Miscellanous small improvements

.github/workflows/main.yml

@@ -248,7 +248,7 @@ jobs:
         # See https://github.com/conda-forge/boost-cpp-feedstock/issues/41 for why we
         # use boost-cpp rather than boost from conda-forge
         run: |
-          conda install -q sundials=${{ matrix.sundials-ver }} scons numpy ruamel_yaml \
+          conda install -q sundials=${{ matrix.sundials-ver }} scons numpy ruamel.yaml \
           cython boost-cpp fmt eigen yaml-cpp h5py pandas libgomp openblas
       - name: Build Cantera
         run: |

SConstruct

@@ -1300,11 +1300,11 @@ if env['python_package'] != 'none':
     if check_for_ruamel_yaml:
         ru_script = textwrap.dedent("""\
             try:
-                import ruamel_yaml as yaml
+                from ruamel import yaml
                 print(yaml.__version__)
             except ImportError as ru_err:
                 try:
-                    from ruamel import yaml
+                    import ruamel_yaml as yaml
                     print(yaml.__version__)
                 except ImportError as ru_err_2:
                     print('0.0.0')

data/inputs/ptcombust.cti

@@ -18,7 +18,7 @@
 #****                                                                  *
 #***********************************************************************
 #
-#  Ref:- 1.) Deutschman et al., 26th Symp. (Intl.) on Combustion,1996
+#  Ref:- 1.) Deutschmann et al., 26th Symp. (Intl.) on Combustion,1996
 #            pp. 1747-1754
 #----------------------------------------------------------------------
 #

data/ptcombust.yaml

@@ -18,7 +18,7 @@ description: |-
   ****                                                                  *
   ***********************************************************************
 
-    Ref:- 1.) Deutschman et al., 26th Symp. (Intl.) on Combustion, 1996
+    Ref:- 1.) Deutschmann et al., 26th Symp. (Intl.) on Combustion, 1996
               pp. 1747-1754
   -----------------------------------------------------------------------
 

doc/sphinx/cython/thermo.rst

@@ -49,11 +49,21 @@ ConstantCp
 .. autoclass:: ConstantCp(T_low, T_high, P_ref, coeffs)
     :no-undoc-members:
 
+Mu0Poly
+^^^^^^^
+.. autoclass:: Mu0Poly(T_low, T_high, P_ref, coeffs)
+    :no-undoc-members:
+
 NasaPoly2
 ^^^^^^^^^
 .. autoclass:: NasaPoly2(T_low, T_high, P_ref, coeffs)
     :no-undoc-members:
 
+Nasa9PolyMultiTempRegion
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: Nasa9PolyMultiTempRegion(T_low, T_high, P_ref, coeffs)
+    :no-undoc-members:
+
 ShomatePoly2
 ^^^^^^^^^^^^
 .. autoclass:: ShomatePoly2(T_low, T_high, P_ref, coeffs)

doc/sphinx/yaml/reactions.rst

@@ -14,7 +14,7 @@ The fields common to all ``reaction`` entries are:
     must be separated by a space.
 
     Reversible reactions may be written using ``<=>`` or ``=`` to separate
-    reactants and products. Irreversible reacions are written using ``=>``.
+    reactants and products. Irreversible reactions are written using ``=>``.
 
 ``type``
     A string specifying the type of reaction or rate coefficient
@@ -292,7 +292,7 @@ Example::
 ``interface``
 -------------
 
-A reaction occuring on a surface between two bulk phases, or along an edge
+A reaction occurring on a surface between two bulk phases, or along an edge
 at the intersection of two surfaces, as
 `described here <https://cantera.org/science/reactions.html#sec-surface>`__.
 

include/cantera/base/Units.h

@@ -55,7 +55,7 @@ class Units
 
     //! Raise these Units to a power, changing both the conversion factor and
     //! the dimensions of these Units.
-    Units pow(double expoonent) const;
+    Units pow(double exponent) const;
 
     bool operator==(const Units& other) const;
 

include/cantera/equil/MultiPhase.h

@@ -687,7 +687,7 @@ std::ostream& operator<<(std::ostream& s, MultiPhase& x);
  * @param[in] orderVectorElements Order vector for the elements. The element
  *         rows in the formula matrix are rearranged according to this vector.
  * @param[in] orderVectorSpecies Order vector for the species. The species are
- *         rearranged according to this formula. The first nCompoments of this
+ *         rearranged according to this formula. The first nComponents of this
  *         vector contain the calculated species components on exit.
  * @param[in] doFormRxn  If true, the routine calculates the formation
  *         reaction matrix based on the calculated component species. If
@@ -748,7 +748,7 @@ void ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
                    std::vector<size_t>& orderVectorElements);
 
