Hi @ischoegl , I've started migrating the MATLAB interface to the generated Clib. It won't work with the generated Clib as-is due to the following two points:

• Only ct.h includes <stdint.h>, but several other generated headers in cantera_clib also declare functions using int32_t.
  When the MATLAB interface generator (clibgen.generateLibraryDefinition) parses these headers individually, compilation fails with:

/Users/ssun30/cantera/interfaces/clib/include/cantera_clib/ctconnector.h(139): 
error: identifier "int32_t" is undefined'

On my local machine, I got around this issue by adding <stdint.h> to other header files.

• Several function docstrings in ct.h contain the substring %Cantera, for example, in ct_version:

/**
 * Returns the %Cantera version.
 */

MATLAB’s clibgen treats % as a comment character in MATLAB syntax. During parsing, the line is truncated at %, producing an unterminated string in the generated definectMatlab.m file and causing:

Error: String is not terminated properly.

Affected functions:
ct_version
ct_gitCommit
ct_getDataDirectories
ct_make_warnings_fatal
ct_getCanteraError

On my local machine, I got around this issue by removing the % symbol from %Cantera.

@ssun30 ... I pushed some fixes. I can compile things without needing to edit on my machine, and the toolbox loads, but the unit tests fail. Please ensure that you reset your local branch to this one to preserve my edits.

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@ssun30 ... I pushed some fixes. I can compile things without needing to edit on my machine, and the toolbox loads, but the unit tests fail. Please ensure that you reset your local branch to this one to preserve my edits.

Hi @ischoegl , I've fixed most of the issues with the unit tests. But five tests remain and I'll list each of them:

sample ignite.m

Unable to resolve the name 'clib.ctMatlab.kin_getSourceTerms'.

Error in [ctArray](matlab:matlab.lang.internal.introspective.errorDocCallback('ctArray', '/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctArray.m', 6)) ([line 6](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctArray.m',6,0)))
    iok = clib.ctMatlab.(funcName)(varargin{:}, buf);
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in [Kinetics/get.massProdRate](matlab:matlab.lang.internal.introspective.errorDocCallback('Kinetics/get.massProdRate', '/Users/ssun30/cantera/interfaces/matlab_experimental/Base/Kinetics.m', 458)) ([line 458](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/Base/Kinetics.m',458,0)))
            ydot = ctArray('kin_getSourceTerms', nsp, kin.kinID);
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in [reactor_ode](matlab:matlab.lang.internal.introspective.errorDocCallback('reactor_ode', '/Users/ssun30/cantera/samples/matlab_experimental/reactor_ode.m', 44)) ([line 44](matlab: opentoline('/Users/ssun30/cantera/samples/matlab_experimental/reactor_ode.m',44,0)))
        ydt = total_mass * gas.massProdRate;

I didn't find the new equivalent function to kin_getSourceTerms in the generated clib.

The next sample is catacomb.m

Error using [clib.ctMatlab.domain_index](matlab:matlab.lang.internal.introspective.errorDocCallback('clib.ctMatlab.domain_index'))
No method 'clib.ctMatlab.domain_index' with matching signature found.

Error in [ctFunc](matlab:matlab.lang.internal.introspective.errorDocCallback('ctFunc', '/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctFunc.m', 5)) ([line 5](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctFunc.m',5,0)))
    output = clib.ctMatlab.(funcName)(varargin{:});
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in [Domain1D/get.domainIndex](matlab:matlab.lang.internal.introspective.errorDocCallback('Domain1D/get.domainIndex', '/Users/ssun30/cantera/interfaces/matlab_experimental/OneDim/Domain1D.m', 200)) ([line 200](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/OneDim/Domain1D.m',200,0)))
            i = ctFunc('domain_index', d.domainID) + 1;
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in [Boundary1D/massFraction](matlab:matlab.lang.internal.introspective.errorDocCallback('Boundary1D/massFraction', '/Users/ssun30/cantera/interfaces/matlab_experimental/OneDim/Boundary1D.m', 81)) ([line 81](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/OneDim/Boundary1D.m',81,0)))
            if d.domainIndex == 0
               ^^^^^^^^^^^^^
Error in [catcomb](matlab:matlab.lang.internal.introspective.errorDocCallback('catcomb', '/Users/ssun30/cantera/samples/matlab_experimental/catcomb.m', 144)) ([line 144](matlab: opentoline('/Users/ssun30/cantera/samples/matlab_experimental/catcomb.m',144,0)))
    y = inlt.massFraction(k);

The function signature for domain_index has changed:

    /**
     *  Returns the index of the solution vector, which corresponds to component n at grid point j.
     *
     *  Wraps C++ method: `size_t Domain1D::index(size_t, size_t)`
     *
     *  @param handle       Handle to queried Domain1D object.
     *  @param n            component index
     *  @param j            grid point index
     */
    int32_t domain_index(int32_t handle, int32_t n, int32_t j);

sample surf_reactor.m

Error using [ctFunc](matlab:matlab.lang.internal.introspective.errorDocCallback('ctFunc', '/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctFunc.m', 10)) ([line 10](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/Utility/ctFunc.m',10,0)))

*******************************************************************************
CanteraError thrown by Cabinet::as:
Item is not of the correct type.
*******************************************************************************

Error in [ReactorSurface/set.area](matlab:matlab.lang.internal.introspective.errorDocCallback('ReactorSurface/set.area', '/Users/ssun30/cantera/interfaces/matlab_experimental/Reactor/ReactorSurface.m', 56)) ([line 56](matlab: opentoline('/Users/ssun30/cantera/interfaces/matlab_experimental/Reactor/ReactorSurface.m',56,0)))
            ctFunc('reactor_setArea', s.id, a);
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in [surf_reactor](matlab:matlab.lang.internal.introspective.errorDocCallback('surf_reactor', '/Users/ssun30/cantera/samples/matlab_experimental/surf_reactor.m', 48)) ([line 48](matlab: opentoline('/Users/ssun30/cantera/samples/matlab_experimental/surf_reactor.m',48,0)))
rsurf.area = A;
^^^^^^^^^^

I didn't find the equivalent methods for reactorsurface_area and reactorsurface_setArea in the new clib.

