Clean up line wrapping and indentation

Cantera · Aug 5, 2023 · 53396d4 · 53396d4
1 parent c50b8b4
commit 53396d4
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Showing 100 changed files with 244 additions and 423 deletions.
diff --git a/include/cantera/base/AnyMap.h b/include/cantera/base/AnyMap.h
@@ -533,7 +533,7 @@ class AnyMap : public AnyBase
      *     thrown if this condition is not met.
      */
     vector<double> convertVector(const string& key, const string& units,
-                            size_t nMin=npos, size_t nMax=npos) const;
+                                 size_t nMin=npos, size_t nMax=npos) const;
 
     //! Defined to allow use with range-based for loops. Iteration automatically
     //! skips over keys that start and end with double underscores.
@@ -771,9 +771,8 @@ class InputFileError : public CanteraError
         return "InputFileError";
     }
 protected:
-    static string formatError(const string& message,
-                                   int line, int column,
-                                   const shared_ptr<AnyMap>& metadata);
+    static string formatError(const string& message, int line, int column,
+                              const shared_ptr<AnyMap>& metadata);
     static string formatError2(const string& message,
         int line1, int column1, const shared_ptr<AnyMap>& metadata1,
         int line2, int column2, const shared_ptr<AnyMap>& metadata2);

diff --git a/include/cantera/base/ExtensionManager.h b/include/cantera/base/ExtensionManager.h
@@ -74,8 +74,7 @@ class ExtensionManager
     //! @param rateName  The name of the reaction rate type, which corresponds to the
     //!     name used to register the wrapper generator using registerReactionDataLinker
     //! @param data  The ReactionData object to be wrapped
-    static void wrapReactionData(const string& rateName,
-                                 ReactionDataDelegator& data);
+    static void wrapReactionData(const string& rateName, ReactionDataDelegator& data);
 
     //! Create an object in an external language that wraps the specified Solution
     //! object.
@@ -108,8 +107,7 @@ class ExtensionManager
 
 protected:
     //! Functions for wrapping and linking ReactionData objects
-    static map<string,
-        function<void(ReactionDataDelegator&)>> s_ReactionData_linkers;
+    static map<string, function<void(ReactionDataDelegator&)>> s_ReactionData_linkers;
 
     //! Functions for wrapping and linking Solution objects
     static map<string,

diff --git a/include/cantera/base/Units.h b/include/cantera/base/Units.h
@@ -207,8 +207,7 @@ class UnitSystem
     void setDefaultActivationEnergy(const string& e_units);
 
     //! Convert `value` from the units of `src` to the units of `dest`.
-    double convert(double value, const string& src,
-                   const string& dest) const;
+    double convert(double value, const string& src, const string& dest) const;
     double convert(double value, const Units& src, const Units& dest) const;
 
     //! Convert `value` to the specified `dest` units from the appropriate units

diff --git a/include/cantera/base/ctexceptions.h b/include/cantera/base/ctexceptions.h
@@ -80,8 +80,7 @@ class CanteraError : public std::exception
      * @param args Arguments which will be used to interpolate the format string
      */
     template <typename... Args>
-    CanteraError(const string& procedure, const string& msg,
-                 const Args&... args)
+    CanteraError(const string& procedure, const string& msg, const Args&... args)
         : procedure_(procedure)
     {
         if (sizeof...(args) == 0) {
@@ -202,8 +201,7 @@ class NotImplementedError : public CanteraError
 
     //! Alternative constructor taking same arguments as CanteraError
     template <typename... Args>
-    NotImplementedError(const string& func, const string& msg,
-                        const Args&... args) :
+    NotImplementedError(const string& func, const string& msg, const Args&... args) :
         CanteraError(func, msg, args...) {}
 
     virtual string getClass() const {

diff --git a/include/cantera/base/global.h b/include/cantera/base/global.h
@@ -224,8 +224,7 @@ void _warn_deprecated(const string& method, const string& extra="");
  * @param args  arguments for the format string
  */
 template <typename... Args>
-void warn_deprecated(const string& method, const string& msg,
-                     const Args&... args) {
+void warn_deprecated(const string& method, const string& msg, const Args&... args) {
     if (sizeof...(args) == 0) {
         _warn_deprecated(method, msg);
     } else {
@@ -236,8 +235,7 @@ void warn_deprecated(const string& method, const string& msg,
 //! @cond
 
 //! helper function passing generic warning to global handler
-void _warn(const string& warning,
-           const string& method, const string& extra);
+void _warn(const string& warning, const string& method, const string& extra);
 
