Merge wombatlite + cable 3 changes into dev/preindustrial+concentrations

README.md

@@ -1,16 +1,8 @@
 # preindustrial+concentrations
-Standard configuration for a coupled CO<sub>2</sub> concentration driven [ACCESS-ESM1.5](https://github.com/ACCESS-NRI/ACCESS-ESM1.5) under pre-industrial forcings.
+Test configuration for a coupled CO<sub>2</sub> concentration driven [ACCESS-ESM1.6](https://github.com/ACCESS-NRI/ACCESS-ESM1.6) under pre-industrial forcings.
 
 For usage instructions, see the [ACCESS-Hive docs](https://access-hive.org.au/models/run-a-model/run-access-esm/)
 
-This configution is based on and maintains reproducibility with the CMIP6 configuration developed at [CSIRO](https://www.csiro.au/en/research/environmental-impacts/climate-change/climate-science-centre).
-
 ## Conditions of use
 
-The developers of ACCESS-ESM1.5 request that users of this model configuration:
-1. Cite https://doi.org/10.1071/ES19035
-2. Include an acknowledgment such as the following:
-   "The authors thank CSIRO for developing the ACCESS-ESM1.5 model configuration and making it freely available to researchers."
-   ACCESS-NRI requests users follow the guidelines for acknowledging ACCESS-NRI and include a statement such as:
-   "This research used the ACCESS-ESM1.5 model infrastructure provided by ACCESS-NRI, which is enabled by the Australian Government's National Collaborative Research Infrastructure Strategy (NCRIS)."
-
+`<TO DO>`

atmosphere/cable.nml

@@ -1,7 +1,4 @@
 &cable
-!
- filename%veg     = 'INPUT/def_veg_params.txt'
- filename%soil    = 'INPUT/def_soil_params.txt'
 !
 !
 !! cable_user flags
@@ -53,6 +50,6 @@
   l_laiFeedbk   = .TRUE.  ! using prognostic LAI
   l_vcmaxFeedbk = .TRUE.  ! using prognostic Vcmax
 ! filenames for CASA-CNP input files
-  casafile%cnpbiome='INPUT/pftlookup_csiro_v16_17tiles_wtlnds.csv'  ! biome specific BGC parameters
+  casafile%cnpbiome='INPUT/pftlookup_cable3.csv'  ! biome specific BGC parameters
   casafile%phen='INPUT/modis_phenology_csiro.txt' ! phenology by latitude (modis derived)
 &end

config.yaml

@@ -24,9 +24,9 @@ jobfs: 1500MB
 # Modules for loading model executables
 modules:
   use:
-      - /g/data/vk83/modules
+      - /g/data/vk83/prerelease/modules
   load:
-      - access-esm1p5/2024.05.1
+      - access-esm1p6/pr26-4
 
 # Model configuration
 model: access
@@ -53,7 +53,7 @@ submodels:
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/land/soiltype/global.N96/2020.05.19/qrparm.soil_igbp_vg
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/land/vegetation/global.N96/2020.05.19/cable_vegfunc_N96.anc
         - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeochemistry/resolution_independent/2020.05.19/modis_phenology_csiro.txt
-        - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeochemistry/resolution_independent/2020.05.19/pftlookup_csiro_v16_17tiles_wtlnds.csv
+        - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2024.12.18/pftlookup_cable3.csv
         - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeophysics/resolution_independent/2020.05.19/def_soil_params.txt
         - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/land/biogeophysics/resolution_independent/2020.05.19/def_veg_params.txt
         # Spectral
@@ -68,12 +68,11 @@ submodels:
     - name: ocean
       model: mom
       ncpus: 180
-      exe: fms_ACCESS-CM.x
+      exe: fms_ACCESS-ESM.x
       input:
         # Biogeochemistry
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/biogeochemistry/global.1deg/2020.05.19/dust.nc
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/biogeochemistry/global.1deg/2020.05.19/ocmip2_press_monthly_om1p5_bc.nc
-        - /g/data/vk83/configurations/inputs/access-esm1p5/share/ocean/biogeochemistry/global.1deg/2024.07.12/bgc_param.nc
         # Tides
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/tides/global.1deg/2020.05.19/roughness_amp.nc
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/tides/global.1deg/2020.05.19/tideamp.nc
@@ -118,7 +117,7 @@ collate:
     walltime: 1:00:00
     mpi: false
 
-restart: /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/restart/
+restart: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/restart/2024.12.10
 
