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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 ...)
 
 
(21 intermediate revisions by the same user not shown)
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==Main Processes==
 
==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.
+
Main processes in SedimentQuality are organic matter mineralization, nitrification, denitrification and immobilization driven by microorganisms. These processes and microorganisms death are simulated using a standard rate (s.day-1.pop-1) that is afected by temperature, pH, oxygen in case of aerobic processes and substrate concentrations if exist.
−
A maximum rate is computed calculating the standard rate at the actual temperature times bacteria population that conducts the process.
+
An old formulation based on RZWQM was adapted in order to be consistent in units and in the new formulation a maximum rate exists and "stress" factors (from 0 to 1) are computed accordingly to pH, aerobiose and aerobiose conditions, oxygen and susbtrate availability. Aerobiose and aerobiose conditions are computed from realtive water content.
  
 +
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> MaximumRate = \left [\frac{K_{b}\times T_{p}}{h_{p}}\times A_{decay}\times e^\left [{\frac{-Ea}{Rg\times T_{p}}}  \right ] \right ]\times Micro_{pop}</math>
 +
 +
<math> MaximumDeathRate = \left [\frac{\frac{K_{b}\times T_{p}}{h_{p}}\times A_{decay}}{e^\left [\frac{-Ea}{Rg\times T_{p}}  \right ]} \right ]\times Micro_{pop}</math>
 +
where:
 +
Kb - Boltzman constant [J.K−1]
 +
Tp - temperature [K]
 +
hp - Planck constant [J.s]
 +
Rg - Universal gas constant [Kcal.mole-1.K-1]
 +
Adecay - decay coefficient [s. day-1.pop-1]
 +
Ea - Apparent activation energy [Kcal.mole−1]
 +
 +
 +
<math> NonDeathRate = MaximumRate \times \varphi (Aerobiose/Anaerobiose)\times \varphi (Oxygen)\times \varphi (pH)\times \varphi (Substrate_nonDeath) </math>
 +
 +
<math> DeathRate = MaximumDeathRate \times \frac{1}{\varphi (Aerobiose/Anaerobiose)}\times (1 -\varphi (Oxygen))\times (1 -\varphi (pH))\times \varphi (Substrate_Death) </math>
 +
 +
 +
'''pHTerm'''
 +
This term has a value of 1 in pHopt and symetric descending behaviour up to acid and basic pH's. In the case that is used in death rates the term is (1 - pHterm) since value 1 (maximum death rate) will be for the worst conditions (pH acid or basic) and 0 for best conditions.
 +
 +
<math>if pH > pHopt => pHused = 2* pHopt - pH</math>
 +
 +
<math>pHTerm=\frac{pHused}{2\times pHopt-pHused}</math>
 +
 +
 +
'''OxygenTerm and Sustrate in non death rates'''
 +
The oxygen term and substrate term represent the abundance of substance that has not a negative effect on high concentrations. As so, for higher concentrations than optimum the value will be always 1. for lower concentrations than optimum there is a linear decrease of the term up to zero concentration and zero term.
 +
In the case that oxygen term is used in death rates it will become (1 - OxygenTerm) since the value 1 represents a maximum death rate and 0 represents no death.
 +
 +
<math>Term = min\left [\frac{Conc}{ConcOpt} , 1 \right ]</math>
 +
 +
 +
'''SubstrateTerm in Death Rates'''
 +
In the case that the substrate term is used in death rates it becomes a exponential decay with increasing substrate (higher than a mimimum) to represent the same behaviour as old formulation.
 +
For concentration lower than the minimum, the term is 1 and death rate is maximum. For concentrations higher than the minimum the term as an exponential decay showing the effect of increasing material on lowering death rate.
 +
 +
<math>Term=min\left [\frac{MinConc}{Conc} , 1 \right ]</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.
 +
 +
 +
'''LPOM mineralization rate'''
 +
 +
<math>LPOMRate = LPOM_MaximumRate(HeterotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm </math>
  
  
 +
'''RPOM mineralization rate'''
  
−
===Property Transformation===
+
<math>RPOMRate = RPOM_MaximumRate(HeterotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm</math>
  
−
====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).
+
'''Immobilization rate'''
−
Also immobilization of inorganic species is done if bacteria have nutrient needs to mantain ratios.
 
  
−
====Chemical reactions - PREEQC Module=====
+
<math>Insert formula here</math>
  
−
PREEQC Module handles chemical equilibrium between species in soil, giving the new equilibrium at each computation.
 
  
−
====Partition====
+
===Nitrification===
 +
Nitrification is driven by autotrophic microorganisms. Also immobilization is associated.
  
