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(New page: ==Overview== This is the 0D module that handles sediment biological processes made by bacteria as organic matter mineralization, nitrification, denitrification and immobilization. ==Main ...)
 
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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.
 
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.
+
A maximum rate is computed calculating the standard rate at the actual temperature (day-1.pop-1) times bacteria population that conducts the process.
  
 +
<math> MaxRate (day-1) = Standard Rate at actual Temperature (day-1.pop-1) * BacteriaPopulation </math>
  
 +
<math> ActualRate (day-1) = MaxRate (day-1) * Aerobiose/AnaerobioseTerm * pHTerm * OxygenTerm * SubstrateTerm </math>
  
  
 
===Organic Matter Mineralization===
 
===Organic Matter Mineralization===
 +
Organic matter is mineralized to ammonia with heterotrophic bacteria and also immobilization may occur in order to maintain bacteria C:N ratios.
  
 +
Heterotrophic LPOM mineralization rate
  
 +
<math>Insert formula here</math>
  
−
===Property Transformation===
 
  
−
====Biological activity - Sediment Quality Module====
+
Heterotrophic RPOM mineralization rate
  
−
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).
+
<math>Insert formula here</math>
−
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.
+
Immobilization rate
 +
 
 +
<math>Insert formula here</math>
 +
 
 +
 
 +
 
 +
===Nitrification===
 +
 
 +
Nitrification rate
 +
 
 +
<math>Insert formula here</math>
 +
 
 +
 
 +
===Denitrification===
 +
 
 +
 
 +
Denitrification rate
 +
 
 +
<math>Insert formula here</math>
  
−
====Partition====
 
  
−
Partition between particulated and dissolved species is done using a user ratio.
 
  
 
==Other Features==
 
==Other Features==
Line 41: Line 59:
 
===Keywords===
 
===Keywords===
  
−
  Units in porous media properties
+
  Properties Units:
−
  Transported properties (soluble) : g/m3 (or mg/L)                    (needs to convert concentrations to SedimentQuality and
+
  dissolved                - as from called - in MOHID Land mg/L
−
                                                                          PREEQC at entrance and exit)
+
adsorbed/particulated    - as from called - in MOHID Land mg/kgsoil
−
  Adsorbed properties (non soluble) : mg/kgsoil                         (needs to convert concentrations to PREEQC )
+
gases:
−
  Solid Phases (non soluble)        : mg/kgsoil                          (used in PhreeqC to make equilibrium with soil solution)
+
CO2 and CH4              - same as adsorbed/particulated properties
−
  Gas Phases (non soluble)          : mol (mass); atm (partial pressure) (used in PhreeqC to make equilibrium with soil solution)
+
N2                        - same as dissolved properties
−
  Gas Phases (assumed soluble)      : mg/L                               (used in SedimentQuality - N2, CH4 and CO2)
+
exceptions:
 +
oxygen                    - mol/L
 +
hydrogen                  - mol/L
 +
microorganisms population - #org/kgsoil
 +
wind                      - km/day
 
   
 
   
−
  Soil Dry Density                  : kg/m3                             
+
OXYGEN              : [0/1]      0      !Connect/Disconnect Oxygen computation
−
  H+ and Ionic Strenght            : mol/L                              (used in SedimentQuality)
+
SOL_BACTERIA             : [0/1]      0   !Connect/Disconnect Solubilizing bacteria computation
−
  Microorganisms Population        : #org/kgsoil                        (used in SedimentQuality)
 
 
   
 
   
−
  Keywords:
+
  DTSECONDS                  : [s]      86400.  !dt to evaluate
 +
NO3_LIMIT                  :  [mg/L]      0.    !Minimum value for denitrification or maximum value for
 +
                                                    !methane production in organic matter decay
 +
NEW_RATES                  : [0/1]        0      !Connect/Disconnect new rates formulation using maximum * factors
 +
IMOBILIZATION              : [0/1]        1      !Connect/Disconnect immobilization
 
