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stream_hyporheic_conservative_tracer_reach.xml
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stream_hyporheic_conservative_tracer_reach.xml
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<ParameterList name="Main" type="ParameterList">
<ParameterList name="mesh" type="ParameterList">
<ParameterList name="surface" type="ParameterList">
<Parameter name="mesh type" type="string" value="aliased" />
<ParameterList name="aliased parameters">
<Parameter name="target" type="string" value="domain" />
</ParameterList>
</ParameterList>
<ParameterList name="domain" type="ParameterList">
<Parameter name="mesh type" type="string" value="logical mesh" />
<ParameterList name="logical mesh parameters" type="ParameterList">
<ParameterList name="segments" type="ParameterList">
<ParameterList name="Stream" type="ParameterList">
<Parameter name="number of cells" type="int" value="10" />
<Parameter name="total length" type="double" value="1000" />
<Parameter name="cross sectional area [m^2]" type="double" value="0.5496" />
<Parameter name="first tip" type="Array(double)" value="{ 0, 0, 0}" />
<Parameter name="first tip type" type="string" value="boundary" />
<Parameter name="last tip" type="Array(double)" value="{1000, 0, 0}" />
<Parameter name="last tip type" type="string" value="boundary" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="subgrid" type="ParameterList">
<Parameter name="mesh type" type="string" value="domain set indexed" />
<ParameterList name="domain set indexed parameters" type="ParameterList">
<Parameter name="indexing parent domain" type="string" value="surface" />
<Parameter name="entity kind" type="string" value="CELL" />
<Parameter name="regions" type="Array(string)" value="{surface domain}" />
<ParameterList name="subgrid:*" type="ParameterList">
<Parameter name="mesh type" type="string" value="logical mesh" />
<ParameterList name="logical mesh parameters" type="ParameterList">
<Parameter name="infer cell centroids" type="bool" value="true" />
<ParameterList name="segments">
<ParameterList name="tau_space">
<Parameter name="number of cells" type="int" value="20" />
<Parameter name="cross sectional area [m^2]" type="double" value=" 1" />
<Parameter name="first tip" type="Array(double)" value="{ 0, 0, 0}" />
<Parameter name="orientation" type="Array(double)" value="{ 0, 0, 1}" />
<Parameter name="first tip type" type="string" value="boundary" />
<Parameter name="last tip type" type="string" value="boundary" />
<Parameter name="cell lengths [m]" type="Array(double)" value="{3649.63,1805.57,1626.54,1613.26,1678.51,1801.08,1978.1,2215.79,2527.87,2937.04,3479.01,4210.42,5224.11,6679.84,8870.96,12384.6,18542.1,30867.6,61695.7,185036}" />
</ParameterList>
</ParameterList>
<ParameterList name="sets" type="ParameterList">
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="regions" type="ParameterList">
<ParameterList name="surface domain" type="ParameterList">
<ParameterList name="region: all" type="ParameterList">
</ParameterList>
</ParameterList>
<ParameterList name="hyporheic domain" type="ParameterList">
<ParameterList name="region: all" type="ParameterList">
</ParameterList>
</ParameterList>
<ParameterList name="tracer source surface" type="ParameterList">
<ParameterList name="region: enumerated set" type="ParameterList">
<Parameter name="entity" type="string" value="cell" />
<Parameter name="entity gids" type="Array(int)" value="{0}" />
</ParameterList>
</ParameterList>
<ParameterList name="tracer source subgrid" type="ParameterList">
<ParameterList name="region: enumerated set" type="ParameterList">
<Parameter name="entity" type="string" value="face" />
<Parameter name="entity gids" type="Array(int)" value="{0}" />
</ParameterList>
</ParameterList>
<ParameterList name="surface outlet" type="ParameterList">
<ParameterList name="region: enumerated set" type="ParameterList">
<Parameter name="entity" type="string" value="cell" />
<Parameter name="entity gids" type="Array(int)" value="{9}" />
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="cycle driver" type="ParameterList">
<Parameter name="end cycle" type="int" value="20000" />
<Parameter name="start time" type="double" value=" 0" />
<Parameter name="start time units" type="string" value="s" />
<Parameter name="end time" type="double" value=" 2" />
<Parameter name="end time units" type="string" value="d" />
<ParameterList name="PK tree" type="ParameterList">
<ParameterList name="coupler" type="ParameterList">
<Parameter name="PK type" type="string" value="weak MPC" />
