Module PorousMediaProperties - Revision history

Lucian: /* Properties needed to run with sediment quality */

2019-02-07T15:14:36Z

‎Properties needed to run with sediment quality

Lucian: /* Properties needed to run with sediment quality */

2019-02-07T15:13:55Z

‎Properties needed to run with sediment quality

Lucian: /* Properties needed to run with sediment quality */

2019-02-07T15:13:04Z

‎Properties needed to run with sediment quality

Lucian: /* Properties needed to run with sediment quality */

2019-02-07T15:11:36Z

‎Properties needed to run with sediment quality

Lucian at 15:03, 7 February 2019

2019-02-07T15:03:00Z

Lucian at 14:57, 7 February 2019

2019-02-07T14:57:53Z

Davidbrito at 12:02, 17 January 2014

2014-01-17T12:02:31Z

Davidbrito: /* Lateral Boundary */

2013-09-13T18:00:53Z

‎Lateral Boundary

Davidbrito: /* Boundary Conditions */

2013-09-13T17:50:34Z

‎Boundary Conditions

Davidbrito at 17:48, 13 September 2013

2013-09-13T17:48:16Z

@@ Line 260: / Line 260: @@
 ===Properties needed to run with sediment quality===
-- properties simulated -
+- properties simulated:
 ammonia, nitrate, particulated refractory organic nitrogen, particulate organic nitrogen, nitrogen gas, heterotrophic microorganism nitrogen, autotrophic microorganism nitrogen, anaerobic microorganism nitrogen, urea
@@ Line 267: / Line 267: @@
 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) -
+- 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 -
+- properties that can be defined by user or computed:
 oxygen. oxygen is computed based on temperature and salinity.

@@ Line 262: / Line 262: @@
 - 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

@@ Line 260: / Line 260: @@
 ===Properties needed to run with sediment quality===
-- properties simulated:
+- 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 defined by user (sediment quality does not change them) -
-- properties that can be defined by user or computed: oxygen. oxygen is computed based on temperature and salinity.
+- properties that can be defined by user or computed -
   '''ATTENTION:''' When using soil quality modules DTINTERVAL here in each property should be the same as 0D model DT.

@@ Line 260: / Line 260: @@
 ===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 simulated:
 - properties defined by user (sediment quality does not change them): temperature, salinity, pH, ionic strength, phosphorus adsortion index, soil dry density

@@ Line 157: / Line 157: @@
 ==Data File ==
-====Units====
+==Units==
   Units in porous media properties
     Transported properties (soluble)  : g/m3 (or mg/L)                     (needs to convert concentrations to SedimentQuality and
@@ Line 259: / Line 259: @@
- properties needed to run with sediment quality:
+===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,
+- 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
- 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,
+- properties defined by user (sediment quality does not change them): temperature, salinity, pH, ionic strength, phosphorus adsortion index, soil dry density
- 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.
-  ATTENTION : When using soil quality modules DTINTERVAL here in each property should be the same as 0D model DT.
+  '''ATTENTION:''' When using soil quality modules DTINTERVAL here in each property should be the same as 0D model DT.

