ode45 error: dimension mismatch in line 345 column 17

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ode45 error: dimension mismatch in line 345 column 17

daltonj283
I am trying to solve this complex ODE with ode45 and no matter which solver I use I get a similar error from each solver (using odepkg 0.8.5). I've used octave online to solve the very same ode as well as matlab, but I need to be able to solve it using my octave version 4.0.3.

function dydt=bangodefun(y,t,T,N)
  X=[Delta1(t,T(1:N(1))); Delta2(t,T(N(1)+1:sum(N(1:2)))); Delta3(t,T(sum(N(1:2))+1:sum(N(1:3)))); Delta4(t,T(sum(N(1:3))+1:sum(N(1:4)))); Delta5(t,T(sum(N(1:4))+1:sum(N(1:5)))); Delta6(t,T(sum(N(1:5))+1:sum(N(1:6))))];
  H=Hamil(X);
  dydt=-i*H*y;
endfunction

%The Delta functions simply return values 0 or 1 depending on t, T and N are defined inputs
%Hamil(X) returns a 3x3 Hamiltonian matrix which means y is a 3x1 vector

Command:
>> T=[0; 0; 0; 0; .28; .56; .28; .56];
>> N=[1 1 1 1 2 2];
>> Y0=[1; 0; 0];
>> [t,Y]=ode45(@(t,y)bangodefun(t,y,T,N), [0 1], Y0)
warning: Option "RelTol" not set, new value 0.000001 is used
warning: called from
    ode45 at line 113 column 5
warning: Option "AbsTol" not set, new value 0.000001 is used
warning: Option "InitialStep" not set, new value 0.010000 is used
warning: Option "MaxStep" not set, new value 0.010000 is used
error: ode45: A(I,J,...) = X: dimensions mismatch
error: called from
    ode45 at line 345 column 17

I'm not sure why I'm only getting this error on my downloaded version of Octave. Please help.

Thank you,
Dalton

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Re: ode45 error: dimension mismatch in line 345 column 17

Sebastian Schöps
Dalton Jones wrote
function dydt=bangodefun(y,t,T,N)
...
endfunction
...
[t,Y]=ode45(@(t,y)bangodefun(t,y,T,N), [0 1], Y0)
I cannot help debugging as you did not give us the Delta functions. However, I guess your trouble is that you swapped the arguments t and y in the definition of the anonymous function.

Seb.
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Re: ode45 error: dimension mismatch in line 345 column 17

daltonj283
That was actually just a typo when I wrote it on the website, I just checked to make sure I was calling ode45 with t and y in the correct order and got the same error message. The first time I posted my question, the Delta functions literally just returned values 1 or 0 independent of inputs. I did this because when I called ode45 with the time dependent Delta's it tells me that the return values are left unassigned even though I can call each Delta function from the command line and it works as expected. With all of my other functions (Hamil and bangodefun) the same here are my current Delta functions now that I have made them dependent on what time it is again and the current error message:

function [B1]=Delta1(t,tB1)
  n1=length(tB1);
  tsB1=sort(tB1);
  n=1;
  while n<=n1
    if t<=tsB1(n)
        B1=(1+(-1)^(n))/2;
        n=n1+1;
    elseif t>tsB1(n1)
        B1=mod(n1,2);
        n=n1+1;
    else
        n=n+1;
    end
  end
end

function [B2]=Delta2(t,tB2)
  n2=length(tB2);
  tsB2=sort(tB2);
  n=1;
  while n<=n2
    if t<=tsB2(n)
        B2=(1+(-1)^(n))/2;
        n=n2+1;
    elseif t>tsB2(n2)
        B2=mod(n2,2);
        n=n2+1;
    else
        n=n+1;
    end
  end
end

function [B3]=Delta3(t,tB3)
  n3=length(tB3);
  tsB3=sort(tB3);
  n=1;
  while n<=n3
    if t<=tsB3(n)
        B3=(1+(-1)^(n))/2;
        n=n3+1;
    elseif t>tsB3(n3)
        B3=mod(n3,2);
        n=n3+1;
    else
        n=n+1;
    end
  end
end

function [J1]=Delta4(t,tJ1)
  n4=length(tJ1);
  tsJ1=sort(tJ1);
  n=1;
  while n<=n4
    if t<=tsJ1(n)
        J1=(1+(-1)^(n))/2;
        n=n4+1;
    elseif t>tsJ1(n4)
        J1=mod(n4,2);
        n=n4+1;
    else
        n=n+1;
    end
  end
end

function J2=Delta5(t,tJ2)
  n5=length(tJ2);
  tsJ2=sort(tJ2);
  n=1;
  while (n <= n5)
    if t<=tsJ2(n)
        J2=(1+(-1)^(n+1))/2;
        n=n5+1;
    elseif t>tsJ2(n5)
        J2=-1*(mod(n5,2)-1);
        n=n5+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

function [J3]=Delta6(t,tJ3)
  n6=length(tJ3);
  tsJ3=sort(tJ3);
  n=1;
  while n<=n6
    if t<=tsJ3(n)
        J3=(1+(-1)^(n+1))/2;
        n=n6+1;
    elseif t>tsJ3(n6)
        J3=-1*(mod(n6,2)-1);
        n=n6+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