<ParameterList name="surface transport" type="ParameterList">
<Parameter name="PK type" type="string" value="transport ATS" />
</ParameterList>
<ParameterList name="subgrid:*-coupler" type="ParameterList">
<Parameter name="PK type" type="string" value="domain set weak MPC" />
<ParameterList name="subgrid:*-transport" type="ParameterList">
<Parameter name="PK type" type="string" value="transport ATS" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="observations">
<ParameterList name="surface-component_concentration">
<Parameter name="variable" type="string" value="surface-total_component_concentration" />
<Parameter name="functional" type="string" value="point" />
<Parameter name="region" type="string" value="surface outlet" />
<Parameter name="delimiter" type="string" value=" " />
<Parameter name="location name" type="string" value="cell" />
<Parameter name="write interval" type="int" value="1" />
<Parameter name="observation output filename" type="string" value="surface-outlet.dat" />
<Parameter name="times start period stop" type="Array(double)" value="{ 0,3600,-1}" />
</ParameterList>
</ParameterList>
<ParameterList name="visualization" type="ParameterList">
<ParameterList name="surface" type="ParameterList">
<Parameter name="file name base" type="string" value="visdump" />
<Parameter name="times start period stop" type="Array(double)" value="{ 0,120,-1}" />
</ParameterList>
</ParameterList>
<ParameterList name="checkpoint" type="ParameterList">
<Parameter name="file name base" type="string" value="checkpoint" />
<Parameter name="times start period stop" type="Array(double)" value="{ 0,18000,-1}" />
</ParameterList>
<ParameterList name="PKs" type="ParameterList">
<ParameterList name="coupler" type="ParameterList">
<Parameter name="PK type" type="string" value="weak MPC" />
<Parameter name="PKs order" type="Array(string)" value="{surface transport, subgrid:*-coupler}" />
</ParameterList>
<ParameterList name="subgrid:*-coupler" type="ParameterList">
<Parameter name="PK type" type="string" value="domain set weak MPC" />
<Parameter name="PKs order" type="Array(string)" value="{subgrid:*-transport}" />
<Parameter name="entity kind" type="string" value="CELL" />
<Parameter name="parent domain" type="string" value="surface" />
<Parameter name="subgrid region name" type="string" value="surface domain" />
</ParameterList>
<ParameterList name="subgrid:*-transport" type="ParameterList">
<Parameter name="PK type" type="string" value="transport ats" />
<Parameter name="PK origin" type="string" value="Amanzi" />
<Parameter name="domain name" type="string" value="subgrid:*" />
<Parameter name="component names" type="Array(string)" value="{Tracer1}" />
<Parameter name="number of liquid components" type="int" value="1" />
<Parameter name="component molar masses" type="Array(double)" value="{ 1}" />
<Parameter name="spatial discretization order" type="int" value="1" />
<Parameter name="temporal discretization order" type="int" value="1" />
<Parameter name="cfl" type="double" value=" 1" />
<Parameter name="solver" type="string" value="PCG with Hypre AMG" />
<Parameter name="transport subcycling" type="bool" value="true" />
<Parameter name="number of aqueous components" type="int" value="1" />
<Parameter name="number of gaseous components" type="int" value="0" />
<Parameter name="runtime diagnostics: regions" type="Array(string)" value="{}" />
<ParameterList name="verbose object" type="ParameterList">
<Parameter name="verbosity level" type="string" value="none" />
<Parameter name="name" type="string" value="Transport" />
</ParameterList>
<ParameterList name="reconstruction" type="ParameterList">
<Parameter name="polynomial order" type="int" value="0" />
<Parameter name="limiter" type="string" value="tensorial" />
<Parameter name="limiter extension for transport" type="bool" value="true" />
</ParameterList>
<ParameterList name="boundary conditions" type="ParameterList">
<ParameterList name="concentration" type="ParameterList">
<ParameterList name="subgrid" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{tracer source subgrid}" />
<Parameter name="spatial distribution method" type="string" value="subgrid" />
<ParameterList name="boundary concentration" type="ParameterList">
<Parameter name="field_out_key" type="string" value="surface-total_component_concentration" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="initial condition" type="ParameterList">
<ParameterList name="function" type="ParameterList">
<ParameterList name="All" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{hyporheic domain}" />
