Merge pull request #268 from ACCESS-NRI/255-combined-changes

Combined updates to the configuration prior to optimisation

Author: blimlim

atmosphere/cable.nml

@@ -4,12 +4,6 @@
 !! cable_user flags
 !
   cable_user%GS_SWITCH = 'medlyn' ! alternative is 'leuning' - used for ESM1.5
-  cable_user%CABLE_RUNTIME_COUPLED = .TRUE. ! controls whether snow initialised if
-                                            ! ktau_gl=1
-                                            ! must be set true for coupled run
-                                            ! use true for atmosphere only runs if
-                                            ! want to take snow from start dump
-                                            ! default is .false.
   cable_user%FWSOIL_SWITCH = 'Haverd2013' ! Controls root water uptake function
                                         ! choices are: 
                                         ! 'standard' - used for ESM1.5
@@ -61,7 +55,7 @@
   l_vcmaxFeedbk = .TRUE.  ! using prognostic Vcmax
 ! filenames for CASA-CNP input files
 ! updated pftlookup file for CABLE3 format
-  casafile%cnpbiome='INPUT/pftlookup_cable3_1213_exp6_c4crop.csv'  ! biome specific BGC parameters
+  casafile%cnpbiome='INPUT/pftlookup_cable3_OctB_update.csv'  ! biome specific BGC parameters
   cable_user%PHENOLOGY_SWITCH = 'MODIS' 
   casafile%phen='INPUT/modis_phenology_csiro_13evergreen.txt' ! phenology by latitude (modis derived)
 &end

atmosphere/input_atm.nml

@@ -3,8 +3,9 @@
  xfactor=1.0
  SC=1361.617
  co2_init=284.725
- VOLCTS_val=137.31
+ VOLCTS_val=135.2
  ocn_sss=.false.
  sdump_enable=.false.
  rdump_enable=.false.
+ ocean_albedo_factor=0.92
 &end

atmosphere/namelists

@@ -388,7 +388,7 @@
  L_HYDROLOGY=.TRUE.,
  L_SOIL_SAT_DOWN=.TRUE.,
  L_SCVARY=.false.,
- L_VOLCTS=.true.,
+ L_VOLCTS_VARY=.false.,
  l_anthrop_heat_src=.FALSE.,
  L_ICOUNT=.FALSE.,
  L_UKCA=.FALSE.,
@@ -575,7 +575,7 @@
  L_CCW=.TRUE.,
  L_CLOUD_DEEP=.TRUE.,
  A_CONVECT_SEGMENTS=-99, 
- A_CONVECT_SEG_SIZE=80,
+ A_CONVECT_SEG_SIZE=20,
  MPARWTR=1.0000e-03,
  ANVIL_FACTOR=0.0000, 
  TOWER_FACTOR=0.0000, 
@@ -639,9 +639,9 @@
  PEN_RAD_FRAC=0.170,
  SW_BETA=0.400,
  A_SW_SEGMENTS=-99, 
- A_SW_SEG_SIZE=80,
+ A_SW_SEG_SIZE=20,
  A_LW_SEGMENTS=-99, 
- A_LW_SEG_SIZE=80,
+ A_LW_SEG_SIZE=20,
  L_EQT=.TRUE.,
  L_SEC_VAR=.FALSE.,
  L_CLIM_AERO_HGT=.FALSE.,
@@ -905,7 +905,7 @@
 
  &FILENATFORCE
  FILE_SCVARY  = '',
- FILE_VOLCTS  = 'INPUT/volcts_18502000ave.dat'
+ FILE_VOLCTS  = ''
  /
 
