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Moved table to the top and the example files to the bottom.
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@tammasloughran
tammasloughran committed Sep 15, 2023
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136 changes: 68 additions & 68 deletions documentation/docs/user_guide/inputs/cable_nml.md
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Expand Up @@ -16,73 +16,6 @@ applications. The following are annotated examples of cable.nml:
[obsolete and deprecated user features](../obsolete_and_deprecated_features/obsolete_and_deprecated_features.md) page.


## For offline applications ##

```fortran
&cable
filename%met = '/projects/access/CABLE-AUX/offline/TumbaFluxnet.1.3_met.nc'
filename%out = 'out_cable.nc'
filename%log = 'log_cable.txt'
filename%restart_in = ' '
filename%restart_out = './restart_out.nc'
filename%type = '/projects/access/CABLE-AUX/offline/gridinfo_CSIRO_1x1.nc'
vegparmnew = .TRUE. ! using new format when true
soilparmnew = .TRUE. ! using new format when true
spinup = .TRUE. ! do we spin up the model?
delsoilM = 0.001 ! allowed variation in soil moisture for spin up
delsoilT = 0.01 ! allowed variation in soil temperature for spin up
output%restart = .TRUE. ! should a restart file be created?
output%met = .TRUE. ! input met data
output%flux = .TRUE. ! convective, runoff, NEE
output%soil = .TRUE. ! soil states
output%snow = .TRUE. ! snow states
output%radiation = .TRUE. ! net rad, albedo
output%carbon = .TRUE. ! NEE, GPP, NPP, stores
output%veg = .TRUE. ! vegetation states
output%params = .TRUE. ! input parameters used to produce run
output%balances = .TRUE. ! energy and water balances
check%ranges = .FALSE. ! variable ranges, input and output
check%energy_bal = .TRUE. ! energy balance
check%mass_bal = .TRUE. ! water/mass balance
verbose = .TRUE. ! write details of every grid cell init and params to log?
leaps = .TRUE. ! calculate timing with leap years
logn = 88 ! log file number - declared in input module
fixedCO2 = 350.0 ! if not found in met file, in ppmv
spincasa = .FALSE. ! spin casa before running the model if TRUE, and should be set to FALSE if spincasainput = .TRUE.
l_casacnp = .FALSE. ! using casaCNP with CABLE
l_laiFeedbk = .FALSE. ! using prognostic LAI
l_vcmaxFeedbk = .FALSE. ! using prognostic Vcmax
icycle = 0 ! BP pull it out from casadimension and put here; 0 for not using casaCNP, 1 for C, 2 for C+N, 3 for C+N+P
casafile%cnpipool='/projects/access/CABLE-AUX/core/biogeochem/poolcnpInTumbarumba.csv' !
casafile%cnpbiome='/projects/access/CABLE-AUX/core/biogeochem/pftlookup_csiro_v16_17tiles.csv' ! biome specific BGC parameters
casafile%cnpepool='poolcnpOut.csv' ! end of run pool size
casafile%cnpmetout='casamet.nc' ! output daily met forcing for spinning casacnp
casafile%cnpmetin='' ! list of daily met files for spinning casacnp
casafile%phen='/projects/access/CABLE-AUX/core/biogeochem/modis_phenology_csiro.txt' ! modis phenology
casafile%cnpflux='cnpfluxOut.csv'
ncciy = 0 ! 0 for not using gswp; 4-digit year input for year of gswp met
gswpfile%rainf = 'gswp/Rainf_gswp1987.nc'
gswpfile%snowf = 'gswp/Snowf_gswp1987.nc'
gswpfile%LWdown= 'gswp/LWdown_srb1987.nc'
gswpfile%SWdown= 'gswp/SWdown_srb1987.nc'
gswpfile%PSurf = 'gswp/PSurf_ecor1987.nc'
gswpfile%Qair = 'gswp/Qair_cru1987.nc'
gswpfile%Tair = 'gswp/Tair_cru1987.nc'
gswpfile%wind = 'gswp/Wind_ncep1987.nc'
redistrb = .FALSE. ! Turn on/off the hydraulic redistribution
wiltParam = 0.5
satuParam = 0.8
cable_user%FWSOIL_SWITCH = 'standard' ! choices are: 'standard', 'non-linear extrapolation' or 'Lai and Ktaul 2000'
cable_user%DIAG_SOIL_RESP = 'ON '
cable_user%LEAF_RESPIRATION = 'ON '
cable_user%RUN_DIAG_LEVEL= 'BASIC' ! choices are: 'BASIC', 'NONE'
cable_user%CONSISTENCY_CHECK= .TRUE. ! TRUE outputs combined fluxes at each timestep for comparison to a control run
cable_user%CASA_DUMP_READ = .FALSE. ! TRUE reads CASA forcing from netcdf format
cable_user%CASA_DUMP_WRITE = .FALSE. ! TRUE outputs CASA forcing in netcdf format
cable_user%SSNOW_POTEV= 'HDM' ! Humidity Deficit Method
&end
```

