6.13. jules_deposition.nml

This file contains options and parameters for modelling of dry deposition of atmospheric trace constituents. It contains a variable number of namelists depending on the required model configuration. The namelist JULES_DEPOSITION is always required, the namelist JULES_DEPOSITION_SPECIES_SPECIFIC and one or more instances of the namelist JULES_DEPOSITION_SPECIES is required if dry deposition has been selected.

Warning

Atmospheric deposition in JULES is still in development. In this version, two options are provided: (1) dry_dep_model = 1, which implements the existing UKCA interactive gas-phase dry deposition routines in JULES. The parameters are hard-wired in the code and only 4 surface tile configurations are permitted; and (2) dry_dep_model = 2, which removes the surface tile restrictions and uses namelists to define the various deposition parameters. Deposition parameters specific to a single deposited species are input on JULES_DEPOSITION_SPECIES_SPECIFIC namelist. There is a separate JULES_DEPOSITION_SPECIES namelist for each deposited species for deposition parameters common to more than one deposited species. To activate the deposition code: set l_deposition to TRUE.

6.13.1. JULES_DEPOSITION namelist members

JULES_DEPOSITION::l_deposition

Type:

logical

Default:

FALSE

Switch to activate deposition code in JULES.

TRUE

Model deposition in JULES.

FALSE

Do not model deposition in JULES.

Note

There is now a requirement to specify all surface types in JULES_SURFACE_TYPES (the plant functional types need to be defined, e.g. brd_leaf =1, ndl_leaf =2, c3_grass =3, c4_grass =4, shrub =5 for the 5-pft configuration).

Only used if l_deposition = TRUE.

JULES_DEPOSITION::dry_dep_model

Type:

integer

Permitted:

1, 2

Default:

none

Choice for model of dry deposition.

Possible values are:

1. Parameterisation based on the interactive dry deposition scheme in the UKCA.
2. Parameterisation based on the interactive dry deposition scheme in the UKCA, with the restriction on the allowable surface tile configuration removed.

JULES_DEPOSITION::dep_h2_soil_scheme

Type:

integer

Permitted:

1, 2

Default:

none

Choice for scheme for soil uptake of H2 from the atmosphere.

Possible values are:

1. Parameterisation based on Conrad & Seiler uptake scheme in the UKCA.
2. Parameterisation based on Paulot et al. scheme.

Note: The Paulot et al. scheme is currently not available in UM-coupled JULES applications.

JULES_DEPOSITION::l_deposition_flux

Type:

logical

Default:

FALSE

Switch for calculation of deposition fluxes as opposed to deposition velocities.

TRUE

Calculate deposition fluxes. This requires that the concentrations of atmopsheric tracer species are provided as prescribed data (see List of supported variables).

FALSE

Calculate deposition velocities.

JULES_DEPOSITION::ndry_dep_species

Type:

integer

Permitted:

>= 1 and <= 200 (ndep_species_max)

Default:

none

Number of species for which dry deposition is calculated.

JULES_DEPOSITION::tundra_s_limit

Type:

real

Default:

none

Latitude of southern limit of tundra (radians). This is used to alter the calculation of deposition of certain species in the tundra region (actually for all points north of this limit). Only used if the list of species (see dep_species_name_io) includes one or more of ‘CO’, ‘NO2’, ‘O3’, ‘PAN’, ‘PPAN’, ‘MPAN’ or ‘ONITU’.

JULES_DEPOSITION::dzl_const

Type:

real

Default:

none

Constant value for separation of boundary layer levels (m). All layer thicknesses are set to this value. This is used as a simple way to prescribe the layer thicknesses in standalone mode. This value can be overriden by prescribed data - see JULES_PRESCRIBED. This can be considered as the representative depth for tracer concentration and the depth over which the deposition flux is removed.

JULES_DEPOSITION::l_deposition_from_ukca

Type:

logical

Default:

FALSE

Switch to determine calling routine for the JULES-based interactive deposition routines.

