Improve formatting

include/cantera/base/AnyMap.h

@@ -74,7 +74,7 @@ class AnyMap;
  * Elements are set using assignment, and the assignment operator has been
  * overloaded for specific types so that only those types are allowed to be
  * used in an AnyValue. The allowed types are:
- * - AnyMap
+ * - `AnyMap`
  * - `double`
  * - `long int`
  * - `bool`
@@ -341,7 +341,8 @@ vector<double>& AnyValue::asVector<double>(size_t nMin, size_t nMax);
 
 //! Implicit conversion of long int to double if accessed as a vector<vector<double>>
 template<>
-const vector<vector<double>>& AnyValue::asVector<vector<double>>(size_t nMin, size_t nMax) const;
+const vector<vector<double>>& AnyValue::asVector<vector<double>>(size_t nMin,
+                                                                 size_t nMax) const;
 
 template<>
 vector<vector<double>>& AnyValue::asVector<vector<double>>(size_t nMin, size_t nMax);
@@ -499,7 +500,7 @@ class AnyMap : public AnyBase
 
     //! If `key` exists, return it as a `string`, otherwise return `default_`.
     const string& getString(const string& key,
-                                 const string& default_) const;
+                            const string& default_) const;
 
     //! Convert the item stored by the given `key` to the units specified in
     //! `units`. If the stored value is a double, convert it using the default

include/cantera/base/Delegator.h

@@ -524,13 +524,10 @@ class Delegator
     map<string, function<void(bool)>*> m_funcs_v_b;
     map<string, function<void(double)>*> m_funcs_v_d;
     map<string, function<void(AnyMap&)>*> m_funcs_v_AMr;
-    map<string,
-        function<void(const AnyMap&, const UnitStack&)>*> m_funcs_v_cAMr_cUSr;
+    map<string, function<void(const AnyMap&, const UnitStack&)>*> m_funcs_v_cAMr_cUSr;
     map<string, function<void(const string&, void*)>*> m_funcs_v_csr_vp;
-    map<string,
-        function<void(std::array<size_t, 1>, double*)>*> m_funcs_v_dp;
-    map<string,
-        function<void(std::array<size_t, 1>, double, double*)>*> m_funcs_v_d_dp;
+    map<string, function<void(std::array<size_t, 1>, double*)>*> m_funcs_v_dp;
+    map<string, function<void(std::array<size_t, 1>, double, double*)>*> m_funcs_v_d_dp;
     map<string,
         function<void(std::array<size_t, 2>, double, double*, double*)>*> m_funcs_v_d_dp_dp;
     map<string,
@@ -540,15 +537,11 @@ class Delegator
     map<string, function<double(void*)>> m_base_d_vp;
     map<string, function<double(void*)>*> m_funcs_d_vp;
 
-    map<string,
-        function<string(size_t)>> m_base_s_sz;
-    map<string,
-        function<string(size_t)>*> m_funcs_s_sz;
+    map<string, function<string(size_t)>> m_base_s_sz;
+    map<string, function<string(size_t)>*> m_funcs_s_sz;
 
-    map<string,
-        function<size_t(const string&)>> m_base_sz_csr;
-    map<string,
-        function<size_t(const string&)>*> m_funcs_sz_csr;
+    map<string, function<size_t(const string&)>> m_base_sz_csr;
+    map<string, function<size_t(const string&)>*> m_funcs_sz_csr;
     //! @}
 
     //! Handles to wrappers for the delegated object in external language interfaces.

include/cantera/base/Units.h

@@ -27,7 +27,7 @@ class AnyMap;
 /*!
  * Used for converting quantities between unit systems and checking for
  * dimensional consistency. Units objects are mainly used within UnitSystem
- * class to convert values from a user-specified Unit system to Cantera's
+ * class to convert values from a user-specified Unit system to %Cantera's
  * base units (SI + kmol).
  * @ingroup unitsGroup
  */
@@ -238,10 +238,8 @@ class UnitSystem
     //! Convert an array of AnyValue nodes to the units specified in `dest`. For
     //! each node, if the value is a double, convert it using the default units,
     //! and if it is a string, treat it as a value with the given dimensions.
-    vector<double> convert(const vector<AnyValue>& vals,
-                      const string& dest) const;
-    vector<double> convert(const vector<AnyValue>& vals,
-                      const Units& dest) const;
+    vector<double> convert(const vector<AnyValue>& vals, const string& dest) const;
+    vector<double> convert(const vector<AnyValue>& vals, const Units& dest) const;
 
