function m = gpt_demosubdivision_20121116( m )
%m = gpt_demosubdivision_20121116( m )
%   Morphogen interaction function.
%   Written at 2012-11-16 11:02:05.
%   GFtbox revision 4351, .

% The user may edit any part of this function between delimiters
% of the form "USER CODE..." and "END OF USER CODE...".  The
% delimiters themselves must not be moved, edited, deleted, or added.

    if isempty(m), return; end

    fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );

    try
        m = local_setproperties( m );
    catch
    end

    realtime = m.globalDynamicProps.currenttime;

%%% USER CODE: INITIALISATION

% In this section you may modify the mesh in any way whatsoever.
    if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration
        % Zero out a lot of stuff to create a blank slate.  
        % If no morphogens are set in the GUI it may be useful to
        % zero some arrays by uncommenting the following.
        % m.morphogens(:) = 0;
        % m.morphogenclamp(:) = 0;
        % m.mgen_production(:) = 0;
        % m.mgen_absorption(:) = 0;
        % m.seams(:) = false;
        % m.mgen_dilution(:) = false;

        % Set up names for variant models.  Useful for running multiple models on a cluster.
        m.userdata.ranges.modelname.range = { 'NOSUBDIVISION', 'WITHSUBDIVISION' };  % CLUSTER
        m.userdata.ranges.modelname.index = 2;                       % CLUSTER
    end
    modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index};  % CLUSTER
    
    disp(sprintf('\nRunning %s model %s\n',mfilename, modelname));    	
    % to plot polariser on the A side and resultant areal growth rate on the B side:
    m = leaf_plotoptions( m, 'morphogenA', 'KAPAR', 'morphogenB', 'KBPAR' ); 
%%% END OF USER CODE: INITIALISATION

%%% SECTION 1: ACCESSING MORPHOGENS AND TIME.
%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.

    if isempty(m), return; end

    setGlobals();
    global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
    global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
    dt = m.globalProps.timestep;
    polariser_i = gNEW_POLARISER;
    P = m.morphogens(:,polariser_i);
    [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
    [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
    [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
    [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
    [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
    [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
    [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
    [id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
    [id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );
    [id_subdivide_i,id_subdivide_p,id_subdivide_a,id_subdivide_l] = getMgenLevels( m, 'ID_SUBDIVIDE' );

% Mesh type: rectangle
%            base: 0
%          centre: 0
%      randomness: 0.1
%         version: 1
%           xdivs: 16
%          xwidth: 16
%           ydivs: 8
%          ywidth: 8

%            Morphogen    Diffusion   Decay   Dilution   Mutant
%            --------------------------------------------------
%                KAPAR         ----    ----       ----     ----
%                KAPER         ----    ----       ----     ----
%                KBPAR         ----    ----       ----     ----
%                KBPER         ----    ----       ----     ----
%                 KNOR         ----    ----       ----     ----
%            POLARISER         ----    ----       ----     ----
%            STRAINRET         ----    ----       ----     ----
%               ARREST         ----    ----       ----     ----
%                 ID_A         ----    ----       ----     ----
%                 ID_B         ----    ----       ----     ----
%         ID_SUBDIVIDE         ----    ----       ----     ----


%%% USER CODE: MORPHOGEN INTERACTIONS

% In this section you may modify the mesh in any way that does not
% alter the set of nodes.

    if (Steps(m)==0) && m.globalDynamicProps.doinit  % Initialisation code.
        % Put any code here that should only be performed at the start of
        % the simulation, for example, to set up initial morphogen values.
        id_a_p((m.nodes(:,1)>0)&(m.nodes(:,1)<=2))=1;
        id_b_p((m.nodes(:,1)>-2)&(m.nodes(:,1)<=0))=1;
        id_subdivide_p((m.nodes(:,1)>=-2)&(m.nodes(:,1)<=2))=1;
        P=m.nodes(:,1);
    end
    if realtime<=1
        kapar_p(:) = 0;
        kaper_p(:) = 0;
        kbpar_p(:) = 0;
        kbper_p(:) = 0;
        knor_p(:)  = 0;
    else
        kapar_p(:) = 0.05*id_a_p;
        kaper_p(:) = 0;
        kbpar_p(:) = 0.05*id_b_p;
        kbper_p(:) = 0;
        knor_p(:)  = 0;
    end
%%% END OF USER CODE: MORPHOGEN INTERACTIONS

