6.12. jules_soil_ecosse.nml

This file sets options and parameters for the ECOSSE model of soil biogeochemistry. It is used only if the ECOSSE model is chosen (soil_bgc_model = 3).

Warning

The ECOSSE model in JULES is still in development and is not fully functional in this version. The code is included to allow further development. Users should not try to use ECOSSE.

See also

References:

• Smith et al., 2010, Estimating changes in Scottish soil carbon stocks using ECOSSE. I. Model description and uncertainties, Climate Research, 45: 179-192. (https://doi.org/10.3354/cr00899).

• Clark, D. B., Mercado, L. M., Sitch, S., Jones, C. D., Gedney, N., Best, M. J., Pryor, M., Rooney, G. G., Essery, R. L. H., Blyth, E., Boucher, O., Harding, R. J., Huntingford, C., and Cox, P. M.: The Joint UK Land Environment Simulator (JULES), model description – Part 2: Carbon fluxes and vegetation dynamics, Geosci. Model Dev., 4, 701–722, (https://doi.org/10.5194/gmd-4-701-2011), 2011.

6.12.1. JULES_SOIL_ECOSSE namelist members

JULES_SOIL_ECOSSE::l_soil_n

Type

logical

Default

T

Switch to include soil nitrogen in ECOSSE.

TRUE

Model soil carbon and nitrogen.

FALSE

Model only soil carbon.

JULES_SOIL_ECOSSE::l_match_layers

Type

logical

Default

T

Switch to match ECOSSE soil C and N layers to those for soil moisture.

TRUE

Use the same layering as for soil moisture. The number of soil carbon layers will equal sm_levels, with layer thicknesses given by dzsoil_io.

FALSE

The number of layers will be specified by dim_cslayer and the thicknesses by dz_soilc_io.

JULES_SOIL_ECOSSE::dim_cslayer

Type

integer

Permitted

>= 1

Default

None

The number of ECOSSE soil carbon layers. Not used if l_match_layers = TRUE. Despite the similar name, this parameter is unrelated to sclayer_dim_name.

JULES_SOIL_ECOSSE::dz_soilc_io

Type

real(dim_cslayer)

Permitted

> 0

Default

None

Thicknesses of the ECOSSE soil carbon layers (m). Not used if l_match_layers = TRUE. In most cases the total depth must equal that of the soil moisture layers (see dzsoil_io). The exception is the case of a single layer, bulk model (dim_cslayer = 1), for which dz_soilc(1) is interpreted as the representative or averaging depth for the bulk layer (e.g. the temperature of the bulk model is taken as the average over this depth).

JULES_SOIL_ECOSSE::dt_soilc

Type

REAL

Permitted

>= timestep_len

Default

timestep_len

The timestep length for ECOSSE (seconds). The main JULES timestep length timestep_len must be a multiple of this timestep length, so that ECOSSE is called on JULES timesteps. The TRIFFID timestep length triffid_period (converted to seconds) must also be a multiple of the ECOSSE timestep length.

JULES_SOIL_ECOSSE::l_driver_ave

Type

logical

Default

T

Switch controlling the averaging of the physical driving variables that are input to ECOSSE (e.g. soil temperature).

TRUE

Average the driving variables over the ECOSSE timestep length.

FALSE

Use instantaneous values of the driving variables at the time when ECOSSE is called.

JULES_SOIL_ECOSSE::plant_input_profile

Type

INTEGER

Permitted

1 or 2

Default

1

Switch for the vertical distribution of litterfall inputs of C and N to the soil.

Possible values are:

1. Fraction pi_sfc_frac of inputs are distributed uniformly in a surface layer of depth pi_sfc_depth, the remainder are distributed according to the distribution of roots.
2. Inputs decrease exponentially with depth with decay constant tau_lit.

JULES_SOIL_ECOSSE::pi_sfc_frac

Type

REAL

Default

0.3

Fraction of plant litterfall that is added to the surface soil layer of depth pi_sfc_depth. Only used if plant_input_profile = 1.

JULES_SOIL_ECOSSE::pi_sfc_depth

Type

REAL

Default

0.1

Depth of soil over which fraction pi_sfc_frac of plant litterfall is added (m). Only used if plant_input_profile = 1.

JULES_SOIL_ECOSSE::temp_modifier

Type

INTEGER

Permitted

1 or 2

Default

2

Switch for the form of the temperature rate modifier for decomposition.

1. Use a Q10 approach (Eqn. 65 of Clark et al. (2011))
2. Use the Smith et al. (2010) form of the modifier (Eqn.1 of Smith et al. (2010))

JULES_SOIL_ECOSSE::water_modifier

type

INTEGER

permitted

1 or 2

default

2

Switch for the form of the water rate modifier for decomposition and nitrification.

1. Use the Clark et al. (2011) form of the modifier (Eqn. 67 of Clark et al. (2011)). Note however that only the unfrozen water is considered here.
2. Use the Smith et al. (2010) form of the modifier.

JULES_SOIL_ECOSSE::decomp_rate

Type

REAL(4)

Default

3.22e-7, 9.65e-9, 2.12e-8, 6.43e-10

Rate constant for decomposition of each soil carbon pool (s^-1).

Note that these default values are also those for use with the 4-pool model (kaps_4pool).

JULES_SOIL_ECOSSE::decomp_ph_rate_min

Type

REAL

Default

0.2

Minimum allowed value of pH rate modifier for decomposition.

JULES_SOIL_ECOSSE::decomp_ph_min

Type

REAL

Permitted

decomp_ph_min <= decomp_ph_max

Default

1.0

Soil pH below which rate of decomposition is minimum.