   
 
   
−
  ADVDIFF_EXPLICIT              : 0/1                [1]        !REMARK: Horizontal diffusion is always explicit
+
  EXPLICIT                  : [0/1]        1      !Explicit computation for time dicretization
−
                                                              !(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===
 
===Sample===
  
 
[[Category:MOHID Land]]
 
[[Category:MOHID Land]]
  
 +
!!!!!!!!!!!!!!!!!MAIN SEDIMENT OPTIONS!!!!!!!!!!!!!!!!
 +
!++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +
 +
!NITROGEN : 1
 +
!CARBON  : 1
 +
!PHOSPHORUS  : 1
 +
OXYGEN  : 1
 +
SOL_BACTERIA : 0
 +
 +
DTSECONDS    : 86400.
 +
NO3_LIMIT    : 0. ![mg/L] Minimum value for denitrification or maximum value for methane production in organic matter decay
 +
CHANGE_RATES : 0  !0 - original rates; 1-changed rates (removing concentrations from rates so do not change units)
 +
NEW_RATES    : 1  !1 - new rates using maximum * factors
 +
!IMOBILIZATION : 0
 +
 +
EXPLICIT : 1
 +
!IMPLICIT  ! not working?
 +
!SEMIIMP
 +
 +
 +
 +
 +
!!!!!!!!!!!!!!!!!!!!!!RATES!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 +
!++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +
 +
!!!! Organic Matter Decay !!!!
 +
 +
<begin_Labil_OM_C_Rate>
 +
AE          : 15.1        ![kcal.mole-1] Initial Activation Energy
 +
Acoef        : 0.391E-9    !same rate as original rates  !1E-7        ![s.day-1.pop-1] Rate Coefficient
 +
kp     : 12.3     ![L/mol] Salinity coefficient
 +
Temperature  : 35          ![ºC] Optimal Temperature   
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_Labil_OM_C_Rate>
 +
 +
<begin_RefractOM_C_Rate>
 +
AE          : 15.1
 +
Acoef        : 0.653E-11    !0.653E-10    !same rate as original rates  !1.67E-8
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_RefractOM_C_Rate>
 +
 
 +
 +
!!!! Microorganisms Death !!!!!
 +
 +
<begin_Heterotrophs_Rate>
 +
AE          : 15.19
 +
Acoef        : 1.01E-33    !5.00E-34    !5.00E-35 testing
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
ConcMinCarbon : 1000.        ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_Heterotrophs_Rate>
 +
 +
<begin_Autotrophs_Rate>
 +
AE          : 12.64
 +
Acoef        : 1.35E-25    !1.34E-25      !same rate as original rates  !6.68E-30  testing
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
ConcMinAmmonia : 1.          ![mg/L] - ammonia min. below rate is maximum
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_Autotrophs_Rate>
 +
 +
<begin_Anaerobic_Rate>
 +
AE          : 12.83
 +
Acoef        : 4.522E-30    !4.76E-33      !4.76E-30      !4.76E-23
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
ConcMinNitrate : 1.          ![mg/L] - nitrate min. below rate is maximum
 +
ConcMinCarbon : 1000.        ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
<end_Anaerobic_Rate>
 +
 
 +
 +
!!!! Nitrification !!!!!
 +
 +
<begin_AmmoniaToNitrate_Rate>
 +
AE          : 21
 +
Acoef        : 0.    !3.33E-04          ! 3.33E-01                          !Need for a standard value.
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_AmmoniaToNitrate_Rate>
 +
 +
 +
!!!! Ammonia Immobilization !!!!!
 +
 +
<begin_AmmoniaImobilization_Rate>
 +
AE          : 15.1
 +
Acoef        : 5E-07
 +
kp     : 12.3
 +
Temperature  : 35
 +
<end_AmmoniaImobilization_Rate>
 +
 +
 +
!!!! Denitrification !!!!!
 +
 +
<begin_NitrateToNgas_Rate>
 +
AE          : 12.6
 +
Acoef        : 1.431E-10  !1.746E-8      !1.00E-13  2E-7 gave similar results as original rates with 1E-13
 +
kp     : 0
 +
Temperature  : 35
 +
 +
ConcOptCarbon : 10000.        ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
<end_NitrateToNgas_Rate>
 +
 
