[Matlab] Fixed issue causing crash when getting diffusion coefficients

Other miscellaneous updates

interfaces/matlab_experimental/1D/CounterFlowDiffusionFlame.m

@@ -167,7 +167,7 @@
     % Set the profile of the flame with the estimated axial velocities,
     % radial velocities, temperature, and mass fractions calculated above.
     flame = Stack([left flow right]);
-    flame.setProfile(2, {'u', 'V'}, [zrel; u; v]);
+    flame.setProfile(2, {'velocity', 'spread_rate'}, [zrel; u; v]);
     flame.setProfile(2, 'T', [zrel; t] );
     for n = 1:nsp
         nm = tp_f.speciesName(n);

interfaces/matlab_experimental/1D/Domain1D.m

@@ -205,7 +205,7 @@ function clear(d)
             end
         end
 
-        function n = componentName(d, index)
+        function s = componentName(d, index)
             % Get the name of a component given its index.
             %
             % n = d.componentName(index)
@@ -219,7 +219,7 @@ function clear(d)
             %     Cell array of component names.
             %
             n = length(index);
-            s = cell(m);
+            s = cell(1, n);
             for i = 1:n
                 id = index(i)-1;
                 output = callct2('domain_componentName', d.domainID, id);
@@ -650,7 +650,7 @@ function setSteadyTolerances(d, component, rtol, atol)
                 nc = d.nComponents;
                 for ii = 1:nc
                     callct('domain_setSteadyTolerances', ...
-                            d.domainID, ii, rtol, atol);
+                            d.domainID, ii-1, rtol, atol);
                 end
             elseif iscell(component)
                 nc = length(component);
@@ -662,7 +662,7 @@ function setSteadyTolerances(d, component, rtol, atol)
             else
                 n = d.componentIndex(component);
                 callct('domain_setSteadyTolerances', ...
-                        d.domainID, ii, rtol, atol);
+                        d.domainID, n, rtol, atol);
             end
         end
 
@@ -686,7 +686,7 @@ function setTransientTolerances(d, component, rtol, atol)
                 nc = d.nComponents;
                 for ii = 1:nc
                     callct('domain_setTransientTolerances', ...
-                            d.domainID, ii, rtol, atol);
+                            d.domainID, ii-1, rtol, atol);
                 end
             elseif iscell(component)
                 nc = length(component);
@@ -698,7 +698,7 @@ function setTransientTolerances(d, component, rtol, atol)
             else
                 n = d.componentIndex(component);
                 callct('domain_setTransientTolerances', ...
-                        d.domainID, ii, rtol, atol);
+                        d.domainID, n, rtol, atol);
             end
         end
 

interfaces/matlab_experimental/1D/Sim1D.m

@@ -355,12 +355,12 @@ function setProfile(s, name, comp, p)
                 for j = 1:np
                     ic = d.componentIndex(c{j});
                     callct('sim1D_setProfile', s.stID, ...
-                            n - 1, ic - 1, sz(1), p(1, :), sz(1), p(j+1, :));
+                            n - 1, ic - 1, sz(2), p(1, :), sz(2), p(j+1, :));
                 end
             elseif sz(2) == np + 1;
                 ic = d.componentIndex(c{j});
                 callct('sim1D_setProfile', s.stID, ...
-                        n - 1, ic - 1, sz(2), p(:, 1), sz(2), p(:, j+1));
+                        n - 1, ic - 1, sz(1), p(:, 1), sz(1), p(:, j+1));
             else
                 error('Wrong profile shape.');
             end

interfaces/matlab_experimental/Base/Solution.m

@@ -24,12 +24,11 @@
             %     >> s = Solution('input.yaml'[, phase_name[, transport_model]])
             %
             % constructs a :mat:func:`Solution` object from a specification contained in
-            % file ``input.yaml``. Optionally, the name of the phase to be imported
-            % can be specified with ``phase_name``. If a :mat:func:`Transport` model is
-            % included in ``input.yaml``, it will be included in the :mat:func:`Solution`
-            % instance with the default transport modeling as set
-            % in the input file. To specify the transport modeling, set the input
-            % argument ``trans`` to one of ``'default'``, ``'None'``, ``'Mix'``, or ``'Multi'``.
+            % file ``input.yaml`` with the name of the phase to be imported specified with
+            % ``phase_name``. If a :mat:func:`Transport` model is included in ``input.yaml``,
+            % it will be included in the :mat:func:`Solution` instance with the default transport modeling as set
+            % in the input file. To specify the transport modeling, set the input argument
+            % ``trans`` to one of ``'default'``, ``'None'``, ``'Mix'``, or ``'Multi'``.
             % In this case, the phase name must be specified as well. Alternatively,
             % change the ``transport`` node in the YAML file, or ``transport``
             % property in the CTI file before loading the phase. The transport
@@ -47,16 +46,15 @@
             % :param src:
             %     Input string of YAML file name.
             % :param id:
-            %     Optional unless ``trans`` is specified. ID of the phase to
-            %     import as specified in the YAML file.
+            %     ID of the phase to import as specified in the YAML file.
             % :param trans:
             %     String, transport modeling. Possible values are ``'default'``, ``'None'``,
             %     ``'Mix'``, or ``'Multi'``. If not specified, ``'default'`` is used.
             % :return:
             %     Instance of class :mat:func:`Solution`
 