TRUE

Calls the JULES-based deposition routines from the same UKCA routine ukca_chemistry_ctl (or the equivalents: ukca_chemistry_ctl_BE or ukca_chemistry_ctl_col), which is used to call the UKCA-based interactive deposition routines.

FALSE

Calls the JULES-based deposition routines from the JULES routine surf_couple_extra.

Note

For JULES standalone applications, the JULES-based deposition routines can only be called from surf_couple_extra() and l_deposition_from_ukca is false and not enabled. For UM-coupled JULES applications, the JULES-based deposition routines can currently only be called from the UKCA and l_deposition_from_ukca should be set to true.

(1) Switches that are only available for use in standalone JULES applications.

JULES_DEPOSITION::l_deposition_gc_corr

Type:

logical

Default:

FALSE

Switch to use stomatal conductances with or without bare soil evaporation.

TRUE

Use calculation of stomatal conductance without bare soil evaporation.

FALSE

Use calculation of stomatal conductance with bare soil evaporation.

(2) For UM-coupled JULES applications, the following switches are set during the run to be equivalent to the corresponding switches in the UKCA (which are set in the UM run_ukca namelist).

JULES_DEPOSITION::l_ukca_ddep_lev1

Type:

logical

Default:

FALSE

Switch from the UKCA controlling which atmospheric levels in the boundary layer are used for dry deposition. For UM-coupled JULES applications, the UKCA interactive dry deposition switch (l_ukca_intdd in the run_ukca namelist) needs to be true.

TRUE

Deposition occurs only from the lowest level in the atmospheric boundary layer.

FALSE

Deposition occurs from all levels within the atmospheric boundary layer.

JULES_DEPOSITION::l_ukca_emsdrvn_ch4

Type:

logical

Default:

FALSE

Switch from the UKCA in which the UKCA chemistry scheme uses methane (CH₄) emissions instead of prescribed CH₄ surface mole fractions.

TRUE

UKCA chemistry scheme uses methane (CH₄) emissions.

FALSE

UKCA chemistry scheme uses prescribed CH₄ surface mole fractions.

(3) Switches that are only available for UM-coupled JULES applications. The following switches are set during the run to be equivalent to the corresponding switches in the UKCA (which are set in the UM run_ukca namelist).

JULES_DEPOSITION::l_ukca_ddepo3_ocean

Type:

logical

Default:

FALSE

Switch from the UKCA to use a mechanistic calculation for deposition of ozone to the ocean from Luhar et al. (2018).

TRUE

Use the mechanistic calculation of Luhar et al. (2018).

FALSE

Use the surface resistance term for water provided in rsurf_std_io.

JULES_DEPOSITION::l_ukca_dry_dep_so2wet

Type:

logical

Default:

FALSE

Switch from the UKCA to account for surface wetness in the dry deposition for SO₂. The calculation uses the parameterisation in Erisman, Pul and Wyers (1994).

TRUE

Account for surface wetness in the dry deposition for SO₂.

FALSE

Do not account for surface wetness in the dry deposition for SO₂.

6.13.2. Notes on the JULES_DEPOSITION namelist

The height of the atmospheric boundary layer is required and is set to a default constant value of 1000 m. This value can be overridden via the namelist variable bl_height, or can be prescribed (i.e. allowed to vary in time and/or space) by providing bl_height as prescribed data (see List of supported variables).

The number of model levels in the boundary layer is required and is set to a default balues of 1. This can be overridden via the namelist variable bl_levels. The number of levels is only used to communicate with the atmospheric model (e.g. UKCA).

The separation of the model levels in the boundary layer is required and is set to a constant value via dzl_const. The separation can be prescribed (i.e. allowed to vary in time and/or space) by providing level_separation as prescribed data (see List of supported variables). This can be considered as the representative depth for tracer concentration and the depth over which the deposition flux is removed.

