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

    <reactionSchemeFile>Reac_gradedkdiff_PKAc_times_3_gigs_switching_L_pump_neurogranin</reactionSchemeFile>
    <morphologyFile>morph_dend_0.2um_0.1_diameter_with_spine_and_injection_spines</morphologyFile>
    <stimulationFile>Stim_ISO_bath_3_min_5_Hz_L_pump_higher_Ca_1000_nM.xml</stimulationFile>
    <initialConditionsFile>IC_switching_steady_L_pump_neurogranin_2.0_x_PDE4_AC</initialConditionsFile>
    <outputSchemeFile>../Model_one_short_dendrite_PKAc_times_3_switching_L_pump_neurogranin_2.0_4_trains_massed_whole_output</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>    245         </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>20000</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>.0029</fixedStepDt>


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

    <outputInterval>1000</outputInterval>



    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
