Cantera · speth · Feb 25, 2023 · Feb 24, 2023 · Feb 24, 2023 · Feb 24, 2023
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -58,7 +58,8 @@ jobs:
     - name: Build Cantera
       run: |
         python3 `which scons` build env_vars=all -j2 debug=n --debug=time \
-        hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR
+        hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR \
+        cc_flags=-D_GLIBCXX_ASSERTIONS
     - name: Upload shared library
       uses: actions/upload-artifact@v3
       if: matrix.python-version == '3.10' && matrix.os == 'ubuntu-22.04'

diff --git a/SConstruct b/SConstruct
@@ -1036,8 +1036,8 @@ if conda_prefix is not None:
     env["extra_lib_dirs"].append(conda_lib_dir)
     logger.info(f"Adding conda include and library paths: {conda_prefix}")
 
-env.Append(CPPPATH=env['extra_inc_dirs'],
-           LIBPATH=env['extra_lib_dirs'])
+add_system_include(env, env['extra_inc_dirs'])
+env.Append(LIBPATH=env['extra_lib_dirs'])
 
 if env['use_rpath_linkage']:
     env.Append(RPATH=env['extra_lib_dirs'])
@@ -1054,7 +1054,7 @@ else:
 
 if env['boost_inc_dir']:
     env["boost_inc_dir"] = Path(env["boost_inc_dir"]).as_posix()
-    env.Append(CPPPATH=env['boost_inc_dir'])
+    add_system_include(env, env['boost_inc_dir'])
 
 if env['blas_lapack_dir']:
     env["blas_lapack_dir"] = Path(env["blas_lapack_dir"]).as_posix()
@@ -1065,7 +1065,7 @@ if env['blas_lapack_dir']:
 if env['system_sundials'] in ('y','default'):
     if env['sundials_include']:
         env["sundials_include"] = Path(env["sundials_include"]).as_posix()
-        env.Append(CPPPATH=[env['sundials_include']])
+        add_system_include(env, env['sundials_include'])
         env['system_sundials'] = 'y'
     if env['sundials_libdir']:
         env["sundials_libdir"] = Path(env["sundials_libdir"]).as_posix()
@@ -1100,7 +1100,7 @@ int main(int argc, char** argv) {
     return result
 
 # Set up compiler options before running configuration tests
-env['CXXFLAGS'] = listify(env['cxx_flags'])
+env.Append(CXXFLAGS=listify(env['cxx_flags']))
 env['CCFLAGS'] = listify(env['cc_flags']) + listify(env['thread_flags'])
 env['LINKFLAGS'] += listify(env['thread_flags'])
 env['CPPDEFINES'] = {}
@@ -1531,7 +1531,7 @@ else: # env['system_sundials'] == 'n'
 
 if env["hdf_include"]:
     env["hdf_include"] = Path(env["hdf_include"]).as_posix()
-    env.Append(CPPPATH=[env["hdf_include"]])
+    add_system_include(env, env["hdf_include"])
     env["hdf_support"] = "y"
 if env["hdf_libdir"]:
     env["hdf_libdir"] = Path(env["hdf_libdir"]).as_posix()

diff --git a/interfaces/cython/setup.cfg.in b/interfaces/cython/setup.cfg.in
@@ -46,12 +46,18 @@ install_requires =
 python_requires = >=@py_min_ver_str@
 packages =
     cantera
+    cantera.data
+    cantera.test
+    cantera.examples
 
 [options.package_data]
 # The module extension needs to be here since we don't want setuptools to compile
 # the extension, so there are no ``source`` files in the setup.py ``extension`` and
 # we have to treat the module as package data.
-cantera = *.pxd, *.dll, *@py_module_ext@, test/*.txt, examples/*.txt, data/*.*
+cantera = *.pxd, *.dll, *@py_module_ext@
+cantera.data = *.*
+cantera.test = *.txt
+cantera.examples = *.txt
 
