Merge pull request #83 from COSIMA/declutter_notebook

Declutter example notebook

demos/premade_run_directories/README.md

@@ -0,0 +1,6 @@
+
+## Premade Run Directories
+
+These folders are used for the demo notebooks, and can be used as templates for setting up a new experiment. The difference in the choices is the surface forcing, affecting the `data_table`. 
+
+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. If you call `.setup_rundir` and specify `jra` 

demos/premade_run_directories/common_files/MOM_layout

@@ -0,0 +1,27 @@
+! === 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.

demos/premade_run_directories/common_files/MOM_override

@@ -0,0 +1,9 @@
+## Add override files here
+
+!#override OBC_SEGMENT_001 = "J=0,I=0:N,ORLANSKI" !
+!#override OBC_SEGMENT_002 = "J=0,I=0:N,ORLANSKI" !
+!#override OBC_SEGMENT_003 = "J=0,I=0:N,ORLANSKI" !
+!#override OBC_SEGMENT_004 = "J=0,I=0:N,ORLANSKI" !
+
+#override DT=50
+#override DT_THERM=300

regional_mom6/default_rundir/era5_surface/SIS_input → demos/premade_run_directories/common_files/SIS_input

@@ -12,11 +12,6 @@ DO_ICEBERGS = False
 ! time between writes of global ice diags and conservation
 ICE_STATS_INTERVAL = 0.25
 
-NIGLOBAL = 80
-NJGLOBAL = 129
-LAYOUT = 10,10
-MASKTABLE = "mask_table.18.10x10"
-
 GRID_CONFIG = "mosaic"
 GRID_FILE = "hgrid.nc"
 INPUTDIR = "INPUT"

demos/premade_run_directories/common_files/config.yaml

@@ -0,0 +1,24 @@
+project: x77
+queue: normal
+walltime: 05:00:00
+jobname: jobname
+ncpus: 1234
+jobfs: 10GB
+shortpath: /scratch/nm03
+
+model: mom6
+input:
+    - path_to_input_files
+
+exe: /g/data/v45/ab8992/mom_executables/dec-23-build
+collate: false
+#runlog: true
+storage:
+  gdata:
+    - ua8
+    - x77
+    - ik11
+
+mpi:
+  module: openmpi/4.1.2
+

demos/premade_run_directories/common_files/data_table

@@ -0,0 +1,22 @@
+
+"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/default_rundir/era5_surface/diag_table → demos/premade_run_directories/common_files/diag_table

@@ -1,6 +1,3 @@
-eac
-1991 1 1 0 0 0
-
 "ocean_daily",            1, "days",   1, "days", "time"
 "ocean_month",            1, "months", 1, "days", "time"
 "ocean_month_z",          1, "months", 1, "days", "time"
@@ -87,4 +84,4 @@ eac
 "ice_model", "siconc",     "siconc",       "ice_month", "all", "mean", "none", 2
 "ice_model", "siconc",     "siconc",       "ice_daily", "all", "mean", "none", 2
 "ice_model", "sithick",    "sithick",      "ice_month", "all", "mean", "none", 2
-"ice_model", "sithick",    "sithick",      "ice_daily", "all", "mean", "none", 2
+"ice_model", "sithick",    "sithick",      "ice_daily", "all", "mean", "none", 2

regional_mom6/default_rundir/era5_surface/input.nml → demos/premade_run_directories/common_files/input.nml

@@ -3,15 +3,15 @@
 	input_filename = 'n',
 	restart_input_dir = 'INPUT',
 	restart_output_dir = 'RESTART',
-	parameter_filename = 'MOM_input', 'MOM_override'
+	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'
+	parameter_filename = 'SIS_input','MOM_layout'
 /
 
 &fms_nml
@@ -28,10 +28,10 @@
 
 &coupler_nml
 	months = 0,
-	days = 5,
+	days = 1,
 	hours = 0,
-	current_date = 1991,1,1,0,0,0,
-	calendar = 'NOLEAP',
+	current_date = 2015,1,1,0,0,0,
+	calendar = 'JULIAN',
 	dt_cpld = 3600,
 	dt_atmos = 3600,
 	do_atmos = .false.,

demos/premade_run_directories/era5_surface/data_table

@@ -0,0 +1,22 @@
+"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", "", "", "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/default_rundir/jra_surface/input.nml → demos/premade_run_directories/era5_surface/input.nml

@@ -3,15 +3,15 @@
 	input_filename = 'n',
 	restart_input_dir = 'INPUT',
 	restart_output_dir = 'RESTART',
-	parameter_filename = 'MOM_input', 'MOM_override'
+	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'
+	parameter_filename = 'SIS_input','MOM_layout'
 /
 
 &fms_nml
@@ -28,10 +28,10 @@
 
 &coupler_nml
 	months = 0,
-	days = 5,
+	days = 1,
 	hours = 0,
-	current_date = 1991,1,1,0,0,0,
-	calendar = 'NOLEAP',
+	current_date = 2015,1,1,0,0,0,
+	calendar = 'JULIAN',
 	dt_cpld = 3600,
 	dt_atmos = 3600,
 	do_atmos = .false.,
@@ -73,9 +73,10 @@
 /
 
 &surface_flux_nml
-	ncar_ocean_flux = .true.,
-	raoult_sat_vap = .true.
-/
+    ncar_ocean_flux_multilevel = .true.
+    bulk_zu = 10.
+    bulk_zt = 2.
+    bulk_zq = 2.
 
 &xgrid_nml
 	make_exchange_reproduce = .false.,

regional_mom6/default_rundir/era5_surface/config.yaml → demos/premade_run_directories/jra_surface/config.yaml

@@ -1,7 +1,9 @@
+## Example of a config.yaml file for running mom6 via payu
+
 project: x77
 queue: normal
 walltime: 02:00:00
-jobname: mom6_GIPPSLAND
+jobname: mom6_regional
 ncpus: 82
 jobfs: 10GB
 
@@ -10,15 +12,11 @@ shortpath: /scratch/x77
 model: mom6
 input:
     - /scratch/v45/ab8992/mom6/regional_configs/gippsland
-#    - /g/data/ua8/JRA55-do/RYF/v1-3/
     - /g/data/ik11/inputs/JRA-55/RYF/v1-3/
-# release exe
 exe: /g/data/x77/ahg157/exes/MOM6_SIS2/symmetric_FMS2-e7d09b7
-# debug exe
-#exe: /g/data/x77/ahg157/exes/MOM6_SIS2/symmetric_FMS2-9bc3419a
+
 
 collate: false
-#runlog: true
 storage:
   gdata:
     - ua8