  &PPRINTXN

atmosphere/pft_params.nml

@@ -524,7 +524,7 @@
  vegin% canst1   (           10 ) =    1.0000000E-01
  vegin% length   (           10 ) =    3.0000000E-01
  vegin% width    (           10 ) =    9.9999998E-03
- vegin% vcmax    (           10 ) =    2.0E-05
+ vegin% vcmax    (           10 ) =    2.0000000E-05
  vegin% ejmax    (           10 ) =    0.0000000E+00
  vegin% hc       (           10 ) =    5.5000000E-01
  vegin% xfang    (           10 ) =    -3.0000000E-01
@@ -638,11 +638,11 @@
  vegin% dleaf    (           11 ) =    5.4772258E-02
  vegin% lai      (           11 ) =    0.0000000E+00
  vegin% canst1   (           12 ) =    1.0000000E-01
- vegin% length   (           12 ) =    1.1293175E-01
- vegin% width    (           12 ) =    2.3409716E-02
+ vegin% length   (           12 ) =    1.1350000E-01
+ vegin% width    (           12 ) =    2.3520000E-02
  vegin% vcmax    (           12 ) =    5.7499999E-05
  vegin% ejmax    (           12 ) =    0.0000000E+00
- vegin% hc       (           12 ) =    2.5610882E+01
+ vegin% hc       (           12 ) =    2.4900000E+01
  vegin% xfang    (           12 ) =    -5.0000000E-01
  vegin% rp20     (           12 ) =    1.4000000E+00
  vegin% rpcoef   (           12 ) =    8.3200000E-02
@@ -693,14 +693,14 @@
  vegin% taul1    (           12 ) =    9.0000004E-02
  vegin% taul2    (           12 ) =    2.9000000E-01
  vegin% taul3    (           12 ) =    9.9999998E-03
- vegin% dleaf    (           12 ) =    5.1416925E-02
+ vegin% dleaf    (           12 ) =    5.1667398E-02
  vegin% lai      (           12 ) =    2.5000000E+00
  vegin% canst1   (           13 ) =    1.0000000E-01
- vegin% length   (           13 ) =    9.7057207E-02
- vegin% width    (           13 ) =    1.4283113E-02
+ vegin% length   (           13 ) =    1.0210000E-01
+ vegin% width    (           13 ) =    1.5460000E-02
  vegin% vcmax    (           13 ) =    4.9999999E-05
  vegin% ejmax    (           13 ) =    0.0000000E+00
- vegin% hc       (           13 ) =    1.2014615E+01
+ vegin% hc       (           13 ) =    1.7800000E+01
  vegin% xfang    (           13 ) =    1.0000000E-02
  vegin% rp20     (           13 ) =    1.6000000E+00
  vegin% rpcoef   (           13 ) =    8.3200000E-02
@@ -751,7 +751,7 @@
  vegin% taul1    (           13 ) =    9.0000004E-02
  vegin% taul2    (           13 ) =    2.9500000E-01
  vegin% taul3    (           13 ) =    9.9999998E-03
- vegin% dleaf    (           13 ) =    3.7232769E-02
+ vegin% dleaf    (           13 ) =    3.9729913E-02
  vegin% lai      (           13 ) =    0.0000000E+00
  vegin% canst1   (           14 ) =    1.0000000E-01
  vegin% length   (           14 ) =    2.9999999E-02
@@ -985,4 +985,4 @@
  vegin% taul3    (           17 ) =    9.9999998E-03
  vegin% dleaf    (           17 ) =    5.4772259E-03
  vegin% lai      (           17 ) =    0.0000000E+00
- /
+ /

atmosphere/um_env.yaml

@@ -10,9 +10,9 @@ RPSEED: ''
 RUNID: PI-01
 TYPE: NRUN
 UM_ATM_NPROCX: '16'
-UM_ATM_NPROCY: '13'
+UM_ATM_NPROCY: '16'
 UM_NAM_MAX_SECONDS: '300'
-UM_NPES: '208'
+UM_NPES: '256'
 UM_SECTOR_SIZE: '2048'
 UM_STDOUT_FILE: atm.fort6.pe
 VN: '7.3'
@@ -42,7 +42,7 @@ ARCLBIOG: INPUT/biogenic_351sm.N96L38
 BIOMASS: INPUT/Bio_1850_cmip7.anc
 CHEMOXID: INPUT/sulpc_oxidants_N96_L38
 DMSCONC: INPUT/DMS_conc.N96
-NDEPFIL: INPUT/Ndep_1850_ESM1.anc
+NDEPFIL: INPUT/Ndep_1850_cmip7.anc
 OCFFEMIS: INPUT/OCFF_1850_cmip7.anc
 OZONE: INPUT/ozone_1850_ESM1.anc
 SOOTEMIS: INPUT/BC_1850_cmip7.anc

config.yaml

@@ -30,15 +30,15 @@ modules:
   use:
       - /g/data/vk83/modules
   load:
-      - access-esm1p6/2025.09.002
+      - access-esm1p6/2025.11.000
 
