Module SedimentQuality

Overview

This is the 0D module that handles sediment biological processes made by bacteria as organic matter mineralization, nitrification, denitrification and immobilization.

Main Processes

Main processes in SedimentQuality are organic matter mineralization, nitrification, denitrification and immobilization. These processes are simulated using a standard rate (s.day-1.pop-1) that is afected by temperature, pH, oxygen in case of aerobic processes and sustrate concentrations if exist. A maximum rate is computed calculating the standard rate at the actual temperature times bacteria population that conducts the process.

Property Transformation

Biological activity - Sediment Quality Module

Sediment Quality module simulates biological processes by bacteria. Heterotrophic bacteria perform mineralization of organic matter (organic matter to inorganic material), Autotrophic bacteria perform nitrification (ammonia to nitrate) and Anaerobic bacteria denitrification (nitrate to nitrogen gas). Also immobilization of inorganic species is done if bacteria have nutrient needs to mantain ratios.

Chemical reactions - PREEQC Module=

PREEQC Module handles chemical equilibrium between species in soil, giving the new equilibrium at each computation.

Partition

Partition between particulated and dissolved species is done using a user ratio.

Outputs

Output is done in terms of timeseries, HDF, and boxes following the MOHID standards.

Data File

Keywords

Units in porous media properties
  Transported properties (soluble)  : g/m3 (or mg/L)                     (needs to convert concentrations to SedimentQuality and 
                                                                          PREEQC at entrance and exit)
  Adsorbed properties (non soluble) : mg/kgsoil                          (needs to convert concentrations to PREEQC )
  Solid Phases (non soluble)        : mg/kgsoil                          (used in PhreeqC to make equilibrium with soil solution)
  Gas Phases (non soluble)          : mol (mass); atm (partial pressure) (used in PhreeqC to make equilibrium with soil solution)
  Gas Phases (assumed soluble)      : mg/L                               (used in SedimentQuality - N2, CH4 and CO2)

  Soil Dry Density                  : kg/m3                              
  H+ and Ionic Strenght             : mol/L                              (used in SedimentQuality)
  Microorganisms Population         : #org/kgsoil                        (used in SedimentQuality)

Keywords:

ADVDIFF_EXPLICIT              : 0/1                [1]        !REMARK: Horizontal diffusion is always explicit
                                                              !(1 - adv and diff are explicit in all directions; 0 - adv and diff 
                                                              !are implicit in vertical, horizontal adv may be explicit or impl) 
  ADVDIFF_ADVECTION_H_IMP_EXP : 0/1                [1]        !(read if ADVDIFF_EXPLICIT : 0; 0 - horiz adv implicit; 
                                                                1 - horiz adv explicit)
NEW_FORMULATION               : 0/1                [0]        !if 1 then spatial methods will be the same for all properties
                                                             
    ADVDIFF_METHOD_H          : integer      [UpwindOrder1]   !Spatial methods for horizontal advection
                                                              !UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
                                                               CentralDif = 5, LeapFrog = 6    
    ADVDIFF_METHOD_V          : integer      [UpwindOrder1]   !Spatial methods for vertical advection
                                                              !UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
                                                               CentralDif = 5, LeapFrog = 6!
<beginproperty>
  ADVECTION_DIFFUSION         : 0/1               [0]         !Property advection - diffusion
      ADVDIFF_METHOD_H        : integer      [UpwindOrder1]   !Spatial methods for horizontal advection
                                                              !UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
                                                               CentralDif = 5, LeapFrog = 6    
      ADVDIFF_METHOD_V        : integer      [UpwindOrder1]   !Spatial methods for vertical advection
                                                              !UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
                                                               CentralDif = 5, LeapFrog = 6
      ADVDIFF_TVD_LIMIT_H     : integer        [Superbee]     !Horizontal advection non-linear stability conditions
                                                               MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
      ADVDIFF_TVD_LIMIT_V     : integer        [Superbee]     !Vertical advection non-linear stability conditions
                                                              !MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
      ADVDIFF_VOLUME_RELATION_MAX : real          5.          !The relation between adjacent volumes above which 
                                                              !the advection is upwind

