6.9. jules_vegetation.nml

This file sets the vegetation options. It contains one namelist called JULES_VEGETATION.

HCTN24 refers to Hadley Centre Technical Note 24, available from the Met Office Library.

6.9.1. JULES_VEGETATION namelist members

JULES_VEGETATION::l_trait_phys

Type:logical Default:F

Switch for using trait-based physiology.

TRUE

Vcmax is calculated based on observed leaf traits. Leaf nitrogen (nmass: kgN kgLeaf-1) and leaf mass (LMA: kgLeaf m-2) can be based on observations from the TRY database. Vcmax (umol CO2 m-2 s-1) is based on linear regressions as in Kattge et al. 2009. Two additional parameters are needed: vint and vsl - the intercept and slope, respectively, that relate the leaf nitrogen to vcmax. Sigl is replaced with LMA (sigl=LMA*Cmass, where Cmass is the kgC/kgLeaf and is 0.4).

FALSE

Vcmax is calculated based on parameters nl0 (kgN kgC-1) and neff.

JULES_VEGETATION::l_phenol

Type:logical Default:F

Switch for vegetation phenology model.

TRUE

Use phenology model.

FALSE

Do not use phenology model.

JULES_VEGETATION::l_triffid

Type:logical Default:F

Switch for dynamic vegetation model (TRIFFID) except for competition.

TRUE

Use TRIFFID. In this case soil carbon is modelled using four pools (biomass, humus, decomposable plant material, resistant plant material).

FALSE

Do not use TRIFFID. A single soil carbon pool is used.

JULES_VEGETATION::l_veg_compete

Type:logical Default:T

Switch for competing vegetation.

Only used if l_triffid = TRUE.

TRUE

TRIFFID will let the different PFTs compete against each other and modify the vegetation fractions.

FALSE

Vegetation fractions do not change.

JULES_VEGETATION::l_ht_compete

Type:logical Default:F

Only used if l_triffid = TRUE.

TRUE

Use height-based vegetation competition (recommended).

This allows for a generic number of PFTs. When l_trif_eq = TRUE, this is implemented by lotka_eq_jls.F90. When l_trif_eq = FALSE, it is implemented in lotka_noeq_jls.F90 when l_trif_crop = FALSE and in lotka_noeq_subset_jls.F90 when l_trif_crop = TRUE.

FALSE

Use the vegetation competition described in HCTN24.

This is hard-wired for 5 PFTs (BT, NT, C3, C4, SH, in that order) with co-competition for grasses and trees in lokta_jls.F90.

JULES_VEGETATION::l_nitrogen

Type:logical Default:F

Only used if l_triffid = TRUE.

TRUE

Enable Nitrogen limitation of carbon uptake. A nitrogen deposition field should be provided otherwise no N deposition is assumed.

FALSE

No Nitrogen limitation. Nitrogen fluxes are calculated as diagnostics only.

JULES_VEGETATION::l_trif_eq

Type:logical Default:T

Switch for equilibrium vegetation model (i.e., an equilibrium solution of TRIFFID).

Only used if l_triffid = TRUE.

TRUE

Use equilibrium TRIFFID.

FALSE

Do not use equilibrium TRIFFID.

JULES_VEGETATION::phenol_period

Type:integer Permitted:>= 1 Default:None

Period for calls to phenology model in days. Only relevant if l_phenol = TRUE.

JULES_VEGETATION::triffid_period

Type:integer Permitted:>= 1 Default:None

Period for calls to TRIFFID model in days. Only relevant if one of l_triffid or l_trif_eq is TRUE.

JULES_VEGETATION::l_gleaf_fix

Type:logical Default:T

Switch for fixing a bug in the accumulation of g_leaf_phen_acc.

This bug occurs because veg2 is called on TRIFFID timesteps and veg1 is called on phenol timesteps, but veg1 did not previously accumulate g_leaf_phen_acc in the same way as veg2.

TRUE

veg1 accumulates g_leaf_phen_acc between calls to TRIFFID. This is important if triffid_period > phenol_period.

FALSE

veg1 does not accumulate g_leaf_phen_acc between calls to TRIFFID.

JULES_VEGETATION::l_bvoc_emis

Type:logical Default:F

Switch to enable calculation of BVOC emissions.

TRUE

BVOC emissions diagnostics will be calculated.

FALSE

BVOC emissions diagnostics will not be calculated.

JULES_VEGETATION::l_o3_damage

Type:logical Default:F

Switch for ozone damage.

TRUE

Ozone damage is on.

Note

Ozone concentration in ppb must be prescribed in prescribed_data.nml.