 # Model configuration
 model: access-esm1.6
 
 submodels:
     - name: atmosphere
       model: um
-      ncpus: 208
+      ncpus: 256
       exe: um_hg3.exe
       input:
         # Aerosols
@@ -51,13 +51,12 @@ submodels:
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/aerosol/global.N96/2020.05.19/DMS_conc.N96
         # Forcing
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/forcing/global.N96/2020.05.19/ozone_1850_ESM1.anc
-        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/forcing/resolution_independent/2020.05.19/volcts_18502000ave.dat
         # Land
-        - /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/land/biogeochemistry/global.N96/2020.05.19/Ndep_1850_ESM1.anc
+        - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/atmosphere/land/biogeochemistry/global.N96/2025.11.18/Ndep_1850_cmip7.anc
         - /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/land/soiltype/global.N96/2020.05.19/qrparm.soil_igbp_vg
         - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/vegetation/global.N96/2025.08.29/cable_vegfunc_N96.anc
         - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2025.08.29/modis_phenology_csiro_13evergreen.txt
-        - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2025.08.29/pftlookup_cable3_1213_exp6_c4crop.csv
+        - /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2025.11.18/pftlookup_cable3_OctB_update.csv
         # Spectral
         - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/spectral/resolution_independent/2020.05.19/spec3a_sw_hadgem1_6on
         - /g/data/vk83/configurations/inputs/access-esm1p5/share/atmosphere/spectral/resolution_independent/2020.05.19/spec3a_lw_hadgem1_6on
@@ -69,7 +68,7 @@ submodels:
 
     - name: ocean
       model: mom
-      ncpus: 196
+      ncpus: 240
       exe: mom5_access_cm 
       input:
         # Biogeochemistry
@@ -119,7 +118,7 @@ submodels:
 collate:
     enable: false
 
-restart: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/restart/2025.09.26
+restart: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/restart/2025.11.20
 
 # Timing controls
 calendar:
@@ -146,7 +145,7 @@ qsub_flags: -W umask=027
 mpi:
   flags:
     - --mca mpi_yield_when_idle true
-payu_minimum_version: 1.1.7
+payu_minimum_version: 1.2.0
 
 # Sync options for automatically copying data from ephemeral scratch space to
 # longer term storage

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/oneapi-2025.2.0/um7-git.access-esm1.6-2025.09.000_access-esm1.6-s7ckahfudhpeh547lksszvuqt44usnq3/bin/um_hg3.exe
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.2.0/um7-git.2025.11.000_access-esm1.6-nwpmrxgu3rst7i3mpucbsyzsbr6nbeqq/bin/um_hg3.exe
   hashes:
-    binhash: 6f8b323ac3b87cc25dce32cf14b90188
-    md5: 5580604dab9ed80b2f869fde88bb3603
+    binhash: 4f43750a722b4be2d3c4a9ca650e1f7d
+    md5: 38bbaca9e1b13b55d59f0aed5263ffff
 work/ice/cice_access-esm1.6_360x300_12x1_12p.exe:
-  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.2.0/cice5-git.access-esm1.6-2025.09.000_access-esm1.6-nlh32pdhysi5qlht7mk3revvjk4hn3un/bin/cice_access-esm1.6_360x300_12x1_12p.exe
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.2.0/cice5-git.access-esm1.6-2025.09.000_access-esm1.6-upsemjp76eyjszivtpvmonw2dyqaq2rj/bin/cice_access-esm1.6_360x300_12x1_12p.exe
   hashes:
-    binhash: e6f0aa66a4e6e6c67686294496e25129
-    md5: 19575002899af412795b2eb26a0d5696
+    binhash: d5ca8f242306c1a01f2f5b71ee02f3ca
+    md5: 21f4176d7ec28702ebf6483fc9529886
 work/ocean/mom5_access_cm:
-  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.2.0/mom5-git.2025.05.000_access-esm1.6-q7acqikepkutcdxofim77qzjbul2lkc7/bin/mom5_access_cm
+  fullpath: /g/data/vk83/apps/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/oneapi-2025.2.0/mom5-git.2025.05.000_access-esm1.6-tzlv4hwxcbh4u2alvbiwnpnxjg67crnu/bin/mom5_access_cm
   hashes:
-    binhash: bbe76179c6b55a7f83c8aeef8a44927b
-    md5: 70f590d05f1a582dff3dd458a3f9c296
+    binhash: c54fa44a8d0c20975b42bdd915ff7bef
+    md5: 8e404189b0972fb1beb916ed0dcba88c

