 <CompuCell3D>
 <Potts>
   <Dimensions x="40" y="40" z="40"/>
   <Anneal>0</Anneal>
   <Steps>20000</Steps>
   <Temperature>1</Temperature>
   <Offset>-0.1</Offset>
   <Flip2DimRatio>1.0</Flip2DimRatio>
 </Potts>

 <Plugin Name="PlayerSettings">
    <Project2D XYProj="5"/>
    <InitialProjection Projection="XY"/>
    <Rotate3D XRot="27" YRot="-11"/>
 </Plugin>


 <Plugin Name="Volume">
   <TargetVolume>68</TargetVolume>
   <LambdaVolume>8.5</LambdaVolume>
 </Plugin>


 <Plugin Name="Surface">
   <TargetSurface>104</TargetSurface>
   <LambdaSurface>0.1</LambdaSurface>
 </Plugin>

<!--
 <Plugin Name="VolumeFlex">
    <VolumeEnergyParameters CellType="Prestalk" TargetVolume="68" LambdaVolume="15"/>
    <VolumeEnergyParameters CellType="Prespore" TargetVolume="68" LambdaVolume="15"/>
    <VolumeEnergyParameters CellType="Autocycling" TargetVolume="68" LambdaVolume="15"/>
    <VolumeEnergyParameters CellType="Ground" TargetVolume="0" LambdaVolume="0"/>
    <VolumeEnergyParameters CellType="Wall" TargetVolume="0" LambdaVolume="0"/>
 </Plugin>


 <Plugin Name="SurfaceFlex">
    <SurfaceEnergyParameters CellType="Prestalk" TargetSurface="100" LambdaSurface="0.15"/>
    <SurfaceEnergyParameters CellType="Prespore" TargetSurface="100" LambdaSurface="0.15"/>
    <SurfaceEnergyParameters CellType="Autocycling" TargetSurface="100" LambdaSurface="0.15"/>
    <SurfaceEnergyParameters CellType="Ground" TargetSurface="0" LambdaSurface="0"/>    
    <SurfaceEnergyParameters CellType="Wall" TargetSurface="0" LambdaSurface="0"/>        
 </Plugin>

-->

 <Plugin Name="CellType">
    <CellType TypeName="Medium" TypeId="0"/>
    <CellType TypeName="Prestalk" TypeId="1"/>
    <CellType TypeName="Prespore" TypeId="2"/>
    <CellType TypeName="Autocycling" TypeId="3"/>
    <CellType  TypeName="Ground" TypeId="4" Freeze=""/>
    <CellType  TypeName="Wall" TypeId="5" Freeze="" />
 </Plugin>
 

 <Plugin Name="Contact">
 
   <Energy Type1="Autocycling" Type2="Autocycling"> 2.5 </Energy>
   <Energy Type1="Prestalk" Type2="Prestalk"> 3.5 </Energy>
   <Energy Type1="Prespore" Type2="Prespore"> 4 </Energy>
   <Energy Type1="Autocycling" Type2="Medium"> 3 </Energy>
   <Energy Type1="Prestalk" Type2="Medium"> 2 </Energy>
   <Energy Type1="Prespore" Type2="Medium"> 2 </Energy>
   <Energy Type1="Prestalk" Type2="Prespore"> 4 </Energy>
   <Energy Type1="Prestalk" Type2="Autocycling"> 4 </Energy>
   <Energy Type1="Prespore" Type2="Autocycling"> 4 </Energy> 
   <Energy Type1="Medium" Type2="Medium"> 0 </Energy>
  
   <Energy Type1="Ground" Type2="Ground">0</Energy>
   <Energy Type1="Ground" Type2="Medium">0</Energy>
   <Energy Type1="Ground" Type2="Autocycling">2.5</Energy>
   <Energy Type1="Ground" Type2="Prestalk">2.0</Energy>
   <Energy Type1="Ground" Type2="Prespore">2.0</Energy>

   <Energy Type1="Wall" Type2="Wall">0</Energy>
   <Energy Type1="Wall" Type2="Medium">0</Energy>
   <Energy Type1="Wall" Type2="Autocycling">20</Energy>
   <Energy Type1="Wall" Type2="Prestalk">20</Energy>
   <Energy Type1="Wall" Type2="Prespore">20</Energy>
   <Energy Type1="Wall" Type2="Ground">20</Energy>

<!--Current simulation -->
<!--
   <Energy Type1="Autocycling" Type2="Autocycling">3</Energy>
   <Energy Type1="Prestalk" Type2="Prestalk">3</Energy>
   <Energy Type1="Prespore" Type2="Prespore">3</Energy>
   <Energy Type1="Autocycling" Type2="Medium">2</Energy>
   <Energy Type1="Prestalk" Type2="Medium">2</Energy>
   <Energy Type1="Prespore" Type2="Medium">2</Energy>
   <Energy Type1="Prestalk" Type2="Prespore">4</Energy>
   <Energy Type1="Prestalk" Type2="Autocycling">4</Energy>
   <Energy Type1="Prespore" Type2="Autocycling">4</Energy> 
   <Energy Type1="Medium" Type2="Medium">0</Energy>
   <Energy Type1="Ground" Type2="Ground">0</Energy>
   <Energy Type1="Ground" Type2="Medium">1</Energy>
   <Energy Type1="Ground" Type2="Autocycling">2</Energy>
   <Energy Type1="Ground" Type2="Prestalk">2</Energy>
   <Energy Type1="Ground" Type2="Prespore">2</Energy>
 -->  
<!--   <Energy Type1="Water" Type2="Water">3</Energy>
   <Energy Type1="Water" Type2="Autocycling">4</Energy>
   <Energy Type1="Water" Type2="Prestalk">4</Energy>
   <Energy Type1="Water" Type2="Prespore">4</Energy>
   <Energy Type1="Water" Type2="Medium">4</Energy>
   <Energy Type1="Water" Type2="Ground">2</Energy>-->
   <Depth>2</Depth>
 </Plugin>

