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 =20;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 48 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 BG_Hpump (second)');
LEGEND_CONSTANTS(:,1) = strpad('R in component params_BG (J_per_K_mol)');
LEGEND_CONSTANTS(:,2) = strpad('T in component params_BG (kelvin)');
LEGEND_CONSTANTS(:,3) = strpad('F in component params_BG (C_per_mol)');
LEGEND_CONSTANTS(:,4) = strpad('K_Hi in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,37) = strpad('q_init_Hi in component params_BG (fmol)');
LEGEND_CONSTANTS(:,5) = strpad('K_Ho in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,34) = strpad('q_init_Ho in component params_BG (fmol)');
LEGEND_CONSTANTS(:,6) = strpad('K_Pi in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,40) = strpad('q_init_Pi in component params_BG (fmol)');
LEGEND_CONSTANTS(:,7) = strpad('K_ATPi in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,43) = strpad('q_init_ATPi in component params_BG (fmol)');
LEGEND_CONSTANTS(:,8) = strpad('K_ADPi in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,46) = strpad('q_init_ADPi in component params_BG (fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_1 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('q_init_1 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,11) = strpad('K_2 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,12) = strpad('q_init_2 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,13) = strpad('K_3 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,14) = strpad('q_init_3 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,15) = strpad('K_4 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,16) = strpad('q_init_4 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,17) = strpad('kappa_r1 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,18) = strpad('kappa_r2 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,19) = strpad('kappa_r3 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,20) = strpad('kappa_r4 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,39) = strpad('mu_Hi in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,36) = strpad('mu_Ho in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,42) = strpad('mu_Pi in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,45) = strpad('mu_ATPi in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,48) = strpad('mu_ADPi in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,1) = strpad('mu_1 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,19) = strpad('v_1 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('mu_2 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,11) = strpad('v_2 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,3) = strpad('mu_3 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,15) = strpad('v_3 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,4) = strpad('mu_4 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,20) = strpad('v_4 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('A_f_r1 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('v_r1 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('A_r_r1 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,8) = strpad('A_f_r2 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,10) = strpad('v_r2 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,9) = strpad('A_r_r2 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,12) = strpad('A_f_r3 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,14) = strpad('v_r3 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,13) = strpad('A_r_r3 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,16) = strpad('A_f_r4 in component BG_Hpump (J_per_mol)');
LEGEND_ALGEBRAIC(:,18) = strpad('v_r4 in component BG_Hpump (fmol_per_s)');
LEGEND_ALGEBRAIC(:,17) = strpad('A_r_r4 in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,38) = strpad('q_Hi in component BG_Hpump (fmol)');
LEGEND_CONSTANTS(:,35) = strpad('q_Ho in component BG_Hpump (fmol)');
LEGEND_CONSTANTS(:,41) = strpad('q_Pi in component BG_Hpump (fmol)');
LEGEND_CONSTANTS(:,44) = strpad('q_ATPi in component BG_Hpump (fmol)');
LEGEND_CONSTANTS(:,47) = strpad('q_ADPi in component BG_Hpump (fmol)');
LEGEND_STATES(:,1) = strpad('q_1 in component BG_Hpump (fmol)');
LEGEND_STATES(:,2) = strpad('q_2 in component BG_Hpump (fmol)');
LEGEND_STATES(:,3) = strpad('q_3 in component BG_Hpump (fmol)');
LEGEND_STATES(:,4) = strpad('q_4 in component BG_Hpump (fmol)');
LEGEND_CONSTANTS(:,21) = strpad('z_zr1 in component params_BG (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('z_zr2 in component params_BG (dimensionless)');
LEGEND_CONSTANTS(:,32) = strpad('mu_zr1 in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,33) = strpad('mu_zr2 in component BG_Hpump (J_per_mol)');
LEGEND_CONSTANTS(:,31) = strpad('V_Vm in component BG_Hpump (volt)');
LEGEND_CONSTANTS(:,23) = strpad('V_E in component params_BG (volt)');
LEGEND_CONSTANTS(:,24) = strpad('V_i in component params_BG (pL)');
LEGEND_CONSTANTS(:,25) = strpad('H_i in component params_BG (mM)');
LEGEND_CONSTANTS(:,26) = strpad('H_o in component params_BG (mM)');
