8 Silica

8.1 Contributors

Matthew R. Hipsey

8.1.1 Variable Summary

The default variables created by this module, and the optionally required linked variables needed for full functionality of this module are summarised in Table 8.1. The diagnostic outputs able to be output are summarised in Table 8.2.

State variables

Table 8.1: Silica - *state* variables
AED name	Symbol	Description	Unit	Type	Typical Range	Comments
aed_silica
`SIL_rsi`	\[\mathbf{RSi}\]	dissolved reactive silica concentration	\[\small{mmol\:Si/m^3}\]	pelagic	0 - 500	.
Dependent variables
`SDF_Fsed_rsi`	\[\mathbf{F}_{sed}^{rsi}\]	reference sediment \(RSi\) flux	\[\small{mmol \:Si/m^2/s}\]	benthic	-300 - 300	read and output as /day, but internally used as /s

Diagnostics

Table 8.2: Silica - *diagnostic* variables
AED name	Symbol	Description	Unit	Type	Typical Range	Comments
diag_level = 2+
`SIL_sed_rsi`	\[\mathbf{\mathcal{F}}_{sed}^{rsi}\]	\(RSi\) exchange across sediment-water interface	\[\small{mmol\: Si/m^2/d}\]	benthic	0 - 50	.

8.1.2 Parameter Summary

The parameters and settings used by this module are summarised in Table 8.3.

Table 8.3: Silica module parameters and configuration options
AED name	Symbol	Description	Unit	Type	Typical Range	Comments
Initialisation
`rsi_initial`	\[RSi\|_{t=0}\]	initial \(RSi\) concentration	\[\small{mmol\: Si/m^3}\]	float	0 - 5000	can be overwritten by initial condition files
`rsi_min`	\[RSi\rfloor_{min}\]	minimum \(RSi\) concentration	\[\small{mmol\: Si/m^3}\]	float	0	optional limitier
`rsi_max`	\[RSi\rceil^{max}\]	maximum \(RSi\) concentration	\[\small{mmol\: Si/m^3}\]	float	600	optional limitier
Sediment exchange
`Fsed_rsi`	\[F_{sed}^{rsi}\]	reference sediment \(RSi\) flux at \(20^{\circ}C\)	\[\small{mmol\: Si/m^2/d}\]	float	-300 - 300	.
`Ksed_rsi`	\[K_{sed}^{rsi}\]	half-saturation oxygen conc. controlling \(Si\) flux	\[\small{mmol\: Si/m^3}\]	float	20 - 100	.
`theta_sed_rsi`	\[\theta_{sed}^{rsi}\]	Arrhenius temperature multiplier for sediment \(Si\) flux	\[\small{-}\]	float	1.0 - 1.2	.
`Fsed_rsi_variable`		variable name to link to for spatially resolved sediment zones	\[\small{-}\]	string	`SDF_Fsed_rsi`	optional link to enable spatially resolved fluxes
`silica_reactant_variable`	\[O_2\]	state variable used to control \(Si\) sediment release	\[\small{-}\]	string	`OXY_oxy`	optional link for oxygen control on sediment \(Si\) release

8.2 Setup & Configuration

An example aed.nml parameter specification block for the aed_silica module is shown below:

  &aed_silica
    !-- Initial value
     rsi_initial              = 12.5
    !-- Sediment flux
     Fsed_rsi                 = 1.8
     Ksed_rsi                 = 50.0
     theta_sed_rsi            = 1.08
     silica_reactant_variable = 'OXY_oxy'
     Fsed_rsi_variable        = 'SDF_Fsed_rsi'
  /