MSPNmodel_A_5DaStim_12spine_newa50_long.xml

<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>        MSPNreactions_12spine_new50             </reactionSchemeFile>
    <morphologyFile>            MSPNmorph_12spine_long                  </morphologyFile>
    <stimulationFile>           MSPNstim_5DaStim_12spine_50_long        </stimulationFile>
    <initialConditionsFile>     MSPNic_A_12spine_new_long               </initialConditionsFile>
    <outputSchemeFile>          MSPNio_12spine_newmorph_long            </outputSchemeFile>

    <!--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>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    0000123      </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>          500000         </runtime>
<!-- 100001 -->
    <!-- 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="dend1">  0.20    </MaxElementSide>
       <MaxElementSide region="dend1a"> 0.20    </MaxElementSide>
       <MaxElementSide region="dend2">  0.20    </MaxElementSide>
       <MaxElementSide region="dend3">  0.20    </MaxElementSide>
       <MaxElementSide region="dend3a"> 0.20    </MaxElementSide>
       <MaxElementSide region="dend4">  0.20    </MaxElementSide>
       <MaxElementSide region="dend4a"> 0.20    </MaxElementSide>
       <MaxElementSide region="dend5">  0.20    </MaxElementSide>
       <MaxElementSide region="dend6">  0.20    </MaxElementSide>
       <MaxElementSide region="dend6a"> 0.20    </MaxElementSide>
       <MaxElementSide region="dend7">  0.20    </MaxElementSide>
       <MaxElementSide region="dend7a"> 0.20    </MaxElementSide>
       <MaxElementSide region="dend8">  0.20    </MaxElementSide>
       <MaxElementSide region="dend9">  0.20    </MaxElementSide>
       <MaxElementSide region="dend9a"> 0.20    </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 -->


<!--
        <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>      3000000.0   </outputInterval>

    <!-- the tolerace is not used yet -->
    <tolerance>           0.001       </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>

</SDRun>