Fixing some typos and formatting based on comments for PR #575

include/cantera/numerics/FuncEval.h

@@ -76,7 +76,7 @@ class FuncEval
      *  @returns 0 for a successful evaluation; 1 after a potentially-
      *      recoverable error; -1 after an unrecoverable error.
      */
-    int eval_nothrow(double t, double* y, double* ydot, double* residaul);
+    int eval_nothrow(double t, double* y, double* ydot, double* residual);
 
     /*! Evaluate the setup processes for the Jacobian preconditioner.
      * @param[in] t time.

include/cantera/numerics/IDAIntegrator.h

@@ -4,7 +4,7 @@
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
-// at http://www.cantera.org/license.txt for license and copyright information.
+// at https://www.cantera.org/license.txt for license and copyright information.
 
 #ifndef CT_IDAIntegrator_H
 #define CT_IDAIntegrator_H
@@ -67,7 +67,7 @@ class IDAIntegrator : public Integrator
     //! responsible for integrator failures or unexpected small timesteps.
     virtual std::string getErrorInfo(int N);
 
-    //! Error message information provide by CVodes
+    //! Error message information provide by IDAS
     std::string m_error_message;
 
     virtual void setMaxNonlinIterations(int n);
@@ -78,7 +78,7 @@ class IDAIntegrator : public Integrator
 
 protected:
     protected:
-    //! Applies user-specified options to the underlying CVODES solver. Called
+    //! Applies user-specified options to the underlying IDAS solver. Called
     //! during integrator initialization or reinitialization.
     void applyOptions();
 

include/cantera/numerics/Integrator.h

@@ -3,7 +3,7 @@
  */
 
 /**
- * @defgroup intGroup Zero-dimensional Integrators
+ * @defgroup intGroup Integrators for initial value problems
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
@@ -68,8 +68,8 @@ class Integrator
      * @param n      Number of equations
      * @param abstol array of N absolute tolerance values
      */
-    virtual void setTolerances(doublereal reltol, size_t n,
-                               doublereal* abstol) {
+    virtual void setTolerances(double reltol, size_t n,
+                               double* abstol) {
         warn("setTolerances");
     }
 
@@ -78,7 +78,7 @@ class Integrator
      * @param reltol scalar relative tolerance
      * @param abstol scalar absolute tolerance
      */
-    virtual void setTolerances(doublereal reltol, doublereal abstol) {
+    virtual void setTolerances(double reltol, double abstol) {
         warn("setTolerances");
     }
 
@@ -87,7 +87,7 @@ class Integrator
      * @param reltol scalar relative tolerance
      * @param abstol scalar absolute tolerance
      */
-    virtual void setSensitivityTolerances(doublereal reltol, doublereal abstol)
+    virtual void setSensitivityTolerances(double reltol, double abstol)
     { }
 
     //! Set the problem type.
@@ -164,11 +164,11 @@ class Integrator
      * @param t0   initial time
      * @param func RHS evaluator object for system of equations.
      */
-    virtual void initialize(doublereal t0, FuncEval& func) {
+    virtual void initialize(double t0, FuncEval& func) {
         warn("initialize");
     }
 
-    virtual void reinitialize(doublereal t0, FuncEval& func) {
+    virtual void reinitialize(double t0, FuncEval& func) {
         warn("reinitialize");
     }
 
@@ -177,7 +177,7 @@ class Integrator
      * @param tout Integrate to this time. Note that this is the
      *             absolute time value, not a time interval.
      */
-    virtual void integrate(doublereal tout) {
+    virtual void integrate(double tout) {
         warn("integrate");
     }
 
@@ -186,19 +186,19 @@ class Integrator
      * @param tout integrate to this time. Note that this is the
      * absolute time value, not a time interval.
      */
-    virtual doublereal step(doublereal tout) {
+    virtual double step(double tout) {
         warn("step");
         return 0.0;
     }
 
     //! The current value of the solution of equation k.
-    virtual doublereal& solution(size_t k) {
+    virtual double& solution(size_t k) {
         warn("solution");
         return m_dummy;
     }
 