 //! External int that is used to turn on debug printing for the
-//! BasisOptimze program.
+//! BasisOptimize program.
 /*!
  *   Set this to 1 if you want debug printing from BasisOptimize.
  */

include/cantera/kinetics/Kinetics.h

@@ -680,7 +680,7 @@ class Kinetics
      *              concentrations (no change to legacy behavior). After Cantera 2.6,
      *              results will no longer include third-body concentrations and be
      *              consistent with conventional definitions (see Eq. 9.75 in
-     *              Kee, Coltrin and Glarborg, 'Chemically eacting Flow', Wiley
+     *              Kee, Coltrin and Glarborg, 'Chemically Reacting Flow', Wiley
      *              Interscience, 2003).
      *              For new behavior, set 'Cantera::use_legacy_rate_constants(false)'.
      */
@@ -706,7 +706,7 @@ class Kinetics
      *              concentrations (no change to legacy behavior). After Cantera 2.6,
      *              results will no longer include third-body concentrations and be
      *              consistent with conventional definitions (see Eq. 9.75 in
-     *              Kee, Coltrin and Glarborg, 'Chemically eacting Flow', Wiley
+     *              Kee, Coltrin and Glarborg, 'Chemically Reacting Flow', Wiley
      *              Interscience, 2003).
      *              For new behavior, set 'Cantera::use_legacy_rate_constants(false)'.
      */

include/cantera/numerics/FuncEval.h

@@ -92,7 +92,7 @@ class FuncEval
     // If true, errors are accumulated in m_errors. Otherwise, they are printed
     bool m_suppress_errors;
 
-    //! Errors occuring during function evaluations
+    //! Errors occurring during function evaluations
     std::vector<std::string> m_errors;
 };
 

include/cantera/numerics/ResidJacEval.h

@@ -22,7 +22,7 @@ enum ResidEval_Type_Enum {
     Base_ResidEval = 0,
     //! Base residual calculation for the Jacobian calculation
     JacBase_ResidEval,
-    //! Delta residual calculation for the Jacbobian calculation
+    //! Delta residual calculation for the Jacobian calculation
     JacDelta_ResidEval,
     //! Base residual calculation for the showSolution routine
     /*!
@@ -32,7 +32,7 @@ enum ResidEval_Type_Enum {
     //! Base residual calculation containing any lagged components
     /*!
      * We use this to calculate residuals when doing line searches along
-     * irections determined by Jacobians that are missing contributions from
+     * directions determined by Jacobians that are missing contributions from
      * lagged entries.
      */
     Base_LaggedSolutionComponents

include/cantera/oneD/OneDim.h

@@ -349,7 +349,6 @@ class OneDim
     std::vector<size_t> m_loc;
     vector_int m_mask;
     size_t m_pts;
-    doublereal m_solve_time;
 
     // options
     int m_ss_jac_age, m_ts_jac_age;

include/cantera/thermo/ThermoPhase.h

@@ -1241,7 +1241,7 @@ class ThermoPhase : public Phase
      * @param element    either "Bilger" to compute the mixture fraction
      *                   in terms of the Bilger mixture fraction, or
      *                   an element name, to compute the mixture fraction
-     *                   bsaed on a single element (default: "Bilger")
+     *                   based on a single element (default: "Bilger")
      * @returns          mixture fraction (kg fuel / kg mixture)
      */
     double mixtureFraction(const double* fuelComp, const double* oxComp,

include/cantera/zeroD/Reactor.h

@@ -154,7 +154,7 @@ class Reactor : public ReactorBase
     //! @returns           True if at least one limit is set, False otherwise
     bool getAdvanceLimits(double* limits);
 
-    //! Set individual step size limit for compoment name *nm*
+    //! Set individual step size limit for component name *nm*
     //! @param nm component name
     //! @param limit value for step size limit
     void setAdvanceLimit(const std::string& nm, const double limit);

include/cantera/zeroD/flowControllers.h

@@ -160,7 +160,7 @@ class Valve : public FlowDevice
         return m_coeff;
     }
 