     //! Convert `value` from the units of `src` to the units of `dest`, allowing
     //! for the different dimensions that can be used for activation energies
@@ -261,8 +259,7 @@ class UnitSystem
     //! input is a double, convert it using the default units. If the input is a
     //! string, treat this as a dimensioned value, such as '2.7e4 J/kmol', and
     //! convert from the specified units.
-    double convertActivationEnergy(const AnyValue& val,
-                                   const string& dest) const;
+    double convertActivationEnergy(const AnyValue& val, const string& dest) const;
 
     //! Get the changes to the defaults from `other` to this UnitSystem
     AnyMap getDelta(const UnitSystem& other) const;

include/cantera/base/stringUtils.h

@@ -26,7 +26,7 @@ namespace Cantera
  * @param sep   Separator
  */
 string vec2str(const vector<double>& v, const string& fmt="%g",
-                    const string& sep=", ");
+               const string& sep=", ");
 
 //! Strip non-printing characters wherever they are
 /*!
@@ -59,7 +59,7 @@ string stripnonprint(const string& s);
  * @return     map of names to values
  */
 Composition parseCompString(const string& ss,
-        const vector<string>& names=vector<string>());
+                            const vector<string>& names=vector<string>());
 
 //! Translate a string into one double value
 /*!
@@ -104,8 +104,7 @@ double fpValueCheck(const string& val);
  * @param oval   String to be broken up
  * @param v     Output vector of tokens.
  */
-void tokenizeString(const string& oval,
-                    vector<string>& v);
+void tokenizeString(const string& oval, vector<string>& v);
 
 //! This function separates a string up into tokens according to the location of
 //! path separators.
@@ -117,8 +116,7 @@ void tokenizeString(const string& oval,
  *
  * @since New in %Cantera 3.0.
  */
-void tokenizePath(const string& oval,
-                  vector<string>& v);
+void tokenizePath(const string& oval, vector<string>& v);
 
 //! Copy the contents of a string into a char array of a given length
 /*!

include/cantera/equil/MultiPhaseEquil.h

@@ -66,7 +66,7 @@ class MultiPhaseEquil
     }
 
     double equilibrate(int XY, double err = 1.0e-9,
-                           int maxsteps = 1000, int loglevel=-99);
+                       int maxsteps = 1000, int loglevel=-99);
     double error();
 
     string reactionString(size_t j) {

include/cantera/kinetics/InterfaceRate.h

@@ -117,7 +117,8 @@ class InterfaceRateBase
     //! Add a coverage dependency for species *sp*, with exponential dependence
     //! *a*, power-law exponent *m*, and activation energy dependence *e*,
     //! where *e* is in Kelvin, that is, energy divided by the molar gas constant.
-    virtual void addCoverageDependence(const string& sp, double a, double m, const vector<double>& e);
+    virtual void addCoverageDependence(const string& sp, double a, double m,
+                                       const vector<double>& e);
 
     //! Boolean indicating whether rate uses exchange current density formulation
     bool exchangeCurrentDensityFormulation() {
@@ -441,7 +442,9 @@ class InterfaceRate : public RateType, public InterfaceRateBase
         return RateType::activationEnergy() + m_ecov * GasConstant;
     }
 
-    void addCoverageDependence(const string& sp, double a, double m, const vector<double>& e) override {
+    void addCoverageDependence(const string& sp, double a, double m,
+                               const vector<double>& e) override
+    {
         InterfaceRateBase::addCoverageDependence(sp, a, m, e);
         RateType::setCompositionDependence(true);
     }

include/cantera/kinetics/ReactionPath.h

@@ -226,8 +226,7 @@ class ReactionPathDiagram
         m_local = k;
     }
 
-    void linkNodes(size_t k1, size_t k2, size_t rxn, double value,
-                   string legend = "");
+    void linkNodes(size_t k1, size_t k2, size_t rxn, double value, string legend = "");
 
     void include(const string& aaname) {
         m_include.push_back(aaname);

include/cantera/kinetics/StoichManager.h

@@ -334,7 +334,8 @@ class C_AnyN
 public:
     C_AnyN() = default;
 