 //! @endcond
 
@@ -266,8 +264,7 @@ void warn(const string& warning, const string& method,
  * @param args  arguments for the format string
  */
 template <typename... Args>
-void warn_user(const string& method, const string& msg,
-               const Args&... args) {
+void warn_user(const string& method, const string& msg, const Args&... args) {
     if (sizeof...(args) == 0) {
         _warn("Cantera", method, msg);
     } else {

diff --git a/include/cantera/base/stringUtils.h b/include/cantera/base/stringUtils.h
@@ -25,8 +25,7 @@ namespace Cantera
  * @param fmt   Format to be used (printf style) for each element
  * @param sep   Separator
  */
-string vec2str(const vector<double>& v, const string& fmt="%g",
-               const string& sep=", ");
+string vec2str(const vector<double>& v, const string& fmt="%g", const string& sep=", ");
 
 //! Strip non-printing characters wherever they are
 /*!

diff --git a/include/cantera/base/utilities.h b/include/cantera/base/utilities.h
@@ -79,8 +79,7 @@ inline double dot5(const V& x, const V& y)
  * @return The return is hard-coded to return a double.
  */
 template<class InputIter, class InputIter2>
-inline double dot(InputIter x_begin, InputIter x_end,
-                      InputIter2 y_begin)
+inline double dot(InputIter x_begin, InputIter x_end, InputIter2 y_begin)
 {
     return std::inner_product(x_begin, x_end, y_begin, 0.0);
 }

diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
@@ -1512,8 +1512,7 @@ class Kinetics
      *  @return 0.0 if the stoichiometries are not multiples of one another
      *    Otherwise, it returns the ratio of the stoichiometric coefficients.
      */
-    double checkDuplicateStoich(map<int, double>& r1,
-                                map<int, double>& r2) const;
+    double checkDuplicateStoich(map<int, double>& r1, map<int, double>& r2) const;
 
     //! @name Stoichiometry management
     //!

diff --git a/include/cantera/kinetics/Reaction.h b/include/cantera/kinetics/Reaction.h
@@ -327,8 +327,7 @@ unique_ptr<Reaction> newReaction(const AnyMap& rxn_node,
 //! Create Reaction objects for each item (an AnyMap) in `items`. The species
 //! involved in these reactions must exist in the phases associated with the
 //! Kinetics object `kinetics`.
-vector<shared_ptr<Reaction>> getReactions(const AnyValue& items,
-                                               Kinetics& kinetics);
+vector<shared_ptr<Reaction>> getReactions(const AnyValue& items, Kinetics& kinetics);
 
 //! Parse reaction equation
 void parseReactionEquation(Reaction& R, const string& equation,

diff --git a/include/cantera/kinetics/ReactionPath.h b/include/cantera/kinetics/ReactionPath.h
@@ -95,8 +95,7 @@ class Path
      * Add a reaction to the path. Increment the flow from this reaction, the
      * total flow, and the flow associated with this label.
      */
-    void addReaction(size_t rxnNumber, double value,
-                     const string& label = "");
+    void addReaction(size_t rxnNumber, double value, const string& label = "");
 
     //! Upstream node.
     const SpeciesNode* begin() const {

diff --git a/include/cantera/kinetics/StoichManager.h b/include/cantera/kinetics/StoichManager.h
@@ -363,31 +363,27 @@ class C_AnyN
         }
     }
 
-    void incrementSpecies(const double* input,
-                          double* output) const {
+    void incrementSpecies(const double* input, double* output) const {
         double x = input[m_rxn];
         for (size_t n = 0; n < m_n; n++) {
             output[m_ic[n]] += m_stoich[n]*x;
         }
     }
 
-    void decrementSpecies(const double* input,
-                          double* output) const {
+    void decrementSpecies(const double* input, double* output) const {
         double x = input[m_rxn];
         for (size_t n = 0; n < m_n; n++) {
             output[m_ic[n]] -= m_stoich[n]*x;
         }
     }
 
-    void incrementReaction(const double* input,
-                           double* output) const {
+    void incrementReaction(const double* input, double* output) const {
         for (size_t n = 0; n < m_n; n++) {
             output[m_rxn] += m_stoich[n]*input[m_ic[n]];
         }
     }
 
-    void decrementReaction(const double* input,
-                           double* output) const {
+    void decrementReaction(const double* input, double* output) const {
         for (size_t n = 0; n < m_n; n++) {
             output[m_rxn] -= m_stoich[n]*input[m_ic[n]];
         }
@@ -677,7 +673,7 @@ class StoichManagerN
     void add(size_t rxn, const vector<size_t>& k, const vector<double>& order,
              const vector<double>& stoich) {
         if (order.size() != k.size()) {
-            throw CanteraError(\
+            throw CanteraError(
                 "StoichManagerN::add()", "size of order and species arrays differ");
         }
         if (stoich.size() != k.size()) {

diff --git a/include/cantera/numerics/funcs.h b/include/cantera/numerics/funcs.h
@@ -35,8 +35,7 @@ namespace Cantera
  * @returns the value of of the interpolated function at x.
  * @ingroup mathUtils
  */
-double linearInterp(double x, const vector<double>& xpts,
-                        const vector<double>& fpts);
+double linearInterp(double x, const vector<double>& xpts, const vector<double>& fpts);
 