@@ Line 12: / Line 12: @@
 [[Image:EqnPropertyTransport_Text.png|1000px|thumb|center|]]
-This "equation" may be written in integral form meaning that the accumulation terms are summed in infinitesimal volumes and the fluxes trough the faces of the volume are summed in infinitesimal areas. These fluxes trough the faces enter with the velocity (transport from other volumes) and because there is diffusion (the property has different concentrations in different volumes and spreads). So the inputs and outputs will create two terms, the first the advection (driven trough velocity) and the second the diffusion (driven trough property gradient).
+This "equation" may be written in integral form meaning that the accumulation terms are summed in infinitesimal volumes and the fluxes through the faces of the volume are summed in infinitesimal areas. These fluxes through the faces enter with the velocity (transport from other volumes) and because there is diffusion (the property has different concentrations in different volumes and spreads). So the inputs and outputs will create two terms, the first the advection (driven trough velocity) and the second the diffusion (driven trough property gradient).
 The property transport equation in integral form:
@@ Line 24: / Line 24: @@
   dt is infinitesimal variation of time
-In a finite volume approach the control volume (or cell) has a defined volume and all the properties are homogeneous inside the control volume (and refered to the cell center) and velocities are homogeneous in the faces of the volume (and refered to the face).
+In a finite volume approach, the control volume (or cell) has a defined volume and all the properties are homogeneous inside the control volume (and referred to the cell center) and velocities are homogeneous in the faces of the volume (and referred to the face).
-So the latter equation may be simplified because property, velocity and diffusivity are homogeneous inside control volume or in the faces so they may exit the integral and the various flux directions (3 directions trough 6 faces have to be analyzed).
+So the latter equation may be simplified because property, velocity, and diffusivity are homogeneous inside control volume or in the faces so they may exit the integral and the various flux directions (3 directions through 6 faces have to be analyzed).
 The property transport equation in "infinitesimal volume" form::
@@ Line 51: / Line 51: @@
   * is t in case of explicit model and t+deltat in case of implicit
-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).
+Time discretization of property transport in Module PorousMediaProperties can be explicit or implicit. If a 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 a source to soil and sources or sinks from vegetation (uptake or organic matter generation) are always computed explicitly. Vegetation uptakes cannot be simulated implicitly because this uptake may be disconnected from evapotranspiration flux (SWAT formulation).
@@ Line 71: / Line 71: @@
   * is t in case of explicit model and t+deltat in case of implicit
-Water content at face can be obtained by several methods chosen by user: average of adjacent cells, minimum, maximum.
+Water content at face can be obtained by several methods chosen by the user: average of adjacent cells, minimum, maximum.
 Tortuosity is defined as:
@@ Line 86: / Line 86: @@
 [[Module SedimentQuality | 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.
+Also, immobilization of inorganic species is done if bacteria have nutrient needs to maintain ratios.
 ====Chemical reactions - PREEQC Module====
@@ Line 99: / Line 99: @@
 In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.
-In the case of lateral boundary flux if water enters domain from outside the properties values in the boundary need to be defined.
+In the case of lateral boundary flux if water enters the domain from outside the properties values in the boundary need to be defined.
 For the bottom boundary condition is assumed "free-flow" or "null gradient" and water only exits soil so the properties in boundary do not need to be defined.
@@ Line 105: / Line 105: @@
 ====Lateral Boundary====
 Boundary propertie values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
-The boundary flow from Module Porous Media and the imposed concentration in boundary are used to define transport coefficients for advection diffusion.
+The boundary flow from Module Porous Media and the imposed concentration in boundary are used to define transport coefficients for advection-diffusion.
-In advection diffusion solving (if user chooses implicit) the fluxes entering the domain are solved explicitly and fluxes exiting are computed implicitly.
+In advection diffusion solving (if the user chooses implicit), the fluxes entering the domain are solved explicitly and fluxes exiting are computed implicitly.
 ====Bottom Boundary====
-Bottom fluxes do not need for a boundary property definition (water exiting domain) and in the advection diffusion solving (if user chooses implicit) the fluxes are computed implicitly.
+Bottom fluxes do not need for a boundary property definition (water exiting domain) and in the advection-diffusion solving (if the user chooses implicit) the fluxes are computed implicitly.
 ===Keywords===
@@ Line 132: / Line 132: @@
 ==Discharges==
-In PorousMediaProperties the discharges may be positive or negative (PorousMediaProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges.
+In PorousMediaProperties the discharges may be positive or negative (PorousMediaProperties uses discharge flow and concentration) and are dealt with ModuleDischarges.
-In Porous Media Properties it was also introduced the option to use properties discharged.
+In Porous Media Properties, it was also introduced the option to use properties discharged.
 If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.
@@ Line 140: / Line 140: @@
 The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.
-In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).
+In Modification phase, the discharges are explicit and computed before transport (they were not included in transport scheme).
 ===Keywords===
@@ Line 157: / Line 157: @@
 ==Data File ==
-===Keywords===
+====Units====
   Units in porous media properties
     Transported properties (soluble)  : g/m3 (or mg/L)                     (needs to convert concentrations to SedimentQuality and
@@ Line 170: / Line 169: @@
     H+ and Ionic Strenght             : mol/L                              (used in SedimentQuality)
     Microorganisms Population         : #org/kgsoil                        (used in SedimentQuality)
-−
- Keywords:
+===Keywords===
   ADVDIFF_EXPLICIT              : 0/1                [1]        !REMARK: Horizontal diffusion is always explicit

@@ Line 129: / Line 129: @@
 ====Bottom Boundary====
 For bottom boundary is no need for property definition
 ==Other Features==

← Older revision		Revision as of 17:48, 13 September 2013
Line 95:		Line 95:

	Partition between particulated and dissolved species is done using a user ratio.		Partition between particulated and dissolved species is done using a user ratio.
		+
		+	==Boundary Conditions==
		+	In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.
		+
		+	In the case of lateral boundary flux if water enters domain from outside the properties values in the boundary need to be defined.
		+	For the bottom boundary condition is assumed "free-flow" or "null gradient" and water only exits soil so the properties in boundary do not need to be defined.
		+
		+	===Computation===
		+	====Lateral Boundary====
		+	Boundary propertie values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
		+	The boundary flow from runoff and the imposed concentration in boundary are used to define transport coefficients for advection diffusion.
		+	In advection diffusion solving (if user chooses implicit) the fluxes entering the domain are solved explicitly and fluxes exiting are computed implicitly.
		+
		+	====Bottom Boundary====
		+	Bottom fluxes do not need for a boundary property definition (water exiting domain) and in the advection diffusion solving (if user chooses implicit) the fluxes are computed implicitly.
		+
		+	===Keywords===
		+	====Lateral Boundary====
		+	The keyword in property block in PorousMediaProperties_X.dat that allows to define the boundary condition method is:
		+	<beginproperty>
		+	...
		+	BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
		+	...
		+	<endproperty>
		+
		+	In case of using imposed value than the imposed concentration has to be defined:
		+	<beginproperty>
		+	...
		+	DEFAULTBOUNDARY : 1.
		+	...
		+	<endproperty>
		+
		+
		+	====Bottom Boundary====
		+	For bottom boundary is no need for property definition
		+
		+

	==Other Features==		==Other Features==