FALSE

No effect.

JULES_VEGETATION::l_stem_resp_fix

Type:logical Default:F

Switch for bug fix for stem respiration to use balanced LAI to derive respiring stem mass. The switch is included for backwards compatability with existing configurations. Future updates should include this change.

TRUE

Respiring stem mass is derived allometrically.

FALSE

Respiring stem mass varies with seasonal LAI

JULES_VEGETATION::l_scale_resp_pm

Type:logical Default:F

Scale whole plant maintanence respiration by the soil moisture stress factor, instead of only scaling leaf respiration.

TRUE

Soil moisture stress reduces leaf, root, and stem maintanence respiration.

FALSE

Soil moisture stress only reduces leaf maintanence respiration.

JULES_VEGETATION::fsmc_shape

Type:integer Permitted:0,1 Default:0

Shape of soil moisture stress function on vegetation (fsmc).

0. Piece-wise linear in vol. soil moisture.
1. Piece-wise linear in soil potential. Currently only allowed when const_z = T and l_use_pft_psi = T.

Note

The option fsmc_shape = 1 is still in development. Users should ensure that results are as expected, and provide feedback where deficiencies are identified.

JULES_VEGETATION::l_use_pft_psi

Type:logical Default:F

Switch for parameters in the soil moisture stress on vegetation function (fsmc).

TRUE

Fsmc is calculated from psi_close_io and psi_open_io.

FALSE

Fsmc is calculated from sm_wilt and sm_crit in JULES_SOIL_PROPS and fsmc_p0_io.

Note

Soil respiration and surface conductance of bare soil respectively will depend on sm_wilt and sm_crit in JULES_SOIL_PROPS, regardless of the setting of fsmc_shape.

Note

The option l_use_pft_psi = T is still in development. Users should ensure that results are as expected, and provide feedback where deficiencies are identified.

JULES_VEGETATION::l_vegcan_soilfx

Type:logical Default:F

Switch for enhancement to canopy model to allow for conduction in the soil below the vegetative canopy, reducing coupling between the soil and the canopy.

TRUE

Allow for conduction in the soil.

FALSE

No effect.

JULES_VEGETATION::l_leaf_n_resp_fix

Type:logical Default:F

Switch for bug fix for leaf nitrogen content used in the calculation of plant maintenance respiration. The switch is included for backwards compatability with existing configurations. Runs with can_rad_mod =1, 4 or 5 are affected.

TRUE

Use correct forms for canopy-average leaf N content.

FALSE

No effect.

JULES_VEGETATION::l_landuse

Type:logical Default:F

Switch for using landuse change in conjunction with TRIFFID

Only used if l_triffid = TRUE.

TRUE

Land use change is implemented within TRIFFID. Litter fluxes are split between soil and wood product pools. Requires additional prognostics covering the product pools and the agricultural fraction from the previous TRIFFID call.

FALSE

All litter fluxes enter the soil

JULES_VEGETATION::l_recon

Type:logical Default:T

Switch for reconfiguring vegetation fractions. Also initialises vegetation and soil biogeochemistry at land ice points. With the ECOSSE soil model this switch also ensures that the initial condition for soil biogeochemistry is internally consistent.

TRUE

For soil points (land points with no ice) ensure vegetation fractions are at least a minimum value and reduce other fractions accordingly.

FALSE

Do not apply the minimum vegation fractions. This is useful when some points are 100% lake and urban, in which case reconfiguration leads to a total tile fraction of greater than 1.

JULES_VEGETATION::l_prescsow

Type:logical Default:F

Switch that determines how crop sowing dates are defined. Only used if ncpft > 0.

TRUE

Sowing dates prescribed in JULES_CROP_PROPS are used.

FALSE

Sowing dates are determined by the model.

JULES_VEGETATION::l_irrig_dmd

Type:logical Default:F

Switch controlling the implementation of irrigation demand code.

TRUE

Tiles are irrigated.

FALSE

No effect.

JULES_VEGETATION::l_irrig_limit

Type:logical Default:F

Switch controlling whether the amount of water used to irrigate tiles is limited.

TRUE

Water for irrigation is taken first from the deep soil (groundwater) store, and then from the river storage when the deep soil store is exhausted. Tiles are irrigated up to the critical point if the necessary water is available. This option requires l_irrig_dmd = TRUE, l_top = TRUE, l_rivers = TRUE and i_river_vn = 1,3.

Warning

The irrigation supply code in JULES is still in development, and is available in this release to support beta testing activities.

Users should ensure that results are as expected, and provide feedback where deficiencies are identified.

