Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =16;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 11 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('t in component main (second)');
LEGEND_CONSTANTS(:,1) = strpad('RT in component main (J_per_mol)');
LEGEND_STATES(:,1) = strpad('q_1 in component main (mole)');
LEGEND_STATES(:,2) = strpad('q_2 in component main (mole)');
LEGEND_STATES(:,3) = strpad('q_3 in component main (mole)');
LEGEND_STATES(:,4) = strpad('q_4 in component main (mole)');
LEGEND_STATES(:,5) = strpad('q_e0 in component main (mole)');
LEGEND_STATES(:,6) = strpad('q_e1 in component main (mole)');
LEGEND_ALGEBRAIC(:,15) = strpad('v_1 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,16) = strpad('v_2 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,1) = strpad('u_1 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,3) = strpad('u_2 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,5) = strpad('u_3 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('u_4 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,9) = strpad('u_e0 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,12) = strpad('u_e1 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,10) = strpad('u_f_1 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,13) = strpad('u_r_1 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,14) = strpad('u_f_2 in component main (J_per_mol)');
LEGEND_ALGEBRAIC(:,11) = strpad('u_r_2 in component main (J_per_mol)');
LEGEND_CONSTANTS(:,2) = strpad('K_q_1 in component main (per_mol)');
LEGEND_CONSTANTS(:,3) = strpad('K_q_2 in component main (per_mol)');
LEGEND_CONSTANTS(:,4) = strpad('K_q_3 in component main (per_mol)');
LEGEND_CONSTANTS(:,5) = strpad('K_q_4 in component main (per_mol)');
LEGEND_CONSTANTS(:,6) = strpad('K_q_e0 in component main (per_mol)');
LEGEND_CONSTANTS(:,7) = strpad('K_q_e1 in component main (per_mol)');
LEGEND_CONSTANTS(:,8) = strpad('kappa_1 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,9) = strpad('kappa_2 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('q_e_tot in component main (mole)');
LEGEND_ALGEBRAIC(:,4) = strpad('A_f in component main (per_mol3_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('A_r in component main (per_mol3_per_s)');
LEGEND_CONSTANTS(:,10) = strpad('B_f in component main (per_mol3)');
LEGEND_CONSTANTS(:,11) = strpad('B_r in component main (per_mol3)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_SS in component main (mol_per_s)');
LEGEND_RATES(:,1) = strpad('d/dt q_1 in component main (mole)');
LEGEND_RATES(:,2) = strpad('d/dt q_2 in component main (mole)');
LEGEND_RATES(:,3) = strpad('d/dt q_3 in component main (mole)');
LEGEND_RATES(:,4) = strpad('d/dt q_4 in component main (mole)');
LEGEND_RATES(:,5) = strpad('d/dt q_e0 in component main (mole)');
LEGEND_RATES(:,6) = strpad('d/dt q_e1 in component main (mole)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
CONSTANTS(:,1) = 2578.73058;
STATES(:,1) = 3;
STATES(:,2) = 1;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 1;
STATES(:,6) = 1;
CONSTANTS(:,2) = 2;
CONSTANTS(:,3) = 2;
CONSTANTS(:,4) = 2;
CONSTANTS(:,5) = 2;
CONSTANTS(:,6) = 2;