<Parameter name="component" type="string" value="cell" />
<ParameterList name="function" type="ParameterList">
<Parameter name="number of dofs" type="int" value="1" />
<Parameter name="function type" type="string" value="composite function" />
<ParameterList name="dof 1 function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 0" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="surface transport" type="ParameterList">
<Parameter name="PK type" type="string" value="transport ats" />
<Parameter name="PK origin" type="string" value="Amanzi" />
<Parameter name="domain name" type="string" value="surface" />
<Parameter name="saturation liquid key suffix" type="string" value="ponded_depth" />
<Parameter name="component names" type="Array(string)" value="{Tracer1}" />
<Parameter name="number of liquid components" type="int" value="1" />
<Parameter name="component molar masses" type="Array(double)" value="{ 1}" />
<Parameter name="spatial discretization order" type="int" value="1" />
<Parameter name="temporal discretization order" type="int" value="1" />
<Parameter name="cfl" type="double" value=" 1" />
<Parameter name="solver" type="string" value="PCG with Hypre AMG" />
<Parameter name="transport subcycling" type="bool" value="true" />
<Parameter name="number of aqueous components" type="int" value="1" />
<Parameter name="number of gaseous components" type="int" value="0" />
<Parameter name="runtime diagnostics: regions" type="Array(string)" value="{}" />
<ParameterList name="verbose object" type="ParameterList">
<Parameter name="verbosity level" type="string" value="none" />
<Parameter name="name" type="string" value="Transport" />
</ParameterList>
<ParameterList name="reconstruction" type="ParameterList">
<Parameter name="polynomial order" type="int" value="0" />
<Parameter name="limiter" type="string" value="tensorial" />
<Parameter name="limiter extension for transport" type="bool" value="true" />
</ParameterList>
<ParameterList name="inverse">
<Parameter name="preconditioning method" type="string" value="boomer amg" />
<Parameter name="iterative method" type="string" value="pcg" />
<ParameterList name="boomer amg parameters">
<Parameter name="tolerance" type="double" value=" 0" />
<Parameter name="smoother sweeps" type="int" value="3" />
<Parameter name="cycle applications" type="int" value="5" />
<Parameter name="strong threshold" type="double" value="0.5" />
</ParameterList>
<ParameterList name="pcg parameters">
<Parameter name="maximum number of iterations" type="int" value="400" />
<Parameter name="error tolerance" type="double" value="1e-20" />
<Parameter name="convergence criteria" type="Array(string)" value="{relative rhs, make one iteration}" />
<Parameter name="size of Krylov space" type="int" value="5" />
<ParameterList name="verbose object">
<Parameter name="verbosity level" type="string" value="low" />
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="source terms" type="ParameterList">
<ParameterList name="component mass source" type="ParameterList">
<ParameterList name="SOURCE: Tracer" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{tracer source surface}" />
<Parameter name="spatial distribution method" type="string" value="volume" />
<Parameter name="component names" type="Array(string)" value="{Tracer1}" />
<ParameterList name="source function" type="ParameterList">
<ParameterList name="function-tabular" type="ParameterList">
<Parameter name="y values" type="Array(double)" value="{0.1, 0}" />
<Parameter name="x values" type="Array(double)" value="{ 0,86400}" />
<Parameter name="forms" type="Array(string)" value="{constant}" />
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="SINK: to subgrid" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{surface domain}" />
<Parameter name="spatial distribution method" type="string" value="first order exchange" />
<Parameter name="component names" type="Array(string)" value="{Tracer1}" />
<ParameterList name="source function" type="ParameterList">
<Parameter name="domain name" type="string" value="surface" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value="1.7e-05" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="SOURCE: from subgrid" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{surface domain}" />
<Parameter name="spatial distribution method" type="string" value="subgrid return" />
<Parameter name="component names" type="Array(string)" value="{Tracer1}" />
<ParameterList name="source function" type="ParameterList">
