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 =39; end % There are a total of 11 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('time in component environment (second)'); LEGEND_CONSTANTS(:,1) = strpad('q_Cai_init in component environment (fmol)'); LEGEND_CONSTANTS(:,2) = strpad('q_TRPN_init in component environment (fmol)'); LEGEND_CONSTANTS(:,3) = strpad('q_Ca_TRPN_init in component environment (fmol)'); LEGEND_CONSTANTS(:,4) = strpad('q_B_init in component environment (fmol)'); LEGEND_CONSTANTS(:,5) = strpad('q_U_init in component environment (fmol)'); LEGEND_CONSTANTS(:,6) = strpad('q_W_init in component environment (fmol)'); LEGEND_CONSTANTS(:,7) = strpad('q_S_init in component environment (fmol)'); LEGEND_ALGEBRAIC(:,3) = strpad('q_TRPN in component environment (fmol)'); LEGEND_ALGEBRAIC(:,6) = strpad('q_Cai in component environment (fmol)'); LEGEND_ALGEBRAIC(:,9) = strpad('q_Ca_TRPN in component environment (fmol)'); LEGEND_ALGEBRAIC(:,10) = strpad('q_B in component environment (fmol)'); LEGEND_ALGEBRAIC(:,11) = strpad('q_U in component environment (fmol)'); LEGEND_ALGEBRAIC(:,12) = strpad('q_W in component environment (fmol)'); LEGEND_ALGEBRAIC(:,13) = strpad('q_S in component environment (fmol)'); LEGEND_STATES(:,1) = strpad('q_TRPN in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,2) = strpad('q_Cai in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,3) = strpad('q_Ca_TRPN in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,4) = strpad('q_B in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,5) = strpad('q_U in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,6) = strpad('q_W in component crossbridge_TRPN (fmol)'); LEGEND_STATES(:,7) = strpad('q_S in component crossbridge_TRPN (fmol)'); LEGEND_ALGEBRAIC(:,36) = strpad('T_total in component crossbridge_TRPN (kPa)'); LEGEND_STATES(:,8) = strpad('SL in component crossbridge_TRPN (metre)'); LEGEND_CONSTANTS(:,8) = strpad('kappa_R_TRPNCa in component crossbridge_TRPN_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,9) = strpad('kappa_R_BU in component crossbridge_TRPN_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,10) = strpad('kappa_R_UW in component crossbridge_TRPN_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,11) = strpad('kappa_R_WS in component crossbridge_TRPN_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,12) = strpad('kappa_R_SU in component crossbridge_TRPN_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,13) = strpad('K_TRPN in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,14) = strpad('K_Cai in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,15) = strpad('K_Ca_TRPN in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,16) = strpad('K_B in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,17) = strpad('K_U in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,18) = strpad('K_W in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,19) = strpad('K_S in component crossbridge_TRPN_parameters (per_fmol)'); LEGEND_CONSTANTS(:,20) = strpad('R in component constants (J_per_K_per_mol)'); LEGEND_CONSTANTS(:,21) = strpad('T in component constants (kelvin)'); LEGEND_CONSTANTS(:,22) = strpad('n_Tm in component crossbridge_TRPN (dimensionless)'); LEGEND_ALGEBRAIC(:,14) = strpad('mu_TRPN in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,15) = strpad('mu_Cai in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,16) = strpad('mu_Ca_TRPN in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,17) = strpad('mu_B in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,19) = strpad('mu_U in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,21) = strpad('mu_W in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,23) = strpad('mu_S in component crossbridge_TRPN (J_per_mol)'); LEGEND_ALGEBRAIC(:,39) = strpad('v_R_TRPNCa in component crossbridge_TRPN (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,25) = strpad('v_R_BU in component crossbridge_TRPN (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,31) = strpad('v_R_UW in component crossbridge_TRPN (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,33) = strpad('v_R_WS in component crossbridge_TRPN (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,35) = strpad('v_R_SU in component crossbridge_TRPN (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,37) = strpad('tension in component crossbridge_TRPN (N_per_mm2)'); LEGEND_ALGEBRAIC(:,38) = strpad('mu_tension in component crossbridge_TRPN (J_per_mol)'); LEGEND_CONSTANTS(:,23) = strpad('kf_coeff in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,44) = strpad('n in component crossbridge_TRPN (J_per_mol)'); LEGEND_CONSTANTS(:,24) = strpad('hh in component crossbridge_TRPN (mm2_per_N)'); LEGEND_CONSTANTS(:,25) = strpad('SL_0 in component crossbridge_TRPN (metre)'); LEGEND_CONSTANTS(:,26) = strpad('q_MS in component crossbridge_TRPN (fmol)'); LEGEND_CONSTANTS(:,27) = strpad('r_s in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,28) = strpad('r_w in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,29) = strpad('A_eff in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,30) = strpad('phi in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,31) = strpad('k_uw in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,32) = strpad('k_ws in component crossbridge_TRPN (per_sec)'); LEGEND_STATES(:,9) = strpad('G_w in component crossbridge_TRPN (metre)'); LEGEND_STATES(:,10) = strpad('G_s in component crossbridge_TRPN (metre)'); LEGEND_CONSTANTS(:,41) = strpad('c_w in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,42) = strpad('c_s in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,43) = strpad('A_w in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,45) = strpad('A_s in component crossbridge_TRPN (dimensionless)'); LEGEND_ALGEBRAIC(:,4) = strpad('mu_1 in component crossbridge_TRPN (J_per_m)'); LEGEND_CONSTANTS(:,46) = strpad('mu_2 in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,1) = strpad('mu_3 in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,5) = strpad('mu_4 in component crossbridge_TRPN (J_per_m)'); LEGEND_CONSTANTS(:,47) = strpad('mu_5 in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,2) = strpad('mu_6 in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,7) = strpad('v_1 in component crossbridge_TRPN (m_per_s)'); LEGEND_CONSTANTS(:,33) = strpad('v_2 in component crossbridge_TRPN (m_per_s)'); LEGEND_ALGEBRAIC(:,8) = strpad('v_4 in component crossbridge_TRPN (m_per_s)'); LEGEND_CONSTANTS(:,34) = strpad('v_to_mu in component crossbridge_TRPN (Js_per_m2)'); LEGEND_ALGEBRAIC(:,24) = strpad('T_active in component crossbridge_TRPN (kPa)'); LEGEND_CONSTANTS(:,35) = strpad('T_ref in component crossbridge_TRPN (kPa)'); LEGEND_ALGEBRAIC(:,22) = strpad('mu_T_a in component crossbridge_TRPN (kPa)'); LEGEND_ALGEBRAIC(:,18) = strpad('mu_T_S in component crossbridge_TRPN (kPa)'); LEGEND_ALGEBRAIC(:,20) = strpad('mu_T_W in component crossbridge_TRPN (kPa)'); LEGEND_STATES(:,11) = strpad('Cdd in component crossbridge_TRPN (metre)'); LEGEND_ALGEBRAIC(:,26) = strpad('eta in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,36) = strpad('eta_l in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,37) = strpad('eta_s in component crossbridge_TRPN (per_sec)'); LEGEND_CONSTANTS(:,38) = strpad('k in component crossbridge_TRPN (dimensionless)'); LEGEND_CONSTANTS(:,39) = strpad('alpha in component crossbridge_TRPN (kPa)'); LEGEND_ALGEBRAIC(:,30) = strpad('v_Cdd in component crossbridge_TRPN (m_per_s)'); LEGEND_ALGEBRAIC(:,27) = strpad('mu_d in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,28) = strpad('mu_k in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,29) = strpad('mu_f in component crossbridge_TRPN (J_per_m)'); LEGEND_ALGEBRAIC(:,32) = strpad('mu_T_passive in component crossbridge_TRPN (kPa)'); LEGEND_ALGEBRAIC(:,34) = strpad('T_passive in component crossbridge_TRPN (kPa)'); LEGEND_CONSTANTS(:,40) = strpad('F in component constants (C_per_mol)'); LEGEND_RATES(:,2) = strpad('d/dt q_Cai in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,1) = strpad('d/dt q_TRPN in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,3) = strpad('d/dt q_Ca_TRPN in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,4) = strpad('d/dt q_B in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,5) = strpad('d/dt q_U in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,6) = strpad('d/dt q_W in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,7) = strpad('d/dt q_S in component crossbridge_TRPN (fmol)'); LEGEND_RATES(:,9) = strpad('d/dt G_w in component crossbridge_TRPN (metre)'); LEGEND_RATES(:,8) = strpad('d/dt SL in component crossbridge_TRPN (metre)'); LEGEND_RATES(:,10) = strpad('d/dt G_s in component crossbridge_TRPN (metre)'); LEGEND_RATES(:,11) = strpad('d/dt Cdd in component crossbridge_TRPN (metre)'); 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) = 6.82e-1; CONSTANTS(:,2) = 2.57; CONSTANTS(:,3) = 1e-6; CONSTANTS(:,4) = 1; CONSTANTS(:,5) = 0; CONSTANTS(:,6) = 0; CONSTANTS(:,7) = 0; STATES(:,1) = 1e-16; STATES(:,2) = 1e-16; STATES(:,3) = 1e-16; STATES(:,4) = 1e-16; STATES(:,5) = 1e-16; STATES(:,6) = 1e-16; STATES(:,7) = 1e-16; STATES(:,8) = 1e-6; CONSTANTS(:,8) = 52.0453; CONSTANTS(:,9) = 2.90875; CONSTANTS(:,10) = 0.332501; CONSTANTS(:,11) = 0.00782356; CONSTANTS(:,12) = 140824; CONSTANTS(:,13) = 1.27424; CONSTANTS(:,14) = 1.27424; CONSTANTS(:,15) = 0.11171; CONSTANTS(:,16) = 6.06164; CONSTANTS(:,17) = 