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 =8;
end
% There are a total of 1 entries in each of the rate and state variable arrays.
% There are a total of 12 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 (second)');
LEGEND_ALGEBRAIC(:,1) = strpad('F_isom in component contraction (newton)');
LEGEND_CONSTANTS(:,12) = strpad('c in component contraction (newton)');
LEGEND_STATES(:,1) = strpad('L_ce in component contraction (metre)');
LEGEND_CONSTANTS(:,1) = strpad('L_ce_opt in component contraction (metre)');
LEGEND_ALGEBRAIC(:,2) = strpad('L in component contraction (metre)');
LEGEND_CONSTANTS(:,2) = strpad('width in component contraction (metre)');
LEGEND_CONSTANTS(:,3) = strpad('Factor in component contraction (per_second)');
LEGEND_CONSTANTS(:,4) = strpad('A_REL in component contraction (newton)');
LEGEND_CONSTANTS(:,5) = strpad('B_REL in component contraction (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('v_ce in component contraction (metre_per_second)');
LEGEND_ALGEBRAIC(:,6) = strpad('F in component contraction (newton)');
LEGEND_CONSTANTS(:,6) = strpad('F_max in component contraction (newton)');
LEGEND_CONSTANTS(:,7) = strpad('q in component contraction (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('c1 in component contraction (per_second)');
LEGEND_ALGEBRAIC(:,3) = strpad('c2 in component contraction (newton)');
LEGEND_ALGEBRAIC(:,7) = strpad('c3 in component contraction (per_newton_second)');
LEGEND_CONSTANTS(:,8) = strpad('slope in component contraction (newton)');
LEGEND_CONSTANTS(:,9) = strpad('F_asympt in component contraction (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('L_see in component contraction (metre)');
LEGEND_CONSTANTS(:,10) = strpad('L_slack in component contraction (metre)');
LEGEND_CONSTANTS(:,11) = strpad('alpha in component contraction (newton_per_metre)');
LEGEND_RATES(:,1) = strpad('d/dt L_ce in component contraction (metre)');
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) = 0.05;
CONSTANTS(:,1) = 0.055;
CONSTANTS(:,2) = 0.888;
CONSTANTS(:,3) = 1;
CONSTANTS(:,4) = 0.41;
CONSTANTS(:,5) = 5.2;
CONSTANTS(:,6) = 3277.4;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 2;
CONSTANTS(:,9) = 1.5;
CONSTANTS(:,10) = 0.42;
CONSTANTS(:,11) = 1449.027;
CONSTANTS(:,12) = - 1.00000./power(CONSTANTS(:,2), 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(:,12).*power(STATES(:,1)./CONSTANTS(:,1), 2.00000) - ( 2.00000.*CONSTANTS(:,12).*STATES(:,1))./CONSTANTS(:,1))+CONSTANTS(:,12)+1.00000;
ALGEBRAIC(:,2) = piecewise({VOI<=1.00000, 1.00000 , VOI>1.00000&VOI<5.00000, 0.920000 }, 0.900000);
ALGEBRAIC(:,4) = ALGEBRAIC(:,2) - STATES(:,1);
ALGEBRAIC(:,6) = CONSTANTS(:,11).*(ALGEBRAIC(:,4) - CONSTANTS(:,10));
ALGEBRAIC(:,8) = - CONSTANTS(:,3).*STATES(:,1).*(( (ALGEBRAIC(:,1)+CONSTANTS(:,4)).*CONSTANTS(:,5))./( 1.00000.*(ALGEBRAIC(:,6)./( CONSTANTS(:,6).*CONSTANTS(:,7)))+CONSTANTS(:,4)) - CONSTANTS(:,5));
RATES(:,1) = ALGEBRAIC(:,8);
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(:,12).*power(STATES(:,1)./CONSTANTS(:,1), 2.00000) - ( 2.00000.*CONSTANTS(:,12).*STATES(:,1))./CONSTANTS(:,1))+CONSTANTS(:,12)+1.00000;
ALGEBRAIC(:,2) = piecewise({VOI<=1.00000, 1.00000 , VOI>1.00000&VOI<5.00000, 0.920000 }, 0.900000);
ALGEBRAIC(:,4) = ALGEBRAIC(:,2) - STATES(:,1);
ALGEBRAIC(:,6) = CONSTANTS(:,11).*(ALGEBRAIC(:,4) - CONSTANTS(:,10));
ALGEBRAIC(:,8) = - CONSTANTS(:,3).*STATES(:,1).*(( (ALGEBRAIC(:,1)+CONSTANTS(:,4)).*CONSTANTS(:,5))./( 1.00000.*(ALGEBRAIC(:,6)./( CONSTANTS(:,6).*CONSTANTS(:,7)))+CONSTANTS(:,4)) - CONSTANTS(:,5));
ALGEBRAIC(:,3) = ALGEBRAIC(:,1).*CONSTANTS(:,9);
ALGEBRAIC(:,5) = ( CONSTANTS(:,3).*CONSTANTS(:,5).*power(ALGEBRAIC(:,1)+ALGEBRAIC(:,3), 2.00000))./( (ALGEBRAIC(:,1)+CONSTANTS(:,4)).*CONSTANTS(:,8));
ALGEBRAIC(:,7) = ALGEBRAIC(:,5)./(ALGEBRAIC(:,1)+ALGEBRAIC(:,3));
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