Model_simple.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_glubuf.xml" />
    <xi:include href="Morph1.5um.xml" />
    <xi:include href="IC_glubuf.xml" />
  <StimulationSet>
    <InjectionStim specieID="glu"  injectionSite="pointA">
        <onset>               100        </onset>
        <duration>            10        </duration>
        <rate>                6.25         </rate>
    </InjectionStim>
    <InjectionStim specieID="buf"  injectionSite="pointA">
        <onset>               200        </onset>
        <duration>            10        </duration>
        <rate>                6.2          </rate>
    </InjectionStim>
  </StimulationSet>

    <!--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  -->
    <geometry>          2D           </geometry>
    <depth2D>           0.6         </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
<!--    <simulationSeed>    971263          </simulationSeed>-->


    <!-- run time for the calculation, milliseconds -->
    <runtime>          1000       </runtime>
    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>        9897623       </spineSeed>

    <discretization>
        <!-- default largest size for elements in bulk volumes (dendrites), microns -->
        <defaultMaxElementSide> 1.0  </defaultMaxElementSide>

    </discretization>

    <outputInterval>      2.0   </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>