<Parameter name="subgrid field suffix" type="string" value="total_component_concentration" />
<Parameter name="domain subgrid field" type="string" value="subgrid" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value="1.7e-05" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="physical models and assumptions" type="ParameterList">
<Parameter name="effective transport porosity" type="bool" value="false" />
<Parameter name="permeability field is required" type="bool" value="false" />
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="state" type="ParameterList">
<Parameter name="domain sets" type="Array(string)" value="{subgrid}" />
<ParameterList name="evaluators" type="ParameterList">
<ParameterList name="surface-ponded_depth" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="surface domain" />
<Parameter name="components" type="Array(string)" value="{cell}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="surface-water_flux" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="surface domain" />
<Parameter name="components" type="Array(string)" value="{face}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value="-0.1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="surface-porosity" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="surface domain" />
<Parameter name="components" type="Array(string)" value="{cell}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="surface-molar_density_liquid" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="surface domain" />
<Parameter name="components" type="Array(string)" value="{cell}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="subgrid:*-saturation_liquid" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="hyporheic domain" />
<Parameter name="components" type="Array(string)" value="{cell}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="subgrid:*-water_flux" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="checkpoint" type="bool" value="true" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="hyporheic domain" />
<Parameter name="components" type="Array(string)" value="{face}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value="-1" />
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="top face" type="ParameterList">
<Parameter name="region" type="string" value="tracer source subgrid" />
<Parameter name="components" type="Array(string)" value="{face}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value="-1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="subgrid:*-porosity" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="domain" type="ParameterList">
<Parameter name="region" type="string" value="tau_space" />
<Parameter name="component" type="string" value="cell" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="verbose object" type="ParameterList">
<Parameter name="verbosity level" type="string" value="low" />
</ParameterList>
</ParameterList>
<ParameterList name="subgrid:*-molar_density_liquid" type="ParameterList">
<Parameter name="evaluator type" type="string" value="independent variable" />
<Parameter name="constant in time" type="bool" value="true" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="rest domain" type="ParameterList">
<Parameter name="region" type="string" value="hyporheic domain" />
<Parameter name="components" type="Array(string)" value="{cell}" />
<ParameterList name="function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 1" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
<ParameterList name="initial conditions" type="ParameterList">
<ParameterList name="atmospheric_pressure" type="ParameterList">
<Parameter name="value" type="double" value="101325" />
</ParameterList>
<ParameterList name="gravity" type="ParameterList">
<Parameter name="value" type="Array(double)" value="{ 0, 0,-9.80665}" />
</ParameterList>
<ParameterList name="surface-total_component_concentration" type="ParameterList">
<ParameterList name="function" type="ParameterList">
<ParameterList name="All" type="ParameterList">
<Parameter name="regions" type="Array(string)" value="{surface domain}" />
<Parameter name="component" type="string" value="cell" />
<ParameterList name="function" type="ParameterList">
<Parameter name="number of dofs" type="int" value="1" />
<Parameter name="function type" type="string" value="composite function" />
<ParameterList name="dof 1 function" type="ParameterList">
<ParameterList name="function-constant" type="ParameterList">
<Parameter name="value" type="double" value=" 0" />
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>