JULES_SOIL_ECOSSE::decomp_ph_max

Type

REAL

Permitted

decomp_ph_max >= decomp_ph_min

Default

4.5

Soil pH above which rate of decomposition is maximum.

JULES_SOIL_ECOSSE::decomp_temp_coeff_smith

Type

REAL(3)

Default

47.9, 106.0, 18.3

Constants in the 4-pool from of the decomposition temperature modifier (temp_modifier = 2).

Note that these default values are also those harwired in the code for use with the 4-pool model (soil_bgc_model = 2, l_q10 = F ).

JULES_SOIL_ECOSSE::decomp_wrate_min_smith

Type

REAL

Default

0.2

Minimum allowed value of the water rate modifier for decomposition when the 4-pool form is used (water_modifier = 2).

JULES_SOIL_ECOSSE::decomp_wrate_min_clark

Type

REAL

Default

0.2

Minimum allowed value of the water rate modifier for decomposition when the Clark et al. (2011) form is used (water_modifier = 1).

Note that this default value is also that harwired in the code for use with the 4-pool model (soil_bgc_model = 2).

Parameters for ECOSSE that are only used if soil N is included (l_soil_n = TRUE).

JULES_SOIL_ECOSSE::l_decomp_slow

Type

logical

Default

T

Switch controlling how lack of nitrogen affects soil decomposition.

TRUE

Reduce the decomposition rate.

FALSE

Reduce the efficiency of decomposition, so that decomposition results in increased production of CO₂ and decreased production of further soil C. This is the approach used in the standalone version of ECOSSE.

JULES_SOIL_ECOSSE::depo_nit_frac

Type

REAL

Permitted

0 <= depo_nit_frac <= 1

Default

1.0

The fraction of nitrogen deposition that is aded to the soil nitrate pool. The complement is aded to the ammonium pool.

JULES_SOIL_ECOSSE::bacteria_min_frac

Type

REAL

Permitted

0 <= bacteria_min_frac <= 1

Default

0.2

The minimum fraction of the decomposer community that are bacteria.

JULES_SOIL_ECOSSE::bacteria_max_frac

Type

REAL

Permitted

bacteria_min_frac <= bacteria_max_frac <= 1

Default

0.5

The maximum fraction of the decomposer community that are bacteria.

JULES_SOIL_ECOSSE::bacteria_min_frac_pH

Type

REAL

Default

4.0

The soil pH at or below which the fraction of bacteria is at a minimum.

JULES_SOIL_ECOSSE::bacteria_max_frac_pH

Type

REAL

Permitted

bacteria_min_frac_pH <= bacteria_max_frac_pH

Default

5.5

The soil pH at or above which the fraction of bacteria is at a maximum.

JULES_SOIL_ECOSSE::cn_bacteria

Type

REAL

Default

5.5

The C:N ratio of soil bacteria.

JULES_SOIL_ECOSSE::cn_fungi

Type

REAL

Default

5.5

The C:N ratio of soil fungi.

JULES_SOIL_ECOSSE::depth_nitrif

Type

REAL

Default

0.25

Greatest depth at which nitrification and denitrification are allowed (m).

JULES_SOIL_ECOSSE::nitrif_rate

Type

REAL

Default

9.921e-7

Rate constant for nitrification (s^-1).

JULES_SOIL_ECOSSE::nitrif_wrate_min

Type

REAL

Default

0.6

Minimum allowed value of the water rate modifier for nitrification when 4-pool form is used. Only used if water_modifier = 2.).

JULES_SOIL_ECOSSE::nitrif_max_factor

Type

REAL

Default

0.1

Shape factor in rate modifier for nitrification (kg m^-3).

JULES_SOIL_ECOSSE::nitrif_frac_n2o_fc

Type

REAL

Permitted

0 <= nitrif_frac_n2o_fc <= 1

Default

0.02

Fraction of nitrification lost as N₂O by partial nitrification at field capacity.

JULES_SOIL_ECOSSE::nitrif_frac_gas

Type

REAL

Permitted

0 <= nitrif_frac_gas <= 1

Default

0.02

Fraction of nitrification lost as gas through full nitrification.

JULES_SOIL_ECOSSE::nitrif_frac_no

Type

REAL

Permitted

0 <= nitrif_frac_no <= 1

Default

0.4

Fraction of nitrification gas loss through full nitrification that is NO.

JULES_SOIL_ECOSSE::denit50

Type

REAL

Default

0.033

Amount of nitrate at which denitrification rate is 50% of the potential rate (kg m^-3).

JULES_SOIL_ECOSSE::denit_bio_factor

Type

REAL

Default

0.005

Factor in denitrification calculation to convert flux of CO₂ into a representation of biological activity (m² kg^-1).

JULES_SOIL_ECOSSE::denit_frac_n2_fc

Type

REAL

Permitted

0 <= denit_frac_n2_fc <= 1

Default

0.55

Proportion of denitrified N that becomes N₂ when soil moisture is at field capacity.

JULES_SOIL_ECOSSE::denit_nitrate_equal

Type

REAL

Default

0.4

Amount of N in soil nitrate at which denitrified N is released as equal amounts of N₂ and N<sub>2`O (kg m:sup:</sub>-3`).

JULES_SOIL_ECOSSE::denit_water_coeff

Type

REAL(3)

Default

0.62, 0.38, 1.74

Constants describing water modifier for denitrification.

JULES_SOIL_ECOSSE::amm_leach_min

Type

REAL

Default

0.02

Minimum allowed amount of N in soil ammonium after leaching (kg m^-3).

JULES_SOIL_ECOSSE::n_inorg_max_conc

Type

REAL

Default

-1.0

Maximum-allowed concentration of inorganic N in a layer (kg m^-3). A value less than zero means no maximum concentration is imposed.