UchiModel12mar20desen025lowrG_5s5dhpg20sCa12-3.xml

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

    <reactionSchemeFile>mglu_2ag_reac12mar20desens025</reactionSchemeFile>
    <morphologyFile>       mglur_morph                      </morphologyFile>
    <stimulationFile>      UchiStim5s5dhpg20sCa12-3-3-2-2 </stimulationFile>
    <initialConditionsFile>mglur_2ag_init12mar1lowrGabg</initialConditionsFile>
    <outputSchemeFile>     mglur_outPIKnewCaM               </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>           2.0          </depth2D> -->
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    971263          </simulationSeed>
    <outputQuantity>NUMBER</outputQuantity>

    <!-- run time for the calculation, milliseconds.  200 s for initial sims, 350 s later -->
    <runtime>          40000       </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 -->	
<!-- Use 0.2 for rough tuning the model 
	<defaultMaxElementSide>0.2</defaultMaxElementSide> -->
<!-- make it 0.15 once rates and init values are close -->
	<defaultMaxElementSide>0.15</defaultMaxElementSide>
        
	<!-- 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="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->

    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds -->
    <fixedStepDt>         0.0025       </fixedStepDt>

    <outputInterval>1000</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>