Commands:

>> T=[0; 0; 0; 0; .28; .56; .28; .56];
>> N=[1 1 1 1 2 2];
>> Y0=[1; 0; 0];
>>[t,y]=ode45(@(y,t)bangodefun(y,t,T,N),[0 1],Y0)
warning: Option "RelTol" not set, new value 0.000001 is used
warning: called from
    ode45 at line 113 column 5
warning: Option "AbsTol" not set, new value 0.000001 is used
warning: Option "InitialStep" not set, new value 0.010000 is used
warning: Option "MaxStep" not set, new value 0.010000 is used
warning: Delta1: some elements in list of return values are undefined
warning: Delta2: some elements in list of return values are undefined
warning: Delta3: some elements in list of return values are undefined
warning: Delta4: some elements in list of return values are undefined
warning: Delta5: some elements in list of return values are undefined
warning: Delta6: some elements in list of return values are undefined
error: Hamil: A(I): index out of bounds; value 1 out of bound 0
error: called from
    Hamil at line 2 column 4
    bangodefun at line 3 column 4
    ode45 at line 345 column 17

On Mon, Aug 28, 2017 at 12:57 AM, Sebastian Schöps <[hidden email]> wrote:
Dalton Jones wrote
> function dydt=bangodefun(y,t,T,N)
> ...
> endfunction
> ...
> [t,Y]=ode45(@(t,y)bangodefun(t,y,T,N), [0 1], Y0)

I cannot help debugging as you did not give us the Delta functions. However,
I guess your trouble is that you swapped the arguments t and y in the
definition of the anonymous function.

Seb.



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Re: ode45 error: dimension mismatch in line 345 column 17

Sebastian Schöps
Dalton Jones wrote
error: ode45: A(I,J,...) = X: dimensions mismatch
...
That was actually just a typo when I wrote it on the website
The error before was about dimensions. Now the error is different:

Dalton Jones wrote
error: Hamil: A(I): index out of bounds; value 1 out of bound 0
error: called from
    Hamil at line 2 column 4
Something is wrong in your Hamil function ("index out of bounds").
You did not show this function, so again, I cannot help.

Sebastian
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Re: ode45 error: dimension mismatch in line 345 column 17

daltonj283
No the Hamil function returns a 3x3 matrix based on the values of X, and it along with every other function works fine in the command line. It seems that for some reason the Delta functions are not returning values when called in ode45, making X=[ ].

function [ H ] = Hamil( X )
  H=[X(1)+X(2)-X(3)   -2*X(5)   -2*X(6); -2*X(5)   X(1)-X(2)+X(3)   -2*X(4); -2*X(6)   -2*X(4)   X(2)-X(1)+X(3)];
endfunction
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Re: ode45 error: dimension mismatch in line 345 column 17

Sebastian Schöps
In reply to this post by Sebastian Schöps
Hi,

please keep the mailing list in cc.

> No the Hamil function returns a 3x3 matrix based on the values of X, and it along with every other function works fine in the command line. It seems that for some reason the Delta functions are not returning values when called in ode45, making X=[ ].
>
> function [ H ] = Hamil( X )
>   H=[X(1)+X(2)-X(3)   -2*X(5)   -2*X(6); -2*X(5)   X(1)-X(2)+X(3)   -2*X(4); -2*X(6)   -2*X(4)   X(2)-X(1)+X(3)];
> endfunction
>
> Dalton

I tried your functions and they work for me using "[t,Y]=ode45(@(t,y)bangodefun(y,t,T,N), [0 1], Y0)". I am using them with octave 4.3.0+ on macOS. Maybe you have several incompatible versions in your path?

