[Matlab] Construct objects directly from input file names

Bypass reading and manipulation of XML files within Matlab, so that XML, CTI,
and YAML input files can all be used.

interfaces/matlab/toolbox/@Interface/Interface.m

@@ -21,19 +21,17 @@ function s = Interface(src, id, p1, p2, p3, p4)
 %     Instance of class :mat:func:`Interface`
 %
 
-doc = XML_Node('doc', src);
+t = ThermoPhase(src, id);
-node = findByID(doc, id);
-t = ThermoPhase(node);
 if nargin == 2
-    k = Kinetics(node, t);
+    k = Kinetics(t, src, id);
 elseif nargin == 3
-    k = Kinetics(node, t, p1);
+    k = Kinetics(t, src, id, p1);
 elseif nargin == 4
-    k = Kinetics(node, t, p1, p2);
+    k = Kinetics(t, src, id, p1, p2);
 elseif nargin == 5
-    k = Kinetics(node, t, p1, p2, p3);
+    k = Kinetics(t, src, id, p1, p2, p3);
 elseif nargin == 6
-    k = Kinetics(node, t, p1, p2, p3, p4);
+    k = Kinetics(t, src, id, p1, p2, p3, p4);
 end
 
 s.kin = k;

interfaces/matlab/toolbox/@Kinetics/Kinetics.m

@@ -1,4 +1,4 @@
-function k = Kinetics(r, ph, neighbor1, neighbor2, neighbor3, neighbor4)
+function k = Kinetics(ph, src, id, neighbor1, neighbor2, neighbor3, neighbor4)
 % KINETICS  Kinetics class constructor.
 % k = Kinetics(r, ph, neighbor1, neighbor2, neighbor3, neighbor4)
 % Class Kinetics represents kinetics managers, which are classes
@@ -8,10 +8,13 @@ function k = Kinetics(r, ph, neighbor1, neighbor2, neighbor3, neighbor4)
 % of progress, species production rates, and other quantities pertaining to
 % a reaction mechanism.
 %
-% :param r:
-%     An instance of class :mat:func:`XML_Node`.
 % :param ph:
-%     An instance of class :mat:func:`ThermoPhase`.
+%     An instance of class :mat:func:`ThermoPhase` representing the phase
+%     in which reactions occur
+% :param src:
+%     Input string of YAML, CTI, or XML file name.
+% :param id:
+%     ID of the phase to import as specified in the input file. (optional)
 % :param neighbor1:
 %     Instance of class :mat:func:`ThermoPhase` or :mat:func:`Solution` representing a
 %     neighboring phase.
@@ -34,32 +37,28 @@ ineighbor1 = -1;
 ineighbor2 = -1;
 ineighbor3 = -1;
 ineighbor4 = -1;
-
+if nargin == 2
-% First argument must be an XML_Node instance representing the XML tree
+    id = '-';
-if ~isa(r, 'XML_Node')
-    error('first argument must be an XML_Node object')
 end
 
 k.owner = 1;
-ixml = xml_hndl(r);
-
 % get the integer indices used to find the stored objects
 % representing the phases participating in the mechanism.
 iphase = thermo_hndl(ph);
-if nargin > 2
+if nargin > 3
     ineighbor1 = thermo_hndl(neighbor1);
-    if nargin > 3
+    if nargin > 4
         ineighbor2 = thermo_hndl(neighbor2);
-        if nargin > 4
+        if nargin > 5
             ineighbor3 = thermo_hndl(neighbor3);
-            if nargin > 5
+            if nargin > 6
                 ineighbor4 = thermo_hndl(neighbor4);
             end
         end
     end
 end
-k.id = kinetics_get(ixml, 0, iphase, ineighbor1, ineighbor2, ineighbor3, ...
+k.id = kinetics_get(0, 0, src, id, iphase, ineighbor1, ineighbor2, ...
-    ineighbor4);
+    ineighbor3, ineighbor4);
 if k.id < 0
     error(geterr);
 end

interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m

@@ -1,4 +1,4 @@
-function v = kinetics_get(n, job, a, b, c, d, e, f)
+function v = kinetics_get(n, job, a, b, c, d, e, f, g)
 % KINETICS_GET - get kinetics attributes
 %
 if nargin == 2
@@ -15,4 +15,6 @@ elseif nargin == 7
     v = ctmethods(40, n, job, a, b, c, d, e);
 elseif nargin == 8
     v = ctmethods(40, n, job, a, b, c, d, e, f);
+elseif nargin == 9
+    v = ctmethods(40, n, job, a, b, c, d, e, f, g);
 end