−
Partition between particulated and dissolved species is done using a user ratio.
+
<math>NitrificationRate = Nitrification_MaximumRate(AutotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm</math>
 +
 
 +
 
 +
===Denitrification===
 +
Denitrification is driven by anaerobic microorganisms. Also immobilization is associated.
 +
 
 +
<math>DenitrificationRate = Denitrification_MaximumRate(AnaerobicPop) * AnaerobioseTerm * pHTerm * Substrate_Carbon(</math>
 +
 
 +
 
 +
===Microorganisms Growth===
 +
Microorganisms incorporate carbon, nitrogen and phosphorus in the processes described above. However, they also have sinks as respiration and death.
 +
 
 +
'''Death Rates'''
 +
 
 +
Heterotrohpic microorganisms
 +
<math>HeterotrophicDeathRate = Heterotrophic_MaximumDeathRate(HeterotrophicPop) * (1 /AerobioseTerm) * (1 - pHTerm) * (1 - OxygenTerm) * SubstrateTerm_Carbon</math>
 +
 +
 
 +
Autotrohpic  microorganisms
 +
<math>AutotrophicDeathRate = Autotrophic_MaximumDeathRate(AutotrophicPop) * (1 /AerobioseTerm) * (1 - pHTerm) * (1 - OxygenTerm) * SubstrateTerm_Ammonia</math>
 +
 
 +
 
 +
Anaerobic  microorganisms
 +
<math>AnaerobicDeathRate = Anaerobic_MaximumDeathRate(AnaerobicPop) * (1 /AnaerobioseTerm) * (1 - pHTerm) * SubstrateTerm_Nitrate * SubstrateTerm_Carbon</math>
  
 
==Other Features==
 
==Other Features==
Line 41: Line 107:
 
===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]]
+
====New Formulation====
−
 
 
  
−
  OUTPUT_TIME              : 0 3600
+
  !!!!!!!!!!!!!!!!!MAIN SEDIMENT OPTIONS!!!!!!!!!!!!!!!!
−
  TIME_SERIE_LOCATION      : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat
+
  !++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
   
 
   
−
  !Advectin diffusion options
+
  NITROGEN : 1
−
  ADVDIFF_EXPLICIT          : 1
+
  CARBON  : 1
−
  !Horizontal diffusion is always explicit
+
  PHOSPHORUS  : 1
−
  !(1 - adv and diff are explicit in all directions; 0 - adv and diff
+
  OXYGEN  : 1  
−
  !are implicit in vertical. horizontal adv may be explicit or impl)
+
SOL_BACTERIA : 0  
 
   
 
   
−
  ADVDIFF_ADVECTION_H_IMP_EXP :  1
+
  DTSECONDS    : 86400.
−
  !(read if ADVDIFF_EXPLICIT : 0; 0 - horiz adv implicit;
+
  NO3_LIMIT    : 0.    ![mg/L] Minimum value for denitrification or maximum value for methane production in organic matter decay
−
  ! 1 - horiz adv explicit)
+
  NEW_RATES    : 1      !1 - new rates using maximum * factors; 0 - old formulation
 +
  IMOBILIZATION : 0    !1 - immobilization is connected; 0 - immobilization is disconnected 
 
   
 
   
 +
EXPLICIT : 1          !explicit method
 +
 
 +
 
 +
 +
====Old Formulation====
 +
 +
!!!!!!!!!!!!!!!!!MAIN SEDIMENT OPTIONS!!!!!!!!!!!!!!!!
 +
!++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
   
 
   
−
  NEW_FORMULATION          : 1   !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
+
  NITROGEN : 1
−
  ADVDIFF_METHOD_H          : 1   !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
+
  CARBON  : 1
−
  !CentralDif = 5. LeapFrog = 6
+
  PHOSPHORUS  : 1
−
  ADVDIFF_METHOD_V          : 1   !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
+
  OXYGEN  : 1  
−
  !CentralDif = 5. LeapFrog = 6
+
  SOL_BACTERIA : 0
 
   
 
   
−
  !dispersion
+
  DTSECONDS    : 86400.
−
<begin_dispersion_long>
+
  NO3_LIMIT    : 0.     ![mg/L] Minimum value for denitrification or maximum value for methane production in organic matter decay
−
NAME                      : dispersion long
+
  IMOBILIZATION : 0    !1 - immobilization is connected; 0 - immobilization is disconnected 
−
INITIALIZATION_METHOD    : CONSTANT
 
−
  DEFAULTVALUE              : 0.0
 
−
  REMAIN_CONSTANT          : 1
 
−
<end_dispersion_long>
 
 
   
 
   
−
  <begin_dispersion_trans>
+
  EXPLICIT : 1         !explicit method
−
NAME                      : dispersion trans
+
 
−
INITIALIZATION_METHOD    : CONSTANT
+
 
−
DEFAULTVALUE              : 0.0
+
 
−
REMAIN_CONSTANT          : 1
+
[[Category:MOHID Base 1]]
−
<end_dispersion_trans>
+
[[Category:MOHID Land]]
−
 
−
 
−
!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>
 

Latest revision as of 19:46, 8 December 2013

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 driven by microorganisms. These processes and microorganisms death are simulated using a standard rate (s.day-1.pop-1) that is afected by temperature, pH, oxygen in case of aerobic processes and substrate concentrations if exist. An old formulation based on RZWQM was adapted in order to be consistent in units and in the new formulation a maximum rate exists and "stress" factors (from 0 to 1) are computed accordingly to pH, aerobiose and aerobiose conditions, oxygen and susbtrate availability. Aerobiose and aerobiose conditions are computed from realtive water content.

