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 =2;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 20 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 environment (second)');
LEGEND_CONSTANTS(:,1) = strpad('D_Ca in component parameters (second)');
LEGEND_CONSTANTS(:,2) = strpad('k_1 in component parameters (per_second)');
LEGEND_CONSTANTS(:,3) = strpad('k_2 in component parameters (per_second)');
LEGEND_CONSTANTS(:,4) = strpad('f in component parameters (per_second)');
LEGEND_CONSTANTS(:,5) = strpad('g in component parameters (per_second)');
LEGEND_CONSTANTS(:,6) = strpad('Ca_max in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('Total_Tn in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('Total_CB in component parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ca_t in component Ca_t (dimensionless)');
LEGEND_STATES(:,1) = strpad('TnCa in component TnCa (dimensionless)');
LEGEND_STATES(:,2) = strpad('CB_on in component CB_on (dimensionless)');
LEGEND_STATES(:,3) = strpad('CumCB_on in component CumCB (dimensionless)');
LEGEND_STATES(:,4) = strpad('CumCB_off in component CumCB (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('F in component force_development (force)');
LEGEND_STATES(:,5) = strpad('FTI in component force_development (force_second)');
LEGEND_CONSTANTS(:,16) = strpad('FLA in component force_development (energy)');
LEGEND_CONSTANTS(:,9) = strpad('phi in component force_development (force)');
LEGEND_CONSTANTS(:,10) = strpad('s in component force_development (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('L in component force_development (meter)');
LEGEND_CONSTANTS(:,12) = strpad('L_0 in component force_development (meter)');
LEGEND_CONSTANTS(:,13) = strpad('F_max in component force_development (force)');
LEGEND_CONSTANTS(:,18) = strpad('ATP in component ATP (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('ATP_energy in component ATP (energy)');
LEGEND_CONSTANTS(:,14) = strpad('epsilon in component ATP (energy)');
LEGEND_CONSTANTS(:,15) = strpad('CumCB_on_end in component ATP (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('Efficiency in component equations_main (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('Economy in component equations_main (second_per_meter)');
LEGEND_RATES(:,1) = strpad('d/dt TnCa in component TnCa (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt CB_on in component CB_on (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt CumCB_on in component CumCB (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt CumCB_off in component CumCB (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt FTI in component force_development (force_second)');
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) = 0.1;
CONSTANTS(:,2) = 40;
CONSTANTS(:,3) = 20;
CONSTANTS(:,4) = 10;
CONSTANTS(:,5) = 10;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 1;
STATES(:,1) = 0;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 0;
CONSTANTS(:,13) = 0.228;
CONSTANTS(:,14) = 1;
CONSTANTS(:,15) = 1;
CONSTANTS(:,16) = CONSTANTS(:,13).*CONSTANTS(:,10).*(CONSTANTS(:,11) - CONSTANTS(:,12));
CONSTANTS(:,17) = (CONSTANTS(:,9)./CONSTANTS(:,14)).*(1.00000./CONSTANTS(:,5));
CONSTANTS(:,18) = CONSTANTS(:,15);
CONSTANTS(:,19) = CONSTANTS(:,18).*CONSTANTS(:,14);
CONSTANTS(:,20) = CONSTANTS(:,16)./CONSTANTS(:,19);
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(:,2) = CONSTANTS(:,4).*STATES(:,1).*(CONSTANTS(:,8) - STATES(:,2)) - CONSTANTS(:,5).*STATES(:,2);
RATES(:,3) = CONSTANTS(:,4).*STATES(:,1).*(CONSTANTS(:,8) - STATES(:,2));
RATES(:,4) = CONSTANTS(:,5).*STATES(:,2);
ALGEBRAIC(:,1) = piecewise({VOI>=0.00000&VOI< 0.300000.*CONSTANTS(:,1), ( CONSTANTS(:,6).*(1.00000+ sin(( pi.*(VOI./CONSTANTS(:,1) - 0.150000))./0.300000)))./2.00000 , VOI>= 0.300000.*CONSTANTS(:,1)&VOI<CONSTANTS(:,1), ( CONSTANTS(:,6).*(1.00000 - sin(( pi.*(VOI./CONSTANTS(:,1) - 0.650000))./0.700000)))./2.00000 }, 0.00000);
RATES(:,1) = CONSTANTS(:,2).*ALGEBRAIC(:,1).*(CONSTANTS(:,7) - STATES(:,1)) - CONSTANTS(:,3).*STATES(:,1);
ALGEBRAIC(:,2) = STATES(:,2).*CONSTANTS(:,9);
RATES(:,5) = ALGEBRAIC(:,2);
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) = piecewise({VOI>=0.00000&VOI< 0.300000.*CONSTANTS(:,1), ( CONSTANTS(:,6).*(1.00000+ sin(( pi.*(VOI./CONSTANTS(:,1) - 0.150000))./0.300000)))./2.00000 , VOI>= 0.300000.*CONSTANTS(:,1)&VOI<CONSTANTS(:,1), ( CONSTANTS(:,6).*(1.00000 - sin(( pi.*(VOI./CONSTANTS(:,1) - 0.650000))./0.700000)))./2.00000 }, 0.00000);
ALGEBRAIC(:,2) = STATES(:,2).*CONSTANTS(:,9);
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