 # Timing controls
 calendar:
@@ -137,10 +136,10 @@ runspersub: 1
 # Misc
 restart_freq: 10YS
 
-runlog: true
+runlog: false
 manifest:
   reproduce:
-    exe: True
+    exe: False
 
 
 stacksize: unlimited

make_wombatlite_restart.py

@@ -0,0 +1,63 @@
+import xarray as xr
+import numpy as np
+import matplotlib.pyplot as plt
+
+_ = xr.set_options(keep_attrs=True)
+
+restart_path = "/g/data/tm70/ds0092/model/inputs/access-esm1.5/modern/pre-industrial/restart/ocean/"
+
+rho = 1035
+mmol_to_mol = 1e-3
+mmol_m3_to_mol_kg = mmol_to_mol / rho
+umol_m3_to_mol_kg = mmol_to_mol * mmol_m3_to_mol_kg
+
+unit_convert = {
+    "adic": mmol_m3_to_mol_kg,
+    "caco3": mmol_m3_to_mol_kg,
+    "alk": mmol_m3_to_mol_kg,
+    "dic": mmol_m3_to_mol_kg,
+    "no3": mmol_m3_to_mol_kg,
+    "phy": mmol_m3_to_mol_kg,
+    "o2": mmol_m3_to_mol_kg,
+    "fe": umol_m3_to_mol_kg,
+    "zoo": mmol_m3_to_mol_kg,
+    "det": mmol_m3_to_mol_kg,
+    "caco3_sediment": mmol_to_mol,
+    "det_sediment": mmol_to_mol
+}
+
+old_res = xr.open_mfdataset(
+    f"{restart_path}/csiro_bgc*.nc",
+    decode_cf=False,
+    decode_times=False,
+    decode_timedelta=False,
+    decode_coords=False
+)
+
+zero_array = 0 * old_res["adic"]
+
+wombatlite_res = []
+for var in old_res:
+    da_old = old_res[var]
+    da_new = da_old * unit_convert[var]
+    da_new.encoding = da_old.encoding
+    del da_new.attrs["checksum"]
+    if var in ["caco3_sediment", "det_sediment"]:
+        # Make 3D
+        da_new = da_new + zero_array.rename(var)
+        da_new = da_new.transpose(*list(zero_array.dims))
+        da_new = da_new.where(da_new.zaxis_1 < 1.5, 0)
+    da_new.encoding['_FillValue'] = None
+    wombatlite_res.append(da_new)
+
+wombatlite_res = xr.merge(wombatlite_res)
+wombatlite_res.attrs = old_res.attrs
+
+for coord in wombatlite_res.coords:
+    wombatlite_res[coord].encoding['_FillValue'] = None
+
+wombatlite_res.to_netcdf(
+    f"{restart_path}/ocean_wombatlite.res.nc",
+    format="NETCDF3_CLASSIC",
+    unlimited_dims=["Time"],
+)

manifests/exe.yaml

@@ -2,17 +2,17 @@ format: yamanifest
 version: 1.0
 ---
 work/atmosphere/um_hg3.exe:
-  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/um7-git.2024.07.03_access-esm1.5-kgxooyp2s476dd4zc5mgtwhxfknkhnoe/bin/um_hg3.exe
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/um7-git.2024.07.03_access-esm1.5-kgxooyp2s476dd4zc5mgtwhxfknkhnoe/bin/um_hg3.exe
   hashes:
-    binhash: 3180dda616c7dfe63d8134e00bff2641
-    md5: 1b7874ffb5e34ec50b6a68abbb7769a6
+    binhash: cc7e4e1ad8f67c4594e62769fc48a917
+    md5: 37e5f7c1ce39d40011ca7eae556fcd17
 work/ice/cice_access_360x300_12x1_12p.exe:
-  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cice4-git.2024.05.21_access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra/bin/cice_access_360x300_12x1_12p.exe
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cice4-git.2024.05.21_access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra/bin/cice_access_360x300_12x1_12p.exe
   hashes:
-    binhash: 818f213e53d30fc307b565c35939382c
-    md5: 04fd88249ebc16e3f560fc265838e9d1
-work/ocean/fms_ACCESS-CM.x:
-  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/mom5-git.access-esm1.5_2024.08.23_access-esm1.5-ougudnkjcdkuuu6wuxne3uy7tr4y6oes/bin/fms_ACCESS-CM.x
+    binhash: 224441384273cfc7bd37b859acccb5cd
+    md5: b50c8f77304eea6548f571fa6ca9ba8c
+work/ocean/fms_ACCESS-ESM.x:
+  fullpath: /g/data/vk83/prerelease/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/mom5-git.2024.08.23_access-esm1.6-oycrxfrimqhonk4i6iowchxru4hzfvm5/bin/fms_ACCESS-ESM.x
   hashes:
-    binhash: 711dd9e382eee06aba1f38ce83f7e7d5
-    md5: 96863931103def85ed76b152ba01b5c1
+    binhash: 70d3e4603aa6cfa5b55b3cb4c726cc77
+    md5: 1165f3f6312a2107086d155926240438

manifests/input.yaml

@@ -296,11 +296,6 @@ work/ice/INPUT/monthly_sstsss.nc:
   hashes:
     binhash: 49aab10f25c58a9a0ffa5617847050ff
     md5: 323d4c605f83f4d7d3126da70153c2ed
-work/ocean/INPUT/bgc_param.nc:
-  fullpath: /g/data/vk83/configurations/inputs/access-esm1p5/share/ocean/biogeochemistry/global.1deg/2024.07.12/bgc_param.nc
-  hashes:
-    binhash: 69340d523fddf842e3e7a030eb139111
-    md5: 9defb35e7a7181e9170a6ae57a4d3348
 work/ocean/INPUT/dust.nc:
   fullpath: /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/ocean/biogeochemistry/global.1deg/2020.05.19/dust.nc
   hashes: