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 =7;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 23 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_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_5 in component main (mole)');
LEGEND_ALGEBRAIC(:,1) = strpad('q_6 in component main (mole)');
LEGEND_CONSTANTS(:,1) = strpad('q_tot in component main (mole)');
LEGEND_ALGEBRAIC(:,4) = strpad('v_1 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('v_2 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('v_3 in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,7) = strpad('v_4 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,2) = strpad('kappa_1 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,3) = strpad('kappa_2 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,4) = strpad('kappa_3 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,5) = strpad('kappa_4 in component main (mol_per_s)');
LEGEND_CONSTANTS(:,6) = strpad('K_1 in component main (per_mol)');
LEGEND_CONSTANTS(:,7) = strpad('K_2 in component main (per_mol)');
LEGEND_CONSTANTS(:,8) = strpad('K_s in component main (per_mol)');
LEGEND_CONSTANTS(:,9) = strpad('K_3 in component main (per_mol)');
LEGEND_CONSTANTS(:,10) = strpad('K_4 in component main (per_mol)');
LEGEND_CONSTANTS(:,11) = strpad('K_5 in component main (per_mol)');
LEGEND_CONSTANTS(:,12) = strpad('K_6 in component main (per_mol)');
LEGEND_CONSTANTS(:,13) = strpad('K_m in component main (per_mol)');
LEGEND_CONSTANTS(:,14) = strpad('k_m in component main (mole)');
LEGEND_CONSTANTS(:,15) = strpad('v_max in component main (mol_per_s)');
LEGEND_CONSTANTS(:,16) = strpad('k_f_1 in component main (per_mol_per_s)');
LEGEND_CONSTANTS(:,17) = strpad('k_r_1 in component main (per_s)');
LEGEND_CONSTANTS(:,18) = strpad('k_f_2 in component main (per_s)');
LEGEND_CONSTANTS(:,19) = strpad('k_r_2 in component main (per_mol_per_s)');
LEGEND_CONSTANTS(:,20) = strpad('k_f_3 in component main (per_s)');
LEGEND_CONSTANTS(:,21) = strpad('k_r_3 in component main (per_s)');
LEGEND_CONSTANTS(:,22) = strpad('k_f_4 in component main (per_s)');
LEGEND_CONSTANTS(:,23) = strpad('k_r_4 in component main (per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('v_SF in component main (mol_per_s)');
LEGEND_ALGEBRAIC(:,3) = strpad('v_MM 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_5 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 = [];
STATES(:,1) = 100;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,1) = 1;
CONSTANTS(:,2) = 100;
CONSTANTS(:,3) = 100;
CONSTANTS(:,4) = 1;
CONSTANTS(:,5) = 0.1;
CONSTANTS(:,6) = 0.1;
CONSTANTS(:,7) = 0.1;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 1;
CONSTANTS(:,13) = 1;
CONSTANTS(:,14) = 2.00000./( CONSTANTS(:,8).*(1.00000+CONSTANTS(:,4)./CONSTANTS(:,5)));
CONSTANTS(:,15) = ( CONSTANTS(:,1).*CONSTANTS(:,4).*CONSTANTS(:,13))./(1.00000+CONSTANTS(:,4)./CONSTANTS(:,5));
CONSTANTS(:,16) = CONSTANTS(:,2).*CONSTANTS(:,6).*CONSTANTS(:,12);
CONSTANTS(:,17) = CONSTANTS(:,2).*CONSTANTS(:,9);
CONSTANTS(:,18) = CONSTANTS(:,3).*CONSTANTS(:,10);
CONSTANTS(:,19) = CONSTANTS(:,3).*CONSTANTS(:,7).*CONSTANTS(:,11);
CONSTANTS(:,20) = CONSTANTS(:,4).*CONSTANTS(:,9);
CONSTANTS(:,21) = CONSTANTS(:,4).*CONSTANTS(:,10);
CONSTANTS(:,22) = CONSTANTS(:,5).*CONSTANTS(:,11);
CONSTANTS(:,23) = CONSTANTS(:,5).*CONSTANTS(:,12);
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) - STATES(:,3)) - STATES(:,4)) - STATES(:,5);
ALGEBRAIC(:,4) = CONSTANTS(:,16).*STATES(:,1).*ALGEBRAIC(:,1) - CONSTANTS(:,17).*STATES(:,3);
RATES(:,1) = - ALGEBRAIC(:,4);
ALGEBRAIC(:,5) = CONSTANTS(:,18).*STATES(:,4) - CONSTANTS(:,19).*STATES(:,2).*STATES(:,5);
RATES(:,2) = ALGEBRAIC(:,5) - 1000.00.*STATES(:,2);
ALGEBRAIC(:,6) = CONSTANTS(:,20).*STATES(:,3) - CONSTANTS(:,21).*STATES(:,4);
RATES(:,3) = ALGEBRAIC(:,4) - ALGEBRAIC(:,6);
RATES(:,4) = ALGEBRAIC(:,6) - ALGEBRAIC(:,5);
ALGEBRAIC(:,7) = CONSTANTS(:,22).*STATES(:,5) - CONSTANTS(:,23).*ALGEBRAIC(:,1);
RATES(:,5) = ALGEBRAIC(:,5) - ALGEBRAIC(:,7);
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) - STATES(:,3)) - STATES(:,4)) - STATES(:,5);
ALGEBRAIC(:,4) = CONSTANTS(:,16).*STATES(:,1).*ALGEBRAIC(:,1) - CONSTANTS(:,17).*STATES(:,3);
ALGEBRAIC(:,5) = CONSTANTS(:,18).*STATES(:,4) - CONSTANTS(:,19).*STATES(:,2).*STATES(:,5);
ALGEBRAIC(:,6) = CONSTANTS(:,20).*STATES(:,3) - CONSTANTS(:,21).*STATES(:,4);
ALGEBRAIC(:,7) = CONSTANTS(:,22).*STATES(:,5) - CONSTANTS(:,23).*ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = ( CONSTANTS(:,1).*CONSTANTS(:,4).*CONSTANTS(:,5).*CONSTANTS(:,13).*CONSTANTS(:,8).*(STATES(:,1) - STATES(:,2)))./( 2.00000.*CONSTANTS(:,5)+ (CONSTANTS(:,4)+CONSTANTS(:,5)).*CONSTANTS(:,8).*(STATES(:,1)+STATES(:,2))+ 2.00000.*CONSTANTS(:,4).*CONSTANTS(:,8).*CONSTANTS(:,8).*STATES(:,1).*STATES(:,2));
ALGEBRAIC(:,3) = ( CONSTANTS(:,15).*STATES(:,1))./(CONSTANTS(:,14)+STATES(:,1));
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