A maximum rate is computed calculating the standard rate at the actual temperature (day-1.pop-1) times bacteria population that conducts the process. 

 MaximumRate = \left [\frac{K_{b}\times T_{p}}{h_{p}}\times A_{decay}\times e^\left [{\frac{-Ea}{Rg\times T_{p}}}  \right ] \right ]\times Micro_{pop}

 MaximumDeathRate = \left [\frac{\frac{K_{b}\times T_{p}}{h_{p}}\times A_{decay}}{e^\left [\frac{-Ea}{Rg\times T_{p}}  \right ]} \right ]\times Micro_{pop}

where: 

Kb - Boltzman constant [J.K−1]
Tp - temperature [K]
hp - Planck constant [J.s]
Rg - Universal gas constant [Kcal.mole-1.K-1]
Adecay - decay coefficient [s. day-1.pop-1]
Ea - Apparent activation energy [Kcal.mole−1]



 NonDeathRate = MaximumRate \times \varphi (Aerobiose/Anaerobiose)\times \varphi (Oxygen)\times \varphi (pH)\times \varphi (Substrate_nonDeath) 

 DeathRate = MaximumDeathRate \times \frac{1}{\varphi (Aerobiose/Anaerobiose)}\times (1 -\varphi (Oxygen))\times (1 -\varphi (pH))\times \varphi (Substrate_Death)


pHTerm This term has a value of 1 in pHopt and symetric descending behaviour up to acid and basic pH's. In the case that is used in death rates the term is (1 - pHterm) since value 1 (maximum death rate) will be for the worst conditions (pH acid or basic) and 0 for best conditions. 

if pH > pHopt => pHused = 2* pHopt - pH

pHTerm=\frac{pHused}{2\times pHopt-pHused}


OxygenTerm and Sustrate in non death rates The oxygen term and substrate term represent the abundance of substance that has not a negative effect on high concentrations. As so, for higher concentrations than optimum the value will be always 1. for lower concentrations than optimum there is a linear decrease of the term up to zero concentration and zero term. In the case that oxygen term is used in death rates it will become (1 - OxygenTerm) since the value 1 represents a maximum death rate and 0 represents no death. 

Term = min\left [\frac{Conc}{ConcOpt} , 1 \right ]


SubstrateTerm in Death Rates In the case that the substrate term is used in death rates it becomes a exponential decay with increasing substrate (higher than a mimimum) to represent the same behaviour as old formulation. For concentration lower than the minimum, the term is 1 and death rate is maximum. For concentrations higher than the minimum the term as an exponential decay showing the effect of increasing material on lowering death rate. 

Term=min\left [\frac{MinConc}{Conc} , 1 \right ]


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.


LPOM mineralization rate 

LPOMRate = LPOM_MaximumRate(HeterotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm


RPOM mineralization rate 

RPOMRate = RPOM_MaximumRate(HeterotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm


Immobilization rate 

Insert formula here


Nitrification

Nitrification is driven by autotrophic microorganisms. Also immobilization is associated. 

NitrificationRate = Nitrification_MaximumRate(AutotrophsPop) * AerobioseTerm * pHTerm * OxygenTerm


Denitrification

Denitrification is driven by anaerobic microorganisms. Also immobilization is associated. 

DenitrificationRate = Denitrification_MaximumRate(AnaerobicPop) * AnaerobioseTerm * pHTerm * Substrate_Carbon(


Microorganisms Growth

Microorganisms incorporate carbon, nitrogen and phosphorus in the processes described above. However, they also have sinks as respiration and death.

Death Rates 

Heterotrohpic microorganisms
HeterotrophicDeathRate = Heterotrophic_MaximumDeathRate(HeterotrophicPop) * (1 /AerobioseTerm) * (1 - pHTerm) * (1 - OxygenTerm) * SubstrateTerm_Carbon


Autotrohpic  microorganisms
AutotrophicDeathRate = Autotrophic_MaximumDeathRate(AutotrophicPop) * (1 /AerobioseTerm) * (1 - pHTerm) * (1 - OxygenTerm) * SubstrateTerm_Ammonia



Anaerobic  microorganisms
AnaerobicDeathRate = Anaerobic_MaximumDeathRate(AnaerobicPop) * (1 /AnaerobioseTerm) * (1 - pHTerm) * SubstrateTerm_Nitrate * SubstrateTerm_Carbon

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

New Formulation

!!!!!!!!!!!!!!!!!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
NEW_RATES    : 1      !1 - new rates using maximum * factors; 0 - old formulation
IMOBILIZATION : 0    !1 - immobilization is connected; 0 - immobilization is disconnected   

EXPLICIT : 1          !explicit method

Old Formulation

!!!!!!!!!!!!!!!!!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
IMOBILIZATION : 0    !1 - immobilization is connected; 0 - immobilization is disconnected   

EXPLICIT : 1          !explicit method
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