%%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE
%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
    m.morphogens(:,polariser_i) = P;
    m.morphogens(:,kapar_i) = kapar_p;
    m.morphogens(:,kaper_i) = kaper_p;
    m.morphogens(:,kbpar_i) = kbpar_p;
    m.morphogens(:,kbper_i) = kbper_p;
    m.morphogens(:,knor_i) = knor_p;
    m.morphogens(:,strainret_i) = strainret_p;
    m.morphogens(:,arrest_i) = arrest_p;
    m.morphogens(:,id_a_i) = id_a_p;
    m.morphogens(:,id_b_i) = id_b_p;
    m.morphogens(:,id_subdivide_i) = id_subdivide_p;

%%% USER CODE: FINALISATION

% In this section you may modify the mesh in any way whatsoever.
    switch modelname
        case 'NOSUBDIVISION' 
            % do nothing
        case 'WITHSUBDIVISION' 
            % subdivide on the first step
            if realtime>0 && realtime<=0+dt
                m = leaf_subdivide( m, 'morphogen','id_subdivide',...
                    'min',0.5,'max',1,...
                    'mode','mid','levels','all');
            end
            if realtime>0 && realtime<=0+dt
                m = leaf_subdivide( m, 'morphogen','id_subdivide',...
                    'min',0.5,'max',1,...
                    'mode','mid','levels','all');
            end
        otherwise
            % If this happens, maybe you forgot a model.
    end

    % If needed force FE to subdivide (increase number FE's) here
    % if realtime==280+dt
         % m = leaf_subdivide( m, 'morphogen','id_vent',...
         %       'min',0.5,'max',1,...
         %       'mode','mid','levels','all');
    % end
% Cut the mesh along the seams (see above)
    % if m.userdata.CutOpen==1
    %    m=leaf_dissect(m);
    %    m.userdata.CutOpen=2;        
    %    Relax accumulated stresses slowly i.e. 0.95 to 0.999
    %    m = leaf_setproperty( m, 'freezing', 0.999 );
    % end
%%% END OF USER CODE: FINALISATION

end


%%% USER CODE: SUBFUNCTIONS

function m = local_setproperties( m )
% This function is called at time zero in the INITIALISATION section of the
% interaction function.  It provides commands to set each of the properties
% that are contained in m.globalProps.  Uncomment whichever ones you would
% like to set yourself, and put in whatever value you want.
%
% Some of these properties are for internal use only and should never be
% set by the user.  At some point these will be moved into a different
% component of m, but for the present, just don't change anything unless
% you know what it is you're changing.

