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p4zsms

Overview

The p4zsms module manages the Source Minus Sink (SMS) terms for biogeochemical tracers, handling biological and chemical reactions, sedimentation, and mass conservation based on the model configuration.

Module Name: p4zsms
Model: PISCES (version NEMO 5.0)
Subroutines: p4z_sms, p4z_sms_init, p4z_rst, p4z_dmp, p4z_budget

p4z_sms

Primary routine that manages the biological and chemical sources and sinks.

Functionality

  1. Initializes chemical constants and pH at first timestep
  2. Applies tracer damping if enabled
  3. Computes time step variables for biological SMS processes
  4. Stores initial tracer concentrations
  5. Processes external nutrient sources
  6. Computes chemical constants
  7. Computes auxiliary fields/rates
  8. Executes sub-timestep iterations:
    • Calls biological processes
    • Handles calcite saturation
    • Manages bottom boundary conditions
    • Computes surface fluxes
    • Corrects negative tracer concentrations
  9. Calls sediment module if enabled
  10. Calculates trends and updates tracers
  11. Writes PISCES restart
  12. Performs budget checking

Input parameters

Parameter Type Intent Description
kt INTEGER IN Current time step index
Kbb INTEGER IN Time level index (before)
Kmm INTEGER IN Time level index (now/middle)
Krhs INTEGER IN Right-hand side index

Negative Concentration Handling

The module implements a scaling approach to prevent negative tracer concentrations:

  1. Identifies cells where tracers would become negative
  2. Calculates scaling factor (xnegtr) to limit the magnitude of sinks
  3. Applies the scaling factor to all SMS terms at that location

p4z_sms_init

Initializes the PISCES model by reading namelist parameters in the nampisbio block.

Configuration Parameters

  • nrdttrc: Frequency for biology calculations (time splitting)
  • wsbio: POC sinking speed (small particles)
  • xkmort: Half-saturation constant for phytoplankton and zooplankton mortality
  • feratz, feratm, no3rat3, po4rat3: Fe/C, N/C, P/C ratios of zoophytoplankton
  • wsbio2, wsbio2max, wsbio2scale : Parameters for big particles sinking speed
  • ldocp, ldocz, lthet: Prognostic ligand production parameters
  • ln_pisdmp, ln_pisdmp_alk: Damping/relaxation configuration

p4z_rst

Handles reading/writing of restart files. If the variables are not present in the restart file or if the restart file does not exist, then they are initialised to characteristic values.

Variables Managed

  • pH
  • Thetanano (ln_p2z)
  • Silica limitation and maximum values
  • Fe\(^3\) consumption by phytoplankton
  • Mean remineralization rates of particles (POC, GOC)
  • Cumulative CO\(_2\) fluxes
  • Size proxies for phytoplankton groups

Input Parameters

Parameter Type Intent Description
kt INTEGER IN Current time step index
Kbb INTEGER IN Time level index (before)
Kmm INTEGER IN Time level index (now/middle)
cdrw CHARACTER IN "READ" or "WRITE" flag

p4z_dmp

Performs the damping/relaxation of total budget for some tracers. This damping prevents the model from deviating too much from the observed mean values in these tracers.

Tracer Relaxation Targets

  • Alkalinity: 2426 (mean value)
  • PO\(_4\): 2.174 (mean value)
  • NO\(_3\): 31.00 (mean value)
  • Silicate: 90.33 (mean value)

Input parameters

Parameter Type Intent Description
kt INTEGER IN Current time step index
Kmm INTEGER IN Time level index (now/middle)

p4z_budget

Checks the mass conservation of several tracers.

Budgets Calculated

  • NO\(_3\)
  • Iron
  • Total Alkalinity
  • PO\(_4\)
  • Silicate
  • Nitrogen fixation by diazotrophs
  • Denitrification in the water column and the sediment

Input parameters

Parameter Type Intent Description
kt INTEGER IN Current time step index
Kmm INTEGER IN Time level index (now/middle)

Additional Information

Multiple Model Configurations

The code supports multiple configurations via logical flags:

  • ln_p2z: Two-component model
  • ln_p4z: Four-component model
  • ln_p5z: Five-component model
  • ln_ligand: Controls ligand processes
  • ln_sediment: Enables coupled sediment model

Time Management

  • rfact: Main PISCES time step
  • rfact2: Biological SMS time step (allows sub-stepping)
  • xstep: Time step relative to day length
  • Multiple iterations (nrdttrc) can be performed within each tracers time step

Notes on Implementation

  • ORCA grid configuration is specifically addressed for global calculations
  • Includes both local-grid and global-sum operations
  • Uses XIOS library for standardized output management
  • Restart capabilities ensure simulation continuity

Document Version: 1.0
Last Updated: October 2025
Source code: NEMO 5.0