 +
 +
!!!! Nitrate Immobilization !!!!!
 +
 +
<begin_NitrateImobilization_Rate>
 +
AE          : 15.1
 +
Acoef        : 5E-07
 +
kp     : 12.3
 +
Temperature  : 35
 +
<end_NitrateImobilization_Rate>
 +
 +
 +
!!!! Urea hydrolysis !!!!!
 +
 +
<begin_Urea_Hydrolysis>
 +
AE     : 12.6
 +
Acoef        : 2.50E-04
 +
kp     : 0
 +
Temperature  : 35
 +
<end_Urea_Hydrolysis>
 +
 +
 +
!!!! Phsphorus Immobilization !!!!!
 +
 +
<begin_PhosphorusImobilization_Rate>
 +
AE     : 15.1
 +
Acoef        : 1.955E-9    !5E-10        !5E-07 testing
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_PhosphorusImobilization_Rate>
 +
 +
 +
!!!! Methane Production !!!!! -> testing
 +
 +
<begin_methane_production>
 +
AE     : 12.6
 +
Acoef        : 1.252E-12      !same rate as original rates !1E-13  testing
 +
kp     : 0
 +
Temperature  : 35
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
<end_methane_production>
 +
 +
 +
!!!! Solubilizing Bacteria  !!!!!
 +
 +
<begin_Sol_Rate>              
 +
AE          : 15.19
 +
Acoef        : 5.00E-35
 +
kp     : 12.3
 +
Temperature  : 35
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_Sol_Rate>
 +
 +
<begin_Labil_OM_C_sol_Rate>
 +
AE          : 1.64E-04
 +
Acoef        : 7.92E-10
 +
kp     : 12.3
 +
Temperature  : 35   
 +
 +
OptimumpH    : 7            ![] Optimum pH for reaction
 +
ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
 +
<end_Labil_OM_C_sol_Rate>
 +
 +
 +
<begin_RefractOM_C_sol_Rate>
 +
AE          : 2.02E-04
 +
Acoef        : 2.58E-10
 +
kp     : 12.3
 +
Temperature  : 35
  
−
  OUTPUT_TIME              : 0 3600
+
  OptimumpH    : 7            ![] Optimum pH for reaction
−
  TIME_SERIE_LOCATION      : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat
+
  ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
−
   
+
  <end_RefractOM_C_sol_Rate>
−
!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)
 
 
   
 
   
 +
<begin_Solubilizing_Rate>        
 +
AE          : 12.6                
 +
Acoef        : 1.10E-13
 +
kp     : 0
 +
Temperature  : 35
 
   
 
   
−
  NEW_FORMULATION          : 1  !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
+
  OptimumpH    : 7            ![] Optimum pH for reaction
−
  ADVDIFF_METHOD_H          : 1  !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
+
  ConcOptO2    : 10          ![mg/L] Maxium conc. above rate will be maximum.
−
!CentralDif = 5. LeapFrog = 6
+
  <end_Solubilizing_Rate>
−
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
+
  !!!!!!!!!!!!!!!!!!MICROORGANISMS!!!!!!!!!!!!!!!!!!!!!!!
−
  BOXFLUXES                : ..\General Data\Boxes\Boxes.dat
+
  !++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
   
 
   