If deposition fluxes (rather than deposition velocities) are to be calculated (see l_deposition_flux), the concentrations of atmospheric tracer species need to be prescribed (see tracer_field in List of supported variables).

6.13.3. JULES_DEPOSITION_SPECIES namelist members

This namelist should occur ndry_dep_species times, with each occurence containing parameters for an atmospheric tracer species that is to be considered in dry deposition.

JULES_DEPOSITION_SPECIES::dep_species_name_io

Type:

character

Default:

none

Name of an atmospheric tracer species to be included in deposition modelling.

JULES_DEPOSITION_SPECIES::dep_species_rmm_io

Type:

real

Default:

none

Relative molecular mass (g mol^-1), as used in the UKCA. It is used in the calculation of the quasi-laminar resistance term (R_b), if no diffusion coefficient is provided.

JULES_DEPOSITION_SPECIES::diffusion_coeff_io

Type:

real

Default:

none

Diffusion coefficient (m^-2 s^-1).

Note

If there is no measured value of the diffusion coefficient for any chemical species in the chemical mechanism, the diffusion coefficient for those species should be set to -1.0. This will be used to indicate that the diffusion coefficient will be calculated from the diffusion coefficient of water and the relative molecular masses of water and the chemical species.

JULES_DEPOSITION_SPECIES::rsurf_std_io

Type:

real(ntype)

Default:

none

Standard value of surface resistance for each surface type (s m^-1).

Only used if dep_species_name_io = NO2, O3, PAN, PPAN, MPAN or ONITU. Values provided for other species will be ignored.

JULES_DEPOSITION_SPECIES::diffusion_corr_io

Type:

real

Default:

none

Diffusion correction factor for stomatal resistance, accounting for the different diffusivities of water and other species (dimensionless).

Only used if dep_species_name_io = CO, NO2, O3, PAN, PPAN, MPAN or ONITU. Values provided for other species will be ignored.

JULES_DEPOSITION_SPECIES::r_tundra_io

Type:

real

Default:

none

Surface resistance used in tundra region (s m^-1).

Only used if dep_species_name_io = HNO3, HONO2, ISON and if l_fix_improve_drydep = true, also for HCl, HOCl, HBr or HOBr.

JULES_DEPOSITION_SPECIES::dd_ice_coeff_io

Type:

real(3)

Default:

none

Coefficients in quadratic function relating dry deposition over ice to temperature.

6.13.4. JULES_DEPOSITION_SPECIES_SPECIFIC namelist members

This namelist is used for deposition parameters specific to a single deposited species. This namelist is used to avoid redundant entries on the JULES_DEPOSITION_SPECIES namelists.

Deposition parameters specific to dep_species_name_io = CH4.

JULES_DEPOSITION_SPECIES_SPECIFIC::ch4_scaling_io

Type:

real

Default:

none

Scaling applied to methane soil uptake (dimensionless). (Originally this was used to match the value from the IPCC Third Assessment Report.)

JULES_DEPOSITION_SPECIES_SPECIFIC::ch4_mml_io

Type:

real

Default:

none

Factor used in UKCA to convert the methane soil uptake flux in (μg m^-2 h^-1) to a dry dep velocity (in m s^-1). The current value of ch4_mml_io = 3600.0 * 0.016 * 1.0 x 10⁹ * 1.75 x 10^-6 = 1.008 x 10⁵, where 0.016 is the relative molecular mass of methane (kg), 1.0 x 10⁹ converts μg to kg, and 1.75 x 10^-6 ppmv is the assumed mean global atmospheric volume mixing ratio of methane.

JULES_DEPOSITION_SPECIES_SPECIFIC::ch4dd_tundra_io

Type:

real(4)

Default:

none

Coefficients of cubic polynomial relating methane loss for tundra to temperature. Flux is in units of μg (CH₄) m^-2 s^-1.