interfaces/matlab/toolbox/@Solution/Solution.m

@@ -44,24 +44,21 @@ function s = Solution(src, id, trans)
 % :return:
 %     Instance of class :mat:func:`Solution`
 %
-doc = XML_Node('doc', src);
 if nargin == 1
-    node = findByName(doc, 'phase');
+    id = '-';
-else
-    node = findByID(doc, id);
 end
-t = ThermoPhase(node);
+t = ThermoPhase(src, id);
-k = Kinetics(node, t);
+k = Kinetics(t, src, id);
 s.kin = k;
 s.th = t;
 if nargin == 3
     if strcmp(trans, 'default') || strcmp(trans, 'Mix') || strcmp(trans, 'Multi')
-        tr = Transport(node, t, trans, 0);
+        tr = Transport(t, trans, 0);
     else
         error('Unknown transport modeling specified.')
     end
 else
-    tr = Transport(node, t, 'default', 0);
+    tr = Transport(t, 'default', 0);
 end
 s.tr = tr;
 s = class(s, 'Solution', t, k, tr);

interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m

@@ -1,19 +1,24 @@
-function t = ThermoPhase(r)
+function t = ThermoPhase(src, id)
 % THERMOPHASE  ThermoPhase class constructor.
-% t = ThermoPhase(r)
+% t = ThermoPhase(src, id)
-% :param r:
+% :param src:
-%     An instance of class :mat:func:`XML_Node`.
+%     Input string of YAML, CTI, or XML file name.
+% :param id:
+%     ID of the phase to import as specified in the input file. (optional)
 % :return:
 %     Instance of class :mat:func:`ThermoPhase`
 %
 
-if nargin ~= 1
+if nargin > 2
-    error('ThermoPhase expects 1 input argument.');
+    error('ThermoPhase expects 1 or 2 input arguments.');
+end
+
+if nargin == 1
+    id = '-';
 end
 
 t.owner = 1;
-hr = xml_hndl(r);
+t.tp_id = thermo_get(0, 0, src, id);
-t.tp_id = thermo_get(hr, 0);
 if t.tp_id < 0
     error(geterr);
 end

interfaces/matlab/toolbox/@Transport/Transport.m

@@ -1,22 +1,18 @@
-function tr = Transport(r, th, model, loglevel)
+function tr = Transport(th, model, loglevel)
 % TRANSPORT  Transport class constructor.
 % tr = Transport(r, th, model, loglevel)
-% Create a new instance of class :mat:func:`Transport`. Three or four arguments
+% Create a new instance of class :mat:func:`Transport`. One to three arguments
-% may be supplied. The first two must be an instance of class:mat:func:`XML_Node`
+% may be supplied. The first must be an instance of class
-% and an instance of class :mat:func:`ThermoPhase` respectively.
+% :mat:func:`ThermoPhase`. The second (optional) argument is the type of
-% The third argument is the type of modeling desired, specified
+% model desired, specified by the string ``'default'``, ``'Mix'`` or
-% by the string ``'default'``, ``'Mix'`` or ``'Multi'``.
+% ``'Multi'``. ``'default'`` uses the default transport specified in the
-% ``'default'`` uses the default transport specified in the
+% :mat:func:`XML_Node`. The third argument is the logging level desired.
-% :mat:func:`XML_Node`. The fourth argument is
-% the logging level desired.
 %
-% :param r:
-%     An instance of class :mat:func:`XML_Node`
 % :param th:
 %     Instance of class :mat:func:`ThermoPhase`
 % :param model:
 %     String indicating the transport model to use. Possible values
-%     are ``'default'``, ``'Mix'``, and ``'Multi'``
+%     are ``'default'``, ``'Mix'``, and ``'Multi'``. Optional.
 % :param loglevel:
 %     Level of diagnostic logging. Default if not specified is 4.
 % :return:
@@ -24,25 +20,22 @@ function tr = Transport(r, th, model, loglevel)
 %
 