−
  <beginSQrate>
+
  <begin_Heterotrophs>
−
  NAME                      : ammonia ammonia
+
  CN_RATIO                : 3.40        !
−
  DESCRIPTION              : nitrification (-); ammonia imombilization (+)
+
  CP_RATIO : 12.09      !
−
  FIRSTPROP                : ammonia
+
POPULATION_CARBON_RATIO : 950        !950        ![(#org/kgsoil)/(mgC/kgsoil)]
−
  SECONDPROP                : ammonia
+
  CARBON_EFICIENCY        : 0.13        !
−
  MODEL                    : SedimentQuality
+
  NITROGEN_EFICIENCY      : 0          !
−
  <endSQrate>
+
  MINIMUM_POPULATION      : 50000.      ![#org/kgsoil]
 +
  <end_Heterotrophs>
 
   
 
   
 +
<begin_Autotrophs>
 +
CN_RATIO                : 2.01
 +
CP_RATIO : 13.82   
 +
POPULATION_CARBON_RATIO : 9500      !9500
 +
CARBON_EFICIENCY        : 0
 +
NITROGEN_EFICIENCY      : 0.01
 +
MINIMUM_POPULATION      : 500.
 +
<end_Autotrophs>
 
   
 
   
−
  properties needed to run with sediment quality:  
+
  <begin_Anaerobic>
−
  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
+
CN_RATIO                : 3.40
−
  properties defined by user (sediment quality does not change them): temperature, salinity, pH, ionic strength, phosphorus adsortion index, soil dry density
+
  CP_RATIO : 13.82   
−
  properties that can be defined by user or computed: oxygen. oxygen is computed based on temperature and salinity.
+
  POPULATION_CARBON_RATIO : 9500      !9500
 +
  CARBON_EFICIENCY        : 0.1
 +
NITROGEN_EFICIENCY      : 0.1
 +
MINIMUM_POPULATION      : 5000.
 +
<end_Anaerobic>
 
   
 
   
−
  <beginproperty>
+
  <begin_Sols>
−
  NAME                      : ammonia
+
  CN_RATIO                :8
−
UNITS                    : mgN/L
+
  CP_RATIO :60   
−
  DESCRIPTION              : ammonia
+
  POPULATION_CARBON_RATIO :950        !950
−
  PARTICULATE              : 0
+
  CARBON_EFICIENCY        :0.1
−
  OLD                      : 0
+
  NITROGEN_EFICIENCY      :0.1
−
MIN_VALUE                : 1E-15
+
  <end_Sols>
−
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>
 

Revision as of 20:48, 1 June 2011

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 (day-1.pop-1) times bacteria population that conducts the process.

MaxRate (day-1) = Standard Rate at actual Temperature (day-1.pop-1) * BacteriaPopulation

ActualRate (day-1) = MaxRate (day-1) * Aerobiose/AnaerobioseTerm * pHTerm * OxygenTerm * SubstrateTerm


Organic Matter Mineralization

Organic matter is mineralized to ammonia with heterotrophic bacteria and also immobilization may occur in order to maintain bacteria C:N ratios.

Heterotrophic LPOM mineralization rate

Insert formula here


Heterotrophic RPOM mineralization rate

Insert formula here


Immobilization rate

Insert formula here


Nitrification

Nitrification rate

Insert formula here


Denitrification

Denitrification rate

Insert formula here


Other Features

Outputs

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

References

Data File

Keywords

Properties Units:
dissolved                 - as from called - in MOHID Land mg/L
adsorbed/particulated     - as from called - in MOHID Land mg/kgsoil
gases:
CO2 and CH4               - same as adsorbed/particulated properties
N2                        - same as dissolved properties
exceptions:
oxygen                    - mol/L
hydrogen                  - mol/L
microorganisms population - #org/kgsoil
wind                      - km/day

OXYGEN   	            :  [0/1]       0      !Connect/Disconnect Oxygen computation 
SOL_BACTERIA 	            :  [0/1]       0	  !Connect/Disconnect Solubilizing bacteria computation 