-    /// Compute the currrent mass flow rate, based on the pressure difference.
+    /// Compute the current mass flow rate, based on the pressure difference.
     virtual void updateMassFlowRate(double time);
 };
 

interfaces/cython/cantera/_cantera.pxd

@@ -932,7 +932,7 @@ cdef extern from "cantera/oneD/Boundary1D.h":
         CxxSurf1D()
 
     cdef cppclass CxxReactingSurf1D "Cantera::ReactingSurf1D":
-        CxxRreactingSurf1D()
+        CxxReactingSurf1D()
         void setKineticsMgr(CxxInterfaceKinetics*) except +translate_exception
         void enableCoverageEquations(cbool) except +translate_exception
         cbool coverageEnabled()

interfaces/cython/cantera/ck2yaml.py

@@ -53,9 +53,9 @@
 from email.utils import formatdate
 
 try:
-    import ruamel_yaml as yaml
-except ImportError:
     from ruamel import yaml
+except ImportError:
+    import ruamel_yaml as yaml
 
 # yaml.version_info is a tuple with the three parts of the version
 yaml_version = yaml.version_info

interfaces/cython/cantera/cti2yaml.py

@@ -20,9 +20,9 @@
 import argparse
 
 try:
-    import ruamel_yaml as yaml
-except ImportError:
     from ruamel import yaml
+except ImportError:
+    import ruamel_yaml as yaml
 
 # yaml.version_info is a tuple with the three parts of the version
 yaml_version = yaml.version_info

interfaces/cython/cantera/ctml2yaml.py

@@ -27,9 +27,9 @@
 import numpy as np
 
 try:
-    import ruamel_yaml as yaml  # type: ignore
-except ImportError:
     from ruamel import yaml
+except ImportError:
+    import ruamel_yaml as yaml  # type: ignore
 
 # yaml.version_info is a tuple with the three parts of the version
 yaml_version = yaml.version_info

interfaces/cython/cantera/examples/surface_chemistry/catalytic_combustion.py

@@ -7,7 +7,7 @@
 catalytically on the platinum surface. Gas-phase chemistry is included too,
 and has some effect very near the surface.
 
-The catalytic combustion mechanism is from Deutschman et al., 26th
+The catalytic combustion mechanism is from Deutschmann et al., 26th
 Symp. (Intl.) on Combustion,1996 pp. 1747-1754
 
 Requires: cantera >= 2.5.0

interfaces/cython/cantera/examples/thermo/vapordome.py

@@ -13,7 +13,7 @@
 
 w = ct.Water()
 
-# create colums
+# create columns
 columns = ['T', 'P',
            'vf', 'vfg', 'vg',
            'uf', 'ufg', 'ug',

interfaces/cython/cantera/onedim.py

@@ -499,7 +499,7 @@ def write_hdf(self, filename, *args, group=None, species='X', mode='a',
         """
         Write the solution vector to a HDF container file.
 
-        The `write_hdf` method preserves the stucture of a `FlameBase`-derived
+        The `write_hdf` method preserves the structure of a `FlameBase`-derived
         object (such as `FreeFlame`). Each simulation is saved as a *group*,
         whereas individual domains are saved as subgroups. In addition to
         datasets, information on `Sim1D.settings` and `Domain1D.settings` is
@@ -1638,7 +1638,7 @@ def __init__(self, gas, grid=None, width=None):
 
     def set_initial_guess(self, data=None, group=None):
         """
-        Set the initial guess for the solution based on an equiibrium solution.
+        Set the initial guess for the solution based on an equilibrium solution.
         Alternatively, a previously calculated result can be supplied as an
         initial guess via 'data' and 'key' inputs (see
         `FlameBase.set_initial_guess`).

interfaces/cython/cantera/test/test_onedim.py

@@ -554,7 +554,7 @@ def test_save_restore_xml(self):
         u3 = self.sim.velocity
         V3 = self.sim.spread_rate
 
-        # TODO: These tolereances seem too loose, but the tests fail on some
+        # TODO: These tolerances seem too loose, but the tests fail on some
         # systems with tighter tolerances.
         self.assertArrayNear(Y1, Y3, 3e-3)
         self.assertArrayNear(u1, u3, 1e-3)

interfaces/cython/cantera/test/test_reaction.py

@@ -353,7 +353,7 @@ class ReactionTests:
     _equation = None # reaction equation string
     _rate = None # parameters for reaction rate object constructor
     _rate_obj = None # reaction rate object
-    _kwargs = {} # additional parameters required by contructor
+    _kwargs = {} # additional parameters required by constructor
     _index = None # index of reaction in "kineticsfromscratch.yaml"
     _yaml = None # YAML parameterization
     _input = None # input parameters (dict corresponding to YAML)

interfaces/cython/cantera/test/utilities.py

@@ -6,9 +6,9 @@
 from pathlib import Path, PurePath
 
 try:
-    import ruamel_yaml as yaml
-except ImportError:
     from ruamel import yaml
+except ImportError:
+    import ruamel_yaml as yaml
 
 import cantera
 

samples/matlab/catcomb.m

@@ -7,7 +7,7 @@
 % chemistry is included too, and has some effect very near the
 % surface.
 %
-% The catalytic combustion mechanism is from Deutschman et al., 26th
+% The catalytic combustion mechanism is from Deutschmann et al., 26th
 % Symp. (Intl.) on Combustion,1996 pp. 1747-1754
 %
 

samples/matlab/surfreactor.m

@@ -13,7 +13,7 @@
 set(gas,'T',t,'P',oneatm,'X','CH4:0.01, O2:0.21, N2:0.78');
 