  SOIL_CHEMISTRY              : 0/1               [0]         !Use PREEQC model to change property (source/sink model)
  SOIL_QUALITY                : 0/1               [0]         !Use SedimentQuality model to change property (source/sink model)
  PARTITION                   : 0/1               [0]         !Compute partition between dissolved-particulate phases
      PARTITION_COUPLE        : char               +          !Name of the property (oposite phase) to compute partition
      PARTITION_FRACTION      : real               -          !Percentage of mass of a property in a determined phase 
      PARTITION_RATE          : real            [1 s-1]       !Kinetic rate of partition to reach equilibrium
<endproperty>

Sample

OUTPUT_TIME               : 0 3600
TIME_SERIE_LOCATION       : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

!Advectin diffusion options
ADVDIFF_EXPLICIT          : 1
!Horizontal diffusion is always explicit
!(1 - adv and diff are explicit in all directions; 0 - adv and diff
!are implicit in vertical. horizontal adv may be explicit or impl)

ADVDIFF_ADVECTION_H_IMP_EXP :  1
!(read if ADVDIFF_EXPLICIT : 0; 0 - horiz adv implicit;
! 1 - horiz adv explicit)


NEW_FORMULATION           : 1   !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H          : 1   !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6
ADVDIFF_METHOD_V          : 1   !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!dispersion
<begin_dispersion_long>
NAME                      : dispersion long
INITIALIZATION_METHOD     : CONSTANT
DEFAULTVALUE              : 0.0
REMAIN_CONSTANT           : 1
<end_dispersion_long>

<begin_dispersion_trans>
NAME                      : dispersion trans
INITIALIZATION_METHOD     : CONSTANT
DEFAULTVALUE              : 0.0
REMAIN_CONSTANT           : 1
<end_dispersion_trans>


!example of rates for use with sediment quality
BOXFLUXES                 : ..\General Data\Boxes\Boxes.dat

<beginSQrate>
NAME                      : ammonia ammonia
DESCRIPTION               : nitrification (-); ammonia imombilization (+)
FIRSTPROP                 : ammonia
SECONDPROP                : ammonia
MODEL                     : SedimentQuality
<endSQrate>


properties needed to run with sediment quality: 
properties simulated: ammonia, nitrate, particulated refractory organic nitrogen, particulate organic nitrogen, nitrogen gas, heterotrophic microorganism nitrogen, autotrophic microorganism nitrogen, anaerobic microorganism nitrogen, urea, particulate labile organic carbon, particulated refractory organic carbon, heterotrophic microorganism carbon, anaerobic microorganism carbon, carbon dioxide, inorganic phosphorus, particulated inorganic phosphorus, particulated refractory organic phosphorus, particulate organic phosphorus, heterotrophic microorganism phosphorus, autotrophic microorganism phosphorus, anaerobic microorganism phosphorus, heterotrophic microorganism population, autotrophic microorganism population, anaerobic microorganism population
properties defined by user (sediment quality does not change them): temperature, salinity, pH, ionic strength, phosphorus adsortion index, soil dry density
properties that can be defined by user or computed: oxygen. oxygen is computed based on temperature and salinity.

<beginproperty>
NAME                      : ammonia
UNITS                     : mgN/L
DESCRIPTION               : ammonia
PARTICULATE               : 0
OLD                       : 0
MIN_VALUE                 : 1E-15
FILE_IN_TIME              : NONE
INITIALIZATION_METHOD     : CONSTANT
DEFAULTVALUE              : 10.           
ADVECTION_DIFFUSION       : 1
ADVDIFF_MOLECULAR_DIFF_COEF :  0.0
DTINTERVAL                : 86400.
SOIL_QUALITY              : 1
SOIL_CHEMISTRY            : 0
TIME_SERIE                : 1
OUTPUT_HDF                : 1
BOX_TIME_SERIE            : 1
<endproperty>