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 =5; end % There are a total of 2 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('H_int in component concentrations (mM)'); LEGEND_ALGEBRAIC(:,2) = strpad('H_ext in component concentrations (mM)'); LEGEND_CONSTANTS(:,1) = strpad('psi_int in component concentrations (volt)'); LEGEND_CONSTANTS(:,2) = strpad('psi_ext in component concentrations (volt)'); LEGEND_CONSTANTS(:,10) = strpad('psi in component concentrations (volt)'); LEGEND_STATES(:,1) = strpad('pH_int in component concentrations (dimensionless)'); LEGEND_STATES(:,2) = strpad('pH_ext in component concentrations (dimensionless)'); LEGEND_CONSTANTS(:,3) = strpad('J_Vtype_H_Max in component H_ATPase (mM_per_s)'); LEGEND_ALGEBRAIC(:,4) = strpad('J_Vtype_H in component H_ATPase (mM_per_s)'); LEGEND_ALGEBRAIC(:,5) = strpad('plot in component fluxes (dimensionless)'); LEGEND_ALGEBRAIC(:,3) = strpad('mu_H in component H_ATPase (joule_per_mmole)'); LEGEND_CONSTANTS(:,4) = strpad('mu_0 in component H_ATPase (joule_per_mmole)'); LEGEND_CONSTANTS(:,5) = strpad('xi in component H_ATPase (mmole_per_joule)'); LEGEND_CONSTANTS(:,6) = strpad('F in component H_ATPase (coulomb_per_mmole)'); LEGEND_CONSTANTS(:,7) = strpad('R in component H_ATPase (joule_per_mmole_kelvin)'); LEGEND_CONSTANTS(:,8) = strpad('T in component H_ATPase (kelvin)'); LEGEND_CONSTANTS(:,9) = strpad('z in component H_ATPase (dimensionless)'); LEGEND_RATES(:,1) = strpad('d/dt pH_int in component concentrations (dimensionless)'); LEGEND_RATES(:,2) = strpad('d/dt pH_ext in component concentrations (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) = -0.03; CONSTANTS(:,2) = 0.0; STATES(:,1) = 7.5; STATES(:,2) = 4.0; CONSTANTS(:,3) = 1.8; CONSTANTS(:,4) = 4.0; CONSTANTS(:,5) = 0.4; CONSTANTS(:,6) = 96.5; CONSTANTS(:,7) = 0.008315; CONSTANTS(:,8) = 300; CONSTANTS(:,9) = -1.57; CONSTANTS(:,10) = CONSTANTS(:,2) - CONSTANTS(:,1); CONSTANTS(:,10) = 0.00000; CONSTANTS(:,11) = 0.100000; 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(:,10); RATES(:,2) = CONSTANTS(:,11); 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) = 1000.00.*power(10.0000, - STATES(:,1)); ALGEBRAIC(:,2) = 1000.00.*power(10.0000, - STATES(:,2)); ALGEBRAIC(:,3) = CONSTANTS(:,7).*CONSTANTS(:,8).*log(ALGEBRAIC(:,2)./ALGEBRAIC(:,1))+ CONSTANTS(:,9).*CONSTANTS(:,6).*CONSTANTS(:,10); ALGEBRAIC(:,4) = CONSTANTS(:,3)./(1.00000+exp( CONSTANTS(:,5).*(ALGEBRAIC(:,3) - CONSTANTS(:,4)))); ALGEBRAIC(:,5) = ALGEBRAIC(:,4)./CONSTANTS(:,3); 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