ode solver error, too many argyments etc

Hello community.

I am working on some code to optimize a protein pump. I keep getting the following errors

>> run script_runSS_CaDoseResponse.m
Error using
script_runSS_CaDoseResponse>@(t,y)rhs(t,y,k_S0_S1,k_S2_S3,k_S7_S8,k_S9_S10,k_S5_S6a,k_S6_S7,k_S0_S11,k_S0_S1a,k_S1a_S0,k_S1a_S2a,k_S2a_S1a,k_S1_S2a,k_S2a_S1,k_S2a_S3a,k_S3a_S2a,k_S2_S3a,k_S3a_S2,k_S3a_S4,k_S4_S3a,Ca,p.Pi_conc)
Too many input arguments.

Error in odearguments (line 90)
f0 = feval(ode,t0,y0,args{:});   % ODE15I sets args{1} to yp0.

Error in ode15s (line 150)
    odearguments(FcnHandlesUsed, solver_name, ode, tspan, y0, options, varargin);

Error in script_runSS_CaDoseResponse (line 78)
    [t,y] = ode15s(@(t,y) rhs(t,y, k_S0_S1, k_S2_S3, k_S7_S8, k_S9_S10, k_S5_S6a, k_S6_S7, k_S0_S11, k_S0_S1a,
        k_S1a_S0, k_S1a_S2a, k_S2a_S1a, k_S1_S2a, k_S2a_S1, k_S2a_S3a, k_S3a_S2a, k_S2_S3a, k_S3a_S2, k_S3a_S4, k_S4_S3a,
        Ca, p.Pi_conc), tspan, ic, 'AbsTol', 1e-8, 'RelTol', 1e-7);

Error in run (line 91)
evalin('caller', strcat(script, ';'));

The code is attached.

I will be eternally greatful for any help!

[Walter Roberson]

Your function named rhs does not expect that many input variables.

You have not posted your rhs.m so we do not know how many it does expect.

Caution: as of R2017a there is rhs() supplied by Mathworks in the Symbolic Toolbox

Answer 1

[Sophie Sophie]

Can you kindly give me an example?

Do I do this everywhere that rhs is mentioned?

[Walter Roberson]

function [rates] = rhs(t,y, k_S0_S1, k_S2_S3, k_S7_S8, k_S9_S10, k_S5_S6a, k_S6_S7, k_S0_S11, k_S0_S1a, k_S1a_S0, k_S1a_S2a, k_S2a_S1a, k_S1_S2a, k_S2a_S1, k_S2a_S3a, k_S3a_S2a, k_S2_S3a, k_S3a_S2, k_S3a_S4, k_S4_S3a, Ca, Ca_sr_conc)

[Sophie Sophie]

Do you mean that p.Pi_conc should be Pi_conc?

[Walter Roberson]

Your code does not refer to Pi_conc anywhere.

Your code refers to Ca_sr_conc without defining it anywhere.

This combination hints that the user should perhaps be passing in p.Pi_conc but that it should be received into the variable Ca_sr_conc .

Does that make sense? What are you expecting Ca_sr_conc to be in your code?

[Sophie Sophie]

Casr_conc is refined in getParams.m

It’s a set value.

Pi_conc is also defined there.

[Walter Roberson]

You are calling getParams() as a function, so any local variable you set there is not made available to the calling function. Perhaps you need to refer to p.Ca_sr_conc ?

When you were constructing the code, what were you intending that last parameter to bring into the function ?

Answer 2

[Torsten]

options = odeset('RelTol',1e-7,'AbsTol',1e-8);
[t,y] = ode15s(@(t,y) rhs(t,y, k_S0_S1, k_S2_S3, k_S7_S8, k_S9_S10, k_S5_S6a, k_S6_S7, k_S0_S11, k_S0_S1a, k_S1a_S0, k_S1a_S2a, k_S2a_S1a, k_S1_S2a, k_S2a_S1, k_S2a_S3a, k_S3a_S2a, k_S2_S3a, k_S3a_S2, k_S3a_S4, k_S4_S3a, Ca, p.Pi_conc), tspan, ic, options);

Best wishes

Torsten.

Answer 3

[madhan ravi]

 [t,y] = ode15s(@rhs, tspan, ic, 'AbsTol', 1e-8, 'RelTol', 1e-7);

[Walter Roberson]

That will not work: it would invoke rhs with no arguments.

[madhan ravi]

edited code sir Walter

Answer 4

[Sophie Sophie]

This is my rhs.m code

function [rates] = rhs(t,y, k_S0_S1, k_S2_S3, k_S7_S8, k_S9_S10, k_S5_S6a, k_S6_S7, k_S0_S11, k_S0_S1a, k_S1a_S0, k_S1a_S2a, k_S2a_S1a, k_S1_S2a, k_S2a_S1, k_S2a_S3a, k_S3a_S2a, k_S2_S3a, k_S3a_S2, k_S3a_S4, k_S4_S3a, Ca, p.Pi_conc)

% setting up kinetic transitions as follows: 
% ------------------------------------------
%
%       [S1-y(1)]      [S2-y(2)]        [S3-y(3)]         [S4-y(4)]            [S5-y(5)]
%          E.Ca <==> E'.Ca  + Ca <==> E'.Ca2 (+ ATP) <==> E'.ATP.Ca2  <==>   E'~P.ADP.Ca2
%           /\  ^        ^                                            //  \\
%           ||   \\      \\ =========================>[S3a-y(16)]             //    \\
%           ||    \\===============>[S2a-y(15)]         E'.ATP.Ca   [S6a-y(7)]//      \\  [S6-y(6)]
%     +Ca   ||    [S1a-y(14)]        E.ATP.Ca                       *E'-P.ADP.Ca2      E'~P.Ca2 (+ ADP)
%           ||      E.ATP                                                     \\      //
%           ||                                                        (+ ADP)  \\    //
%           \/                                                                  \\  //
%    (Pi +) E <==> *E-Pi <==> *E-P + Ca <==> *E-P.Ca  <==> *E'-P.Ca + Ca <==>  *E'-P.Ca2
%  [S0-y(13)]   [S11-y(12)]  [S10-y(11)]    [S9-y(10)]       [S8-y(9)]         [S7-y(8)]
%
% ---------------------------------------------------------------------------------------

   p = getParams();

