problems about dde15s solving delay differential equation

I have a problem solving stiff delay differential equations recently. I just found that there's a paper written by Vikas Agrawal's group and they used a solver called "dde15s" for there calculation.

We can find the paper at the following website: https://onlinelibrary.wiley.com/doi/10.1021/bp034226s

At the bottom of the website, click "Supporting Information", and download the zip file "bp034226ssi20030804_024052.zip", which the dde15s.m is inside (or you may download the attachment form this comment).

But I found a new problem. I try to use dde15s instead of dde23 in my code, then the error appears:

    Error using vertcat
Dimensions of matrices being concatenated are not consistent.
    Error in dde15s>solextend (line 155)
solout.idata.kvec = [sol.idata.kvec; solex.idata.kvec(2:end)];
    Error in dde15s (line 139)
      sol = solextend(sol,solex);

In dde15s.m, function "solextend" is for Concatenate two solution structures produced by ODE15S. And the Author said " This function works with ODE15S from MATLAB 6.5, but it may require modifications to work with other versions."

I think the error exist in my code because I use the Matlab 2017a version. So is there anyone can fix that error and make "dde15s.m" fit to the newest version of Matlab?

Thanks for all your help.

[Valeriia Hutor]

Hi Leo,

Did you resolve this issue? I currently have the same with my equations.

Thank you.

[Shiny Samuel]

Hi Leo,

Were you able to resolve this issue? I am also currently trying to use DDE15s and running into the same problem.

Please do let me know.

Thanks,

Shiny

Answer 1

[George Sarantoglou]

After struggling for two hours I made it work. I use Matlab 2017a.

Fist of all in the solextend function you should change the ";" character with "," in the fourth and last line - solout.idata.kvec, solout.idata.dif3d lines.

function solout = solextend(sol,solex)
% Concatenate two solution structures produced by ODE15S.
% This function works with ODE15S from MATLAB 6.5, but 
% it may require modifications to work with other versions.

solout.solver = 'ode15s';
solout.x = [sol.x, solex.x(2:end)];
solout.y = [sol.y, solex.y(:,2:end)];
solout.idata.kvec = [sol.idata.kvec, solex.idata.kvec(2:end)];  
dim3   = size(  sol.idata.dif3d,3);
dim3ex = size(solex.idata.dif3d,3);
if dim3ex > dim3
  sol.idata.dif3d(:,:,dim3+1:dim3ex) = 0;
  dim3 = dim3ex;
elseif dim3ex < dim3
  solex.idata.dif3d(:,:,dim3ex+1:dim3) = 0;       
end
solout.idata.dif3d = [sol.idata.dif3d , solex.idata.dif3d];

In the main body, I have also made the following modifications and the whole thing works just fine.

solex = ode15s(@(t,y) ddefcn(t,y,ddefun,lags,history,solast,varargin),[b e],solast.y(:,end),options);
%     solex = ode15s(@ddefcn,[b,e],sol.y(:,end),options,...
%                    ddefun,lags,history,sol,varargin{:});
    solast = solex;
    if (i == 2) && (j == 1)    % Initialize solution structure.
      sol = solex;
    else
      sol = solextend(sol,solex);
    end
  end
end
sol.discont = discont;

[Shiny Samuel]

Hi George,

I have changed dde15s using the following edits you've made. However, I keep getting the error: Unrecognized function or variable 'solast'.

Have you defined solast elsewhere in the code?

Thanks in advance for your help!

Answer 2

[Michelle Przedborski]

I have an updated version of the code that works in Matlab R2018b and newer releases (updated by Jacek Kierzenka at Mathworks). The code can be downloaded/viewed from here: https://github.com/mprzedborski/venetoclax-tedizolid/blob/3b4b84df0aa797a0761d9509756aa6f25dcffc17/dde15s_updated.m

Answer 3

[Alec Sargood]

Hi George,

I would be very interested to know if you managed to fix the code for dde15s, as I'm currently working on a project looking to solve stiff ddes.

Thanks