<?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_ERK-d.xml" />
          <xi:include href="../../../Morph.xml" />        
          <xi:include href="../../../IC_ERK_basald-R01.xml" />
          <xi:include href="../../../Out_ERK.xml" />
	   <xi:include href="../../Stim_ERK_Ca-C500-d1.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. depth 2D units are microns  -->
    <geometry>          2D           </geometry>
    <depth2D>           0.40          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    123       </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>          3600000      </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>8</defaultMaxElementSide> 
        
    <!-- surfaceLayers> 0.1 </surfaceLayers -->
    </discretization>

    <outputInterval>      2000.0   </outputInterval>

    <!-- the tolerace is used for adaptive sims -->
    <tolerance>           0.01       </tolerance>
    <!-- calculation types include
	 GRID_STEPPED_STOCHASTIC (old fixedStep tau-leap),
	 GRID_STEPPED_CONTINUOUS (deterministic), and
	 GRID_ADAPTIVE (new adaptive (asynchronous tau-leap).-->
    <calculation>GRID_ADAPTIVE</calculation>
</SDRun>