-    C_AnyN(size_t rxn, const vector<size_t>& ic, const vector<double>& order_, const vector<double>& stoich_) :
+    C_AnyN(size_t rxn, const vector<size_t>& ic,
+           const vector<double>& order_, const vector<double>& stoich_) :
         m_n(ic.size()),
         m_rxn(rxn) {
         m_ic.resize(m_n);
@@ -676,10 +677,12 @@ 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("StoichManagerN::add()", "size of order and species arrays differ");
+            throw CanteraError(\
+                "StoichManagerN::add()", "size of order and species arrays differ");
         }
         if (stoich.size() != k.size()) {
-           throw CanteraError("StoichManagerN::add()", "size of stoich and species arrays differ");
+            throw CanteraError(
+                "StoichManagerN::add()", "size of stoich and species arrays differ");
         }
         bool frac = false;
         for (size_t n = 0; n < stoich.size(); n++) {

include/cantera/kinetics/ThirdBodyCalc.h

@@ -21,7 +21,7 @@ class ThirdBodyCalc
 public:
     //! Install reaction that uses third-body effects in ThirdBodyCalc manager
     void install(size_t rxnNumber, const map<size_t, double>& efficiencies,
-                  double default_efficiency, bool mass_action) {
+                 double default_efficiency, bool mass_action) {
         m_reaction_index.push_back(rxnNumber);
         m_default.push_back(default_efficiency);
 

include/cantera/kinetics/solveSP.h

@@ -226,8 +226,8 @@ class solveSP
      * @returns the 1. /  delta T to be used on the next step
      */
     double calc_t(double netProdRateSolnSP[], double XMolSolnSP[],
-                      int* label, int* label_old,
-                      double* label_factor, int ioflag);
+                  int* label, int* label_old,
+                  double* label_factor, int ioflag);
 
     //! Calculate the solution and residual weights
     /*!

include/cantera/oneD/MultiNewton.h

@@ -43,7 +43,7 @@ class MultiNewton
      * all domains between their specified lower and upper bounds.
      */
     double boundStep(const double* x0, const double* step0,
-                         const OneDim& r, int loglevel);
+                     const OneDim& r, int loglevel);
 
     /**
      * On entry, step0 must contain an undamped Newton step for the solution x0.
@@ -57,16 +57,14 @@ class MultiNewton
                  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;
+    double norm2(const double* x, const double* step, OneDim& r) const;
 
     /**
      * Find the solution to F(X) = 0 by damped Newton iteration. On entry, x0
      * contains an initial estimate of the solution. On successful return, x1
      * contains the converged solution.
      */
-    int solve(double* x0, double* x1, OneDim& r, MultiJac& jac,
-              int loglevel);
+    int solve(double* x0, double* x1, OneDim& r, MultiJac& jac, int loglevel);
 
     //! Set options.
     void setOptions(int maxJacAge = 5) {

include/cantera/oneD/OneDim.h

@@ -193,8 +193,7 @@ class OneDim
      *                  the default value is used.
      * @param count   Set to zero to omit this call from the statistics
      */
-    void eval(size_t j, double* x, double* r, double rdt=-1.0,
-              int count = 1);
+    void eval(size_t j, double* x, double* r, double rdt=-1.0, int count = 1);
 
     //! Return a pointer to the domain global point *i* belongs to.
     /*!
@@ -220,8 +219,7 @@ class OneDim
      * @param loglevel controls amount of printed diagnostics
      * @returns size of last timestep taken
      */
-    double timeStep(int nsteps, double dt, double* x,
-                    double* r, int loglevel);
+    double timeStep(int nsteps, double dt, double* x, double* r, int loglevel);
 
     void resetBadValues(double* x);
 

include/cantera/oneD/StFlow.h

@@ -305,8 +305,7 @@ class StFlow : public Domain1D
      *  j-1, j, and j+1. This option is used to efficiently evaluate the
      *  Jacobian numerically.
      */
-    virtual void eval(size_t j, double* x, double* r,
-                      integer* mask, double rdt);
+    virtual void eval(size_t j, double* x, double* r, integer* mask, double rdt);
 
     //! Evaluate all residual components at the right boundary.
     virtual void evalRightBoundary(double* x, double* res, int* diag,

include/cantera/thermo/HMWSoln.h

@@ -1187,7 +1187,7 @@ class HMWSoln : public MolalityVPSSTP
     }
 
     void setCroppingCoefficients(double ln_gamma_k_min, double ln_gamma_k_max,
-        double ln_gamma_o_min, double ln_gamma_o_max);
+                                 double ln_gamma_o_min, double ln_gamma_o_max);
 
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
@@ -1253,8 +1253,7 @@ class HMWSoln : public MolalityVPSSTP
      * @param pressure    Pressure of the derivative calculation
      *                    or -1 to indicate the current pressure
      */
-    double ADebye_L(double temperature = -1.0,
-                    double pressure = -1.0) const;
+    double ADebye_L(double temperature = -1.0, double pressure = -1.0) const;
 