 tr.id = 0;
-if nargin == 3
+if nargin == 2
+    model = 'default';
+end
+
+if nargin < 3
     loglevel = 4;
 end
-if ~isa(r, 'XML_Node')
+
-    error(['The first argument must be an instance of class XML_Node'])
+if ~isa(th, 'ThermoPhase')
-elseif ~isa(th, 'ThermoPhase')
+    error('The first argument must be an instance of class ThermoPhase')
-    error('The second argument must be an instance of class ThermoPhase')
 else
     tr.th = th;
     if strcmp(model, 'default')
-        try
+        tr.id = trans_get(thermo_hndl(th), -2, loglevel);
-            node = child(r, 'transport');
-            tr.model = attrib(node, 'model');
-        catch
-            tr.model = 'None';
-        end
     else
-        tr.model = model;
+        tr.id = trans_get(thermo_hndl(th), -1, model, loglevel);
     end
-    tr.id = trans_get(thermo_hndl(th), -1, tr.model, loglevel) ;
     tr = class(tr, 'Transport');
 end

src/matlab/kineticsmethods.cpp

@@ -3,6 +3,7 @@
 
 #include "ctmatutils.h"
 #include "cantera/clib/ct.h"
+#include "cantera/base/global.h"
 
 void checkNArgs(const int n, const int nrhs)
 {
@@ -20,14 +21,19 @@ void kineticsmethods(int nlhs, mxArray* plhs[],
 
     // construct a new instance
     if (job == 0) {
-        checkNArgs(8, nrhs);
+        checkNArgs(10, nrhs);
-        int root = getInt(prhs[1]);
+        std::string fileName = getString(prhs[3]);
-        int iph = getInt(prhs[3]);
+        std::string phaseName = getString(prhs[4]);
-        int in1 = getInt(prhs[4]);
+        if (phaseName == "-") {
-        int in2 = getInt(prhs[5]);
+            phaseName = "";
-        int in3 = getInt(prhs[6]);
+        }
-        int in4 = getInt(prhs[7]);
+        int iph = getInt(prhs[5]);
-        vv = static_cast<int>(kin_newFromXML(root, iph, in1, in2, in3, in4));
+        int in1 = getInt(prhs[6]);
+        int in2 = getInt(prhs[7]);
+        int in3 = getInt(prhs[8]);
+        int in4 = getInt(prhs[9]);
+        vv = static_cast<int>(kin_newFromFile(
+            fileName.c_str(), phaseName.c_str(), iph, in1, in2, in3, in4));
         plhs[0] = mxCreateNumericMatrix(1,1,mxDOUBLE_CLASS,mxREAL);
         double* h = mxGetPr(plhs[0]);
         *h = vv;

src/matlab/thermomethods.cpp

@@ -119,12 +119,24 @@ static void thermoget(int nlhs, mxArray* plhs[],
     int n = getInt(prhs[1]);
     int job = getInt(prhs[2]);
 
-    if (job < 30) {
+    if (job == 0) {
+        checkNArgs(5, nrhs);
+        std::string fileName = getString(prhs[3]);
+        std::string phaseName = getString(prhs[4]);
+        if (phaseName == "-") {
+            phaseName = "";
+        }
+        vv = (double) thermo_newFromFile(fileName.c_str(), phaseName.c_str());
+        if (vv == DERR) {
+            reportError();
+        }
+        plhs[0] = mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL);
+        double* h = mxGetPr(plhs[0]);
+        *h = vv;
+        return;
+    } else if (job < 30) {
         bool ok = true;
         switch (job) {
-        case 0:
-            vv = (double) thermo_newFromXML(n);
-            break;
         case 2:
             vv = thermo_enthalpy_mole(n);
             break;

src/matlab/transportmethods.cpp

@@ -27,6 +27,19 @@ void transportmethods(int nlhs, mxArray* plhs[],
             reportError();
         }
 
+        // Create matrix for the return argument.
+        plhs[0] = mxCreateDoubleMatrix(1,1, mxREAL);
+        double* x = mxGetPr(plhs[0]);
+        *x = m;
+        return;
+    } else if (job == -2) {
+        int loglevel = getInt(prhs[3]);
+        int m = -2;
+        m = (int) trans_newDefault(n, loglevel);
+        if (m < 0) {
+            reportError();
+        }
+
         // Create matrix for the return argument.
         plhs[0] = mxCreateDoubleMatrix(1,1, mxREAL);
         double* x = mxGetPr(plhs[0]);