% formulate ODEs w/ Mass action kinetics
dS1dt  = Ca* k_S0_S1 * y(13) + p.k_S2_S1 * y(2) - (p.k_S1_S0 + p.k_S1_S2) * y(1);
dS2dt  = p.k_S1_S2 * y(1) + p.k_S3_S2 * y(3) + k_S3a_S2 * y(16) - (p.k_S2_S1 + Ca* k_S2_S3 + p.MgATP_conc * k_S2_S3a) * y(2); 
dS3dt  = Ca * k_S2_S3 * y(2) + p.k_S4_S3 * y(4) - (p.k_S3_S2 + p.MgATP_conc * p.k_S3_S4) * y(3);
dS4dt  = p.MgATP_conc * p.k_S3_S4 * y(3) + p.k_S5_S4 * y(5) + Ca * k_S3a_S4 * y(16) - (p.k_S4_S3 + p.k_S4_S5 + k_S4_S3a) * y(4);
dS5dt  = p.k_S4_S5 * y(4) + p.k_S6a_S5 * y(7) + p.k_S6_S5 * p.MgADP_conc * y(6) - (p.k_S5_S4 + k_S5_S6a + p.k_S5_S6) * y(5);
dS6dt  = p.k_S5_S6 * y(5) + p.k_S7_S6 * y(8) - (p.k_S6_S5 * p.MgADP_conc + k_S6_S7) * y(6);
dS6adt = k_S5_S6a * y(5) + p.k_S7_S6a * p.MgADP_conc * y(8) - (p.k_S6a_S5 + p.k_S6a_S7) * y(7);
dS7dt  = k_S6_S7 * y(6) + p.k_S6a_S7 * y(7) + Ca_sr_conc * p.k_S8_S7 * y(9) - (p.k_S7_S6 + p.k_S7_S6a * p.MgADP_conc + k_S7_S8) * y(8);
dS8dt  = k_S7_S8 * y(8) + p.k_S9_S8 * y(10) - (Ca_sr_conc * p.k_S8_S7 + p.k_S8_S9) * y(9);
dS9dt  = p.k_S8_S9 * y(9) + Ca_sr_conc * p.k_S10_S9 * y(11) - (p.k_S9_S8 + k_S9_S10) * y(10);
dS10dt = k_S9_S10 * y(10) + p.k_S11_S10 * y(12) - (p.k_S10_S11 + Ca_sr_conc * p.k_S10_S9) * y(11);
dS11dt = p.k_S10_S11 * y(11) + Pi * k_S0_S11 * y(13) - (p.k_S11_S0 + p.k_S11_S10) * y(12);
dS0dt  = p.k_S11_S0 * y(12) + p.k_S1_S0 * y(1) + k_S1a_S0 * y(14) - (Ca * k_S0_S1 + Pi * k_S0_S11 + k_S0_S1a * p.MgATP_conc) * y(13); 
dS1adt = p.MgATP_conc * k_S0_S1a * y(13) + Ca * k_S2a_S1a * y(15) - (k_S1a_S0 + Ca * k_S1a_S2a) * y(14);
dS2adt = Ca * k_S1a_S2a * y(14) + k_S3a_S2a * y(16) + k_S1_S2a * p.MgATP_conc * y(1) - (k_S2a_S1a + k_S2a_S1 + k_S2a_S3a) * y(15);
dS3adt = p.MgATP_conc * k_S2_S3a * y(2) * k_S2a_S3a * y(15) * k_S4_S3a * y(4) - (k_S3a_S2 + k_S3a_S4 + k_S3a_S2a) * y(16); 

rates = [dS1dt;
         dS2dt;
         dS3dt;
         dS4dt;
         dS5dt;
         dS6dt;
         dS6adt;
         dS7dt;
         dS8dt;
         dS9dt;
         dS10dt;
         dS11dt;
         dS0dt;
         dS1adt;
         dS2adt;
         dS3adt;
         ];

end

[madhan ravi]

Provide the input datas , i mean the values

[Walter Roberson]

Structure references are not permitted on a 'function' line.

[Sophie Sophie]

Not certain what that means or how to fix that.

[Sophie Sophie]

@Mahan, the files are attached in a zip file in the original comment.

[Steven Lord]

In your function declaration line (broken across multiple lines to avoid scrolling in Answers):

 function [rates] = rhs(t,y, k_S0_S1, k_S2_S3, k_S7_S8, ...
    k_S9_S10, k_S5_S6a, k_S6_S7, k_S0_S11, k_S0_S1a, k_S1a_S0, ...
    k_S1a_S2a, k_S2a_S1a, k_S1_S2a, k_S2a_S1, k_S2a_S3a, k_S3a_S2a, ...
    k_S2_S3a, k_S3a_S2, k_S3a_S4, k_S4_S3a, Ca, p.Pi_conc)

the input arguments must be the name of a variable, the tilde operator, or varargin (as the last input.) Your last input argument is none of these; it is an expression referring to a field of a struct array or a property of an object. You need to change that to a variable name (or ~ if you don't need it to use it inside your rhs function but need your rhs function to accept it, to keep the syntax consistent with another tool's requirements for example.)