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[Matlab] Construct objects directly from input file names

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Bypass reading and manipulation of XML files within Matlab, so that XML, CTI,
and YAML input files can all be used.
This commit is contained in:
Ray Speth 2019-01-29 16:17:34 -05:00
parent 6a8c378846
commit 901ec2f12c
9 changed files with 103 additions and 78 deletions
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14
interfaces/matlab/toolbox/@Interface/Interface.m
View file

@ -21,19 +21,17 @@ function s = Interface(src, id, p1, p2, p3, p4)
% Instance of class :mat:func:`Interface`
%
doc = XML_Node('doc', src);
node = findByID(doc, id);
t = ThermoPhase(node);
t = ThermoPhase(src, id);
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;

31
interfaces/matlab/toolbox/@Kinetics/Kinetics.m
View file

@ -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;
% First argument must be an XML_Node instance representing the XML tree
if ~isa(r, 'XML_Node')
error('first argument must be an XML_Node object')
if nargin == 2
id = '-';
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, ...
ineighbor4);
k.id = kinetics_get(0, 0, src, id, iphase, ineighbor1, ineighbor2, ...
ineighbor3, ineighbor4);
if k.id < 0
error(geterr);
end

4
interfaces/matlab/toolbox/@Kinetics/private/kinetics_get.m
View file

@ -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

13
interfaces/matlab/toolbox/@Solution/Solution.m
View file

@ -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');
else
node = findByID(doc, id);
id = '-';
end
t = ThermoPhase(node);
k = Kinetics(node, t);
t = ThermoPhase(src, id);
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);

21
interfaces/matlab/toolbox/@ThermoPhase/ThermoPhase.m
View file

@ -1,19 +1,24 @@
function t = ThermoPhase(r)
function t = ThermoPhase(src, id)
% THERMOPHASE ThermoPhase class constructor.
% t = ThermoPhase(r)
% :param r:
% An instance of class :mat:func:`XML_Node`.
% t = ThermoPhase(src, id)
% :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)
% :return:
% Instance of class :mat:func:`ThermoPhase`
%
if nargin ~= 1
error('ThermoPhase expects 1 input argument.');
if nargin > 2
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(hr, 0);
t.tp_id = thermo_get(0, 0, src, id);
if t.tp_id < 0
error(geterr);
end

43
interfaces/matlab/toolbox/@Transport/Transport.m
View file

@ -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
% may be supplied. The first two must be an instance of class:mat:func:`XML_Node`
% and an instance of class :mat:func:`ThermoPhase` respectively.
% The third argument is the type of modeling desired, specified
% by the string ``'default'``, ``'Mix'`` or ``'Multi'``.
% ``'default'`` uses the default transport specified in the
% :mat:func:`XML_Node`. The fourth argument is
% the logging level desired.
% Create a new instance of class :mat:func:`Transport`. One to three arguments
% may be supplied. The first must be an instance of class
% :mat:func:`ThermoPhase`. The second (optional) argument is the type of
% model desired, specified by the string ``'default'``, ``'Mix'`` or
% ``'Multi'``. ``'default'`` uses the default transport specified in the
% :mat:func:`XML_Node`. The third 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'])
elseif ~isa(th, 'ThermoPhase')
error('The second argument must be an instance of class ThermoPhase')
if ~isa(th, 'ThermoPhase')
error('The first argument must be an instance of class ThermoPhase')
else
tr.th = th;
if strcmp(model, 'default')
try
node = child(r, 'transport');
tr.model = attrib(node, 'model');
catch
tr.model = 'None';
end
tr.id = trans_get(thermo_hndl(th), -2, loglevel);
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

22
src/matlab/kineticsmethods.cpp
View file

@ -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);
int root = getInt(prhs[1]);
int iph = getInt(prhs[3]);
int in1 = getInt(prhs[4]);
int in2 = getInt(prhs[5]);
int in3 = getInt(prhs[6]);
int in4 = getInt(prhs[7]);
vv = static_cast<int>(kin_newFromXML(root, iph, in1, in2, in3, in4));
checkNArgs(10, nrhs);
std::string fileName = getString(prhs[3]);
std::string phaseName = getString(prhs[4]);
if (phaseName == "-") {
phaseName = "";
}
int iph = getInt(prhs[5]);
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;

20
src/matlab/thermomethods.cpp
View file

@ -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;

13
src/matlab/transportmethods.cpp
View file

@ -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]);