Difference between revisions of "Module PorousMediaProperties"
From MohidWiki
Davidbrito (talk | contribs) |
Davidbrito (talk | contribs) (→Property Transport) |
||
| Line 24: | Line 24: | ||
<math>Insert formula here</math> | <math>Insert formula here</math> | ||
| − | |||
===Property Transformation=== | ===Property Transformation=== | ||
Revision as of 13:17, 2 June 2011
Contents
Overview
This is the module in Mohid Land that handles porous media properties, meaning that controls transport (dependent on fluxes computed in porous media) and transformation processes (sediment quality and PREEQC modules that concern to biological and chemical processes in soil respectively).
Main Processes
Property Transport
Time discretization of property transport in Module PorousMediaProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between porous media cells are implicit computed and also Runoff or Drainage Network interactions where sinks in soil occur. Runoff and Drainage network interactions acting as source to soil and sources or sinks from vegetation (uptake or organic matter generation) are always computed explicitly. Vegetation uptakes can not be simulated implicitly because this uptake may be disconnected from evapotranspiration flux (SWAT formulation).
Spatial discretization (horizontally and vertically) of property transport in Module PorousMediaProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, PorousMediaProperties has the option of choosing all the same discretization for all the properties (discussed below).
Insert equations for property transport
Insert equation for diffusivity
Insert equation for tortuosity
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.
Other Features
Outputs
Output is done in terms of timeseries, HDF, and boxes following the MOHID standards.
References
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>