FALSE

Tiles will be irrigated to critical point from an unconstrained water supply.

JULES_VEGETATION::l_trif_crop

Type:logical Default:F

Switch controlling the treatment of agricultural PFTs. Where agricultural PFTs are defined by the crop_io parameter.

TRUE

In the non-agricultural area natural PFT competion is calculated by a call to a new version of the lotka routine and in each agricultural area agricultural-PFT competition is calculated by an additional call to the new version of the lotka routine. Crop and pasture areas are defined by the frac_agr and frac_past variables respectively. Additionally, to represent harvesting, a fraction of crop litter is added to the fast wood products pool instead of the soil carbon pools.

FALSE

Vegetation competition is calculated for natural and crop PFTs together, with natural PFTs excluded from the agricultural area that is defined by the frac_agr variable. Agricultural PFTs can also grow in natural areas where they are interpreted as natural grasses.

JULES_VEGETATION::irr_crop

Type:integer Permitted:0, 1 or 2 Default:0

0. Irrigation season (i.e. season in which crops might be growing on the gridbox) lasts the entire year.
1. Irrigation season is determined from driving data according to Doell & Siebert (2002) method. No irrigation is applied outside the irrigation season.
2. Irrigation season is determined by maximum dvi across all tiles. Requires l_crop = T. No irrigation is applied outside the irrigation season.

JULES_VEGETATION::can_model

Type:integer Permitted:1-4 Default:4

Choice of canopy model for vegetation:

1. No distinct canopy.
2. Radiative canopy with no heat capacity.
3. Radiative canopy with heat capacity. This option is deprecated, with 4 preferred.
4. As 3 but with a representation of snow beneath the canopy. This option is preferred to 3.

Note

can_model = 1 does not mean that there is no vegetation canopy. It means that the surface is represented as a single entity, rather than having distinct surface and canopy levels for the purposes of radiative processes.

JULES_VEGETATION::can_rad_mod

Type:integer Permitted:1, 4, 5, 6 Default:4

Switch for treatment of canopy radiation.

1. A single canopy layer for which radiation absorption is calculated using Beer’s law. Leaf-level photosynthesis is scaled to the canopy level using the ‘big leaf’ approach. Leaf nitrogen, photosynthetic capacity, i.e the Vcmax parameter, and leaf photosynthesis vary exponentially through the canopy with radiation.

4. Multi-layer approach for radiation interception following the 2-stream approach of Sellers et al. (1992). This approach takes into account leaf angle distribution, zenith angle, and differentiates absorption of direct and diffuse radiation. It has an exponential decline of leaf N through the canopy and includes inhibition of leaf respiration in the light. Canopy photosynthesis and conductance are calculated as the sum over all layers.
5. This is an improvement of option 4, including:
   • Sunfleck penetration though the canopy.
   • Division of sunlit and shaded leaves within each canopy level.
   • A modified version of inhibition of leaf respiration in the light.
6. This is an improvement of option 5, including an exponential decline of leaf N with canopy height proportional to LAI, following Beer’s law.

Note

can_rad_mod = 1 and 6 are recommended.

Note

When using can_rad_mod = 4, 5 or 6 it is recommended to use driving data that contains direct and diffuse radiation separately rather than a constant diffuse fraction.

See also

Descriptions of option 1 can be found in Jogireddy et al. (2006), and an application of option 4 can be found in Mercado et al. (2007). Options 1 to 5 are described in Clark et al (2011).

JULES_VEGETATION::ilayers

Type:integer Permitted:>= 0 Default:10

Number of layers for canopy radiation model. Only used for can_rad_mod = 4, 5 or 6.

These layers are used for the calculations of radiation interception and photosynthesis.

JULES_VEGETATION::stomata_model

Type:integer Permitted:1 or 2 Default:1

Choice for model of stomatal conductance.

Possible values are:

1. The original JULES model, including the Jacobs closure - see Eqn.9 of Best et al. (2011).
2. The model of Medlyn et al. (2011) - see Eqn.11 of that paper, and Medlyn et al (2012). Note that as implemented the model uses a single parameter (g₁, assuming that g₀ = 0).

See also

References:

• Best et al., 2011, The Joint UK Land Environment Simulator (JULES), model description – Part 1: Energy and water fluxes, Geosci. Model Dev., https://doi.org/10.5194/gmd-4-677-2011.
• Medlyn et al., 2011, Reconciling the optimal and empirical approaches to modelling stomatal conductance, Global Change Biology, https://doi.org/10.1111/j.1365-2486.2010.02375.x.
• Medlyn et al., 2012, Reconciling the optimal and empirical approaches to modelling stomatal conductance, Global Change Biology, https://doi.org/10.1111/j.1365-2486.2012.02790.x.