2.27312; CONSTANTS(:,18) = 14.8627; CONSTANTS(:,19) = 3.71567e-06; CONSTANTS(:,20) = 8.31; CONSTANTS(:,21) = 310; CONSTANTS(:,22) = 1.1; CONSTANTS(:,23) = -0.0118; CONSTANTS(:,24) = 1; CONSTANTS(:,25) = 2e-6; CONSTANTS(:,26) = 1e-6; CONSTANTS(:,27) = 0.25; CONSTANTS(:,28) = 0.5; CONSTANTS(:,29) = 25; CONSTANTS(:,30) = 2.23; CONSTANTS(:,31) = 26; CONSTANTS(:,32) = 4; STATES(:,9) = 1e-6; STATES(:,10) = 1e-6; CONSTANTS(:,33) = 0; CONSTANTS(:,34) = 1; CONSTANTS(:,35) = 40.5; STATES(:,11) = 0; CONSTANTS(:,36) = 200e3; CONSTANTS(:,37) = 200e3; CONSTANTS(:,38) = 7; CONSTANTS(:,39) = 2.1; CONSTANTS(:,40) = 96485; CONSTANTS(:,41) = ( CONSTANTS(:,30).*CONSTANTS(:,31).*(1.00000 - CONSTANTS(:,28)))./CONSTANTS(:,28); CONSTANTS(:,42) = ( CONSTANTS(:,30).*CONSTANTS(:,32).*(1.00000 - CONSTANTS(:,27)).*CONSTANTS(:,28))./CONSTANTS(:,27); CONSTANTS(:,43) = ( CONSTANTS(:,29).*CONSTANTS(:,27))./( (1.00000 - CONSTANTS(:,27)).*CONSTANTS(:,28)+CONSTANTS(:,27)); CONSTANTS(:,44) = CONSTANTS(:,23).*CONSTANTS(:,20).*CONSTANTS(:,21); CONSTANTS(:,47) = CONSTANTS(:,33); CONSTANTS(:,45) = CONSTANTS(:,43); CONSTANTS(:,46) = - CONSTANTS(:,43).*CONSTANTS(:,33).*CONSTANTS(:,34); CONSTANTS(:,47) = - CONSTANTS(:,45).*CONSTANTS(:,33).*CONSTANTS(:,34); 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(:,8) = CONSTANTS(:,47); ALGEBRAIC(:,1) = CONSTANTS(:,41).*STATES(:,9).*CONSTANTS(:,34); ALGEBRAIC(:,4) = - CONSTANTS(:,46) - ALGEBRAIC(:,1); ALGEBRAIC(:,7) = ALGEBRAIC(:,4)./CONSTANTS(:,34); RATES(:,9) = ALGEBRAIC(:,7); ALGEBRAIC(:,2) = CONSTANTS(:,42).*STATES(:,10).*CONSTANTS(:,34); ALGEBRAIC(:,5) = - CONSTANTS(:,47) - ALGEBRAIC(:,2); ALGEBRAIC(:,8) = ALGEBRAIC(:,5)./CONSTANTS(:,34); RATES(:,10) = ALGEBRAIC(:,8); ALGEBRAIC(:,9) = STATES(:,3)+CONSTANTS(:,3); ALGEBRAIC(:,16) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,15).*ALGEBRAIC(:,9)); ALGEBRAIC(:,10) = STATES(:,4)+CONSTANTS(:,4); ALGEBRAIC(:,17) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,16).*ALGEBRAIC(:,10)); ALGEBRAIC(:,11) = STATES(:,5)+CONSTANTS(:,5); ALGEBRAIC(:,19) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,17).*ALGEBRAIC(:,11)); ALGEBRAIC(:,25) = CONSTANTS(:,9).*(exp((ALGEBRAIC(:,17)+ CONSTANTS(:,22).*ALGEBRAIC(:,16))./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp((ALGEBRAIC(:,19)+ CONSTANTS(:,22).*ALGEBRAIC(:,16))./( CONSTANTS(:,20).*CONSTANTS(:,21)))); RATES(:,4) = - ALGEBRAIC(:,25); [CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS, STATES, ALGEBRAIC); ALGEBRAIC(:,30) = ALGEBRAIC(:,27)./CONSTANTS(:,34); RATES(:,11) = ALGEBRAIC(:,30); ALGEBRAIC(:,12) = STATES(:,6)+CONSTANTS(:,6); ALGEBRAIC(:,21) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,18).*ALGEBRAIC(:,12)); ALGEBRAIC(:,31) = CONSTANTS(:,10).*(exp(ALGEBRAIC(:,19)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,21)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); ALGEBRAIC(:,13) = STATES(:,7)+CONSTANTS(:,7); ALGEBRAIC(:,23) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,19).*ALGEBRAIC(:,13)); ALGEBRAIC(:,33) = CONSTANTS(:,11).*(exp(ALGEBRAIC(:,21)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,23)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); RATES(:,6) = ALGEBRAIC(:,31) - ALGEBRAIC(:,33); ALGEBRAIC(:,35) = CONSTANTS(:,12).