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 =1;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 34 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('x in component environment (nanometer)');
LEGEND_STATES(:,1) = strpad('n in component Crossbridges_attached (dimensionless)');
LEGEND_STATES(:,2) = strpad('A_c in component Actin_free (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('f in component f (per_second)');
LEGEND_CONSTANTS(:,25) = strpad('g in component g (per_second)');
LEGEND_CONSTANTS(:,2) = strpad('h in component Crossbridges_attached (nanometer)');
LEGEND_CONSTANTS(:,3) = strpad('f_1 in component f (per_second)');
LEGEND_CONSTANTS(:,4) = strpad('g_1 in component g (per_second)');
LEGEND_CONSTANTS(:,5) = strpad('g_2 in component g (per_second)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ca_f in component Ca_sarcoplasm (molar)');
LEGEND_CONSTANTS(:,6) = strpad('t_d in component Ca_sarcoplasm (second)');
LEGEND_CONSTANTS(:,7) = strpad('a_1 in component Ca_sarcoplasm (per_second_squared)');
LEGEND_CONSTANTS(:,8) = strpad('b_1 in component Ca_sarcoplasm (per_second_squared)');
LEGEND_CONSTANTS(:,9) = strpad('Ca_0 in component Ca_sarcoplasm (molar)');
LEGEND_CONSTANTS(:,10) = strpad('c_1 in component Actin_free (per_second)');
LEGEND_CONSTANTS(:,27) = strpad('c_2 in component Actin_free (per_second)');
LEGEND_CONSTANTS(:,11) = strpad('c_2_0 in component Actin_free (per_second)');
LEGEND_CONSTANTS(:,12) = strpad('k_i in component Actin_free (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('s_h in component s_h (muscle_length)');
LEGEND_CONSTANTS(:,13) = strpad('q in component Actin_free (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('AT_0 in component Actin_free (dimensionless)');
LEGEND_CONSTANTS(:,33) = strpad('F_SE in component Series_Elastic_Element (force)');
LEGEND_CONSTANTS(:,15) = strpad('alpha_s in component Series_Elastic_Element (force)');
LEGEND_CONSTANTS(:,16) = strpad('beta_s in component Series_Elastic_Element (muscle_length)');
LEGEND_CONSTANTS(:,32) = strpad('x_s in component SE_constants (muscle_length)');
LEGEND_CONSTANTS(:,17) = strpad('x_so in component Series_Elastic_Element (muscle_length)');
LEGEND_CONSTANTS(:,31) = strpad('X_M_0 in component X_0 (muscle_length)');
LEGEND_CONSTANTS(:,18) = strpad('L_max in component Series_Elastic_Element (muscle_length)');
LEGEND_CONSTANTS(:,29) = strpad('F_PE in component Parallel_Elastic_Element (force)');
LEGEND_CONSTANTS(:,19) = strpad('alpha_p in component Parallel_Elastic_Element (force)');
LEGEND_CONSTANTS(:,20) = strpad('beta_p in component Parallel_Elastic_Element (muscle_length)');
LEGEND_CONSTANTS(:,28) = strpad('x_p in component PE_constants (muscle_length)');
LEGEND_CONSTANTS(:,21) = strpad('x_po in component Parallel_Elastic_Element (muscle_length)');
LEGEND_CONSTANTS(:,34) = strpad('F_CE in component Contractile_Element (force)');
LEGEND_CONSTANTS(:,22) = strpad('F_PL in component s_h (force)');