The final errors are under ctTestThermo.m, in particular testElementalMassFraction and testNAtoms:

    --> The value does not contain the substring.
    
    Actual char:
        <no Cantera error
    Expected Substring:
        No such element

In the legacy clib, the thermo_elementIndex and thermo_speciesIndex methods have hard-coded error handling:

    size_t thermo_elementIndex(int n, const char* nm)
    {
        try {
             size_t k = ThermoCabinet::at(n)->elementIndex(nm);
             if (k == npos) {
                throw CanteraError("thermo_elementIndex",
                                   "No such element {}.", nm);
             }
             return k;
        } catch (...) {
            return handleAllExceptions(npos, npos);
        }
    }

Now the corresponding methods in the generated clib lack those checks, and thus no error message was returned.

@ssun30 ... thank you - I'll look into the issue you pointed out shortly. We just merged #1995, which changes some of the 1D access routes (good news: things should become somewhat easier). Could you rebase? I'll try to push some fixes to the issues you pointed out thereafter.

PS: I outlined some of my thoughts on the 'onedim' portion in Cantera/enhancements#239. Only a small fraction is applicable to this PR.

I didn't find the new equivalent function to kin_getSourceTerms in the generated clib.

This was hard-coded in the legacy CLib, and won't be replicated as such in the generated CLib. You have two options:

1. Implement what the old function did in MATLAB
2. Add it to the C++ code base

The function signature for domain_index has changed:

Point-wise access should be replaced by domain_value for boundaries and domain_values for flow domains.

The final errors are under ctTestThermo.m, in particular testElementalMassFraction and testNAtoms
[...]

The underlying C++ methods return npos, and Python implements custom exception handling. The way the generated CLib works is that it will simply pass through C++ behavior, with no additional checks added.

The quick fix is to follow the Python approach, although an argument could be made to move this to C++ (which is significantly more difficult, as this changes long-standing behavior with potentially breaking changes). The best approach to implementing a change in C++ would be to create an enhancement request, as it exceeds the scope of the MATLAB toolbox. Edit: see #2004.

PS: #2010

I didn't find the equivalent methods for reactorsurface_area and reactorsurface_setArea in the new clib.

Yes - while there was a setter/getter, it was shadowed by FlowReactor. I implemented a version that handles both in C++ - please use reactor_area and reactor_setArea and add it to the base class. The C++ fix is added to this PR.

@ssun30 ... I will have a look at the 1D components as there have been significant changes. I will try to make this as close to Cantera/enhancements#239 and the corresponding Python framework as possible so this is futureproof.

@ssun30 ... I added a new flamespeed.m example that is an almost identical replica of the C++ example. It runs and gives the same output as C++. I.e., this PR likely fixes #1722 (added this to the top description).

The catcomb.m sample runs mostly through at this point but stalls at the plotting step; the rest should be straightforward debugging. PS: pushed the remaining (trivial) fix.

Overall, there were some issues with MATLAB functions calling incorrect CLib signatures. I created convenience access points as necessary. There are two observations:

• The MATLAB-built interface changes the signatures, which is extremely confusing, as the names still correspond to CLib
• MATLAB does not display C++ output (which is a bug)

@ssun30 and @speth ... I ended up simplifying ctBuildInterface as there is no need to specify two include folders. After installation, the /path/to/cantera_install/include folder holds cantera and cantera_clib in parallel folders.

The main difference is that this requires a scons install, and avoids using the build folders.

PS: I also switched to inprocess defaults on macOS and Windows, but can roll that change back. Edit: rolled back.

The main difference is that this requires a scons install, and avoids using the build folders.

I think being able to test (both the test suite and interactively) without running scons install is incredibly valuable, and not a feature I would want to lose for the MATLAB toolbox or any of the interfaces.

I think being able to test (both the test suite and interactively) without running scons install is incredibly valuable, and not a feature I would want to lose for the MATLAB toolbox or any of the interfaces.

Fair point. Thankfully, the dependency on cantera/base/config.h in clib_defs.h was unnecessary, so I was able to maintain the simplification without needing to install. I.e.,

ctToolboxDir = '/path/to/cantera/source/interfaces/matlab_experimental';
ctIncludeDir = '/path/to/cantera/include';
ctLibDir = '/path/to/cantera/library';
ctBuildInterface(ctToolboxDir, ctIncludeDir, ctLibDir);

I'll leave this for a final review now. There are many rough edges, but the migration to the generated CLib is accomplished (thank you @ssun30!). Additional improvements can be made in follow-up PRs.

@speth / @ssun30 ... I went ahead and made all the requested changes, which also extend to improved exception handling for enabling/disabling energy and chemistry.