 //! Numerical integration of a function using the trapezoidal rule.
 /*!

diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h
@@ -322,8 +322,7 @@ class Domain1D
      *  @param[in] rdt Reciprocal of the timestep (`rdt=0` implies steady-
      *  state.)
      */
-    virtual void eval(size_t j, double* x, double* r,
-                      integer* mask, double rdt=0.0) {
+    virtual void eval(size_t j, double* x, double* r, integer* mask, double rdt=0.0) {
         throw NotImplementedError("Domain1D::eval");
     }
 

diff --git a/include/cantera/oneD/MultiNewton.h b/include/cantera/oneD/MultiNewton.h
@@ -34,8 +34,7 @@ class MultiNewton
 
     //! Compute the undamped Newton step.  The residual function is evaluated
     //! at `x`, but the Jacobian is not recomputed.
-    void step(double* x, double* step,
-              OneDim& r, MultiJac& jac, int loglevel);
+    void step(double* x, double* step, OneDim& r, MultiJac& jac, int loglevel);
 
     /**
      * Return the factor by which the undamped Newton step 'step0'
@@ -52,9 +51,8 @@ class MultiNewton
      * successful, the new solution after taking the damped step is returned in
      * x1, and the undamped step at x1 is returned in step1.
      */
-    int dampStep(const double* x0, const double* step0,
-                 double* x1, double* step1, double& s1,
-                 OneDim& r, MultiJac& jac, int loglevel, bool writetitle);
+    int dampStep(const double* x0, const double* step0, double* x1, double* step1,
+                 double& s1, OneDim& r, MultiJac& jac, int loglevel, bool writetitle);
 
     //! Compute the weighted 2-norm of `step`.
     double norm2(const double* x, const double* step, OneDim& r) const;

diff --git a/include/cantera/oneD/Sim1D.h b/include/cantera/oneD/Sim1D.h
@@ -138,8 +138,7 @@ class Sim1D : public OneDim
      * @param loglevel  Level of diagnostic output
      * @deprecated To be removed after %Cantera 3.0; loglevel is deprecated.
      */
-    void save(const string& fname, const string& id,
-              const string& desc, int loglevel);
+    void save(const string& fname, const string& id, const string& desc, int loglevel);
 
     /**
      * Save current simulation data to a container file or CSV format.
@@ -168,9 +167,8 @@ class Sim1D : public OneDim
      *      if not specified (default=""), the native basis of the underlying
      *      ThermoPhase manager is used - @see nativeState (CSV only)
      */
-    void save(const string& fname, const string& name,
-              const string& desc, bool overwrite=false, int compression=0,
-              const string& basis="");
+    void save(const string& fname, const string& name, const string& desc,
+              bool overwrite=false, int compression=0, const string& basis="");
 
     /**
      * Save the residual of the current solution to a container file.

diff --git a/include/cantera/thermo/ConstCpPoly.h b/include/cantera/thermo/ConstCpPoly.h
@@ -80,20 +80,16 @@ class ConstCpPoly: public SpeciesThermoInterpType
      *  - m_t[0] = tt;
      *
      */
-    void updateProperties(const double* tt,
-                          double* cp_R, double* h_RT,
+    void updateProperties(const double* tt, double* cp_R, double* h_RT,
                           double* s_R) const;
 
-    void updatePropertiesTemp(const double temp,
-                              double* cp_R, double* h_RT,
+    void updatePropertiesTemp(const double temp, double* cp_R, double* h_RT,
                               double* s_R) const;
 
     size_t nCoeffs() const { return 4; }
 
-    void reportParameters(size_t& n, int& type,
-                          double& tlow, double& thigh,
-                          double& pref,
-                          double* const coeffs) const;
+    void reportParameters(size_t& n, int& type, double& tlow, double& thigh,
+                          double& pref, double* const coeffs) const;
 
     virtual void getParameters(AnyMap& thermo) const;
 

diff --git a/include/cantera/thermo/DebyeHuckel.h b/include/cantera/thermo/DebyeHuckel.h
@@ -422,8 +422,7 @@ class DebyeHuckel : public MolalityVPSSTP
      *                    If blank, an empty phase will be created.
      *  @param id         id attribute containing the name of the phase.
      */
-    explicit DebyeHuckel(const string& inputFile="",
-                         const string& id="");
+    explicit DebyeHuckel(const string& inputFile="", const string& id="");
 