Sebastian

---------------------------------------
Just paste this into the octave window ...
---------------------------------------

function dydt=bangodefun(y,t,T,N)
  X=[Delta1(t,T(1:N(1))); Delta2(t,T(N(1)+1:sum(N(1:2)))); Delta3(t,T(sum(N(1:2))+1:sum(N(1:3)))); Delta4(t,T(sum(N(1:3))+1:sum(N(1:4)))); Delta5(t,T(sum(N(1:4))+1:sum(N(1:5)))); Delta6(t,T(sum(N(1:5))+1:sum(N(1:6))))];
  H=Hamil(X);
  dydt=-i*H*y;
endfunction

function [B1]=Delta1(t,tB1)
  n1=length(tB1);
  tsB1=sort(tB1);
  n=1;
  while n<=n1
    if t<=tsB1(n)
        B1=(1+(-1)^(n))/2;
        n=n1+1;
    elseif t>tsB1(n1)
        B1=mod(n1,2);
        n=n1+1;
    else
        n=n+1;
    end
  end
end

function [B2]=Delta2(t,tB2)
  n2=length(tB2);
  tsB2=sort(tB2);
  n=1;
  while n<=n2
    if t<=tsB2(n)
        B2=(1+(-1)^(n))/2;
        n=n2+1;
    elseif t>tsB2(n2)
        B2=mod(n2,2);
        n=n2+1;
    else
        n=n+1;
    end
  end
end

function [B3]=Delta3(t,tB3)
  n3=length(tB3);
  tsB3=sort(tB3);
  n=1;
  while n<=n3
    if t<=tsB3(n)
        B3=(1+(-1)^(n))/2;
        n=n3+1;
    elseif t>tsB3(n3)
        B3=mod(n3,2);
        n=n3+1;
    else
        n=n+1;
    end
  end
end

function [J1]=Delta4(t,tJ1)
  n4=length(tJ1);
  tsJ1=sort(tJ1);
  n=1;
  while n<=n4
    if t<=tsJ1(n)
        J1=(1+(-1)^(n))/2;
        n=n4+1;
    elseif t>tsJ1(n4)
        J1=mod(n4,2);
        n=n4+1;
    else
        n=n+1;
    end
  end
end

function J2=Delta5(t,tJ2)
  n5=length(tJ2);
  tsJ2=sort(tJ2);
  n=1;
  while (n <= n5)
    if t<=tsJ2(n)
        J2=(1+(-1)^(n+1))/2;
        n=n5+1;
    elseif t>tsJ2(n5)
        J2=-1*(mod(n5,2)-1);
        n=n5+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

function [J3]=Delta6(t,tJ3)
  n6=length(tJ3);
  tsJ3=sort(tJ3);
  n=1;
  while n<=n6
    if t<=tsJ3(n)
        J3=(1+(-1)^(n+1))/2;
        n=n6+1;
    elseif t>tsJ3(n6)
        J3=-1*(mod(n6,2)-1);
        n=n6+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

function [ H ] = Hamil( X )
  H=[X(1)+X(2)-X(3)   -2*X(5)   -2*X(6); -2*X(5)   X(1)-X(2)+X(3)   -2*X(4); -2*X(6)   -2*X(4)   X(2)-X(1)+X(3)];
endfunction

T=[0; 0; 0; 0; .28; .56; .28; .56];
N=[1 1 1 1 2 2];
Y0=[1; 0; 0];
[t,Y]=ode45(@(t,y)bangodefun(y,t,T,N), [0 1], Y0)



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Re: ode45 error: dimension mismatch in line 345 column 17

daltonj283
Yeah I'm using octave 4.0.3, I couldn't find anywhere to download anything newer for the Mac. Could you direct me somewhere to download the latest version?

Thanks,
Dalton

On Tue, Aug 29, 2017 at 2:37 PM, Sebastian Schöps [via Octave] <[hidden email]> wrote:
Hi,

please keep the mailing list in cc.

> No the Hamil function returns a 3x3 matrix based on the values of X, and it along with every other function works fine in the command line. It seems that for some reason the Delta functions are not returning values when called in ode45, making X=[ ].
>
> function [ H ] = Hamil( X )
>   H=[X(1)+X(2)-X(3)   -2*X(5)   -2*X(6); -2*X(5)   X(1)-X(2)+X(3)   -2*X(4); -2*X(6)   -2*X(4)   X(2)-X(1)+X(3)];
> endfunction
>
> Dalton

I tried your functions and they work for me using "[t,Y]=ode45(@(t,y)bangodefun(y,t,T,N), [0 1], Y0)". I am using them with octave 4.3.0+ on macOS. Maybe you have several incompatible versions in your path?