 [options.extras_require]
 hdf5 = h5py

diff --git a/site_scons/buildutils.py b/site_scons/buildutils.py
@@ -29,7 +29,7 @@
 __all__ = ("Option", "PathOption", "BoolOption", "EnumOption", "Configuration",
            "logger", "remove_directory", "remove_file", "test_results",
            "add_RegressionTest", "get_command_output", "listify", "which",
-           "ConfigBuilder", "multi_glob", "get_spawn", "quoted",
+           "ConfigBuilder", "multi_glob", "get_spawn", "quoted", "add_system_include",
            "get_pip_install_location", "compiler_flag_list", "setup_python_env")
 
 if TYPE_CHECKING:
@@ -1118,6 +1118,27 @@ def compiler_flag_list(
     return cc_flags
 
 
+def add_system_include(env, include, mode='append'):
+    # Add a file to the include path as a "system" include directory, which will
+    # suppress warnings stemming from code that isn't part of Cantera, and reduces
+    # time spent scanning these files for changes.
+    if mode == 'append':
+        add = env.Append
+    elif mode == 'prepend':
+        add = env.Prepend
+    else:
+        raise ValueError("mode must be 'append' or 'prepend'")
+
+    if env['CC'] == 'cl':
+        add(CPPPATH=include)
+    else:
+        if isinstance(include, (list, tuple)):
+            for inc in include:
+                add(CXXFLAGS=('-isystem', inc))
+        else:
+            add(CXXFLAGS=('-isystem', include))
+
+
 def quoted(s: str) -> str:
     """Return the given string wrapped in double quotes."""
     return f'"{s}"'
@@ -1284,7 +1305,8 @@ def setup_python_env(env):
     py_version_nodot = info["py_version_nodot"]
     plat = info['plat'].replace('-', '_').replace('.', '_')
     numpy_include = info["numpy_include"]
-    env.Prepend(CPPPATH=[Dir('#include'), inc, numpy_include])
+    env.Prepend(CPPPATH=Dir('#include'))
+    add_system_include(env, (inc, numpy_include), 'prepend')
     env.Prepend(LIBS=env['cantera_shared_libs'])
 
     # Fix the module extension for Windows from the sysconfig library.

diff --git a/src/SConscript b/src/SConscript
@@ -40,7 +40,8 @@ libs = [('base', ['cpp'], baseSetup),
         ]
 
 localenv = env.Clone()
-localenv.Prepend(CPPPATH=[Dir('#include'), Dir('#include/cantera/ext'), Dir('.')])
+localenv.Prepend(CPPPATH=[Dir('#include'), Dir('.')])
+add_system_include(localenv, Dir('#include/cantera/ext'), 'prepend')
 localenv.Append(CCFLAGS=env['warning_flags'])
 indicatorEnv = localenv.Clone()  # Get this before any of the PCH complications
 

diff --git a/src/base/SolutionArray.cpp b/src/base/SolutionArray.cpp
@@ -240,7 +240,8 @@ void SolutionArray::writeEntry(const std::string& fname, const std::string& id,
             std::vector<vector_fp> prop;
             for (size_t i = 0; i < m_size; i++) {
                 size_t first = offset + i * m_stride;
-                prop.push_back(vector_fp(&m_data[first], &m_data[first + nSpecies]));
+                prop.emplace_back(m_data.begin() + first,
+                                  m_data.begin() + first + nSpecies);
             }
             file.writeMatrix(id, name, prop);
         } else {
@@ -428,7 +429,7 @@ std::string SolutionArray::detectMode(const std::set<std::string>& names, bool n
     // check set of available names against state acronyms defined by Phase::fullStates
     std::string mode = "";
     const auto& nativeState = m_sol->thermo()->nativeState();
-    bool usesNativeState;
+    bool usesNativeState = false;
     auto surf = std::dynamic_pointer_cast<SurfPhase>(m_sol->thermo());
     for (const auto& item : m_sol->thermo()->fullStates()) {
         bool found = true;

