Declutter notebook (#84)

* Modify notebook to remove mentions of NCI

* modify notebook

* migrate era5 and setup rundir functions from notebook to package

* decluttered notebook, added functions to library instead. reanalysis notebook now has no mention of NCI

* update docstrings

* black

* docstring vgrid

* delete model-forced notebook to migrate it to cosima recipes

* update the model forced example to include for now

* fix diag table

* fix diag table

* execute notebook to keep sphinx happy

regional_mom6/default_rundir/era5_surface/config.yaml

@@ -1,7 +1,9 @@
+## Example of a config.yaml file for using MOM6 with Payu
+
 project: x77
 queue: normal
 walltime: 02:00:00
-jobname: mom6_GIPPSLAND
+jobname: mom6_regional
 ncpus: 82
 jobfs: 10GB
 
@@ -10,15 +12,10 @@ 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

regional_mom6/default_rundir/era5_surface/data_table

@@ -1,21 +1,22 @@
-"ATM", "p_surf", "sp", "./INPUT/forcing/sp_ERA5", "bilinear", 1.0
-"ATM", "p_bot",  "sp", "./INPUT/forcing/sp_ERA5", "bilinear", 1.0
-"ATM", "t_bot",  "t2m", "./INPUT/forcing/2t_ERA5", "bilinear", 1.0
-"ATM", "sphum_bot", "q", "./INPUT/forcing/q_ERA5", "bilinear", 1.0
-"ATM", "u_bot", "u10", "./INPUT/forcing/10u_ERA5", "bicubic", 1.0
-"ATM", "v_bot", "v10", "./INPUT/forcing/10v_ERA5", "bicubic", 1.0
+
+"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", "rlds", "./INPUT/RYF.rlds.1990_1991.nc", "bilinear", 1.0
-"ICE", "sw_flux_vis_dir_dn", "rsds", "./INPUT/RYF.rsds.1990_1991.nc", "bilinear", 0.285
-"ICE", "sw_flux_vis_dif_dn", "rsds", "./INPUT/RYF.rsds.1990_1991.nc", "bilinear", 0.285
-"ICE", "sw_flux_nir_dir_dn", "rsds", "./INPUT/RYF.rsds.1990_1991.nc", "bilinear", 0.215
-"ICE", "sw_flux_nir_dif_dn", "rsds", "./INPUT/RYF.rsds.1990_1991.nc", "bilinear", 0.215
-"ICE", "lprec", "prrn", "./INPUT/RYF.rain.1990_1991.nc", "bilinear", 1.0
-"ICE", "fprec", "prsn", "./INPUT/RYF.snow.1990_1991.nc", "bilinear", 1.0
+"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"""
+"LND", "rough_heat", "", "", "none", 0.1

regional_mom6/default_rundir/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

regional_mom6/default_rundir/jra_surface/diag_table

@@ -1,5 +1,5 @@
-eac
-1991 1 1 0 0 0
+regional_mom6
+1990 1 1 0 0 0
 
 "ocean_daily",            1, "days",   1, "days", "time"
 "ocean_month",            1, "months", 1, "days", "time"