JULES_VEGETATION::frac_min

Type:real Default:1.0e-6

Minimum fraction that a PFT is allowed to cover if TRIFFID is used.

JULES_VEGETATION::frac_seed

Type:real Default:0.01

Seed fraction for TRIFFID.

JULES_VEGETATION::pow

Type:real Default:5.241e-4

Power in sigmodial function used to get competition coefficients.

See Hadley Centre Technical Note 24, Eq.3.

JULES_VEGETATION::l_inferno

Type:logical Default:F

Switch that determines whether interactive fires (INFERNO) is used. This allows for the diagnostic of burnt area, burnt carbon and a variety of fire emissions.

TRUE

INFERNO is used to provide diagnostic fire variables

FALSE

INFERNO is not used.

JULES_VEGETATION::ignition_method

Type:integer Permitted:1, 2, 3 Default:1

Switch to determine the type of ignition used (ubiquitous or prescribed with population and lightning)

1. INFERNO uses ubiquitous (constant) ignitions, of 1.67 fires per km2 per s (1.5 from humans, 0.17 from lightning).
2. INFERNO uses prescribed lightning ignitions, either from an ancillary or the UM. Meanwhile humans are assumed to ignite 1.5 fires per km2 per s.
3. INFERNO uses prescribed ignition using Population Density and Lightning Frequency (Cloud-to-Ground). These must be provided as prescribed data to the JULES run.

JULES_VEGETATION::l_trif_fire

Type:logical Default:F

Switch that determines whether interactive fire is used. This allows for burnt area to link with dynamic vegetation.

Only used if l_triffid = TRUE.

TRUE

Burnt area is calculated in INFERNO and passed to TRIFFID to calculate vegetation dynamics. Carbon is also removed from DPM and RPM pools in SOILCARB.

FALSE

Burnt area is zero unless prescribed via an ancillary file.

JULES_VEGETATION::l_vegdrag_pft

Type:logical(npft) Default:F

Switch for using vegetation canopy drag scheme on each PFT.

TRUE

Use a vegetative drag scheme. This is based on Harman and Finnigan (2007).

FALSE

Do not use vegetative drag scheme.

JULES_VEGETATION::l_rsl_scalar

Type:logical Default:F

Switch for using a roughness sublayer correction scheme in scalar variables. This is based on Harman and Finnigan (2008).

Only use if any l_vegdrag_pft = TRUE.

TRUE

Use a roughness sublayer correction scheme in scalar variables.

FALSE

Do not use a roughness sublayer correction scheme in scalar variables.

JULES_VEGETATION::c1_usuh

Type:real Permitted:>= 0 Default:None

u*/U(h) at the top of dense canopy. See Massman (1997).

Only use if any l_vegdrag_pft = TRUE.

JULES_VEGETATION::c2_usuh

Type:real Permitted:>= 0 Default:None

u*/U(h) at substrate under canopy. See Massman (1997).

Only use if any l_vegdrag_pft = TRUE.

JULES_VEGETATION::c3_usuh

Type:real Permitted:>= 0 Default:None

This is used in the exponent of eqution weighting dense and sparse vegetation to get u*/U(h) in neutral condition. See Massman (1997). The default value is taken from Wang (2012).

Only use if any l_vegdrag_pft = TRUE.

JULES_VEGETATION::cd_leaf

Type:real Permitted:0:1 Default:None

Leaf level drag coefficient.

Only use if any l_vegdrag_pft = TRUE.

JULES_VEGETATION::stanton_leaf

Type:real Permitted:0:1 Default:None

Leaf-level Stanton number

Only use if l_rsl_scalar = TRUE.

JULES_VEGETATION::l_spec_veg_z0

Type:logical Default:F

Switch for using specified values of the vegetation roughness length rather than being determined by the canopy height.

TRUE

Vegetation roughness lengths are specified in z0v_io

FALSE

Vegetation roughenss lengths are calculated using canopy heights and parameter dz0v_dh_io.

JULES_VEGETATION::l_limit_canhc

Type:logical Default:F

Switch for limiting the canopy heat capacity for vegetation, which is calculated from the canopy height.

Using the SIMARD canopy height ancillary gives very large heat capacities in the Amazon, so this switch limits the areal heat calacity to 1.15e5 J Kg-1 m-2, which is the value calculated by the default broadleaf tree height of 19.01 m..

TRUE

Vegetation areal heat capacity limited.

FALSE

Vegetation areal heat capacity unlimited.