diff --git a/src/equil/MultiPhase.cpp b/src/equil/MultiPhase.cpp
@@ -818,7 +818,7 @@ void MultiPhase::uploadMoleFractionsFromPhases()
     size_t loc = 0;
     for (size_t ip = 0; ip < nPhases(); ip++) {
         ThermoPhase* p = m_phase[ip];
-        p->getMoleFractions(&m_moleFractions[loc]);
+        p->getMoleFractions(m_moleFractions.data() + loc);
         loc += p->nSpecies();
     }
     calcElemAbundances();
@@ -828,7 +828,7 @@ void MultiPhase::updatePhases() const
 {
     size_t loc = 0;
     for (size_t p = 0; p < nPhases(); p++) {
-        m_phase[p]->setState_TPX(m_temp, m_press, &m_moleFractions[loc]);
+        m_phase[p]->setState_TPX(m_temp, m_press, m_moleFractions.data() + loc);
         loc += m_phase[p]->nSpecies();
         m_temp_OK[p] = true;
         if (m_temp < m_phase[p]->minTemp() || m_temp > m_phase[p]->maxTemp()) {

diff --git a/src/equil/vcs_solve_TP.cpp b/src/equil/vcs_solve_TP.cpp
@@ -20,6 +20,8 @@ using namespace std;
 namespace {
 enum stages {MAIN, EQUILIB_CHECK, ELEM_ABUND_CHECK,
              RECHECK_DELETED, RETURN_A, RETURN_B};
+
+const int anote_size = 128;
 }
 
 namespace Cantera
@@ -56,7 +58,7 @@ int VCS_SOLVE::vcs_solve_TP(int print_lvl, int printDetails, int maxit)
     bool uptodate_minors = true;
     int forceComponentCalc = 1;
 
-    char ANOTE[128];
+    char ANOTE[anote_size];
     // Set the debug print lvl to the same as the print lvl.
     m_debug_print_lvl = printDetails;
     if (printDetails > 0 && print_lvl == 0) {
@@ -476,7 +478,7 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                 if (iph == iphasePop) {
                     dx = m_deltaMolNumSpecies[kspec];
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + m_deltaMolNumSpecies[kspec];
-                    sprintf(ANOTE, "Phase pop");
+                    snprintf(ANOTE, anote_size, "Phase pop");
                 } else {
                     dx = 0.0;
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec];
@@ -500,15 +502,18 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec];
                     m_deltaMolNumSpecies[kspec] = 0.0;
                     resurrect = false;
-                    sprintf(ANOTE, "Species stays zeroed: DG = %11.4E", m_deltaGRxn_new[irxn]);
+                    snprintf(ANOTE, anote_size, "Species stays zeroed: DG = %11.4E",
+                             m_deltaGRxn_new[irxn]);
                     if (m_deltaGRxn_new[irxn] < 0.0) {
                         if (m_speciesStatus[kspec] == VCS_SPECIES_STOICHZERO) {
-                            sprintf(ANOTE, "Species stays zeroed even though dg neg due to "
-                                    "STOICH/PHASEPOP constraint: DG = %11.4E",
-                                    m_deltaGRxn_new[irxn]);
+                            snprintf(ANOTE, anote_size,
+                                     "Species stays zeroed even though dg neg due to "
+                                     "STOICH/PHASEPOP constraint: DG = %11.4E",
+                                     m_deltaGRxn_new[irxn]);
                         } else {
-                            sprintf(ANOTE, "Species stays zeroed even though dg neg: DG = %11.4E, ds zeroed",
-                                    m_deltaGRxn_new[irxn]);
+                            snprintf(ANOTE, anote_size, "Species stays zeroed even"
+                                " though dg neg: DG = %11.4E, ds zeroed",
+                                m_deltaGRxn_new[irxn]);
                         }
                     }
                 } else {
@@ -519,9 +524,9 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                             if (atomComp > 0.0) {
                                 double maxPermissible = m_elemAbundancesGoal[j] / atomComp;
                                 if (maxPermissible < VCS_DELETE_MINORSPECIES_CUTOFF) {
-                                    sprintf(ANOTE, "Species stays zeroed even though dG "
-                                            "neg, because of %s elemAbund",
-                                            m_elementName[j].c_str());
+                                    snprintf(ANOTE, anote_size, "Species stays zeroed"
+                                        " even though dG neg, because of %s elemAbund",
+                                        m_elementName[j].c_str());
                                     resurrect = false;
                                     break;
                                 }
@@ -554,7 +559,8 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                         dx = m_molNumSpecies_new[kspec] - m_molNumSpecies_old[kspec];
                     }
                     m_deltaMolNumSpecies[kspec] = dx;
-                    sprintf(ANOTE, "Born:IC=-1 to IC=1:DG=%11.4E", m_deltaGRxn_new[irxn]);
+                    snprintf(ANOTE, anote_size, "Born:IC=-1 to IC=1:DG=%11.4E",
+                             m_deltaGRxn_new[irxn]);
                 } else {
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec];
                     m_deltaMolNumSpecies[kspec] = 0.0;
@@ -569,7 +575,7 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec];
                     m_deltaMolNumSpecies[kspec] = 0.0;
                     dx = 0.0;
-                    sprintf(ANOTE,"minor species not considered");
+                    snprintf(ANOTE, anote_size, "minor species not considered");
                     if (m_debug_print_lvl >= 2) {
                         plogf("   --- %-12s%3d% 11.4E %11.4E %11.4E | %s\n",
                               m_speciesName[kspec], m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec],
@@ -623,7 +629,7 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                 }
             } else {
                 // MAJOR SPECIES
-                sprintf(ANOTE, "Normal Major Calc");
+                snprintf(ANOTE, anote_size, "Normal Major Calc");
 
