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 =3; end % There are a total of 1 entries in each of the rate and state variable arrays. % There are a total of 9 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_STATES(:,1) = strpad('Na_int in component concentrations (mM)'); LEGEND_CONSTANTS(:,1) = strpad('Na_ext in component concentrations (mM)'); LEGEND_CONSTANTS(:,2) = strpad('K_int in component concentrations (mM)'); LEGEND_CONSTANTS(:,3) = strpad('K_ext in component concentrations (mM)'); LEGEND_CONSTANTS(:,4) = strpad('NH4_ext in component concentrations (mM)'); LEGEND_ALGEBRAIC(:,1) = strpad('J_NaK_Na in component NaK (mM_per_s)'); LEGEND_ALGEBRAIC(:,2) = strpad('J_NaK_K in component NaK (mM_per_s)'); LEGEND_ALGEBRAIC(:,3) = strpad('J_NaK_NH4 in component NaK (mM_per_s)'); LEGEND_CONSTANTS(:,6) = strpad('K_Na in component NaK (mM)'); LEGEND_CONSTANTS(:,7) = strpad('K_K in component NaK (mM)'); LEGEND_CONSTANTS(:,8) = strpad('K_NH4 in component NaK (mM)'); LEGEND_CONSTANTS(:,5) = strpad('J_NaK_Na_Max in component NaK (mM_per_s)'); LEGEND_RATES(:,1) = strpad('d/dt Na_int in component concentrations (mM)'); 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) = 0.0; CONSTANTS(:,1) = 0.0; CONSTANTS(:,2) = 39.0; CONSTANTS(:,3) = 10.0; CONSTANTS(:,4) = 0.0; CONSTANTS(:,5) = 10.8; CONSTANTS(:,6) = 0.200000.*(1.00000+CONSTANTS(:,2)./8.33000); CONSTANTS(:,7) = 0.100000.*(1.00000+CONSTANTS(:,1)./18.5000); CONSTANTS(:,8) = 1.00000; CONSTANTS(:,8) = 0.200000.*CONSTANTS(:,7); 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(:,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(:,5).*power(STATES(:,1)./(STATES(:,1)+CONSTANTS(:,6)), 3.00000).*power(CONSTANTS(:,3)./(CONSTANTS(:,3)+CONSTANTS(:,7)), 2.00000); ALGEBRAIC(:,2) = ( ( - 2.00000./3.00000).*ALGEBRAIC(:,1))./(1.00000+( CONSTANTS(:,4).*CONSTANTS(:,7))./( CONSTANTS(:,3).*CONSTANTS(:,8))); ALGEBRAIC(:,3) = ALGEBRAIC(:,2).*power(CONSTANTS(:,4)./CONSTANTS(:,8), 1.00000).*power(CONSTANTS(:,7)./CONSTANTS(:,3), 1.00000); 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