     //! @name  Utilities
     //! @{
@@ -623,8 +622,7 @@ class DebyeHuckel : public MolalityVPSSTP
     virtual bool addSpecies(shared_ptr<Species> spec);
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
-    virtual void getSpeciesParameters(const string& name,
-                                  AnyMap& speciesNode) const;
+    virtual void getSpeciesParameters(const string& name, AnyMap& speciesNode) const;
 
     //! Return the Debye Huckel constant as a function of temperature
     //! and pressure (Units = sqrt(kg/gmol))

diff --git a/include/cantera/thermo/IdealGasPhase.h b/include/cantera/thermo/IdealGasPhase.h
@@ -258,8 +258,7 @@ class IdealGasPhase: public ThermoPhase
      * @param id        ID of the phase in the input file. Defaults to the
      *                  empty string.
      */
-    explicit IdealGasPhase(const string& inputFile="",
-                           const string& id="");
+    explicit IdealGasPhase(const string& inputFile="", const string& id="");
 
     virtual string type() const {
         return "ideal-gas";

diff --git a/include/cantera/thermo/IdealMolalSoln.h b/include/cantera/thermo/IdealMolalSoln.h
@@ -76,8 +76,7 @@ class IdealMolalSoln : public MolalityVPSSTP
      *      about the phase. If blank, an empty phase will be created.
      *  @param id          id of the phase within the input file
      */
-    explicit IdealMolalSoln(const string& inputFile="",
-                            const string& id="");
+    explicit IdealMolalSoln(const string& inputFile="", const string& id="");
 
     virtual string type() const {
         return "ideal-molal-solution";

diff --git a/include/cantera/thermo/IdealSolidSolnPhase.h b/include/cantera/thermo/IdealSolidSolnPhase.h
@@ -53,8 +53,7 @@ class IdealSolidSolnPhase : public ThermoPhase
      * @param id     The name of this phase. This is used to look up
      *               the phase in the input file.
      */
-    explicit IdealSolidSolnPhase(const string& infile="",
-                                 const string& id="");
+    explicit IdealSolidSolnPhase(const string& infile="", const string& id="");
 
     virtual string type() const {
         return "ideal-condensed";
@@ -526,8 +525,7 @@ class IdealSolidSolnPhase : public ThermoPhase
     virtual bool addSpecies(shared_ptr<Species> spec);
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
-    virtual void getSpeciesParameters(const string& name,
-                                      AnyMap& speciesNode) const;
+    virtual void getSpeciesParameters(const string& name, AnyMap& speciesNode) const;
     virtual void setToEquilState(const double* mu_RT);
 
     //! Set the form for the standard and generalized concentrations

diff --git a/include/cantera/thermo/IonsFromNeutralVPSSTP.h b/include/cantera/thermo/IonsFromNeutralVPSSTP.h
@@ -79,8 +79,7 @@ class IonsFromNeutralVPSSTP : public GibbsExcessVPSSTP
      * @param id        name (ID) of the phase in the input file. If empty, the
      *                  first phase definition in the input file will be used.
      */
-    explicit IonsFromNeutralVPSSTP(const string& inputFile="",
-                                   const string& id="");
+    explicit IonsFromNeutralVPSSTP(const string& inputFile="", const string& id="");
 
     //! @}
     //! @name  Utilities
@@ -179,7 +178,8 @@ class IonsFromNeutralVPSSTP : public GibbsExcessVPSSTP
      *     This is the mapping between ion species and neutral molecule for
      *     quick invert.
      */
-    void getDissociationCoeffs(vector<double>& fm_neutralMolec_ions, vector<double>& charges, vector<size_t>& neutMolIndex) const;
+    void getDissociationCoeffs(vector<double>& fm_neutralMolec_ions,
+        vector<double>& charges, vector<size_t>& neutMolIndex) const;
 
     //! Return the current value of the neutral mole fraction vector
     /*!

diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h
@@ -553,8 +553,7 @@ class LatticePhase : public ThermoPhase
 
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
-    virtual void getSpeciesParameters(const string& name,
-                                      AnyMap& speciesNode) const;
+    virtual void getSpeciesParameters(const string& name, AnyMap& speciesNode) const;
 
     //! @}
 

diff --git a/include/cantera/thermo/LatticeSolidPhase.h b/include/cantera/thermo/LatticeSolidPhase.h
@@ -435,8 +435,7 @@ class LatticeSolidPhase : public ThermoPhase
                                const AnyMap& rootNode=AnyMap());
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
-    virtual void getSpeciesParameters(const string& name,
-                                      AnyMap& speciesNode) const;
+    virtual void getSpeciesParameters(const string& name, AnyMap& speciesNode) const;
 
     //! Set the Lattice mole fractions using a string
     /*!