model_start.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_start.xml" />
    <xi:include href="morph_dend_single_spine.xml" />
    <xi:include href="IC_basal.xml" />

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
   
    <geometry>          2D           </geometry>
    <depth2D>           0.6          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245         </simulationSeed>
    <outputQuantity>NUMBER</outputQuantity>

    <!-- run time for the calculation, milliseconds -->
    <runtime>1000000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite">0.12</MaxElementSide>

	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->


    </discretization>

    <fixedStepDt>1</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.006</tolerance>

    <outputInterval>200</outputInterval>



    <calculation>GRID_ADAPTIVE</calculation>

</SDRun>