-            if nargin == 1
-                id = '-';
+            if nargin < 2 || nargin > 3
+                error('Solution class constructor expects 2 or 3 input arguments.');
             end
             tp = ThermoPhase(src, id);
             s@ThermoPhase(src, id);

interfaces/matlab_experimental/Base/ThermoPhase.m

@@ -68,31 +68,25 @@
             % t = ThermoPhase(src, id)
             %
             % :param src:
-            %     Input string of YAML, CTI, or XML file name.
+            %     Input string of YAML file name.
             % :param id:
-            %     ID of the phase to import as specified in the input file. (optional)
+            %     ID of the phase to import as specified in the input file.
             % :return:
             %     Instance of class :mat:func:`ThermoPhase`
             %
             checklib;
-            if nargin > 2
-                error('ThermoPhase expects 1 or 2 input arguments.');
-            end
-            if nargin == 1
-                id = '-';
+            if nargin ~= 2
+                error('ThermoPhase expects 2 input arguments.');
             end
             tp.tpID = callct('thermo_newFromFile', src, id);
             tp.basis = 'molar';
         end
 
         %% Utility methods
 
-        function display(tp, threshold)
+        function display(tp)
             % Display thermo properties
 
-            if nargin < 2 || ~isnumeric(threshold)
-                threshold = 1e-14;
-            end
             buflen = 0 - calllib(ct, 'thermo_report', tp.tpID, 0, '', 1);
             aa = char(ones(1, buflen));
             ptr = libpointer('cstring', aa);

interfaces/matlab_experimental/Base/Transport.m

@@ -123,7 +123,7 @@ function trClear(tr)
             %    symmetric: d(i, j) = d(j, i). Unit: m^2/s.
 
             nsp = tr.th.nSpecies;
-            xx = zeros(1, nsp);
+            xx = zeros(nsp, nsp);
             pt = libpointer('doublePtr', xx);
             callct('trans_getBinDiffCoeffs', tr.trID, nsp, pt);
             v = pt.Value;
@@ -137,7 +137,7 @@ function trClear(tr)
             %    diffusion coefficients. Unit: m^2/s.
 
             nsp = tr.th.nSpecies;
-            xx = zeros(1, nsp);
+            xx = zeros(nsp, nsp);
             pt = libpointer('doublePtr', xx);
             callct('trans_getMultiDiffCoeffs', tr.trID, nsp, pt);
             v = pt.Value;

samples/matlab_experimental/catcomb.m

@@ -132,10 +132,10 @@
 sim1D = Stack([inlt, flow, surf]);
 
 % set the initial profiles.
-sim1D.setProfile(2, {'u', 'V', 'T'}, [0.0,    1.0       % z/zmax
-                                      0.06,   0.0       % u
-                                      0.0,    0.0       % V
-                                      tinlet, tsurf]);  % T
+sim1D.setProfile(2, {'velocity', 'spread_rate', 'T'}, [0.0,    1.0       % z/zmax
+                                                       0.06,   0.0       % u
+                                                       0.0,    0.0       % V
+                                                       tinlet, tsurf]);  % T
 names = gas.speciesNames;
 
 for k = 1:gas.nSpecies
@@ -207,11 +207,11 @@
 title('Temperature [K]');
 
 subplot(3, 3, 2);
-sim1D.plotSolution('flow', 'u');
+sim1D.plotSolution('flow', 'velocity');
 title('Axial Velocity [m/s]');
 
 subplot(3, 3, 3);
-sim1D.plotSolution('flow', 'V');
+sim1D.plotSolution('flow', 'spread_rate');
 title('Radial Velocity / Radius [1/s]');
 
 subplot(3, 3, 4);

samples/matlab_experimental/diff_flame.m

@@ -5,13 +5,14 @@
 
 %% Initialization
 
-help diff_flame
-
 clear all
 close all
 cleanup
 clc
 
+tic % total running time of the script
+help diff_flame
+
 runtime = cputime;  % Record the starting time
 
