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Merge pull request #223 from kreft/final-protocols
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Manuscript protocols
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@bascee
bascee authored Nov 9, 2023
2 parents 1399a19 + d9e4499 commit 3607a3a
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214 changes: 214 additions & 0 deletions protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml
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<?xml version="1.0" encoding="UTF-8"?>
<document>
<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
comment="this is a file for testing purposes only.">
<!-- minutes -->
<timer stepSize="12.0" endOfSimulation="120.0[day]" />
<speciesLib>
<species name="heterotroph">
<speciesModule name="coccoid" />
<aspect name="reactions" type="PRIMARY" class="InstantiableList">
<list class="RegularReaction" nodeLabel="reaction"
entryClass="RegularReaction" keyClass="String" keyLabel="name">
<reaction name="hetGrowth">
<expression value="biomass * mumax *
( COD / ( COD + KS ) ) *
( ( oxygen / ( oxygen + Kox ) )">
<!-- pg/µm3 -->
<constant name="KS" value="4.0e-6" />
<constant name="Kox" value="2.0e-7" />
<!-- per minute -->
<constant name="mumax" value="0.004167" />
</expression>
<stoichiometric component="biomass" coefficient="1.0" />
<stoichiometric component="COD" coefficient="-1.5873" />
<stoichiometric component="oxygen" coefficient="-0.5873" />
</reaction>
<reaction name="hetInactivation">
<expression value="inactivationRate * biomass">
<!-- per minute -->
<constant name="inactivationRate" value="5.556e-5" />
</expression>
<stoichiometric component="biomass" coefficient="-1.0" />
<stoichiometric component="inert" coefficient="1.0" />
</reaction>
<reaction name="hetRespiration">
<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
<!-- pg/µm3 -->
<constant name="respirationRate" value="2.222e-4" />
<constant name="Kox" value="2.0e-7" />
</expression>
<stoichiometric component="biomass" coefficient="-1.0" />
<stoichiometric component="oxygen" coefficient="-1.0" />
</reaction>
</list>
</aspect>
</species>

<species name="autotroph">
<speciesModule name="coccoid" />
<aspect name="reactions" type="PRIMARY" class="InstantiableList">
<list class="RegularReaction" nodeLabel="reaction"
entryClass="RegularReaction" keyClass="String" keyLabel="name">
<reaction name="autGrowth">
<expression value="biomass * mumax *
( ammonium / ( ammonium + KN ) ) *
( ( oxygen / ( oxygen + Kox ) )">
<!-- pg/µm3 -->
<constant name="KN" value="1.0e-6" />
<constant name="Kox" value="5.0e-7" />
<!-- per minute -->
<constant name="mumax" value="6.95e-4" />
</expression>
<stoichiometric component="biomass" coefficient="1.0" />
<stoichiometric component="oxygen" coefficient="-18.0417" />
<stoichiometric component="ammonium" coefficient="-4.1667" />
</reaction>
<reaction name="autInactivation">
<expression value="inactivationRate * biomass">
<!-- per minute -->
<constant name="inactivationRate" value="2.083e-5" />
</expression>
<stoichiometric component="biomass" coefficient="-1.0" />
<stoichiometric component="inert" coefficient="1.0" />
</reaction>
<reaction name="autRespiration">
<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
<!-- pg/µm3 -->
<constant name="respirationRate" value="8.333e-5" />
<constant name="Kox" value="5.0e-7" />
</expression>
<stoichiometric component="biomass" coefficient="-1.0" />
<stoichiometric component="oxygen" coefficient="-1.0" />
</reaction>
</list>
</aspect>
</species>