Sebastian

---------------------------------------
Just paste this into the octave window ...
---------------------------------------

function dydt=bangodefun(y,t,T,N)
  X=[Delta1(t,T(1:N(1))); Delta2(t,T(N(1)+1:sum(N(1:2)))); Delta3(t,T(sum(N(1:2))+1:sum(N(1:3)))); Delta4(t,T(sum(N(1:3))+1:sum(N(1:4)))); Delta5(t,T(sum(N(1:4))+1:sum(N(1:5)))); Delta6(t,T(sum(N(1:5))+1:sum(N(1:6))))];
  H=Hamil(X);
  dydt=-i*H*y;
endfunction

function [B1]=Delta1(t,tB1)
  n1=length(tB1);
  tsB1=sort(tB1);
  n=1;
  while n<=n1
    if t<=tsB1(n)
        B1=(1+(-1)^(n))/2;
        n=n1+1;
    elseif t>tsB1(n1)
        B1=mod(n1,2);
        n=n1+1;
    else
        n=n+1;
    end
  end
end

function [B2]=Delta2(t,tB2)
  n2=length(tB2);
  tsB2=sort(tB2);
  n=1;
  while n<=n2
    if t<=tsB2(n)
        B2=(1+(-1)^(n))/2;
        n=n2+1;
    elseif t>tsB2(n2)
        B2=mod(n2,2);
        n=n2+1;
    else
        n=n+1;
    end
  end
end

function [B3]=Delta3(t,tB3)
  n3=length(tB3);
  tsB3=sort(tB3);
  n=1;
  while n<=n3
    if t<=tsB3(n)
        B3=(1+(-1)^(n))/2;
        n=n3+1;
    elseif t>tsB3(n3)
        B3=mod(n3,2);
        n=n3+1;
    else
        n=n+1;
    end
  end
end

function [J1]=Delta4(t,tJ1)
  n4=length(tJ1);
  tsJ1=sort(tJ1);
  n=1;
  while n<=n4
    if t<=tsJ1(n)
        J1=(1+(-1)^(n))/2;
        n=n4+1;
    elseif t>tsJ1(n4)
        J1=mod(n4,2);
        n=n4+1;
    else
        n=n+1;
    end
  end
end

function J2=Delta5(t,tJ2)
  n5=length(tJ2);
  tsJ2=sort(tJ2);
  n=1;
  while (n <= n5)
    if t<=tsJ2(n)
        J2=(1+(-1)^(n+1))/2;
        n=n5+1;
    elseif t>tsJ2(n5)
        J2=-1*(mod(n5,2)-1);
        n=n5+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

function [J3]=Delta6(t,tJ3)
  n6=length(tJ3);
  tsJ3=sort(tJ3);
  n=1;
  while n<=n6
    if t<=tsJ3(n)
        J3=(1+(-1)^(n+1))/2;
        n=n6+1;
    elseif t>tsJ3(n6)
        J3=-1*(mod(n6,2)-1);
        n=n6+1;
    else
        n=n+1;
    endif
  endwhile
endfunction

function [ H ] = Hamil( X )
  H=[X(1)+X(2)-X(3)   -2*X(5)   -2*X(6); -2*X(5)   X(1)-X(2)+X(3)   -2*X(4); -2*X(6)   -2*X(4)   X(2)-X(1)+X(3)];
endfunction

T=[0; 0; 0; 0; .28; .56; .28; .56];
N=[1 1 1 1 2 2];
Y0=[1; 0; 0];
[t,Y]=ode45(@(t,y)bangodefun(y,t,T,N), [0 1], Y0)



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Re: ode45 error: dimension mismatch in line 345 column 17

Sebastian Schöps
daltonj283 wrote
> Yeah I'm using octave 4.0.3, I couldn't find anywhere to download anything
> newer for the Mac. Could you direct me somewhere to download the latest
> version?

Recent octave versions contain ode45 natively, i.e. you do not need odepkg
anymore. You can get it either

1. from homebrew, see https://wiki.octave.org/Octave_for_macOS#Homebrew

In short "brew install octave" will install the most recent stable version
(version 4.2.1) and "brew install octave --HEAD" will compile the current
version from the development sources, i.e. version "4.3.0+").

2. Binary

I recently prepared a binary version of 4.2.1 (based on homebrew). I have
send it to a few colleagues for testing but there might still be bugs
(however, I am rather confident that it is fine). You can get it here:

https://www.dropbox.com/s/7o6w67vfnka1in2/octave_cli_421_appleblas.dmg?dl=0

For verification, the shasum is 4cfa0f4f0136b5a0c4c5c88e30f746e8bc4508c7.

Seb.





