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 =8;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 17 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 (minute)');
LEGEND_CONSTANTS(:,1) = strpad('AMK in component electrolytes (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('TVD in component electrolytes (L_per_minute)');
LEGEND_CONSTANTS(:,3) = strpad('NOD in component electrolytes (monovalent_mEq_per_minute)');
LEGEND_CONSTANTS(:,4) = strpad('STH in component electrolytes (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('KOD in component electrolytes (monovalent_mEq_per_minute)');
LEGEND_CONSTANTS(:,6) = strpad('VUD in component electrolytes (L_per_minute)');
LEGEND_ALGEBRAIC(:,4) = strpad('VEC in component extracellular_fluid_volume (litre)');
LEGEND_ALGEBRAIC(:,5) = strpad('CNA in component extracellular_Na_concentration (monovalent_mEq_per_litre)');
LEGEND_CONSTANTS(:,7) = strpad('NID in component parameter_values (monovalent_mEq_per_minute)');
LEGEND_CONSTANTS(:,8) = strpad('TRPL in component parameter_values (L_per_minute)');
LEGEND_CONSTANTS(:,12) = strpad('NED in component extracellular_Na_concentration (monovalent_mEq_per_minute)');
LEGEND_STATES(:,1) = strpad('NAE in component extracellular_Na_concentration (monovalent_mEq)');
LEGEND_CONSTANTS(:,13) = strpad('AMK1 in component aldosterone_effect_on_cellular_K_distribution (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('ALCLK in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('CKE in component extracellular_K_concentration (monovalent_mEq_per_litre)');
LEGEND_ALGEBRAIC(:,1) = strpad('KE in component extracellular_K_concentration (monovalent_mEq)');
LEGEND_STATES(:,2) = strpad('KTOT in component extracellular_K_concentration (monovalent_mEq)');
LEGEND_CONSTANTS(:,10) = strpad('KID in component parameter_values (monovalent_mEq_per_minute)');
LEGEND_CONSTANTS(:,14) = strpad('KTOTD in component extracellular_K_concentration (monovalent_mEq_per_minute)');
LEGEND_STATES(:,3) = strpad('VIC in component intracellular_fluid_volume (litre)');
LEGEND_ALGEBRAIC(:,3) = strpad('CKI in component intracellular_K_concentration (monovalent_mEq_per_litre)');
LEGEND_ALGEBRAIC(:,2) = strpad('KI in component intracellular_K_concentration (monovalent_mEq)');
LEGEND_ALGEBRAIC(:,8) = strpad('VID in component intracellular_fluid_volume (L_per_minute)');
LEGEND_CONSTANTS(:,11) = strpad('VIDML in component parameter_values (litre2_per_monovalent_mEq_per_minute)');
LEGEND_ALGEBRAIC(:,7) = strpad('CCD in component intracellular_fluid_volume (monovalent_mEq_per_litre)');
LEGEND_STATES(:,4) = strpad('VTW in component total_body_water (litre)');
LEGEND_RATES(:,1) = strpad('d/dt NAE in component extracellular_Na_concentration (monovalent_mEq)');
LEGEND_RATES(:,2) = strpad('d/dt KTOT in component extracellular_K_concentration (monovalent_mEq)');
LEGEND_RATES(:,3) = strpad('d/dt VIC in component intracellular_fluid_volume (litre)');
LEGEND_RATES(:,4) = strpad('d/dt VTW in component total_body_water (litre)');
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) = 1.037;
CONSTANTS(:,2) = 0.000980838;
CONSTANTS(:,3) = 0.0959449;
CONSTANTS(:,4) = 0.977181;
CONSTANTS(:,5) = 0.0804374;
CONSTANTS(:,6) = 0.000989;
CONSTANTS(:,7) = 0.1;
CONSTANTS(:,8) = 0;
STATES(:,1) = 2109.91;
CONSTANTS(:,9) = 0.3;
STATES(:,2) = 3622.54;
CONSTANTS(:,10) = 0.08;
STATES(:,3) = 25.0404;
CONSTANTS(:,11) = 0.01;
STATES(:,4) = 39.8952;
CONSTANTS(:,12) = ( CONSTANTS(:,7).*CONSTANTS(:,4) - CONSTANTS(:,3))+ CONSTANTS(:,8).*142.000;
CONSTANTS(:,13) = (CONSTANTS(:,1) - 1.00000).*CONSTANTS(:,9)+1.00000;
CONSTANTS(:,14) = CONSTANTS(:,10) - CONSTANTS(:,5);
CONSTANTS(:,14) = CONSTANTS(:,2) - CONSTANTS(:,6);
CONSTANTS(:,15) = CONSTANTS(:,12);
CONSTANTS(:,16) = CONSTANTS(:,14);
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(:,4) = CONSTANTS(:,14);
RATES(:,1) = CONSTANTS(:,15);
RATES(:,2) = CONSTANTS(:,16);
ALGEBRAIC(:,4) = STATES(:,4) - STATES(:,3);
ALGEBRAIC(:,5) = STATES(:,1)./ALGEBRAIC(:,4);
ALGEBRAIC(:,1) = (STATES(:,2) - 3000.00)./( CONSTANTS(:,13).*9.33330);
ALGEBRAIC(:,2) = STATES(:,2) - ALGEBRAIC(:,1);
ALGEBRAIC(:,3) = ALGEBRAIC(:,2)./STATES(:,3);
ALGEBRAIC(:,7) = ALGEBRAIC(:,3) - ALGEBRAIC(:,5);
ALGEBRAIC(:,8) = ALGEBRAIC(:,7).*CONSTANTS(:,11);
RATES(:,3) = ALGEBRAIC(:,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(:,4) = STATES(:,4) - STATES(:,3);
ALGEBRAIC(:,5) = STATES(:,1)./ALGEBRAIC(:,4);
ALGEBRAIC(:,1) = (STATES(:,2) - 3000.00)./( CONSTANTS(:,13).*9.33330);
ALGEBRAIC(:,2) = STATES(:,2) - ALGEBRAIC(:,1);
ALGEBRAIC(:,3) = ALGEBRAIC(:,2)./STATES(:,3);
ALGEBRAIC(:,7) = ALGEBRAIC(:,3) - ALGEBRAIC(:,5);
ALGEBRAIC(:,8) = ALGEBRAIC(:,7).*CONSTANTS(:,11);
ALGEBRAIC(:,6) = ALGEBRAIC(:,1)./ALGEBRAIC(:,4);
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