 %% Parameter values of inlet streams
@@ -139,3 +140,5 @@
 plot(z, y(j, :), 'r', z, y(k, :), 'g', z, y(l, :), 'm', z, y(m, :), 'b');
 ylabel('Mass Fraction');
 legend('T', 'O2', 'H2O', 'C2H6', 'CO2');
+
+toc

samples/matlab_experimental/equil.m

@@ -3,12 +3,19 @@ function equil(g)
 %
 % This example computes the adiabatic flame temperature and equilibrium
 % composition for a methane/air mixture as a function of equivalence ratio.
+
+    clear all
+    close all
+    cleanup
+    clc
+
+    tic
     help equil
 
     if nargin == 1
        gas = g;
     else
-       gas = Solution('gri30.yaml');
+       gas = GRI30;
     end
 
     nsp = gas.nSpecies;
@@ -60,4 +67,5 @@ function equil(g)
     ylabel('Mole Fraction');
     title('Equilibrium Composition');
 
+    toc
 end

samples/matlab_experimental/flame.m

@@ -45,9 +45,9 @@
     else
       t1 = right.T;
     end
-    f.setProfile(2, {'u', 'V'}, [0.0            1.0
-                                 mdot0/rho0     -mdot1/rho0
-                                 0.0            0.0]);
+    f.setProfile(2, {'velocity', 'spread_rate'}, [0.0            1.0
+                                                  mdot0/rho0     -mdot1/rho0
+                                                  0.0            0.0]);
     f.setProfile(2, 'T', [0.0, 1.0
                           t0, t1]);
 

samples/matlab_experimental/flame1.m

@@ -5,13 +5,14 @@
 
 %% Initialization
 
-help flame1
-
 clear all
 close all
 cleanup
 clc
 
+tic
+help flame1
+
 t0 = cputime;  % record the starting time
 
 %% Set parameter values
@@ -112,11 +113,13 @@
 plotSolution(fl, 'flow', 'T');
 title('Temperature [K]');
 subplot(2, 2, 2);
-plotSolution(fl, 'flow', 'u');
+plotSolution(fl, 'flow', 'velocity');
 title('Axial Velocity [m/s]');
 subplot(2, 2, 3);
 plotSolution(fl, 'flow', 'H2O');
 title('H2O Mass Fraction');
 subplot(2, 2, 4);
 plotSolution(fl, 'flow', 'O2');
 title('O2 Mass Fraction');
+
+toc

samples/matlab_experimental/flame2.m

@@ -4,13 +4,14 @@
 
 %% Initialization
 
-help flame2
-
 clear all
 close all
 cleanup
 clc
 
+tic
+help flame2
+
 t0 = cputime;  % record the starting time
 
 %% Set parameter values
@@ -119,8 +120,10 @@
 plotSolution(fl, 'flow', 'CH');
 title('CH Mass Fraction');
 subplot(2, 3, 5);
-plotSolution(fl, 'flow', 'V');
+plotSolution(fl, 'flow', 'spread_rate');
 title('Radial Velocity / Radius [s^-1]');
 subplot(2, 3, 6);
-plotSolution(fl, 'flow', 'u');
+plotSolution(fl, 'flow', 'velocity');
 title('Axial Velocity [m/s]');
+
+toc

samples/matlab_experimental/ignite_hp.m

@@ -2,6 +2,12 @@ function ignite_hp(gas)
     %  IGNITE_HP  Solves the same ignition problem as 'ignite', but uses
     %  function conhp instead of reactor.
 
+    clear all
+    close all
+    cleanup
+    clc
+
+    tic
     help ignite_hp
 
     if nargin == 0
@@ -35,4 +41,5 @@ function ignite_hp(gas)
        title('OH Mass Fraction');
     end
 
+    toc
 end

samples/matlab_experimental/ignite_uv.m

@@ -2,6 +2,12 @@ function ignite_uv(gas)
     %  IGNITE_UV  Solves the same ignition problem as 'ignite2', except
     %  function conuv is used instead of reactor.
     %
+    clear all
+    close all
+    cleanup
+    clc
+
+    tic
     help ignite_uv
 
     if nargin == 0
@@ -35,4 +41,5 @@ function ignite_uv(gas)
        title('OH Mass Fraction');
     end
 
+    toc
 end

samples/matlab_experimental/isentropic.m

@@ -4,6 +4,12 @@ function isentropic(g)
 %    In this example, the area ratio vs. Mach number curve is
 %    computed for a hydrogen/nitrogen gas mixture.
 %
+    clear all
+    close all
+    cleanup
+    clc
+
+    tic
     help isentropic
 
     if nargin == 1
@@ -56,4 +62,6 @@ function isentropic(g)
     ylabel('Area Ratio');
     xlabel('Mach Number');
     title('Isentropic Flow: Area Ratio vs. Mach Number');
+
+    toc
 end