DTSECONDS                  :  [s]       86400.   !dt to evaluate
NO3_LIMIT                  :  [mg/L]      0.     !Minimum value for denitrification or maximum value for 
                                                   !methane production in organic matter decay
NEW_RATES                  : [0/1]        0      !Connect/Disconnect new rates formulation using maximum * factors
IMOBILIZATION              : [0/1]        1      !Connect/Disconnect immobilization

EXPLICIT                   : [0/1]        1      !Explicit computation for time dicretization

Sample

!!!!!!!!!!!!!!!!!MAIN SEDIMENT OPTIONS!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

!NITROGEN 	: 1
!CARBON   	: 1
!PHOSPHORUS  	: 1	
OXYGEN   	: 1 
SOL_BACTERIA 	: 0	 

DTSECONDS    : 86400.
NO3_LIMIT    : 0. ![mg/L] Minimum value for denitrification or maximum value for methane production in organic matter decay
CHANGE_RATES : 0  !0 - original rates; 1-changed rates (removing concentrations from rates so do not change units)
NEW_RATES    : 1  !1 - new rates using maximum * factors
!IMOBILIZATION : 0

EXPLICIT : 1
!IMPLICIT  ! not working?
!SEMIIMP




!!!!!!!!!!!!!!!!!!!!!!RATES!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

	!!!! Organic Matter Decay !!!!

<begin_Labil_OM_C_Rate>
AE           : 15.1         ![kcal.mole-1] Initial Activation Energy
Acoef        : 0.391E-9     !same rate as original rates   !1E-7         ![s.day-1.pop-1] Rate Coefficient
kp 	     : 12.3	    ![L/mol] Salinity coefficient		
Temperature  : 35           ![ºC] Optimal Temperature     

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Labil_OM_C_Rate>

<begin_RefractOM_C_Rate>
AE           : 15.1
Acoef        : 0.653E-11     !0.653E-10    !same rate as original rates   !1.67E-8
kp 	     : 12.3
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_RefractOM_C_Rate>
 

	!!!! Microorganisms Death !!!!!

<begin_Heterotrophs_Rate>
AE           : 15.19
Acoef        : 1.01E-33    !5.00E-34    !5.00E-35 testing
kp 	     : 12.3
Temperature  : 35

ConcMinCarbon : 1000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Heterotrophs_Rate>

<begin_Autotrophs_Rate>
AE           : 12.64
Acoef        : 1.35E-25     !1.34E-25      !same rate as original rates  !6.68E-30  testing
kp 	     : 12.3
Temperature  : 35 

ConcMinAmmonia : 1.           ![mg/L] - ammonia min. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Autotrophs_Rate>

<begin_Anaerobic_Rate>
AE           : 12.83
Acoef        : 4.522E-30     !4.76E-33      !4.76E-30       !4.76E-23
kp 	     : 12.3
Temperature  : 35 

ConcMinNitrate : 1.           ![mg/L] - nitrate min. below rate is maximum
ConcMinCarbon : 1000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
<end_Anaerobic_Rate>
 

	!!!! Nitrification !!!!!

<begin_AmmoniaToNitrate_Rate>
AE           : 21
Acoef        : 0.    !3.33E-04           ! 3.33E-01                          !Need for a standard value.
kp 	     : 12.3
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_AmmoniaToNitrate_Rate>


	!!!! Ammonia Immobilization !!!!!

<begin_AmmoniaImobilization_Rate>
AE           : 15.1
Acoef        : 5E-07
kp 	     : 12.3
Temperature  : 35
<end_AmmoniaImobilization_Rate>


	!!!! Denitrification !!!!!

<begin_NitrateToNgas_Rate>
AE           : 12.6
Acoef        : 1.431E-10   !1.746E-8       !1.00E-13   2E-7 gave similar results as original rates with 1E-13
kp 	     : 0
Temperature  : 35 

ConcOptCarbon : 10000.         ![kg/kgsoil] - labil and refractary organic carbon. below rate is maximum
OptimumpH    : 7            ![] Optimum pH for reaction
<end_NitrateToNgas_Rate>
 

	!!!! Nitrate Immobilization !!!!!

