%------------------------------------------------------------------------------------------
%
% Title:    Calcium Signals in Small Structures
% Filename: CaSignal_XDiffKOnSphere.par
% Author:   Ronald van Elburg 
%
%
% Associated Paper:
% Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007) 
% High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: 
% Consequences for Spine Calcium Kinetics and Buffer Capacity. 
% PLoS ONE 2(10): e1073 doi:10.1371/journal.pone.0001073
%
%------------------------------------------------------------------------------------------
Structure           = Sphere_Structure% Make it a sphere
Ca.D        =   D_Calcium*XDiff
Dye.D       =   D_Dye*XDiff         

path = ".\"         % If running under Windows, specify here the path to the
                                    % directory containing the script imported below
file = path "CaSignal_main.par"

include file                        % Import the simulation parameters from the main script


% Auxilary variables for monitoring concentrations at different distances from the membrane

    NoOfSteps = 6    % number of shells in the output (NOT IN THE SIMULATION, THERE THE GRIDSIZE DEFINES THE COMPARTMENTS)
    dR=R_Structure/NoOfSteps
    
    R1k=(NoOfSteps-0.5)*dR
    R6k=(NoOfSteps-5.5)*dR
    
    Ca1 := Ca[R1k] ; Dye1 := Dye[R1k] 
    Ca6 := Ca[R6k] ; Dye6 := Dye[R6k] 

    CaAverage:=Ca[] ; DyeAverage:=Dye[]

% Exporting the variables defined above to file
    Exp='XDiffKOn'
    LoopVar=XDiff*100
    LoopVar2=KPlus_Dye*1000
    Geom='S'
    %print stdout Ca.D ": " Dye.D
    plot point.mute  Ca1 "Output\Exp""Exp""\CSE""Exp""Geom""_Ca1_""LoopVar""_""LoopVar2"
    plot point.mute  Ca6 "Output\Exp""Exp""\CSE""Exp""Geom""_Ca6_""LoopVar""_""LoopVar2"
    plot point.mute  CaAverage "Output\Exp""Exp""\CSE""Exp""Geom""_CaAverage_""LoopVar""_""LoopVar2"
    
    plot point.mute  Dye1 "Output\Exp""Exp""\CSE""Exp""Geom""_Dye1_""LoopVar""_""LoopVar2"
    plot point.mute  Dye6 "Output\Exp""Exp""\CSE""Exp""Geom""_Dye6_""LoopVar""_""LoopVar2"
    plot point.mute  DyeAverage "Output\Exp""Exp""\CSE""Exp""Geom""_DyeAverage_""LoopVar""_""LoopVar2"

% Parameter variation
    for XDiff      = 0.05 to 2 step 0.05
    for KPlus_Dye  = 0.025  to  1   step 0.025

% The adaptive integration method fails for the fast calcium change
% to overcome this problem we run the first 20 ms with a fixed timestep 
% of 0.001 ms, then after the fast changes we switch to the adaptive method 
% for optimal performance.

Run  20.0  1.0e-3 ; current CalciumCurrent

Run  adaptive 480.0  1.0e-3 accuracy; current CalciumCurrent