     //! The current value of the solution of the system of equations.
-    virtual doublereal* solution() {
+    virtual double* solution() {
         warn("solution");
         return 0;
     }
@@ -294,8 +294,8 @@ class Integrator
     virtual void setMaxNonlinConvFailures(int n) {
         warn("setMaxNonlinConvFailures");
     }
-    virtual void inclAlgebraicInErrorTest(bool yesno) {
-        warn("inclAlgebraicInErrorTest");
+    virtual void includeAlgebraicInErrorTest(bool yesno) {
+        warn("includeAlgebraicInErrorTest");
     }
 
 protected:
@@ -308,7 +308,7 @@ class Integrator
     // methods for DAE solvers
 
 private:
-    doublereal m_dummy;
+    double m_dummy;
     void warn(const std::string& msg) const {
         writelog(">>>> Warning: method "+msg+" of base class "
                  +"Integrator called. Nothing done.\n");

include/cantera/zeroD/FlowReactor.h

@@ -66,7 +66,7 @@ class FlowReactor : public IdealGasReactor
         // mark all variables differential equations unless otherwise specified
         std::fill(constraints, constraints + m_nv, 1.0);
         // the species coverages are algebraic constraints
-        std::fill(constraints + m_non_spec_eq + m_nsp, constraints + m_nv, 0.0);
+        std::fill(constraints + m_offset_Y + m_nsp, constraints + m_nv, 0.0);
     }
 
 
@@ -79,7 +79,7 @@ class FlowReactor : public IdealGasReactor
         return m_u;
     }
 
-    //! The area of the reactor [m^2]
+    //! The cross-sectional area of the reactor [m^2]
     double area() const {
         return m_area;
     }
@@ -110,25 +110,25 @@ class FlowReactor : public IdealGasReactor
 
     //! Set the steady state tolerances used to determine the initial state for
     //! surface coverages
-    void setSteadyStateAtol(double atol) {
+    void setInletSurfaceAtol(double atol) {
         m_ss_atol = atol;
     }
 
     //! Set the steady state tolerances used to determine the initial state for
     //! surface coverages
-    void setSteadyStateRtol(double rtol) {
+    void setInletSurfaceRtol(double rtol) {
         m_ss_rtol = rtol;
     }
 
     //! Set the steady state tolerances used to determine the initial state for
     //! surface coverages
-    void setSteadyStateMaxSteps(int max_steps) {
+    void setInletSurfaceMaxSteps(int max_steps) {
         m_max_ss_steps = max_steps;
     }
 
     //! Set the steady state tolerances used to determine the initial state for
     //! surface coverages
-    void setSteadyStateMaxErrorFailures(int max_fails) {
+    void setInletSurfaceMaxErrorFailures(int max_fails) {
         m_max_ss_error_fails = max_fails;
     }
 
@@ -144,7 +144,7 @@ class FlowReactor : public IdealGasReactor
 protected:
     double m_u, m_T, m_P, m_rho;
     //! offset to the species equations
-    const size_t m_non_spec_eq = 4;
+    const size_t m_offset_Y = 4;
     //! reactor area [m^2]
     double m_area;
     //! reactor surface area to volume ratio [m^-1]

include/cantera/zeroD/Reactor.h

@@ -97,20 +97,20 @@ class Reactor : public ReactorBase
     /*!
      *  @param[out] y state vector representing the initial state of the reactor
      */
-    virtual void getState(doublereal* y);
+    virtual void getState(double* y);
 
     //! Get the current state and derivative vector of the reactor for a DAE solver
     /*!
      *  @param[out] y     state vector representing the initial state of the reactor
      *  @param[out] ydot  state vector representing the initial derivatives of the
      *                    reactor
      */
-    virtual void getState(doublereal* y, doublereal* ydot)
+    virtual void getState(double* y, double* ydot)
     {
-        throw CanteraError("Reactor::getState", "Not Implemented");
+        throw CanteraError("Reactor::getState(y, ydot)", "Not Implemented");
     }
 