CONSTANTS(:,7) = 2;
CONSTANTS(:,8) = 0.20;
CONSTANTS(:,9) = 0.1;
CONSTANTS(:,10) = (( (CONSTANTS(:,6)./CONSTANTS(:,7)).*CONSTANTS(:,8))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,2).*power(CONSTANTS(:,3), 2.00000);
CONSTANTS(:,11) = (( (CONSTANTS(:,6)./CONSTANTS(:,7)).*CONSTANTS(:,8))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,4).*power(CONSTANTS(:,5), 2.00000);
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = CONSTANTS(:,1).*log( CONSTANTS(:,2).*STATES(:,1));
ALGEBRAIC(:,3) = CONSTANTS(:,1).*log( CONSTANTS(:,3).*STATES(:,2));
ALGEBRAIC(:,9) = CONSTANTS(:,1).*log( CONSTANTS(:,6).*STATES(:,5));
ALGEBRAIC(:,10) = ALGEBRAIC(:,1)+ 2.00000.*ALGEBRAIC(:,3)+ALGEBRAIC(:,9);
ALGEBRAIC(:,12) = CONSTANTS(:,1).*log( CONSTANTS(:,7).*STATES(:,6));
ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
ALGEBRAIC(:,15) = CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,13)./CONSTANTS(:,1)));
RATES(:,1) = - ALGEBRAIC(:,15);
RATES(:,2) = - 2.00000.*ALGEBRAIC(:,15);
ALGEBRAIC(:,14) = ALGEBRAIC(:,12);
ALGEBRAIC(:,5) = CONSTANTS(:,1).*log( CONSTANTS(:,4).*STATES(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,1).*log( CONSTANTS(:,5).*STATES(:,4));
ALGEBRAIC(:,11) = ALGEBRAIC(:,5)+ 2.00000.*ALGEBRAIC(:,7)+ALGEBRAIC(:,9);
ALGEBRAIC(:,16) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,14)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,11)./CONSTANTS(:,1)));
RATES(:,3) = ALGEBRAIC(:,16);
RATES(:,4) = 2.00000.*ALGEBRAIC(:,16);
RATES(:,5) = ALGEBRAIC(:,16) - ALGEBRAIC(:,15);
RATES(:,6) = ALGEBRAIC(:,15) - ALGEBRAIC(:,16);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = CONSTANTS(:,1).*log( CONSTANTS(:,2).*STATES(:,1));
ALGEBRAIC(:,3) = CONSTANTS(:,1).*log( CONSTANTS(:,3).*STATES(:,2));
ALGEBRAIC(:,9) = CONSTANTS(:,1).*log( CONSTANTS(:,6).*STATES(:,5));
ALGEBRAIC(:,10) = ALGEBRAIC(:,1)+ 2.00000.*ALGEBRAIC(:,3)+ALGEBRAIC(:,9);
ALGEBRAIC(:,12) = CONSTANTS(:,1).*log( CONSTANTS(:,7).*STATES(:,6));
ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
ALGEBRAIC(:,15) = CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,13)./CONSTANTS(:,1)));
ALGEBRAIC(:,14) = ALGEBRAIC(:,12);
ALGEBRAIC(:,5) = CONSTANTS(:,1).*log( CONSTANTS(:,4).*STATES(:,3));
ALGEBRAIC(:,7) = CONSTANTS(:,1).*log( CONSTANTS(:,5).*STATES(:,4));
ALGEBRAIC(:,11) = ALGEBRAIC(:,5)+ 2.00000.*ALGEBRAIC(:,7)+ALGEBRAIC(:,9);
ALGEBRAIC(:,16) = CONSTANTS(:,9).*(exp(ALGEBRAIC(:,14)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,11)./CONSTANTS(:,1)));
ALGEBRAIC(:,2) = STATES(:,5)+STATES(:,6);
ALGEBRAIC(:,4) = (( ALGEBRAIC(:,2).*CONSTANTS(:,6).*CONSTANTS(:,8).*CONSTANTS(:,9))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,2).*power(CONSTANTS(:,3), 2.00000);
ALGEBRAIC(:,6) = (( ALGEBRAIC(:,2).*CONSTANTS(:,6).*CONSTANTS(:,8).*CONSTANTS(:,9))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,4).*power(CONSTANTS(:,5), 2.00000);
ALGEBRAIC(:,8) = ( ALGEBRAIC(:,4).*STATES(:,1).*power(STATES(:,2), 2.00000) - ALGEBRAIC(:,6).*STATES(:,3).*power(STATES(:,4), 2.00000))./(1.00000+ CONSTANTS(:,10).*STATES(:,1).*power(STATES(:,2), 2.00000)+ CONSTANTS(:,11).*STATES(:,3).*power(STATES(:,4), 2.00000));
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end