## List of namelist variables

| Namelist variable | Type | Available values | Default value | Description |
Expand Down Expand Up @@ -170,7 +103,7 @@ applications. The following are annotated examples of cable.nml:
| cable_user%POP_out | character(len=3) | 'epi' 'rst' 'ini' | 'rst' | POP restart file type. `'epi'` is end of year state `'rst'` is a standard restart file, `'ini'` is an initialisation restart file. |
| cable_user%POP_rst | character(len=50) | any string of max. 50 characters | ' ' | POP restart file directory. |
| cable_user%casa_out_freq | character(len=8) | 'daily' 'monthly' 'annually' | 'annually' | CASA output frequency. |
| cable_user%vcmax | character(len=10) | 'standard' 'Walker2014' | 'standard' | Alternative functional form of $V_{cmax}$ (maximum RuBP carboxylation rate). For `'Walker2014'` see [Walker et al., 2014](https://doi.org/10.1002/ece3.1173) |
| cable_user%vcmax | character(len=10) | 'standard' 'Walker2014' | 'standard' | Alternative functional form of $V_{cmax}$ (maximum RuBP carboxylation rate). For `'Walker2014'` see [Walker et al., 2014](https://onlinelibrary.wiley.com/doi/10.1002/ece3.1173) |
| cable_user%POPLUC_RunType | character(len=10) | 'static' 'init' 'restart' | 'static' | Type of POP-LUC run. `'init'` is initial POP-LUC run, `'restart'` is a restart run, `'static'` disables dynamic vegetation and sets `cable_user%POPLUC = .FALSE.`.|
| cable_user%call_pop | logical | .TRUE. .FALSE. | .FALSE. | Enable POP. |
| cable_user%POP_fromZero | logical | .TRUE. .FALSE. | .FALSE. | Run POP initialisation. |
Expand Down Expand Up @@ -202,6 +135,73 @@ applications. The following are annotated examples of cable.nml:
| cable_user%NtilesThruMetFile | logical | .TRUE. .FALSE. | .FALSE. | Specify Ntiles through met file. |