 % The surface reaction mechanism describes catalytic combustion of
-% methane on platinum, and is from Deutschman et al., 26th
+% methane on platinum, and is from Deutschmann et al., 26th
 % Symp. (Intl.) on Combustion,1996, pp. 1747-1754
 surf = importInterface('ptcombust.yaml','Pt_surf', gas);
 setTemperature(surf, t);

src/base/Units.cpp

@@ -144,7 +144,7 @@ Units::Units(const std::string& name, bool force_unity)
     size_t start = 0;
 
     // Determine factor
-    std::regex regexp("[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)");
+    static std::regex regexp("[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)");
     std::smatch matched;
     std::regex_search(name, matched, regexp);
     if (matched.size()) {

src/base/application.h

@@ -381,7 +381,7 @@ class Application
      *              concentrations (no change to legacy behavior). After Cantera 2.6,
      *              results will no longer include third-body concentrations and be
      *              consistent with conventional definitions (see Eq. 9.75 in
-     *              Kee, Coltrin and Glarborg, 'Chemically eacting Flow', Wiley
+     *              Kee, Coltrin and Glarborg, 'Chemically Reacting Flow', Wiley
      *              Interscience, 2003).
      */
     void use_legacy_rate_constants(bool legacy=true) {

src/base/stringUtils.cpp

@@ -147,7 +147,7 @@ doublereal fpValueCheck(const std::string& val)
     ch = str[0];
     if (ch == '+' || ch == '-') {
         if (str.size() == 1) {
-            throw CanteraError("fpValueCheck", "string ends in '{}'", ch);
+            throw CanteraError("fpValueCheck", "string '{}' ends in '{}'", val, ch);
         }
         istart = 1;
     }
@@ -158,33 +158,31 @@ doublereal fpValueCheck(const std::string& val)
             numDot++;
             if (numDot > 1) {
                 throw CanteraError("fpValueCheck",
-                                   "string has more than one .");
+                                   "string '{}' has more than one decimal point.", val);
             }
             if (numExp > 0) {
                 throw CanteraError("fpValueCheck",
-                                   "string has decimal point in exponent");
+                                   "string '{}' has decimal point in exponent", val);
             }
         } else if (ch == 'e' || ch == 'E' || ch == 'd' || ch == 'D') {
             numExp++;
             str[i] = 'E';
             if (numExp > 1) {
                 throw CanteraError("fpValueCheck",
-                                   "string has more than one exp char");
+                                   "string '{}' has more than one exp char", val);
             } else if (i == str.size() - 1) {
-                throw CanteraError("fpValueCheck",
-                                   "string ends in '{}'", ch);
+                throw CanteraError("fpValueCheck", "string '{}' ends in '{}'", val, ch);
             }
             ch = str[i+1];
             if (ch == '+' || ch == '-') {
                 if (i + 1 == str.size() - 1) {
                     throw CanteraError("fpValueCheck",
-                                       "string ends in '{}'", ch);
+                                       "string '{}' ends in '{}'", val, ch);
                 }
                 i++;
             }
         } else {
-            throw CanteraError("fpValueCheck",
-                               "Trouble processing string, " + str);
+            throw CanteraError("fpValueCheck", "Trouble processing string '{}'", str);
         }
     }
     return fpValue(str);

src/kinetics/BulkKinetics.cpp

@@ -124,7 +124,7 @@ bool BulkKinetics::addReaction(shared_ptr<Reaction> r, bool resize)
 
     if (!(r->usesLegacy())) {
         shared_ptr<ReactionRateBase> rate = r->rate();
-        // If neccessary, add new MultiBulkRate evaluator
+        // If necessary, add new MultiBulkRate evaluator
         if (m_bulk_types.find(rate->type()) == m_bulk_types.end()) {
             m_bulk_types[rate->type()] = m_bulk_rates.size();
             m_bulk_rates.push_back(rate->newMultiRate());