%    m = leaf_setproperty( m, 'trinodesvalid', true );
%    m = leaf_setproperty( m, 'prismnodesvalid', true );
%    m = leaf_setproperty( m, 'thicknessRelative', 1.600000 );
%    m = leaf_setproperty( m, 'thicknessArea', 0.000000 );
%    m = leaf_setproperty( m, 'thicknessMode', 'physical' );
%    m = leaf_setproperty( m, 'activeGrowth', 1.000000 );
%    m = leaf_setproperty( m, 'displayedGrowth', 1.000000 );
%    m = leaf_setproperty( m, 'displayedMulti', [] );
%    m = leaf_setproperty( m, 'allowNegativeGrowth', true );
%    m = leaf_setproperty( m, 'usePrevDispAsEstimate', true );
%    m = leaf_setproperty( m, 'perturbInitGrowthEstimate', 0.000010 );
%    m = leaf_setproperty( m, 'perturbRelGrowthEstimate', 0.010000 );
%    m = leaf_setproperty( m, 'perturbDiffusionEstimate', 0.000100 );
%    m = leaf_setproperty( m, 'resetRand', false );
%    m = leaf_setproperty( m, 'mingradient', 0.000000 );
%    m = leaf_setproperty( m, 'relativepolgrad', false );
%    m = leaf_setproperty( m, 'usefrozengradient', true );
%    m = leaf_setproperty( m, 'userpolarisation', false );
%    m = leaf_setproperty( m, 'thresholdsq', 4.000000 );
%    m = leaf_setproperty( m, 'splitmargin', 1.400000 );
%    m = leaf_setproperty( m, 'splitmorphogen', '' );
%    m = leaf_setproperty( m, 'thresholdmgen', 0.500000 );
%    m = leaf_setproperty( m, 'bulkmodulus', 1.000000 );
%    m = leaf_setproperty( m, 'unitbulkmodulus', true );
%    m = leaf_setproperty( m, 'poissonsRatio', 0.300000 );
%    m = leaf_setproperty( m, 'starttime', 0.000000 );
%    m = leaf_setproperty( m, 'timestep', 0.010000 );
%    m = leaf_setproperty( m, 'timeunitname', '' );
%    m = leaf_setproperty( m, 'distunitname', 'mm' );
%    m = leaf_setproperty( m, 'scalebarvalue', 0.000000 );
%    m = leaf_setproperty( m, 'validateMesh', true );
%    m = leaf_setproperty( m, 'rectifyverticals', false );
%    m = leaf_setproperty( m, 'allowSplitLongFEM', true );
%    m = leaf_setproperty( m, 'longSplitThresholdPower', 0.000000 );
%    m = leaf_setproperty( m, 'allowSplitBentFEM', false );
%    m = leaf_setproperty( m, 'allowSplitBio', true );
%    m = leaf_setproperty( m, 'allowFlipEdges', false );
%    m = leaf_setproperty( m, 'allowElideEdges', true );
%    m = leaf_setproperty( m, 'mincellangle', 0.200000 );
%    m = leaf_setproperty( m, 'alwaysFlat', 0.000000 );
%    m = leaf_setproperty( m, 'flattenforceconvex', true );
%    m = leaf_setproperty( m, 'flatten', false );
%    m = leaf_setproperty( m, 'flattenratio', 1.000000 );
%    m = leaf_setproperty( m, 'useGrowthTensors', false );
%    m = leaf_setproperty( m, 'plasticGrowth', false );
%    m = leaf_setproperty( m, 'totalinternalrotation', 0.000000 );
%    m = leaf_setproperty( m, 'stepinternalrotation', 2.000000 );
%    m = leaf_setproperty( m, 'showinternalrotation', false );
%    m = leaf_setproperty( m, 'performinternalrotation', false );
%    m = leaf_setproperty( m, 'internallyrotated', false );
%    m = leaf_setproperty( m, 'maxFEcells', 0 );
%    m = leaf_setproperty( m, 'inittotalcells', 0 );
%    m = leaf_setproperty( m, 'bioApresplitproc', '' );
%    m = leaf_setproperty( m, 'bioApostsplitproc', '' );
%    m = leaf_setproperty( m, 'maxBioAcells', 0 );
%    m = leaf_setproperty( m, 'colors', (6 values) );
%    m = leaf_setproperty( m, 'colorvariation', 0.050000 );
%    m = leaf_setproperty( m, 'colorparams', (12 values) );
%    m = leaf_setproperty( m, 'biocolormode', 'auto' );
%    m = leaf_setproperty( m, 'freezing', 0.000000 );
%    m = leaf_setproperty( m, 'canceldrift', false );
%    m = leaf_setproperty( m, 'mgen_interaction', '' );
%    m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_demosubdivision_20121116' );
%    m = leaf_setproperty( m, 'allowInteraction', true );
%    m = leaf_setproperty( m, 'interactionValid', true );