*(exp(ALGEBRAIC(:,23)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,19)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); RATES(:,5) = (ALGEBRAIC(:,25) - ALGEBRAIC(:,31))+ALGEBRAIC(:,35); RATES(:,7) = ALGEBRAIC(:,33) - ALGEBRAIC(:,35); ALGEBRAIC(:,3) = STATES(:,1)+CONSTANTS(:,2); ALGEBRAIC(:,14) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,13).*ALGEBRAIC(:,3)); ALGEBRAIC(:,6) = STATES(:,2)+CONSTANTS(:,1); ALGEBRAIC(:,15) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,14).*ALGEBRAIC(:,6)); ALGEBRAIC(:,18) = (CONSTANTS(:,35)./( CONSTANTS(:,25).*CONSTANTS(:,26).*CONSTANTS(:,27))).*STATES(:,7).*(STATES(:,10)+CONSTANTS(:,25)); ALGEBRAIC(:,20) = (CONSTANTS(:,35)./( CONSTANTS(:,25).*CONSTANTS(:,26).*CONSTANTS(:,27))).*STATES(:,6).*STATES(:,9); ALGEBRAIC(:,22) = ALGEBRAIC(:,18)+ALGEBRAIC(:,20); ALGEBRAIC(:,24) = ALGEBRAIC(:,22); ALGEBRAIC(:,32) = (( CONSTANTS(:,39).*ALGEBRAIC(:,26))./CONSTANTS(:,25)).*ALGEBRAIC(:,30); ALGEBRAIC(:,34) = ALGEBRAIC(:,32); ALGEBRAIC(:,36) = ALGEBRAIC(:,24)+ALGEBRAIC(:,34); ALGEBRAIC(:,37) = ALGEBRAIC(:,36).*1000.00; ALGEBRAIC(:,38) = CONSTANTS(:,24).*CONSTANTS(:,44).*ALGEBRAIC(:,37); ALGEBRAIC(:,39) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,14))./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,38))./( CONSTANTS(:,20).*CONSTANTS(:,21)))); RATES(:,2) = - ALGEBRAIC(:,39); RATES(:,1) = - ALGEBRAIC(:,39); RATES(:,3) = ALGEBRAIC(:,39); 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(:,41).*STATES(:,9).*CONSTANTS(:,34); ALGEBRAIC(:,4) = - CONSTANTS(:,46) - ALGEBRAIC(:,1); ALGEBRAIC(:,7) = ALGEBRAIC(:,4)./CONSTANTS(:,34); ALGEBRAIC(:,2) = CONSTANTS(:,42).*STATES(:,10).*CONSTANTS(:,34); ALGEBRAIC(:,5) = - CONSTANTS(:,47) - ALGEBRAIC(:,2); ALGEBRAIC(:,8) = ALGEBRAIC(:,5)./CONSTANTS(:,34); ALGEBRAIC(:,9) = STATES(:,3)+CONSTANTS(:,3); ALGEBRAIC(:,16) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,15).*ALGEBRAIC(:,9)); ALGEBRAIC(:,10) = STATES(:,4)+CONSTANTS(:,4); ALGEBRAIC(:,17) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,16).*ALGEBRAIC(:,10)); ALGEBRAIC(:,11) = STATES(:,5)+CONSTANTS(:,5); ALGEBRAIC(:,19) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,17).*ALGEBRAIC(:,11)); ALGEBRAIC(:,25) = CONSTANTS(:,9).*(exp((ALGEBRAIC(:,17)+ CONSTANTS(:,22).*ALGEBRAIC(:,16))./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp((ALGEBRAIC(:,19)+ CONSTANTS(:,22).*ALGEBRAIC(:,16))./( CONSTANTS(:,20).*CONSTANTS(:,21)))); ALGEBRAIC(:,30) = ALGEBRAIC(:,27)./CONSTANTS(:,34); ALGEBRAIC(:,12) = STATES(:,6)+CONSTANTS(:,6); ALGEBRAIC(:,21) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,18).*ALGEBRAIC(:,12)); ALGEBRAIC(:,31) = CONSTANTS(:,10).*(exp(ALGEBRAIC(:,19)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,21)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); ALGEBRAIC(:,13) = STATES(:,7)+CONSTANTS(:,7); ALGEBRAIC(:,23) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,19).*ALGEBRAIC(:,13)); ALGEBRAIC(:,33) = CONSTANTS(:,11).*(exp(ALGEBRAIC(:,21)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,23)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); ALGEBRAIC(:,35) = CONSTANTS(:,12).