                 // Check for superconvergence of the formation reaction. Do
                 // nothing if it is superconverged. Skip to the end of the irxn
@@ -632,7 +638,7 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                     m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec];
                     m_deltaMolNumSpecies[kspec] = 0.0;
                     dx = 0.0;
-                    sprintf(ANOTE, "major species is converged");
+                    snprintf(ANOTE, anote_size, "major species is converged");
                     if (m_debug_print_lvl >= 2) {
                         plogf("   --- %-12s %3d %11.4E %11.4E %11.4E | %s\n",
                               m_speciesName[kspec], m_speciesStatus[kspec], m_molNumSpecies_old[kspec], m_molNumSpecies_new[kspec],
@@ -653,8 +659,8 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                 } else {
                     dx = 0.0;
                     m_deltaMolNumSpecies[kspec] = 0.0;
-                    sprintf(ANOTE, "dx set to 0, DG flipped sign due to "
-                            "changed initial point");
+                    snprintf(ANOTE, anote_size, "dx set to 0, DG flipped sign due to "
+                             "changed initial point");
                 }
 
                 //Form a tentative value of the new species moles
@@ -665,8 +671,8 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                 // the outcome, we branch to sections below, or we restart the
                 // entire iteration.
                 if (m_molNumSpecies_new[kspec] <= 0.0) {
-                    sprintf(ANOTE, "initial nonpos kmoles= %11.3E",
-                            m_molNumSpecies_new[kspec]);
+                    snprintf(ANOTE, anote_size, "initial nonpos kmoles= %11.3E",
+                             m_molNumSpecies_new[kspec]);
                     // NON-POSITIVE MOLES OF MAJOR SPECIES
                     //
                     // We are here when a tentative value of a mole fraction
@@ -705,15 +711,15 @@ void VCS_SOLVE::solve_tp_inner(size_t& iti, size_t& it1,
                         m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] + dx;
                         if (m_molNumSpecies_new[kspec] > 0.0) {
                             m_deltaMolNumSpecies[kspec] = dx;
-                            sprintf(ANOTE,
-                                    "zeroing SS phase created a neg component species "
-                                    "-> reducing step size instead");
+                            snprintf(ANOTE, anote_size,
+                                     "zeroing SS phase created a neg component species "
+                                     "-> reducing step size instead");
                         } else {
                             // We are going to zero the single species phase.
                             // Set the existence flag
                             iph = m_phaseID[kspec];
                             Vphase = m_VolPhaseList[iph].get();
-                            sprintf(ANOTE, "zeroing out SS phase: ");
+                            snprintf(ANOTE, anote_size, "zeroing out SS phase: ");
 