manifests/input.yaml

@@ -16,11 +16,11 @@ work/atmosphere/INPUT/DMS_conc.N96:
   hashes:
     binhash: da1baa25e78ec281c82ea4588e30a340
     md5: 7e8ec8de832c0b9b8c1d9f0eda4d54e5
-work/atmosphere/INPUT/Ndep_1850_ESM1.anc:
-  fullpath: /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/land/biogeochemistry/global.N96/2020.05.19/Ndep_1850_ESM1.anc
+work/atmosphere/INPUT/Ndep_1850_cmip7.anc:
+  fullpath: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/atmosphere/land/biogeochemistry/global.N96/2025.11.18/Ndep_1850_cmip7.anc
   hashes:
-    binhash: 47374849ef42f83e3c02629827a482ee
-    md5: 48462cfa1aeed200c3b8d0bf1b49654a
+    binhash: abdeb4239bb38126280fa2e58eb6f7b9
+    md5: 8341bf43665cdf8d754507885e3abfa8
 work/atmosphere/INPUT/OCFF_1850_cmip7.anc:
   fullpath: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/pre-industrial/atmosphere/aerosol/global.N96/2025.06.04/OCFF_1850_cmip7.anc
   hashes:
@@ -76,11 +76,11 @@ work/atmosphere/INPUT/ozone_1850_ESM1.anc:
   hashes:
     binhash: 7e82d4a83bf18e59277f026cbbee4c74
     md5: a64a01e3b092085fca308524a75a1cee
-work/atmosphere/INPUT/pftlookup_cable3_1213_exp6_c4crop.csv:
-  fullpath: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2025.08.29/pftlookup_cable3_1213_exp6_c4crop.csv
+work/atmosphere/INPUT/pftlookup_cable3_OctB_update.csv:
+  fullpath: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/share/atmosphere/land/biogeochemistry/resolution_independent/2025.11.18/pftlookup_cable3_OctB_update.csv
   hashes:
-    binhash: 28cb640d1f82c866fb2da732ee61a018
-    md5: c67bdd681339f6d9c72223f9f8aaf1b7
+    binhash: 9c4c143d53559b2ac70ea8eb37af48c2
+    md5: bf80c75ce38f147dd46323323d3039e2
 work/atmosphere/INPUT/qrparm.mask:
   fullpath: /g/data/vk83/configurations/inputs/access-esm1p5/modern/share/atmosphere/grids/global.N96/2020.05.19/qrparm.mask
   hashes:
@@ -216,11 +216,6 @@ work/atmosphere/INPUT/vertlevs_G3:
   hashes:
     binhash: 67eeeb98a7de5eee305f026a20482cc7
     md5: 58ca02de69b16bd59771c81e06c4c21a
-work/atmosphere/INPUT/volcts_18502000ave.dat:
-  fullpath: /g/data/vk83/configurations/inputs/access-esm1p5/modern/pre-industrial/atmosphere/forcing/resolution_independent/2020.05.19/volcts_18502000ave.dat
-  hashes:
-    binhash: 34b64995370a775e276c7a270aa659a7
-    md5: 47bd369c750be55d706ab60c78bc7aee
 work/coupler/areas.nc:
   fullpath: /g/data/vk83/configurations/inputs/access-esm1p6/modern/share/coupler/grids/global.oi_1deg.a_N96/2025.07.29/areas.nc
   hashes:
@@ -272,19 +267,16 @@ work/coupler/rmp_um1v_to_cice_CONSERV_FRACNNEI.nc:
     binhash: df320c62a9f91bc48c09172eb56c03d8
     md5: 2a5817b8136e8820fbdd4ed28cfb4098
 work/ice/INPUT/grid.nc:
-  copy: true
   fullpath: /g/data/vk83/configurations/inputs/access-esm1p6/modern/share/ice/grids/global.1deg/2025.07.29/grid.nc
   hashes:
     binhash: fe44237f8bbe8cbcbe8fadef8957f35c
     md5: ff163d91fb6f3e1f5536c8a109d5c04c
 work/ice/INPUT/kmt.nc:
-  copy: true
   fullpath: /g/data/vk83/configurations/inputs/access-esm1p6/modern/share/ice/grids/global.1deg/2025.07.29/kmt.nc
   hashes:
     binhash: c733037d8edd737e43df4335edecb6e8
     md5: f9d11b6fd3c66d6e16a4afde99eec937
 work/ice/INPUT/lice_discharge_iceberg.nc:
-  copy: true
   fullpath: /g/data/vk83/prerelease/configurations/inputs/access-esm1p6/modern/share/ice/iceberg/global.1deg/2025.09.16/lice_discharge_iceberg.nc
   hashes:
     binhash: 02e5fe73a134ce5674b3aa6712443e66