 <CompuCell3D>
 <Potts>
   <Dimensions x="50" y="55" z="50"/>
   <Anneal>0</Anneal>
   <Steps>1000</Steps>
   <Temperature>15</Temperature>
   <Flip2DimRatio>1.0</Flip2DimRatio>
   <Boundary_y>Periodic</Boundary_y>
 </Potts>

 <Plugin Name="Volume">
   <TargetVolume>256</TargetVolume>
   <LambdaVolume>15.0</LambdaVolume>
 </Plugin>

 <Plugin Name="Surface">
   <TargetSurface>260</TargetSurface>
   <LambdaSurface>2.0</LambdaSurface>
 </Plugin>

<Plugin Name="CellType">
    <CellType TypeName="Medium" TypeId="0"/>
    <CellType TypeName="Amoeba" TypeId="1"/>
    <CellType TypeName="Bacteria" TypeId="2"/>
 </Plugin>


<!--
 <Plugin Name="Contact">
   <Energy Type1="Medium" Type2="Medium">0</Energy>
   <Energy Type1="Amoeba" Type2="Amoeba">15</Energy>
   <Energy Type1="Amoeba" Type2="Medium">8</Energy>
   <Depth>2</Depth>
 </Plugin>
-->

 <Plugin Name="ContactFlex">
   <Energy Type1="Medium" Type2="Medium">0</Energy>
   <Energy Type1="Amoeba" Type2="Amoeba">15</Energy>
   <Energy Type1="Amoeba" Type2="Medium">8</Energy>
   <Energy Type1="Bacteria" Type2="Bacteria">15</Energy>
   <Energy Type1="Bacteria" Type2="Amoeba">15</Energy>
   <Energy Type1="Bacteria" Type2="Medium">8</Energy>   
   <Depth>2</Depth>
   <Haptotaxis Source="FlexibleDiffusionSolverFE" Name="FGF" HaptotactingTypes="Medium,Amoeba">1.0</Haptotaxis>
 </Plugin>


 <Plugin Name="CenterOfMass"/>




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

 <Plugin Name="Chemotaxis">
   <ChemicalField Source="FlexibleDiffusionSolverFE" Name="FGF">100</ChemicalField>
   <ChemicalField Source="FlexibleDiffusionSolverFE" Name="FGF8">500</ChemicalField>
 </Plugin>


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

<!-- <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="FlexibleDiffusionSolverFE">
     <DiffusionField>
        <DiffusionData>
	    <FieldName>FGF8</FieldName>
	    <DiffusionConstant>0.0</DiffusionConstant>
	    <DecayConstant>0.000</DecayConstant>
	    <DeltaT>0.1</DeltaT>
	    <DeltaX>1.0</DeltaX>
	    <!--<DoNotDiffuseTo>Amoeba</DoNotDiffuseTo>	-->	    
	</DiffusionData>
	<SecretionData>
	    <Secretion Type="Amoeba">0.1</Secretion>
	</SecretionData>
    </DiffusionField>    
    
    <DiffusionField>
	<DiffusionData>
	    <FieldName>FGF</FieldName>
	    <DiffusionConstant>0.00</DiffusionConstant>
	    <DecayConstant>0.000</DecayConstant>
	    <DeltaT>0.01</DeltaT>
	    <DeltaX>0.1</DeltaX>
<!--	    <DoNotDiffuseTo>Amoeba</DoNotDiffuseTo> -->
	</DiffusionData>
	<SecretionData>
	    <!--<SecretionOnContact Type="Amoeba" SecreteOnContactWith="Medium">0.00</SecretionOnContact>-->
	    <SecretionOnContact Type="Medium" SecreteOnContactWith="Amoeba">0.1</SecretionOnContact>
	    <Secretion Type="Amoeba">0.1</Secretion>
	</SecretionData>
    </DiffusionField>
    

 </Steppable>




 <Steppable Type="AmoebaeInitializer">
    <Radius>3</Radius>
    <Position x="10" y="5" z="10"/>
 </Steppable>

<!--
 <Steppable Type="CellVelocity">
    <NumberOfCOMPoints> 4 </NumberOfCOMPoints> 
    <EnoughDataThreshold> 2 </EnoughDataThreshold> 
 </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>