## For offline applications ##

```fortran
&cable
filename%met = '/projects/access/CABLE-AUX/offline/TumbaFluxnet.1.3_met.nc'
filename%out = 'out_cable.nc'
filename%log = 'log_cable.txt'
filename%restart_in = ' '
filename%restart_out = './restart_out.nc'
filename%type = '/projects/access/CABLE-AUX/offline/gridinfo_CSIRO_1x1.nc'
vegparmnew = .TRUE. ! using new format when true
soilparmnew = .TRUE. ! using new format when true
spinup = .TRUE. ! do we spin up the model?
delsoilM = 0.001 ! allowed variation in soil moisture for spin up
delsoilT = 0.01 ! allowed variation in soil temperature for spin up
output%restart = .TRUE. ! should a restart file be created?
output%met = .TRUE. ! input met data
output%flux = .TRUE. ! convective, runoff, NEE
output%soil = .TRUE. ! soil states
output%snow = .TRUE. ! snow states
output%radiation = .TRUE. ! net rad, albedo
output%carbon = .TRUE. ! NEE, GPP, NPP, stores
output%veg = .TRUE. ! vegetation states
output%params = .TRUE. ! input parameters used to produce run
output%balances = .TRUE. ! energy and water balances
check%ranges = .FALSE. ! variable ranges, input and output
check%energy_bal = .TRUE. ! energy balance
check%mass_bal = .TRUE. ! water/mass balance
verbose = .TRUE. ! write details of every grid cell init and params to log?
leaps = .TRUE. ! calculate timing with leap years
logn = 88 ! log file number - declared in input module
fixedCO2 = 350.0 ! if not found in met file, in ppmv
spincasa = .FALSE. ! spin casa before running the model if TRUE, and should be set to FALSE if spincasainput = .TRUE.
l_casacnp = .FALSE. ! using casaCNP with CABLE
l_laiFeedbk = .FALSE. ! using prognostic LAI
l_vcmaxFeedbk = .FALSE. ! using prognostic Vcmax
icycle = 0 ! BP pull it out from casadimension and put here; 0 for not using casaCNP, 1 for C, 2 for C+N, 3 for C+N+P
casafile%cnpipool='/projects/access/CABLE-AUX/core/biogeochem/poolcnpInTumbarumba.csv' !
casafile%cnpbiome='/projects/access/CABLE-AUX/core/biogeochem/pftlookup_csiro_v16_17tiles.csv' ! biome specific BGC parameters
casafile%cnpepool='poolcnpOut.csv' ! end of run pool size
casafile%cnpmetout='casamet.nc' ! output daily met forcing for spinning casacnp
casafile%cnpmetin='' ! list of daily met files for spinning casacnp
casafile%phen='/projects/access/CABLE-AUX/core/biogeochem/modis_phenology_csiro.txt' ! modis phenology
casafile%cnpflux='cnpfluxOut.csv'
ncciy = 0 ! 0 for not using gswp; 4-digit year input for year of gswp met
gswpfile%rainf = 'gswp/Rainf_gswp1987.nc'
gswpfile%snowf = 'gswp/Snowf_gswp1987.nc'
gswpfile%LWdown= 'gswp/LWdown_srb1987.nc'
gswpfile%SWdown= 'gswp/SWdown_srb1987.nc'
gswpfile%PSurf = 'gswp/PSurf_ecor1987.nc'
gswpfile%Qair = 'gswp/Qair_cru1987.nc'
gswpfile%Tair = 'gswp/Tair_cru1987.nc'
gswpfile%wind = 'gswp/Wind_ncep1987.nc'
redistrb = .FALSE. ! Turn on/off the hydraulic redistribution
wiltParam = 0.5
satuParam = 0.8
cable_user%FWSOIL_SWITCH = 'standard' ! choices are: 'standard', 'non-linear extrapolation' or 'Lai and Ktaul 2000'
cable_user%DIAG_SOIL_RESP = 'ON '
cable_user%LEAF_RESPIRATION = 'ON '
cable_user%RUN_DIAG_LEVEL= 'BASIC' ! choices are: 'BASIC', 'NONE'
cable_user%CONSISTENCY_CHECK= .TRUE. ! TRUE outputs combined fluxes at each timestep for comparison to a control run
cable_user%CASA_DUMP_READ = .FALSE. ! TRUE reads CASA forcing from netcdf format
cable_user%CASA_DUMP_WRITE = .FALSE. ! TRUE outputs CASA forcing in netcdf format
cable_user%SSNOW_POTEV= 'HDM' ! Humidity Deficit Method
&end
```

## For ACCESS applications ##


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