`p4zsed`

Overview

This module implements a simplified representation of sediment processes in the PISCES biogeochemical model. It is not an explicit sediment model but a metamodel that computes organic matter loss in sediments.

Module Name: p4zsed
Model: PISCES (version NEMO 5.0)
Subroutines: p4z_sed, p4z_sed_init, p4z_sed_alloc

Public Variables

sdenit(:,:) - Nitrate reduction in sediment (2D array)

Module Parameters

Namelist: `nampissed`

Parameter	Description	Type
`bureffmin`	Minimum burial efficiency	REAL
`bureffvar`	Variable coefficient for burial efficiency	REAL
`sedsilfrac`	Percentage of silica loss in the sediments	REAL
`sedcalfrac`	Percentage of calcite loss in the sediments	REAL
`sedfactcalmin`	Minimum value for dissolving calcite at the bottom	REAL
`sedfactcalvar`	Variable value for dissolving calcite at the bottom	REAL

`p4z_sed` main subroutine

Purpose

Computes the loss of organic matter in sediments at each bottom grid cell, including:

Sediment denitrification
Burial efficiency of organic matter
Calcite dissolution
Silica loss (for p4z and p5z configurations)

Input Parameters

Parameter	Type	Intent	Description
`kt`	INTEGER	IN	Current time step index
`knt`	INTEGER	IN	Sub-time step counter
`Kbb`	INTEGER	IN	Time level index (before)
`Kmm`	INTEGER	IN	Time level index (now/middle)
`Krhs`	INTEGER	IN	Time level index (right-hand side/tendencies)

Key Processes

1. Sediment Denitrification

Uses the metamodel from Middelburg et al, 1996¹ to compute denitrification proportion:

zpdenit = -2.2567 - 1.185*zflx1 - 0.221*zflx1² - 0.3995*zno3*zo2 
          + 1.25*zno3 + 0.4721*zo2 - 0.0996*log10(zdep) + 0.4256*zflx1*zo2

Where: - zflx1 = log10(flux of POC in g/m²/day) - zo2 = log10(oxygen concentration in µM) - zno3 = log10(nitrate concentration in µM) - zdep = water depth in meters

2. Burial Efficiency

Computed using Dunne's model:

zbureff = bureffmin + bureffvar * zflx² / (7.0 + zflx)² * min(zdep/1000, 1.0)

The fraction that is remineralized: zrivno3 = 1 - zbureff

3. Calcite Dissolution

Depends on carbonate saturation state (excess):

zfactcal = max(-0.1, min(excess, 0.2))
zfactcal = sedfactcalmin + sedfactcalvar * min(1.0, (0.1 + zfactcal)/(0.5 - zfactcal))
zrivalk = sedcalfrac * zfactcal

Affects alkalinity and dissolved inorganic carbon (DIC): - Alkalinity: +2 × calcite loss × zrivalk - DIC: +1 × calcite loss × zrivalk

4. Silica Loss (p4z/p5z only)

Computed as a function of silica flux:

zsiloss2 = sinksilb * (365.0 × 10³ × 10⁻⁴ × 10⁶) / xstep
zrivsil = 1.0 - sedsilfrac * zsiloss2 / (15.0 + zsiloss2)

Model Configurations

The module handles three PISCES versions differently:

P2Z Configuration (`ln_p2z = .TRUE.`)

Simplified nutrient cycling:

DOC remineralization
NO3 consumption/production via denitrification
O2 consumption with factor (o2ut + o2nit)
Alkalinity adjustment
DIC production

P4Z Configuration (default)

Full nutrient cycling including:

DOC, PO4, NH4, NO3, O2
Alkalinity with factor rno3 * (zolimit + (1+rdenit)*zpdenit)
Silica cycling

P5Z Configuration (`ln_p5z = .TRUE.`)

Extended configuration including:

All p4z tracers
Additional DON (dissolved organic nitrogen)
Additional DOP (dissolved organic phosphorus)
Partitioning based on sinking flux ratios

Tracer Updates

For each bottom grid cell (ikt = mbkt(ji,jj)), the following tracers are updated:

All configurations:

jpdoc - Dissolved organic carbon
jptal - Total alkalinity
jpdic - Dissolved inorganic carbon
jpoxy - Oxygen
jpno3 - Nitrate

P4Z/P5Z only:

jppo4 - Phosphate
jpnh4 - Ammonium
jpsil - Silicate (p4z only)

P5Z only:

jpdon - Dissolved organic nitrogen
jpdop - Dissolved organic phosphorus

Diagnostic Outputs

The module provides the following diagnostic fields (when requested via XIOS):

Sdenit - Sediment denitrification rate (molN/m²/s)
SedC - Buried organic carbon (molC/m²/s)
SedCal - Buried calcite (molC/m²/s)
SedSi - Buried silica (molSi/m²/s)

Dependencies

Required Modules

oce_trc - Shared variables between ocean and passive tracers
trc - Passive tracers common variables
sms_pisces - PISCES Source Minus Sink variables
p4zsink - Sinking fluxes
sed - Sediment module
iom - I/O manager
prtctl - Print control for debugging

Required Substitutions

do_loop_substitute.h90 - Loop macros
read_nml_substitute.h90 - Namelist reading macros
domzgr_substitute.h90 - Vertical grid substitutions

Key Variables

Sinking Fluxes (from p4zsink)

sinkpocb(ji,jj) - POC flux at bottom
sinkcalb(ji,jj) - Calcite flux at bottom
sinksilb(ji,jj) - Silica flux at bottom
sinkponb(ji,jj) - PON flux at bottom (p5z)
sinkpopb(ji,jj) - POP flux at bottom (p5z)

Grid Variables

mbkt(ji,jj) - Bottom level index
e3t(ji,jj,ik,Kmm) - Vertical grid spacing
gdepw(ji,jj,ik,Kmm) - Depth of w-points

Important Constants

rtrn - Truncation threshold
rdenit - Denitrification ratio
rno3 - Nitrate ratio
o2ut - Oxygen utilization
o2nit - Oxygen for nitrification (p2z)
rfact2r - Conversion factor
xstep - Time step

Initialization Process

Read namelist parameters from nampissed
Allocate sdenit array
Initialize sdenit to zero
Set lk_sed flag based on sediment coupling options

Performance Considerations

Uses optimized DO_2D loops for horizontal dimensions
Only computes for ocean points (tmask == 1)
Conditional compilation for P2Z/P4Z/P5Z configurations
Minimal I/O with conditional diagnostics

Numerical Stability

Uses MAX/MIN functions to prevent numerical issues
0.5 factor in denitrification calculation prevents negative NO3
Logarithmic transformations for wide-range variables
Truncation threshold rtrn to avoid division by zero

Notes

This is a simplified parameterization, not a mechanistic sediment model
Burial is balanced against surface inputs (rivers, dust)
Denitrification uses empirical relationships
Assumes instant remineralization of non-buried fraction

References

Dunne et al. - Burial efficiency parameterization

Jack J Middelburg, Karline Soetaert, Peter MJ Herman, and Carlo HR Heip. Denitrification in marine sediments: a model study. Global Biogeochemical Cycles, 10(4):661–673, 1996. ↩

p4zsed