LEGEND_CONSTANTS(:,30) = strpad('X_S_0 in component X_0 (muscle_length)');
LEGEND_CONSTANTS(:,23) = strpad('F_PL in component X_0 (force)');
LEGEND_RATES(:,1) = strpad('d/dt n in component Crossbridges_attached (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt A_c in component Actin_free (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) = 10;
STATES(:,1) = 0;
STATES(:,2) = 1;
CONSTANTS(:,2) = 12;
CONSTANTS(:,3) = 70;
CONSTANTS(:,4) = 40;
CONSTANTS(:,5) = 240;
CONSTANTS(:,6) = 0.3;
CONSTANTS(:,7) = 200;
CONSTANTS(:,8) = 5;
CONSTANTS(:,9) = 0.45e-6;
CONSTANTS(:,10) = 200e12;
CONSTANTS(:,11) = 20;
CONSTANTS(:,12) = 30.9;
CONSTANTS(:,13) = 1.45;
CONSTANTS(:,14) = 2;
CONSTANTS(:,15) = 0.1027;
CONSTANTS(:,16) = 20;
CONSTANTS(:,17) = 0.0387;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = 0.00224;
CONSTANTS(:,20) = 20;
CONSTANTS(:,21) = 0.221;
CONSTANTS(:,22) = 3;
CONSTANTS(:,23) = 3;
CONSTANTS(:,24) = piecewise({CONSTANTS(:,1)<0.00000, 0.00000 , CONSTANTS(:,1)>=0.00000&CONSTANTS(:,1)<CONSTANTS(:,2), ( CONSTANTS(:,3).*CONSTANTS(:,1))./CONSTANTS(:,2) }, 0.00000);
CONSTANTS(:,25) = piecewise({CONSTANTS(:,1)<0.00000, CONSTANTS(:,5) , CONSTANTS(:,1)>=0.00000&CONSTANTS(:,1)<CONSTANTS(:,2), ( CONSTANTS(:,4).*CONSTANTS(:,1))./CONSTANTS(:,2) }, ( CONSTANTS(:,4).*CONSTANTS(:,1))./CONSTANTS(:,2));
CONSTANTS(:,26) = CONSTANTS(:,21) - ( 1.00000.*1.00000.*arbitrary_log(1.00000+CONSTANTS(:,22)./CONSTANTS(:,19), 10))./CONSTANTS(:,20);
CONSTANTS(:,27) = CONSTANTS(:,11).*exp( CONSTANTS(:,12).*power(CONSTANTS(:,26)./1.00000, CONSTANTS(:,13)));
CONSTANTS(:,28) = CONSTANTS(:,21) - CONSTANTS(:,26);
CONSTANTS(:,29) = CONSTANTS(:,19).*(exp(( CONSTANTS(:,20).*CONSTANTS(:,28))./( 1.00000.*1.00000)) - 1.00000);
CONSTANTS(:,30) = ( 1.00000.*1.00000.*arbitrary_log(1.00000+CONSTANTS(:,23)./CONSTANTS(:,15), 10))./CONSTANTS(:,16);
CONSTANTS(:,31) = ((CONSTANTS(:,30)+CONSTANTS(:,18)) - CONSTANTS(:,26)) - CONSTANTS(:,17);
CONSTANTS(:,32) = (CONSTANTS(:,17)+CONSTANTS(:,26)+CONSTANTS(:,31)) - CONSTANTS(:,18);
CONSTANTS(:,33) = CONSTANTS(:,15).*(exp(( CONSTANTS(:,16).*CONSTANTS(:,32))./( 1.00000.*1.00000)) - 1.00000);
CONSTANTS(:,34) = CONSTANTS(:,33) - CONSTANTS(:,29);
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(:,24).*(STATES(:,2) - STATES(:,1)) - CONSTANTS(:,25).*STATES(:,1);
ALGEBRAIC(:,1) = CONSTANTS(:,9).*abs(1.00000 - exp( - CONSTANTS(:,7).*power(VOI, 2.00000))).*exp( - CONSTANTS(:,8).*power(VOI - CONSTANTS(:,6), 2.00000));
RATES(:,2) = CONSTANTS(:,10).*power(ALGEBRAIC(:,1)./1.00000, 2.00000).*(CONSTANTS(:,14) - STATES(:,2)) - CONSTANTS(:,27).*STATES(:,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) = CONSTANTS(:,9).*abs(1.00000 - exp( - CONSTANTS(:,7).*power(VOI, 2.00000))).*exp( - CONSTANTS(:,8).*power(VOI - CONSTANTS(:,6), 2.00000));
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
% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
x = log(a) ./ log(base);
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