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 =9;
end
% There are a total of 5 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('time in component environment (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('f in component f (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('a in component f (dimensionless)');
LEGEND_STATES(:,1) = strpad('r in component r (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('p in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('beta in component r (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('alpha in component r (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('ur0 in component ur0 (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('m in component m (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('r0 in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('y in component y (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('r1 in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('ur1 in component ur1 (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('z in component z (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('t1 in component model_parameters (dimensionless)');
LEGEND_STATES(:,2) = strpad('x1 in component x1 (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('q in component q (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('d in component q (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('k in component q (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('uz in component uz (dimensionless)');
LEGEND_STATES(:,3) = strpad('x2 in component x2 (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('t2 in component model_parameters (dimensionless)');
LEGEND_STATES(:,4) = strpad('x3 in component x3 (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('phi in component phi (dimensionless)');
LEGEND_STATES(:,5) = strpad('h in component h (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('t4 in component model_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt r in component r (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt x1 in component x1 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt x2 in component x2 (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt x3 in component x3 (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt h in component h (dimensionless)');
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) = 1.0;
STATES(:,1) = 0.5;
CONSTANTS(:,2) = 1.05;
CONSTANTS(:,3) = 1.0;
CONSTANTS(:,4) = 1.0;
CONSTANTS(:,5) = 0.5;
CONSTANTS(:,6) = 1.2;
CONSTANTS(:,7) = 0.1;
STATES(:,2) = 0.0;
CONSTANTS(:,8) = 5.0;
CONSTANTS(:,9) = 10.5;
STATES(:,3) = 0.0;
CONSTANTS(:,10) = 0.5;
STATES(:,4) = 0.0;
STATES(:,5) = 0.0;
CONSTANTS(:,11) = 20.0;
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(:,4) = (STATES(:,3) - STATES(:,4))./CONSTANTS(:,10);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*CONSTANTS(:,2).*power(STATES(:,1), 4.00000);
RATES(:,5) = (ALGEBRAIC(:,1) - STATES(:,5))./CONSTANTS(:,11);
ALGEBRAIC(:,3) = piecewise({STATES(:,1)>CONSTANTS(:,6), 1.00000 }, 0.00000);
ALGEBRAIC(:,5) = (STATES(:,1) - CONSTANTS(:,6)).*ALGEBRAIC(:,3);
RATES(:,2) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,7);
ALGEBRAIC(:,6) = piecewise({STATES(:,1)>CONSTANTS(:,5), 1.00000 }, 0.00000);
ALGEBRAIC(:,2) = piecewise({STATES(:,1)<0.250000, 0.00000 , STATES(:,1)>2.00000, 0.00000 }, 1.00000 - 1.30612.*(STATES(:,1) - 1.12500).*(STATES(:,1) - 1.12500));
ALGEBRAIC(:,4) = STATES(:,4).*ALGEBRAIC(:,2);
RATES(:,1) = CONSTANTS(:,3).*( CONSTANTS(:,2).*STATES(:,1) - ( CONSTANTS(:,4).*power(STATES(:,1) - CONSTANTS(:,5), 2.00000).*ALGEBRAIC(:,6)+ALGEBRAIC(:,4)));
ALGEBRAIC(:,7) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,7);
ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,7)>0.00000, 1.00000 }, 0.00000);
ALGEBRAIC(:,9) = CONSTANTS(:,9).*(1.00000 - exp( - ( CONSTANTS(:,8).*ALGEBRAIC(:,7)))).*ALGEBRAIC(:,8);
RATES(:,3) = (ALGEBRAIC(:,9) - STATES(:,3))./CONSTANTS(:,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
ALGEBRAIC(:,1) = CONSTANTS(:,1).*CONSTANTS(:,2).*power(STATES(:,1), 4.00000);
ALGEBRAIC(:,3) = piecewise({STATES(:,1)>CONSTANTS(:,6), 1.00000 }, 0.00000);
ALGEBRAIC(:,5) = (STATES(:,1) - CONSTANTS(:,6)).*ALGEBRAIC(:,3);
ALGEBRAIC(:,6) = piecewise({STATES(:,1)>CONSTANTS(:,5), 1.00000 }, 0.00000);
ALGEBRAIC(:,2) = piecewise({STATES(:,1)<0.250000, 0.00000 , STATES(:,1)>2.00000, 0.00000 }, 1.00000 - 1.30612.*(STATES(:,1) - 1.12500).*(STATES(:,1) - 1.12500));
ALGEBRAIC(:,4) = STATES(:,4).*ALGEBRAIC(:,2);
ALGEBRAIC(:,7) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,7);
ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,7)>0.00000, 1.00000 }, 0.00000);
ALGEBRAIC(:,9) = CONSTANTS(:,9).*(1.00000 - exp( - ( CONSTANTS(:,8).*ALGEBRAIC(:,7)))).*ALGEBRAIC(:,8);
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
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