*(exp(ALGEBRAIC(:,23)./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp(ALGEBRAIC(:,19)./( CONSTANTS(:,20).*CONSTANTS(:,21)))); ALGEBRAIC(:,3) = STATES(:,1)+CONSTANTS(:,2); ALGEBRAIC(:,14) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,13).*ALGEBRAIC(:,3)); ALGEBRAIC(:,6) = STATES(:,2)+CONSTANTS(:,1); ALGEBRAIC(:,15) = CONSTANTS(:,20).*CONSTANTS(:,21).*log( CONSTANTS(:,14).*ALGEBRAIC(:,6)); ALGEBRAIC(:,18) = (CONSTANTS(:,35)./( CONSTANTS(:,25).*CONSTANTS(:,26).*CONSTANTS(:,27))).*STATES(:,7).*(STATES(:,10)+CONSTANTS(:,25)); ALGEBRAIC(:,20) = (CONSTANTS(:,35)./( CONSTANTS(:,25).*CONSTANTS(:,26).*CONSTANTS(:,27))).*STATES(:,6).*STATES(:,9); ALGEBRAIC(:,22) = ALGEBRAIC(:,18)+ALGEBRAIC(:,20); ALGEBRAIC(:,24) = ALGEBRAIC(:,22); ALGEBRAIC(:,32) = (( CONSTANTS(:,39).*ALGEBRAIC(:,26))./CONSTANTS(:,25)).*ALGEBRAIC(:,30); ALGEBRAIC(:,34) = ALGEBRAIC(:,32); ALGEBRAIC(:,36) = ALGEBRAIC(:,24)+ALGEBRAIC(:,34); ALGEBRAIC(:,37) = ALGEBRAIC(:,36).*1000.00; ALGEBRAIC(:,38) = CONSTANTS(:,24).*CONSTANTS(:,44).*ALGEBRAIC(:,37); ALGEBRAIC(:,39) = CONSTANTS(:,8).*(exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,14))./( CONSTANTS(:,20).*CONSTANTS(:,21))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,38))./( CONSTANTS(:,20).*CONSTANTS(:,21)))); end % Functions required for solving differential algebraic equation function [CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS_IN, STATES_IN, ALGEBRAIC_IN) ALGEBRAIC = ALGEBRAIC_IN; CONSTANTS = CONSTANTS_IN; STATES = STATES_IN; global initialGuess_0; if (length(initialGuess_0) ~= 4), initialGuess_0 = [0.1,0.1,0.1,0.1];, end options = optimset('Display', 'off', 'TolX', 1E-6); if length(VOI) == 1 residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES); soln = fsolve(residualfn, initialGuess_0, options); initialGuess_0 = soln; ALGEBRAIC(:,26) = soln(1); ALGEBRAIC(:,27) = soln(2); ALGEBRAIC(:,28) = soln(3); ALGEBRAIC(:,29) = soln(4); else SET_ALGEBRAIC(:,26) = logical(1); SET_ALGEBRAIC(:,27) = logical(1); SET_ALGEBRAIC(:,28) = logical(1); SET_ALGEBRAIC(:,29) = logical(1); for i=1:length(VOI) residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC(i,:), VOI(i), CONSTANTS, STATES(i,:)); soln = fsolve(residualfn, initialGuess_0, options); initialGuess_0 = soln; TEMP_ALGEBRAIC(:,26) = soln(1); TEMP_ALGEBRAIC(:,27) = soln(2); TEMP_ALGEBRAIC(:,28) = soln(3); TEMP_ALGEBRAIC(:,29) = soln(4); ALGEBRAIC(i,SET_ALGEBRAIC) = TEMP_ALGEBRAIC(SET_ALGEBRAIC); end end end function resid = residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES) ALGEBRAIC(:,26) = algebraicCandidate(1); ALGEBRAIC(:,27) = algebraicCandidate(2); ALGEBRAIC(:,28) = algebraicCandidate(3); ALGEBRAIC(:,29) = algebraicCandidate(4); resid(1) = ALGEBRAIC(:,26) - piecewise({ALGEBRAIC(:,27)>0.00000, CONSTANTS(:,36) }, CONSTANTS(:,37)); resid(2) = ALGEBRAIC(:,28) - (CONSTANTS(:,38)./ALGEBRAIC(:,26)).*STATES(:,11).*CONSTANTS(:,34); resid(3) = ALGEBRAIC(:,29) - (CONSTANTS(:,38)./ALGEBRAIC(:,26)).*(STATES(:,8) - CONSTANTS(:,25)).*CONSTANTS(:,34); resid(4) = ALGEBRAIC(:,27) - ( - ALGEBRAIC(:,28)+ALGEBRAIC(:,29)); 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