growth_cone_proto_dyk.xml

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<SDRun xmlns:xi="http://www.w3.org/2001/XInclude" xmlns="http://stochdiff.textensor.org">
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <xi:include href="Rxn_IP3R_DYK.xml" />
          <xi:include href="growth_cone_morph_no_spines.xml" />
	  <xi:include href="growth_cone_ic_dyk.xml" />       
          <!--<xi:include href="IO.xml" />-->
 	  <!--<xi:include href="Stim_ACh.xml" />-->

    <!--2D means the morphology is interpreted like a flatworm, 3D for
	roundworms. The 2D case is good for testing as it is eas/Stry to visualize the
results (also, 3D may not work yet...)  -->
    <geometry>          2D           </geometry>
    <depth2D>           .4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    124       </simulationSeed>
    <outputQuantity>NUMBER</outputQuantity>


    <!-- run time for the calculation, milliseconds -->
    <runtime>          300000         </runtime>
<!-- 100001 -->
    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>          450          </spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
      
        <defaultMaxElementSide>.6</defaultMaxElementSide>
       <!--<MaxElementSide region="axon">1.5</MaxElementSide>-->
	<!-- discretization for spines, microns -->
	<!--<spineDeltaX>   1.0          </spineDeltaX>-->
	<surfaceLayers>0.4,0.4</surfaceLayers> 
	<!-- This specifies the surface layers, first implemented in v.2.1.7 -->
	<!--surfaceLayers>0.1,0.2</surfaceLayers-->

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds -->
    <fixedStepDt>         0.005       </fixedStepDt>

    <!-- interval at which stuff should be saved to the output file(s) -->
    <outputInterval>      200.0   </outputInterval>

    <!-- the tolerace is used for adaptive sims -->
    <tolerance>           0.005       </tolerance>
    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <!--calculation>GRID_STEPPED_STOCHASTIC</calculation-->
    <!--use the following for adaptive: -->
    <calculation>GRID_ADAPTIVE</calculation>

</SDRun>