<species name="coccoid">
<!-- pg / µm^3-->
<aspect name="density" type="PRIMARY" class="Double" value="1.008e-2" />
<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
<aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" />
<aspect name="morphology" type="PRIMARY" class="String" value="coccoid" />
<aspect name="volume" type="CALCULATED" class="SimpleVolumeState" />
<aspect name="radius" type="CALCULATED" class="CylinderRadius" />
<aspect name="divide" type="EVENT" class="CoccoidDivision" />
<!-- Dry division mass (pg) -->
<aspect name="divisionMass" class="Double" value="4.0" />
<aspect name="updateBody" type="EVENT" class="UpdateBodySurfaceScaled" />
<aspect name="evaluatePull" type="EVENT" class="ResolveInteractionDistance" />
<!-- µm -->
<aspect name="searchDist" type="PRIMARY" class="Double" value="0.0" />
</species>
</speciesLib>
<compartment name="chemostat">
<shape class="Dimensionless" volume="4.0e6">
<boundary class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
<solute name="ammonium" concentration="3.0E-5"/>
<solute name="oxygen" concentration="1.0E-5"/>
<solute name="COD" concentration="3.0E-5" />
</boundary>
<boundary class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
</boundary>
</shape>
<solutes>
<!-- pg / µm3 -->
<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556" />
<solute name="oxygen" concentration="1.0E-5" defaultDiffusivity="138888.889" />
<solute name="COD" concentration="3.0E-5" defaultDiffusivity="69444.444" />
</solutes>
<processManagers>
<process name="solveChemostat" class="ChemostatSolver" priority="0"
firstStep="0.0">
<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
<aspect name="solver" type="PRIMARY" class="String" value="heun" />
<aspect name="tolerance" class="Double" value="1.0E-6" />
</process>
<process name="summary" class="Summary" priority="2"
firstStep="0.0" timerStepSize="240.0">
<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_1" />
<aspect name="tableSpecification" type="PRIMARY" class="String"
value="%COD | %ammonium" />
<aspect name="fileName" type="PRIMARY" class="String" value="data" />
</process>
</processManagers>
</compartment>
<compartment name="biofilm">
<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
<!-- µm -->
<dimension name="X" isCyclic="true" targetResolution="20.0" max="320.0"/>
<dimension name="Y" isCyclic="false" targetResolution="20.0" max="640.0">
<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
</dimension>
</shape>
<solutes>
<!-- Initial concentrations pg / µm2 -->
<solute name="COD" concentration="3e-5" defaultDiffusivity="69444.444" />
<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"/>
<solute name="oxygen" concentration="1e-5" defaultDiffusivity="138888.889"/>
</solutes>
<reactions>
</reactions>
<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
<templateAgent>
<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
<aspect name="mass" class="InstantiableMap">
<map entryClass="Double" keyType="String">
<item key="biomass" value="10.0" />
<item key="inert" value="0.0" />
</map>
</aspect>
</templateAgent>
</spawn>
<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
<templateAgent>
<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
<aspect name="mass" class="InstantiableMap">
<map entryClass="Double" keyType="String">
<item key="biomass" value="10.0" />
<item key="inert" value="0.0" />
</map>
</aspect>
</templateAgent>
</spawn>
<processManagers>
<!-- minute -->
<process name="agentRelax" class="AgentRelaxation" priority="0"
firstStep="0.0">
<!-- µm -->
<aspect name="maxMovement" type="PRIMARY" class="Double" value="6.0" />
<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
<aspect name="maxAgentOverlap" class="Double" value="3.0" />
</process>
<!-- minute -->
<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
<aspect name="vCycles" class="Integer" value="100" />
<aspect name="preSteps" class="Integer" value="20" />
<aspect name="coarseSteps" class="Integer" value="10" />
<aspect name="postSteps" class="Integer" value="30" />
<aspect name="autoVcycleAdjust" class="Boolean" value="true" />

<!-- µm^2 ms^-1-->
</process>
<process name="scrape" class="AgentScraper" priority="-2"
firstStep="0.0">
<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
</process>
<process name="summary" class="Summary" priority="2"
firstStep="0.0" timerStepSize="240.0">
<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_1_EULER_d_1.008" />
<aspect name="tableSpecification" type="PRIMARY" class="String"
value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
<aspect name="fileName" type="PRIMARY" class="String" value="data" />
</process>
</processManagers>
</compartment>
</simulation>
</document>
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