 <Plugin Name="CenterOfMass"/>
 
 <Plugin Name="SimpleClock"/>
    


<!-- <Plugin Name="MitosisBiofilm">
   <DoublingVolume>29</DoublingVolume>
 </Plugin>
-->

 <Plugin Name="ChemotaxisDicty">
   <Lambda> 200 </Lambda>
   <ChemicalField Source="ReactionDiffusionSolverFE_SavHog">cAMP</ChemicalField>
 </Plugin>


<!--
  <Plugin Name="CellVelocity">
    <VelocityDataHistorySize>5</VelocityDataHistorySize>
    <EnoughDataThreshold>3</EnoughDataThreshold>
  </Plugin>
-->


<!-- <Plugin Name="Concentration"/> -->



<!-- <Steppable Type="OutputData"/>-->

<!-- DiffusionSolverBiofilmFE has to be declared before BlobField initializer so that the field of concentration is non zero already-->
<!-- It has also be declared before TargetVolumeBiofilm as DiffusionSolverBiofilmFE updates cumulative concentration -->
<!--based on which TargetVolumeBiofilm decides what to with a cell-->



 <Steppable Type="DictyInitializer">
   <Gap>1</Gap>
   <Width>4</Width>
<!--   <AmoebaeFieldBorder>73</AmoebaeFieldBorder>-->
   <ZonePoint x="14" y="14" z="3" >10</ZonePoint>
   <PresporeRatio>0.8</PresporeRatio>
 </Steppable>


 <Steppable Type="ReactionDiffusionSolverFE_SavHog">
    <NumberOfFields>3</NumberOfFields>
    <FieldName>cAMP</FieldName>
    <FieldName>Refractoriness</FieldName>
    <DeltaX>0.37</DeltaX>
    <DeltaT>0.01</DeltaT>
    <DiffusionConstant>1.0</DiffusionConstant>
    <DecayConstant>0.0</DecayConstant>
    <MaxDiffusionZ>8</MaxDiffusionZ>
    <IntervalParameters c1="0.0065" c2="0.841"/>
    <fFunctionParameters C1="20" C2="3" C3="15" a="0.15"/>
    <epsFunctionParameters eps1="0.5" eps2="0.0589" eps3="0.5"/>
    <RefractorinessParameters k="3.5" b="0.35"/>
    <MinDiffusionBoxCorner x="0" y="0" z="0"/>
    <MaxDiffusionBoxCorner x="40" y="40" z="8"/> 
    <!-- to get spirals set z=5
    <MaxDiffusionBoxCorner x="40" y="40" z="5"/>     
    -->
 </Steppable>

 <Steppable Type="DictyChemotaxisSteppable">
    <ClockReloadValue>850</ClockReloadValue>
    <ChemotactUntil>750</ChemotactUntil>
    <IgnoreFirstSteps>500</IgnoreFirstSteps>
    <ChetmotaxisActivationThreshold>0.2</ChetmotaxisActivationThreshold>
    <ChemicalField Source="ReactionDiffusionSolverFE_SavHog">cAMP</ChemicalField>
 </Steppable>



<!--
 <Steppable Type="CellVelocity">
    <UpdateFrequency>2</UpdateFrequency>
 </Steppable>
-->


<!--
 <Steppable Type="UniformInitializer">
   <Gap>0</Gap>
   <Width>3</Width>
 </Steppable>
-->

<!--
 <Steppable Type="TargetVolumeBiofilm">
    <DivideThreshold>9.0</DivideThreshold>
    <DieThreshold>7.0</DieThreshold>
    <InitialTargetVolume>27</InitialTargetVolume>
    <InitialTargetSurface>45</InitialTargetSurface>
    <MitosisBoostFactor>1.2</MitosisBoostFactor>
    <OuterDieRadius>48</OuterDieRadius>
 </Steppable>
-->
<!--
 <FieldRenderer Type="Default">
   <CellVisual>
     <Red>10</Red>
     <Green>10</Green>
     <Blue>200</Blue>
     <Opacity>10</Opacity>
   </CellVisual>
 </FieldRenderer>

 <FieldRenderer Type="CenterOfMassType" Frequency="1000">
   <Surface Type="NonCondensing">
     <Red>10</Red>
     <Green>10</Green>
     <Blue>200</Blue>
     <Opacity>100</Opacity>
   </Surface>

   <Surface Type="Condensing">
     <Red>200</Red>
     <Green>10</Green>
     <Blue>10</Blue>
     <Opacity>100</Opacity>
   </Surface>

   <Center>
     <Red>10</Red>
     <Green>200</Green>
     <Blue>10</Blue>
     <Opacity>100</Opacity>
   </Center>
 </FieldRenderer>

 <Steppable Type="OgleDumper" Frequency="1000">
   <Renderer>CenterOfMassType</Renderer>
   <FilePrefix>cellsort</FilePrefix>
 </Steppable>
 -->
</CompuCell3D>