%    m = leaf_setproperty( m, 'gaussInfo', (unknown type ''struct'') );
%    m = leaf_setproperty( m, 'stitchDFs', [] );
%    m = leaf_setproperty( m, 'D', (36 values) );
%    m = leaf_setproperty( m, 'C', (36 values) );
%    m = leaf_setproperty( m, 'G', (6 values) );
%    m = leaf_setproperty( m, 'solver', 'cgs' );
%    m = leaf_setproperty( m, 'solverprecision', 'double' );
%    m = leaf_setproperty( m, 'solvertolerance', 0.001000 );
%    m = leaf_setproperty( m, 'solvertolerancemethod', 'max' );
%    m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 );
%    m = leaf_setproperty( m, 'allowsparse', true );
%    m = leaf_setproperty( m, 'maxIters', 0 );
%    m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 );
%    m = leaf_setproperty( m, 'cgiters', 0 );
%    m = leaf_setproperty( m, 'simsteps', 0 );
%    m = leaf_setproperty( m, 'stepsperrender', 0 );
%    m = leaf_setproperty( m, 'growthEnabled', true );
%    m = leaf_setproperty( m, 'diffusionEnabled', true );
%    m = leaf_setproperty( m, 'flashmovie', false );
%    m = leaf_setproperty( m, 'makemovie', false );
%    m = leaf_setproperty( m, 'moviefile', '' );
%    m = leaf_setproperty( m, 'codec', 'None' );
%    m = leaf_setproperty( m, 'autonamemovie', true );
%    m = leaf_setproperty( m, 'overwritemovie', false );
%    m = leaf_setproperty( m, 'framesize', [] );
%    m = leaf_setproperty( m, 'mov', [] );
%    m = leaf_setproperty( m, 'boingNeeded', false );
%    m = leaf_setproperty( m, 'initialArea', 128.000000 );
%    m = leaf_setproperty( m, 'bendunitlength', 11.313708 );
%    m = leaf_setproperty( m, 'targetRelArea', 1.000000 );
%    m = leaf_setproperty( m, 'defaultinterp', 'min' );
%    m = leaf_setproperty( m, 'readonly', false );
%    m = leaf_setproperty( m, 'projectdir', 'D:\ab\Matlab stuff\Growth models' );
%    m = leaf_setproperty( m, 'modelname', 'GPT_DemoSubdivision_20121116' );
%    m = leaf_setproperty( m, 'allowsave', true );
%    m = leaf_setproperty( m, 'addedToPath', false );
%    m = leaf_setproperty( m, 'bendsplit', 0.300000 );
%    m = leaf_setproperty( m, 'usepolfreezebc', false );
%    m = leaf_setproperty( m, 'dorsaltop', true );
%    m = leaf_setproperty( m, 'defaultazimuth', -45.000000 );
%    m = leaf_setproperty( m, 'defaultelevation', 33.750000 );
%    m = leaf_setproperty( m, 'defaultroll', 0.000000 );
%    m = leaf_setproperty( m, 'defaultViewParams', (unknown type ''struct'') );
%    m = leaf_setproperty( m, 'comment', '' );
%    m = leaf_setproperty( m, 'legendTemplate', '%T: %q\n%m' );
%    m = leaf_setproperty( m, 'bioAsplitcells', true );
%    m = leaf_setproperty( m, 'bioApullin', 0.142857 );
%    m = leaf_setproperty( m, 'bioAfakepull', 0.202073 );
%    m = leaf_setproperty( m, 'interactive', false );
%    m = leaf_setproperty( m, 'coderevision', 0 );
%    m = leaf_setproperty( m, 'coderevisiondate', '' );
%    m = leaf_setproperty( m, 'modelrevision', 0 );
%    m = leaf_setproperty( m, 'modelrevisiondate', '' );
%    m = leaf_setproperty( m, 'savedrunname', '' );
%    m = leaf_setproperty( m, 'savedrundesc', '' );
%    m = leaf_setproperty( m, 'vxgrad', (108 values) );
%    m = leaf_setproperty( m, 'lengthscale', 16.000000 );
end

% Here you may write any functions of your own, that you want to call from
% the interaction function, but never need to call from outside it.
% Remember that they do not have access to any variables except those
% that you pass as parameters, and cannot change anything except by
% returning new values as results.
% Whichever section they are called from, they must respect the same
% restrictions on what modifications they are allowed to make to the mesh.

% For example:

% function m = do_something( m )
%   % Change m in some way.
% end

% Call it from the main body of the interaction function like this:
%       m = do_something( m );