                             // Change the base mole numbers for the iteration.
                             // We need to do this here, because we have decided
@@ -1365,7 +1371,7 @@ double VCS_SOLVE::vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete,
         }
         dg_irxn = std::max(dg_irxn, -200.0);
         if (ANOTE) {
-            sprintf(ANOTE,"minor species alternative calc");
+            snprintf(ANOTE, anote_size, "minor species alternative calc");
         }
         if (dg_irxn >= 23.0) {
             double molNum_kspec_new = w_kspec * 1.0e-10;
@@ -1428,7 +1434,7 @@ double VCS_SOLVE::vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete,
         // Need to check the sign -> This is good for electrons
         double dx = m_deltaGRxn_old[irxn]/ m_Faraday_dim;
         if (ANOTE) {
-            sprintf(ANOTE,"voltage species alternative calc");
+            snprintf(ANOTE, anote_size, "voltage species alternative calc");
         }
         return dx;
     }

diff --git a/src/numerics/AdaptivePreconditioner.cpp b/src/numerics/AdaptivePreconditioner.cpp
@@ -65,7 +65,7 @@ void AdaptivePreconditioner::setup()
     // check for errors
     if (m_solver.info() != Eigen::Success) {
         throw CanteraError("AdaptivePreconditioner::setup",
-                           "error code: {}", m_solver.info());
+                           "error code: {}", static_cast<int>(m_solver.info()));
     }
 }
 
@@ -103,7 +103,7 @@ void AdaptivePreconditioner::solve(const size_t stateSize, double* rhs_vector, d
     xVector = m_solver.solve(bVector);
     if (m_solver.info() != Eigen::Success) {
         throw CanteraError("AdaptivePreconditioner::solve",
-                           "error code: {}", m_solver.info());
+                           "error code: {}", static_cast<int>(m_solver.info()));
     }
 }
 

diff --git a/src/oneD/Sim1D.cpp b/src/oneD/Sim1D.cpp
@@ -217,12 +217,14 @@ AnyMap legacyH5(shared_ptr<SolutionArray> arr, const AnyMap& header={})
     if (header.hasKey("fixed_temperature")) {
         double temp = header.getDouble("fixed_temperature", -1.);
         auto profile = arr->getComponent("T");
-        size_t ix = 0;
+        int ix = 0;
         while (profile[ix] <= temp && ix < arr->size()) {
             ix++;
         }
-        out["fixed-point"]["location"] = arr->getComponent("grid")[ix - 1];
-        out["fixed-point"]["temperature"] = temp;
+        if (ix != 0) {
+            out["fixed-point"]["location"] = arr->getComponent("grid")[ix - 1];
+            out["fixed-point"]["temperature"] = temp;
+        }
     }
 
     return out;
@@ -558,7 +560,9 @@ int Sim1D::refine(int loglevel)
     for (size_t n = 0; n < nDomains(); n++) {
         Domain1D& d = domain(n);
         gridsize = dsize[n];
-        d.setupGrid(gridsize, &znew[gridstart]);
+        if (gridsize != 0) {
+            d.setupGrid(gridsize, &znew[gridstart]);
+        }
         gridstart += gridsize;
     }
 

diff --git a/src/transport/IonGasTransport.cpp b/src/transport/IonGasTransport.cpp
@@ -36,9 +36,9 @@ void IonGasTransport::init(ThermoPhase* thermo, int mode, int log_level)
     // Find the index of electron
     size_t nElectronSpecies = 0;
     for (size_t k = 0; k < m_nsp; k++) {
-        if (m_thermo->molecularWeight(k) ==
-            m_thermo->atomicWeight(m_thermo->elementIndex("E")) &&
-            m_thermo->charge(k)  == -1) {
+        if (m_thermo->molecularWeight(k) == getElementWeight("E") &&
+            m_thermo->charge(k) == -1)
+        {
             m_kElectron = k;
             nElectronSpecies++;
         }

diff --git a/test/general/test_composite.cpp b/test/general/test_composite.cpp
@@ -25,5 +25,5 @@ TEST(Interface, from_AnyMap_and_Solution)
     auto& phase = root["phases"].getMapWhere("name", "Pt_surf");
     auto surf = newInterface(phase, root, {gas});
     ASSERT_EQ(gas.get(), surf->adjacent(0).get());
-    ASSERT_EQ(surf->kinetics()->nReactions(), 24);
+    ASSERT_EQ(surf->kinetics()->nReactions(), 24u);
 }