<begin_NitrateImobilization_Rate>
AE           : 15.1
Acoef        : 5E-07
kp 	     : 12.3
Temperature  : 35
<end_NitrateImobilization_Rate>


	!!!! Urea hydrolysis !!!!!

<begin_Urea_Hydrolysis>
AE	     : 12.6					
Acoef        : 2.50E-04
kp 	     : 0			
Temperature  : 35
<end_Urea_Hydrolysis>


	!!!! Phsphorus Immobilization !!!!!

<begin_PhosphorusImobilization_Rate>
AE	     : 15.1					
Acoef        : 1.955E-9    !5E-10         !5E-07 testing
kp 	     : 12.3			
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_PhosphorusImobilization_Rate>


	!!!! Methane Production !!!!! -> testing

<begin_methane_production>
AE	     : 12.6					
Acoef        : 1.252E-12      !same rate as original rates !1E-13  testing
kp 	     : 0		
Temperature  : 35 

OptimumpH    : 7            ![] Optimum pH for reaction
<end_methane_production>


	!!!! Solubilizing Bacteria  !!!!!

<begin_Sol_Rate>	               
AE           : 15.19
Acoef        : 5.00E-35
kp 	     : 12.3 
Temperature  : 35

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Sol_Rate>

<begin_Labil_OM_C_sol_Rate>
AE           : 1.64E-04
Acoef        : 7.92E-10
kp 	     : 12.3
Temperature  : 35     

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Labil_OM_C_sol_Rate>


<begin_RefractOM_C_sol_Rate>
AE           : 2.02E-04
Acoef        : 2.58E-10
kp 	     : 12.3
Temperature  : 35 

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_RefractOM_C_sol_Rate>


<begin_Solubilizing_Rate>	        
AE           : 12.6	                
Acoef        : 1.10E-13			
kp 	     : 0
Temperature  : 35 

OptimumpH    : 7            ![] Optimum pH for reaction
ConcOptO2    : 10           ![mg/L] Maxium conc. above rate will be maximum.
<end_Solubilizing_Rate>




!!!!!!!!!!!!!!!!!!MICROORGANISMS!!!!!!!!!!!!!!!!!!!!!!!
!++++++++++++++++++++++++++++++++++++++++++++++++++++++

<begin_Heterotrophs>
CN_RATIO                : 3.40        !
CP_RATIO		: 12.09       !
POPULATION_CARBON_RATIO : 950         !950         ![(#org/kgsoil)/(mgC/kgsoil)]
CARBON_EFICIENCY        : 0.13        !
NITROGEN_EFICIENCY      : 0           !
MINIMUM_POPULATION      : 50000.      ![#org/kgsoil]
<end_Heterotrophs>

<begin_Autotrophs>
CN_RATIO                : 2.01 
CP_RATIO		: 13.82    
POPULATION_CARBON_RATIO : 9500       !9500
CARBON_EFICIENCY        : 0
NITROGEN_EFICIENCY      : 0.01
MINIMUM_POPULATION      : 500.
<end_Autotrophs>

<begin_Anaerobic>
CN_RATIO                : 3.40
CP_RATIO		: 13.82    
POPULATION_CARBON_RATIO : 9500       !9500
CARBON_EFICIENCY        : 0.1
NITROGEN_EFICIENCY      : 0.1
MINIMUM_POPULATION      : 5000.
<end_Anaerobic>

<begin_Sols>
CN_RATIO                :8
CP_RATIO		:60    
POPULATION_CARBON_RATIO :950         !950
CARBON_EFICIENCY        :0.1
NITROGEN_EFICIENCY      :0.1
<end_Sols>
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