pres_nml
+	construct_table_wrt_liq = .true.,
+	construct_table_wrt_liq_and_ice = .true.
+/
+
+&surface_flux_nml
+	ncar_ocean_flux = .true.,
+	raoult_sat_vap = .true.
+/
+
+&xgrid_nml
+	make_exchange_reproduce = .false.,
+	interp_method = 'second_order'
+/

regional_mom6/demos/premade_run_directories/era5_surface/data_table

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+"ATM", "p_surf", "sp", "./INPUT/forcing/sp_ERA5.nc", "bilinear", 1.0
+"ATM", "p_bot",  "sp", "./INPUT/forcing/sp_ERA5.nc", "bilinear", 1.0
+"ATM", "t_bot",  "t2m", "./INPUT/forcing/2t_ERA5.nc", "bilinear", 1.0
+"ATM", "sphum_bot", "q", "./INPUT/forcing/q_ERA5.nc", "bilinear", 1.0
+"ATM", "u_bot", "u10", "./INPUT/forcing/10u_ERA5.nc", "bicubic", 1.0
+"ATM", "v_bot", "v10", "./INPUT/forcing/10v_ERA5.nc", "bicubic", 1.0
+"ATM", "z_bot", "", "", "bilinear", 10.0
+"ATM", "gust", "", "", "bilinear", 1.0e-4
+"ICE", "lw_flux_dn", "", "", "bilinear", 1.0
+"ICE", "sw_flux_vis_dir_dn", "msdwswrf", "./INPUT/forcing/msdwswrf_ERA5.nc", "bilinear", 0.285
+"ICE", "sw_flux_vis_dif_dn", "msdwswrf", "./INPUT/forcing/msdwswrf_ERA5.nc", "bilinear", 0.285
+"ICE", "sw_flux_nir_dir_dn", "msdwlwrf", "./INPUT/forcing/msdwlwrf_ERA5.nc", "bilinear", 0.215
+"ICE", "sw_flux_nir_dif_dn", "msdwlwrf", "./INPUT/forcing/msdwlwrf_ERA5.nc", "bilinear", 0.215
+"ICE", "lprec", "trr", "./INPUT/forcing/trr_ERA5.nc", "bilinear", 1.0
+"ICE", "fprec", "", "", "bilinear", 0.0
+"ICE", "runoff", "", "", "none", 0.0
+"ICE", "dhdt", "", "", "none", 80.0
+"ICE", "dedt", "", "", "none", 2.0e-6
+"ICE", "drdt", "", "", "none", 10.0
+"LND", "rough_mom", "", "", "none", 0.01
+"LND", "rough_heat", "", "", "none", 0.1
+

regional_mom6/demos/premade_run_directories/era5_surface/input.nml

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+&MOM_input_nml
+	output_directory = '.',
+	input_filename = 'n',
+	restart_input_dir = 'INPUT',
+	restart_output_dir = 'RESTART',
+	parameter_filename = 'MOM_input', 'MOM_layout', 'MOM_override'
+/
+
+&SIS_input_nml
+	output_directory = '.',
+	input_filename = 'n',
+	restart_input_dir = 'INPUT',
+	restart_output_dir = 'RESTART',
+	parameter_filename = 'SIS_input','MOM_layout'
+/
+
+&fms_nml
+	domains_stack_size = 1600000,
+	stack_size = 0,
+	clock_grain = 'LOOP'
+/
+
+&fms2_io_nml
+        netcdf_default_format = "netcdf4"
+	shuffle = .true.,
+	deflate = 5
+/
+
+&coupler_nml
+	months = 0,
+	days = 1,
+	hours = 0,
+	current_date = 2015,1,1,0,0,0,
+	calendar = 'JULIAN',
+	dt_cpld = 3600,
+	dt_atmos = 3600,
+	do_atmos = .false.,
+	do_land = .false.,
+	do_ice = .true.,
+	do_ocean = .true.,
+	do_flux = .true.,
+	atmos_npes = 0,
+	concurrent = .false.,
+	use_lag_fluxes = .false.,
+	check_stocks = 0
+/
+
+&flux_exchange_nml
+	debug_stocks = .false.,
+	divert_stocks_report = .true.,
+	do_area_weighted_flux = .false.
+/
+
+&ice_albedo_nml
+	t_range = 10.
+/
+
+&monin_obukhov_nml
+	neutral = .true.
+/
+
+&ocean_albedo_nml
+	ocean_albedo_option = 2
+/
+
+&ocean_rough_nml
+	rough_scheme = 'beljaars'
+/
+
+&sat_vapor_pres_nml
+	construct_table_wrt_liq = .true.,
+	construct_table_wrt_liq_and_ice = .true.
+/
+
+&surface_flux_nml
+    ncar_ocean_flux_multilevel = .true.
+    bulk_zu = 10.
+    bulk_zt = 2.
+    bulk_zq = 2.
+
+&xgrid_nml
+	make_exchange_reproduce = .false.,
+	interp_method = 'second_order'
+/