     /**
      * Return Pitzer's definition of A_J. This is basically the temperature
@@ -1271,8 +1270,7 @@ class HMWSoln : public MolalityVPSSTP
      * @param pressure    Pressure of the derivative calculation
      *                    or -1 to indicate the current pressure
      */
-    double ADebye_J(double temperature = -1.0,
-                    double pressure = -1.0) const;
+    double ADebye_J(double temperature = -1.0, double pressure = -1.0) const;
 
     /**
      * Return Pitzer's definition of A_V. This is the derivative wrt pressure of
@@ -1289,8 +1287,7 @@ class HMWSoln : public MolalityVPSSTP
      * @param pressure    Pressure of the derivative calculation
      *                    or -1 to indicate the current pressure
      */
-    double ADebye_V(double temperature = -1.0,
-                    double pressure = -1.0) const;
+    double ADebye_V(double temperature = -1.0, double pressure = -1.0) const;
 
     //! Value of the 2nd derivative of the Debye Huckel constant with respect to
     //! temperature as a function of temperature and pressure.

include/cantera/thermo/LatticePhase.h

@@ -189,8 +189,7 @@ class LatticePhase : public ThermoPhase
      *                  an empty phase will be created.
      * @param id        string id of the phase name
      */
-    explicit LatticePhase(const string& inputFile="",
-                          const string& id="");
+    explicit LatticePhase(const string& inputFile="", const string& id="");
 
     virtual string type() const {
         return "lattice";

include/cantera/thermo/MixtureFugacityTP.h

@@ -418,7 +418,7 @@ class MixtureFugacityTP : public ThermoPhase
      *            return a -2.
      */
     virtual double densityCalc(double TKelvin, double pressure, int phaseRequested,
-                                   double rhoguess);
+                               double rhoguess);
 
 protected:
     //! Utility routine in the calculation of the saturation pressure
@@ -469,8 +469,7 @@ class MixtureFugacityTP : public ThermoPhase
      * @param molarVolLiquid  (return) Molar volume of the liquid
      * @returns the saturation pressure at the given temperature
      */
-    double calculatePsat(double TKelvin, double& molarVolGas,
-                             double& molarVolLiquid);
+    double calculatePsat(double TKelvin, double& molarVolGas, double& molarVolLiquid);
 
 public:
     //! Calculate the saturation pressure at the current mixture content for the

include/cantera/thermo/MolalityVPSSTP.h

@@ -537,8 +537,7 @@ class MolalityVPSSTP : public VPStandardStateTP
         getdlnActCoeffdlnN_numderiv(ld, dlnActCoeffdlnN);
     }
 
-    virtual string report(bool show_thermo=true,
-                               double threshold=1e-14) const;
+    virtual string report(bool show_thermo=true, double threshold=1e-14) const;
 
 protected:
     virtual void getCsvReportData(vector<string>& names,

include/cantera/thermo/PDSS_HKFT.h

@@ -230,8 +230,7 @@ class PDSS_HKFT : public PDSS_Molar
      *                 - 2 2nd derivative wrt temperature
      *                 - 3 derivative wrt pressure
      */
-    double gstar(const double temp, const double pres,
-                     const int ifunc = 0) const;
+    double gstar(const double temp, const double pres, const int ifunc = 0) const;
 
     //! Function to look up Element Free Energies
     /*!

include/cantera/thermo/PengRobinson.h

@@ -164,17 +164,15 @@ class PengRobinson : public MixtureFugacityTP
      *  @param b         @f$ a @f$ parameter in the Peng-Robinson model [m^3/kmol]
      *  @param w         acentric factor
      */
-    void setSpeciesCoeffs(const string& species, double a, double b,
-                          double w);
+    void setSpeciesCoeffs(const string& species, double a, double b, double w);
 
     //! Set values for the interaction parameter between two species
     /*!
      *  @param species_i   Name of one species
      *  @param species_j   Name of the other species
      *  @param a           @f$ a @f$ parameter in the Peng-Robinson model [Pa-m^6/kmol^2]
      */
-    void setBinaryCoeffs(const string& species_i,
-                         const string& species_j, double a);
+    void setBinaryCoeffs(const string& species_i, const string& species_j, double a);
     //! @}
 
 protected:

include/cantera/thermo/PureFluidPhase.h

@@ -186,8 +186,7 @@ class PureFluidPhase : public ThermoPhase
     virtual void initThermo();
     virtual void getParameters(AnyMap& phaseNode) const;
 
-    virtual string report(bool show_thermo=true,
-                               double threshold=1e-14) const;
+    virtual string report(bool show_thermo=true, double threshold=1e-14) const;
 
     virtual bool compatibleWithMultiPhase() const {
         return false;