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 =0;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 15 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('time in component environment (hour)');
LEGEND_STATES(:,1) = strpad('c11 in component c11 (per_millilitre)');
LEGEND_CONSTANTS(:,1) = strpad('p1 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,2) = strpad('p2 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,3) = strpad('p5 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,4) = strpad('p6 in component model_parameters (per_hour)');
LEGEND_STATES(:,2) = strpad('c12 in component c12 (per_millilitre)');
LEGEND_STATES(:,3) = strpad('c21 in component c21 (per_millilitre)');
LEGEND_CONSTANTS(:,5) = strpad('p4 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,6) = strpad('p11 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,7) = strpad('p12 in component model_parameters (per_hour)');
LEGEND_STATES(:,4) = strpad('c22 in component c22 (per_millilitre)');
LEGEND_STATES(:,5) = strpad('c31 in component c31 (per_millilitre)');
LEGEND_CONSTANTS(:,8) = strpad('p3 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,9) = strpad('p7 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,10) = strpad('p8 in component model_parameters (per_hour)');
LEGEND_STATES(:,6) = strpad('c32 in component c32 (per_millilitre)');
LEGEND_STATES(:,7) = strpad('c41 in component c41 (per_millilitre)');
LEGEND_CONSTANTS(:,11) = strpad('p9 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,12) = strpad('p10 in component model_parameters (per_hour)');
LEGEND_STATES(:,8) = strpad('c42 in component c42 (per_millilitre)');
LEGEND_STATES(:,9) = strpad('c51 in component c51 (per_millilitre)');
LEGEND_CONSTANTS(:,13) = strpad('p13 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,14) = strpad('p14 in component model_parameters (per_hour)');
LEGEND_CONSTANTS(:,15) = strpad('p15 in component model_parameters (per_hour)');
LEGEND_STATES(:,10) = strpad('c52 in component c52 (per_millilitre)');
LEGEND_RATES(:,1) = strpad('d/dt c11 in component c11 (per_millilitre)');
LEGEND_RATES(:,3) = strpad('d/dt c21 in component c21 (per_millilitre)');
LEGEND_RATES(:,5) = strpad('d/dt c31 in component c31 (per_millilitre)');
LEGEND_RATES(:,7) = strpad('d/dt c41 in component c41 (per_millilitre)');
LEGEND_RATES(:,9) = strpad('d/dt c51 in component c51 (per_millilitre)');
LEGEND_RATES(:,2) = strpad('d/dt c12 in component c12 (per_millilitre)');
LEGEND_RATES(:,4) = strpad('d/dt c22 in component c22 (per_millilitre)');
LEGEND_RATES(:,6) = strpad('d/dt c32 in component c32 (per_millilitre)');
LEGEND_RATES(:,8) = strpad('d/dt c42 in component c42 (per_millilitre)');
LEGEND_RATES(:,10) = strpad('d/dt c52 in component c52 (per_millilitre)');
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) = 10000;
CONSTANTS(:,1) = 0.019538;
CONSTANTS(:,2) = 0.018813;
CONSTANTS(:,3) = 6.284029;
CONSTANTS(:,4) = 7.463440;
STATES(:,2) = 12000;
STATES(:,3) = 0;
CONSTANTS(:,5) = 0.023533;
CONSTANTS(:,6) = 3.934404;
CONSTANTS(:,7) = 4.167297;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,8) = 0.007776;
CONSTANTS(:,9) = 1.278630;
CONSTANTS(:,10) = 2.003106;
STATES(:,6) = 0;
STATES(:,7) = 0;
CONSTANTS(:,11) = 6.973662;
CONSTANTS(:,12) = 7.849130;
STATES(:,8) = 0;
STATES(:,9) = 0;
CONSTANTS(:,13) = 0.039758;
CONSTANTS(:,14) = 0.361026;
CONSTANTS(:,15) = 0.119765;
STATES(:,10) = 0;
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
RATES(:,1) = (( - CONSTANTS(:,1).*STATES(:,1) - CONSTANTS(:,2).*STATES(:,1)) - CONSTANTS(:,3).*STATES(:,1))+ CONSTANTS(:,4).*STATES(:,2);
RATES(:,3) = (( CONSTANTS(:,1).*STATES(:,1) - CONSTANTS(:,5).*STATES(:,3)) - CONSTANTS(:,6).*STATES(:,3))+ CONSTANTS(:,7).*STATES(:,4);
RATES(:,5) = (( CONSTANTS(:,2).*STATES(:,1) - CONSTANTS(:,8).*STATES(:,5)) - CONSTANTS(:,9).*STATES(:,5))+ CONSTANTS(:,10).*STATES(:,6);
RATES(:,7) = (( CONSTANTS(:,8).*STATES(:,5)+ CONSTANTS(:,5).*STATES(:,3)) - CONSTANTS(:,11).*STATES(:,7))+ CONSTANTS(:,12).*STATES(:,8);
RATES(:,9) = ( CONSTANTS(:,13).*STATES(:,1) - CONSTANTS(:,14).*STATES(:,9))+ CONSTANTS(:,15).*STATES(:,10);
RATES(:,2) = CONSTANTS(:,3).*STATES(:,1) - CONSTANTS(:,4).*STATES(:,2);
RATES(:,4) = CONSTANTS(:,6).*STATES(:,3) - CONSTANTS(:,7).*STATES(:,4);
RATES(:,6) = CONSTANTS(:,9).*STATES(:,5) - CONSTANTS(:,10).*STATES(:,6);
RATES(:,8) = CONSTANTS(:,11).*STATES(:,7) - CONSTANTS(:,12).*STATES(:,8);
RATES(:,10) = CONSTANTS(:,14).*STATES(:,9) - CONSTANTS(:,15).*STATES(:,10);
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
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