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 =13;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 8 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('PPC in component pulmonary_fluid_dynamics (mmHg)');
LEGEND_CONSTANTS(:,2) = strpad('PPA in component pulmonary_fluid_dynamics (mmHg)');
LEGEND_CONSTANTS(:,3) = strpad('PLA in component pulmonary_fluid_dynamics (mmHg)');
LEGEND_CONSTANTS(:,4) = strpad('CPP in component pulmonary_fluid_dynamics (gram_per_L)');
LEGEND_CONSTANTS(:,5) = strpad('RPV in component pulmonary_fluid_dynamics (mmHg_minute_per_L)');
LEGEND_CONSTANTS(:,6) = strpad('RPA in component pulmonary_fluid_dynamics (mmHg_minute_per_L)');
LEGEND_CONSTANTS(:,8) = strpad('PCP in component pulmonary_capillary_pressure (mmHg)');
LEGEND_ALGEBRAIC(:,5) = strpad('POS in component colloid_osmotic_pressure_of_pulmonary_interstitium (mmHg)');
LEGEND_ALGEBRAIC(:,2) = strpad('PPI in component pulmonary_interstitial_fluid_pressure (mmHg)');
LEGEND_ALGEBRAIC(:,6) = strpad('PFI in component fluid_filtration_into_pulmonary_interstitium (L_per_minute)');
LEGEND_CONSTANTS(:,7) = strpad('CPF in component parameter_values (L_per_minute_per_mmHg)');
LEGEND_ALGEBRAIC(:,8) = strpad('PLF in component lung_lymphatic_protein_flow (L_per_minute)');
LEGEND_ALGEBRAIC(:,11) = strpad('DFP in component pulmonary_interstitial_free_fluid_volume (L_per_minute)');
LEGEND_ALGEBRAIC(:,1) = strpad('VPF in component pulmonary_interstitial_free_fluid_volume (litre)');
LEGEND_ALGEBRAIC(:,9) = strpad('DFZ in component pulmonary_interstitial_free_fluid_volume (L_per_minute)');
LEGEND_STATES(:,1) = strpad('VPF1 in component pulmonary_interstitial_free_fluid_volume (litre)');
LEGEND_ALGEBRAIC(:,10) = strpad('PPO in component lung_lymphatic_protein_flow (gram_per_minute)');
LEGEND_ALGEBRAIC(:,7) = strpad('PPN in component protein_leakage_into_pulmonary_interstitium (gram_per_minute)');
LEGEND_ALGEBRAIC(:,13) = strpad('PPD in component concentration_of_protein_in_pulmonary_interstitium (gram_per_minute)');
LEGEND_ALGEBRAIC(:,4) = strpad('CPN in component concentration_of_protein_in_pulmonary_interstitium (gram_per_L)');
LEGEND_ALGEBRAIC(:,12) = strpad('PPZ in component concentration_of_protein_in_pulmonary_interstitium (gram_per_minute)');
LEGEND_STATES(:,2) = strpad('PPR1 in component concentration_of_protein_in_pulmonary_interstitium (gram)');
LEGEND_ALGEBRAIC(:,3) = strpad('PPR in component concentration_of_protein_in_pulmonary_interstitium (gram)');
LEGEND_RATES(:,1) = strpad('d/dt VPF1 in component pulmonary_interstitial_free_fluid_volume (litre)');
LEGEND_RATES(:,2) = strpad('d/dt PPR1 in component concentration_of_protein_in_pulmonary_interstitium (gram)');
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) = 29.9941;
CONSTANTS(:,2) = 15.6376;
CONSTANTS(:,3) = 2;
CONSTANTS(:,4) = 71.9719;
CONSTANTS(:,5) = 1.55719;
CONSTANTS(:,6) = 1.5683;
CONSTANTS(:,7) = 0.0003;
STATES(:,1) = 0.0123238;
STATES(:,2) = 0.419998;
CONSTANTS(:,8) = ( (CONSTANTS(:,2) - CONSTANTS(:,3)).*CONSTANTS(:,5))./(CONSTANTS(:,5)+CONSTANTS(:,6))+CONSTANTS(:,3);
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) = piecewise({STATES(:,1)<0.00100000, 0.00100000 }, STATES(:,1));
ALGEBRAIC(:,3) = piecewise({STATES(:,2)<0.0250000, 0.0250000 }, STATES(:,2));
ALGEBRAIC(:,4) = ALGEBRAIC(:,3)./ALGEBRAIC(:,1);
ALGEBRAIC(:,5) = ALGEBRAIC(:,4).*0.400000;
ALGEBRAIC(:,2) = 2.00000 - 0.150000./ALGEBRAIC(:,1);
ALGEBRAIC(:,6) = (((CONSTANTS(:,8) - ALGEBRAIC(:,2))+ALGEBRAIC(:,5)) - CONSTANTS(:,1)).*CONSTANTS(:,7);
ALGEBRAIC(:,8) = (ALGEBRAIC(:,2)+11.0000).*0.000300000;
ALGEBRAIC(:,9) = ALGEBRAIC(:,6) - ALGEBRAIC(:,8);
ALGEBRAIC(:,11) = ALGEBRAIC(:,9);
RATES(:,1) = ALGEBRAIC(:,11);
ALGEBRAIC(:,10) = ALGEBRAIC(:,8).*ALGEBRAIC(:,4);
ALGEBRAIC(:,7) = (CONSTANTS(:,4) - ALGEBRAIC(:,4)).*0.000225000;
ALGEBRAIC(:,12) = ALGEBRAIC(:,7) - ALGEBRAIC(:,10);
ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
RATES(:,2) = ALGEBRAIC(:,13);
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) = piecewise({STATES(:,1)<0.00100000, 0.00100000 }, STATES(:,1));
ALGEBRAIC(:,3) = piecewise({STATES(:,2)<0.0250000, 0.0250000 }, STATES(:,2));
ALGEBRAIC(:,4) = ALGEBRAIC(:,3)./ALGEBRAIC(:,1);
ALGEBRAIC(:,5) = ALGEBRAIC(:,4).*0.400000;
ALGEBRAIC(:,2) = 2.00000 - 0.150000./ALGEBRAIC(:,1);
ALGEBRAIC(:,6) = (((CONSTANTS(:,8) - ALGEBRAIC(:,2))+ALGEBRAIC(:,5)) - CONSTANTS(:,1)).*CONSTANTS(:,7);
ALGEBRAIC(:,8) = (ALGEBRAIC(:,2)+11.0000).*0.000300000;
ALGEBRAIC(:,9) = ALGEBRAIC(:,6) - ALGEBRAIC(:,8);
ALGEBRAIC(:,11) = ALGEBRAIC(:,9);
ALGEBRAIC(:,10) = ALGEBRAIC(:,8).*ALGEBRAIC(:,4);
ALGEBRAIC(:,7) = (CONSTANTS(:,4) - ALGEBRAIC(:,4)).*0.000225000;
ALGEBRAIC(:,12) = ALGEBRAIC(:,7) - ALGEBRAIC(:,10);
ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
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