JULES_DEPOSITION_SPECIES_SPECIFIC::ch4_up_flux_io

Type:

real(ntype)

Default:

none

Value of uptake flux for methane for each surface type (μg (CH₄) m^-2 s^-1).

Deposition parameters specific to dep_species_name_io = H2.

JULES_DEPOSITION_SPECIES_SPECIFIC::h2dd_c_io

Type:

real(ntype)

Default:

none

Constant in quadratic function relating hydrogen deposition to soil moisture (s m^-1).

JULES_DEPOSITION_SPECIES_SPECIFIC::h2dd_m_io

Type:

real(ntype)

Default:

none

Coefficient of first order term in quadratic function relating hydrogen deposition to soil moisture (s m^-1).

JULES_DEPOSITION_SPECIES_SPECIFIC::h2dd_q_io

Type:

real(ntype)

Default:

none

Coefficient of second order term in quadratic function relating hydrogen deposition to soil moisture (s m^-1).

Deposition parameters specific to dep_species_name_io = O3.

JULES_DEPOSITION_SPECIES_SPECIFIC::cuticle_o3_io

Type:

real

Default:

none

Constant for calculation of cuticular resistance for ozone (s m^-1).

JULES_DEPOSITION_SPECIES_SPECIFIC::r_wet_soil_o3_io

Type:

real

Default:

none

Wet soil surface resistance for ozone (s m^-1).

6.13.4.1. Example

The following gives an example of how you would set up the JULES_DEPOSITION namelist for atmospheric deposition for a JULES standalone run.

&JULES_DEPOSITION
  dep_h2_soil_scheme=1
  dry_dep_model=2
  dzl_const=50.0
  l_deposition=.true.
  l_deposition_flux=.false.
  l_deposition_from_ukca=.false.
  l_deposition_gc_corr=.false.
  l_ukca_ddep_lev1=.false.
  !!l_ukca_ddepo3_ocean=.false.
  !!l_ukca_dry_dep_so2wet=.false.
  l_ukca_emsdrvn_ch4=.false.
  ndry_dep_species=1
  tundra_s_limit=0.866
/

Note: l_deposition_from_ukca should be false for JULES standalone and true for UM-coupled JULES. l_ukca_ddepo3_ocean and l_ukca_dry_dep_so2wet are not available for JULES standalone applications.

The following gives an example of how to set-up the JULES_DEPOSITION_SPECIES and JULES_DEPOSITION_SPECIES_SPECIFIC for the standard 5 pft/9 tile configuration for a single chemical species ‘O3’. In general, ndry_dep_species will be greater than 1 and there will be JULES_DEPOSITION_SPECIES namelists, one for each atmospheric species that is deposited. Some deposition parameters are required for all chemical species, others are species specific and not available (e.g. dd_ice_coeff_io for O3).

&JULES_DEPOSITION_SPECIES
  dep_species_name_io='O3'
  dep_species_rmm_io=48.0
  diffusion_coeff_io=1.400000e-05
  diffusion_corr_io=1.6
  r_tundra_io=800.0
  rsurf_std_io=200.0,200.0,200.0,200.0,400.0,800.0,2200.0,800.0,2500.0
/

&JULES_DEPOSITION_SPECIES_SPECIFIC
  ch4_mml_io=1.008e5
  ch4_scaling_io=15.0
  ch4_up_flux_io=39.5,50.0,30.0,37.0,27.5,0.0,0.0,27.5,0.0
  ch4dd_tundra_io=-4.757e-6,4.0288e-3,-1.13592,106.636
  cuticle_o3_io=5000.0
  h2dd_c_io=0.00197,0.00197,0.00177,1.2346,0.0001,0.0,0.0,0.0,0.0
  h2dd_m_io=-0.00419,-0.00419,-0.00414,-0.472,5*0.0
  h2dd_q_io=0.0,0.0,0.0,0.27,5*0.0
  r_wet_soil_o3_io=500.0
/