ode solver error, too many argyments etc

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Sophie Sophie
Sophie Sophie 2018-10-16
评论： Walter Roberson 2018-10-17
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!
  1 个评论
Walter Roberson
Walter Roberson 2018-10-16
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

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采纳的回答

Sophie Sophie
Sophie Sophie 2018-10-16
Can you kindly give me an example?
Do I do this everywhere that rhs is mentioned?
  5 个评论
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Sophie Sophie
Sophie Sophie 2018-10-17
Casr_conc is refined in getParams.m
It’s a set value.
Pi_conc is also defined there.
Walter Roberson
Walter Roberson 2018-10-17
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 ?

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更多回答（3 个）

Torsten
Torsten 2018-10-16
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.
madhan ravi
madhan ravi 2018-10-16
编辑：madhan ravi 2018-10-16
[t,y] = ode15s(@rhs, tspan, ic, 'AbsTol', 1e-8, 'RelTol', 1e-7);
Sophie Sophie
Sophie Sophie 2018-10-16
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
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Sophie Sophie
Sophie Sophie 2018-10-16
@Mahan, the files are attached in a zip file in the original comment.
Steven Lord
Steven Lord 2018-10-16
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.)

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