LEGEND_CONSTANTS(:,27) = strpad('Pi_i in component params_BG (mM)');
LEGEND_CONSTANTS(:,28) = strpad('ATP_i in component params_BG (mM)');
LEGEND_CONSTANTS(:,29) = strpad('ADP_i in component params_BG (mM)');
LEGEND_CONSTANTS(:,30) = strpad('V_o in component params_BG (pL)');
LEGEND_RATES(:,1) = strpad('d/dt q_1 in component BG_Hpump (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_2 in component BG_Hpump (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_3 in component BG_Hpump (fmol)');
LEGEND_RATES(:,4) = strpad('d/dt q_4 in component BG_Hpump (fmol)');
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) = 8.31;
CONSTANTS(:,2) = 273.15;
CONSTANTS(:,3) = 96485;
CONSTANTS(:,4) = 1;
CONSTANTS(:,5) = 1;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 1;
CONSTANTS(:,8) = 1;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 1;
CONSTANTS(:,13) = 1;
CONSTANTS(:,14) = 1;
CONSTANTS(:,15) = 1;
CONSTANTS(:,16) = 1;
CONSTANTS(:,17) = 1;
CONSTANTS(:,18) = 1;
CONSTANTS(:,19) = 1;
CONSTANTS(:,20) = 1;
CONSTANTS(:,21) = 1;
CONSTANTS(:,22) = 1;
CONSTANTS(:,23) = -0.05;
CONSTANTS(:,24) = 0.09;
CONSTANTS(:,25) = 1;
CONSTANTS(:,26) = 1e-5;
CONSTANTS(:,27) = 1e-5;
CONSTANTS(:,28) = 1e-5;
CONSTANTS(:,29) = 1e-5;
CONSTANTS(:,30) = 0.09;
CONSTANTS(:,31) = CONSTANTS(:,23);
CONSTANTS(:,32) = CONSTANTS(:,21).*CONSTANTS(:,3).*CONSTANTS(:,31);
CONSTANTS(:,33) = CONSTANTS(:,22).*CONSTANTS(:,3).*CONSTANTS(:,31);
CONSTANTS(:,34) = CONSTANTS(:,26).*CONSTANTS(:,30);
CONSTANTS(:,35) = CONSTANTS(:,34);
CONSTANTS(:,36) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,5).*CONSTANTS(:,35));
CONSTANTS(:,37) = CONSTANTS(:,25).*CONSTANTS(:,24);
CONSTANTS(:,38) = CONSTANTS(:,37);
CONSTANTS(:,39) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,4).*CONSTANTS(:,38));
CONSTANTS(:,40) = CONSTANTS(:,27).*CONSTANTS(:,24);
CONSTANTS(:,41) = CONSTANTS(:,40);
CONSTANTS(:,42) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,6).*CONSTANTS(:,41));
CONSTANTS(:,43) = CONSTANTS(:,28).*CONSTANTS(:,24);
CONSTANTS(:,44) = CONSTANTS(:,43);
CONSTANTS(:,45) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,7).*CONSTANTS(:,44));
CONSTANTS(:,46) = CONSTANTS(:,29).*CONSTANTS(:,24);
CONSTANTS(:,47) = CONSTANTS(:,46);
CONSTANTS(:,48) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,8).*CONSTANTS(:,47));
STATES(:,1) = CONSTANTS(:,10);
STATES(:,2) = CONSTANTS(:,12);
STATES(:,3) = CONSTANTS(:,14);
STATES(:,4) = CONSTANTS(:,16);
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(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,9).*STATES(:,1));
ALGEBRAIC(:,5) = ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,2));
ALGEBRAIC(:,6) = ALGEBRAIC(:,2)+CONSTANTS(:,42);
ALGEBRAIC(:,7) = CONSTANTS(:,17).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,8) = ALGEBRAIC(:,2)+CONSTANTS(:,45);
ALGEBRAIC(:,3) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,13).*STATES(:,3));
ALGEBRAIC(:,9) = ALGEBRAIC(:,3);
ALGEBRAIC(:,10) = CONSTANTS(:,18).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,11) = ALGEBRAIC(:,7) - ALGEBRAIC(:,10);
RATES(:,2) = ALGEBRAIC(:,11);
ALGEBRAIC(:,12) = ALGEBRAIC(:,3)+CONSTANTS(:,39);
ALGEBRAIC(:,4) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,15).*STATES(:,4));
ALGEBRAIC(:,13) = ALGEBRAIC(:,4)+CONSTANTS(:,48)+CONSTANTS(:,32);
ALGEBRAIC(:,14) = CONSTANTS(:,19).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,15) = ALGEBRAIC(:,10) - ALGEBRAIC(:,14);
RATES(:,3) = ALGEBRAIC(:,15);
ALGEBRAIC(:,16) = ALGEBRAIC(:,4);
ALGEBRAIC(:,17) = ALGEBRAIC(:,1)+CONSTANTS(:,36)+CONSTANTS(:,33);
ALGEBRAIC(:,18) = CONSTANTS(:,20).*(exp(ALGEBRAIC(:,16)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,19) = ALGEBRAIC(:,18) - ALGEBRAIC(:,7);
RATES(:,1) = ALGEBRAIC(:,19);
ALGEBRAIC(:,20) = ALGEBRAIC(:,14) - ALGEBRAIC(:,18);
RATES(:,4) = ALGEBRAIC(:,20);
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).*log( CONSTANTS(:,9).*STATES(:,1));
ALGEBRAIC(:,5) = ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,2));
ALGEBRAIC(:,6) = ALGEBRAIC(:,2)+CONSTANTS(:,42);
ALGEBRAIC(:,7) = CONSTANTS(:,17).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,8) = ALGEBRAIC(:,2)+CONSTANTS(:,45);
ALGEBRAIC(:,3) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,13).*STATES(:,3));
ALGEBRAIC(:,9) = ALGEBRAIC(:,3);
ALGEBRAIC(:,10) = CONSTANTS(:,18).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,11) = ALGEBRAIC(:,7) - ALGEBRAIC(:,10);
ALGEBRAIC(:,12) = ALGEBRAIC(:,3)+CONSTANTS(:,39);
ALGEBRAIC(:,4) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,15).*STATES(:,4));
ALGEBRAIC(:,13) = ALGEBRAIC(:,4)+CONSTANTS(:,48)+CONSTANTS(:,32);
ALGEBRAIC(:,14) = CONSTANTS(:,19).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,15) = ALGEBRAIC(:,10) - ALGEBRAIC(:,14);
ALGEBRAIC(:,16) = ALGEBRAIC(:,4);
ALGEBRAIC(:,17) = ALGEBRAIC(:,1)+CONSTANTS(:,36)+CONSTANTS(:,33);
ALGEBRAIC(:,18) = CONSTANTS(:,20).*(exp(ALGEBRAIC(:,16)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,19) = ALGEBRAIC(:,18) - ALGEBRAIC(:,7);
ALGEBRAIC(:,20) = ALGEBRAIC(:,14) - ALGEBRAIC(:,18);
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