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Re: ode45 error: dimension mismatch in line 345 column 17

daltonj283
This post has NOT been accepted by the mailing list yet.
So I tried installing Octave using brew install octave, and it worked but I was unable to open Octave with the GUI. It would only allow me to use the command line of Octave. So then I tried brew install octave --HEAD and that resulted in the same problem. I even tried the command octave --force-gui

On Wed, Aug 30, 2017 at 4:46 AM, Sebastian Schöps [via Octave] <[hidden email]> wrote:
daltonj283 wrote
> Yeah I'm using octave 4.0.3, I couldn't find anywhere to download anything
> newer for the Mac. Could you direct me somewhere to download the latest
> version?

Recent octave versions contain ode45 natively, i.e. you do not need odepkg
anymore. You can get it either

1. from homebrew, see https://wiki.octave.org/Octave_for_macOS#Homebrew

In short "brew install octave" will install the most recent stable version
(version 4.2.1) and "brew install octave --HEAD" will compile the current
version from the development sources, i.e. version "4.3.0+").

2. Binary

I recently prepared a binary version of 4.2.1 (based on homebrew). I have
send it to a few colleagues for testing but there might still be bugs
(however, I am rather confident that it is fine). You can get it here:

https://www.dropbox.com/s/7o6w67vfnka1in2/octave_cli_421_appleblas.dmg?dl=0

For verification, the shasum is 4cfa0f4f0136b5a0c4c5c88e30f746e8bc4508c7.

Seb.





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Re: ode45 error: dimension mismatch in line 345 column 17

Sebastian Schöps
daltonj283 wrote
> So I tried installing Octave using *brew install octave*, and it worked
> but
> I was unable to open Octave with the GUI. It would only allow me to use
> the
> command line of Octave. So then I tried *brew install octave --HEAD *and
> that resulted in the same problem. I even tried the command octave
> --force-gui

True. Since homebrew moved to qt 5.9 (which is justified as older version
have significant security issues are unmaintained) we do not build octave
with the GUI anymore. Sorry, it's too buggy to be shipped. Sadly, I have not
the skills to fix the qt issues and the people that might have the skills do
not care about macOS :( For now, you either live with an outdated octave
(using an outdated qt) or a recent octave without GUI.... or you are a qt
expert and you can help me fixing it :)

Personal note: the command line interface is not so bad after all. I would
always go for option 2.

Sebastian




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Re: ode45 error: dimension mismatch in line 345 column 17

daltonj283
This post has NOT been accepted by the mailing list yet.
Ok, yeah it was pretty easy to learn how to use it on the command line. I've gotten most of my scripts running on it now, save for the one I made another post about. Haha I don't think I can help you there, but thanks for all your help, I really appreciate it!

Dalton

On Wed, Aug 30, 2017 at 11:50 PM, Sebastian Schöps [via Octave] <[hidden email]> wrote:
daltonj283 wrote
> So I tried installing Octave using *brew install octave*, and it worked
> but
> I was unable to open Octave with the GUI. It would only allow me to use
> the
> command line of Octave. So then I tried *brew install octave --HEAD *and
> that resulted in the same problem. I even tried the command octave
> --force-gui

True. Since homebrew moved to qt 5.9 (which is justified as older version
have significant security issues are unmaintained) we do not build octave
with the GUI anymore. Sorry, it's too buggy to be shipped. Sadly, I have not
the skills to fix the qt issues and the people that might have the skills do
not care about macOS :( For now, you either live with an outdated octave
(using an outdated qt) or a recent octave without GUI.... or you are a qt
expert and you can help me fixing it :)

Personal note: the command line interface is not so bad after all. I would
always go for option 2.

Sebastian




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Re: ode45 error: dimension mismatch in line 345 column 17

Marius Schamschula-5
In reply to this post by Sebastian Schöps
In MacPorts we still use the old qt (perhaps we should look into the security issues as well).

However, I use Jupyter Notebooks with the octave kernel as my front end, and rarely load the octave GUI anymore.

I have found that this is easier to display to a class when working problems.


On Aug 31, 2017, at 1:48 AM, Sebastian Schöps <[hidden email]> wrote:

daltonj283 wrote
So I tried installing Octave using *brew install octave*, and it worked
but
I was unable to open Octave with the GUI. It would only allow me to use
the
command line of Octave. So then I tried *brew install octave --HEAD *and
that resulted in the same problem. I even tried the command octave
--force-gui

True. Since homebrew moved to qt 5.9 (which is justified as older version
have significant security issues are unmaintained) we do not build octave
with the GUI anymore. Sorry, it's too buggy to be shipped. Sadly, I have not
the skills to fix the qt issues and the people that might have the skills do
not care about macOS :( For now, you either live with an outdated octave
(using an outdated qt) or a recent octave without GUI.... or you are a qt
expert and you can help me fixing it :)

Personal note: the command line interface is not so bad after all. I would
always go for option 2.

Sebastian




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