-    virtual void initialize(doublereal t0 = 0.0);
+    virtual void initialize(double t0 = 0.0);
 
     //! Evaluate the reactor governing equations. Called by ReactorNet::eval.
     //! @param[in] t time.
@@ -126,11 +126,11 @@ class Reactor : public ReactorBase
      * @param[in] y solution vector, length neq()
      * @param[in] ydot rate of change of solution vector, length neq()
      * @param[in] params sensitivity parameter vector, length ReactorNet::nparams()
-     * @param[out] residual resisduals vector, length neq()
+     * @param[out] residual residuals vector, length neq()
      */
-    virtual void evalEqs(doublereal t, doublereal* y,
-                         doublereal* ydot, doublereal* params,
-                         doublereal* residual)
+    virtual void evalEqs(double t, double* y,
+                         double* ydot, double* params,
+                         double* residual)
     {
         throw CanteraError("Reactor::evalEqs", "Not Implemented");
     }
@@ -145,7 +145,7 @@ class Reactor : public ReactorBase
     virtual void syncState();
 
     //! Set the state of the reactor to correspond to the state vector *y*.
-    virtual void updateState(doublereal* y);
+    virtual void updateState(double* y);
 
     //! Number of sensitivity parameters associated with this reactor
     //! (including walls)

include/cantera/zeroD/ReactorNet.h

@@ -69,27 +69,27 @@ class ReactorNet : public FuncEval
     void setSensitivityTolerances(double rtol, double atol);
 
     //! Current value of the simulation time.
-    doublereal time() {
+    double time() {
         return m_time;
     }
 
     //! Relative tolerance.
-    doublereal rtol() {
+    double rtol() {
         return m_rtol;
     }
 
     //! Absolute integration tolerance
-    doublereal atol() {
+    double atol() {
         return m_atols;
     }
 
     //! Relative sensitivity tolerance
-    doublereal rtolSensitivity() const {
+    double rtolSensitivity() const {
         return m_rtolsens;
     }
 
     //! Absolute sensitivity tolerance
-    doublereal atolSensitivity() const {
+    double atolSensitivity() const {
         return m_atolsens;
     }
 
@@ -105,7 +105,7 @@ class ReactorNet : public FuncEval
      * timesteps as necessary to reach *time*.
      * @param time Time to advance to (s).
      */
-    void advance(doublereal time);
+    void advance(double time);
 
     /**
      * Advance the state of all reactors in time. Take as many internal
@@ -150,7 +150,7 @@ class ReactorNet : public FuncEval
 
     //! Update the state of all the reactors in the network to correspond to
     //! the values in the solution vector *y*.
-    void updateState(doublereal* y);
+    void updateState(double* y);
 
     //! Return the sensitivity of the *k*-th solution component with respect to
     //! the *p*-th sensitivity parameter.
@@ -187,8 +187,8 @@ class ReactorNet : public FuncEval
      *  @param[in] p sensitivity parameter vector (unused?)
      *  @param[out] j Jacobian matrix, size neq() by neq().
      */
-    void evalJacobian(doublereal t, doublereal* y,
-                      doublereal* ydot, doublereal* p, Array2D* j);
+    void evalJacobian(double t, double* y,
+                      double* ydot, double* p, Array2D* j);
 
     // overloaded methods of class FuncEval
     virtual size_t neq() {
@@ -199,21 +199,21 @@ class ReactorNet : public FuncEval
         return m_reactors.size();
     }
 
-    virtual void eval(doublereal t, doublereal* y,
-                      doublereal* ydot, doublereal* p);
+    virtual void eval(double t, double* y,
+                      double* ydot, double* p);
 
     //! eval coupling for IDA / DAEs
-    virtual void eval(doublereal t, doublereal* y,
-                      doublereal* ydot, doublereal* p,
-                      doublereal* residaul);
+    virtual void eval(double t, double* y,
+                      double* ydot, double* p,
+                      double* residaul);
 
-    virtual void getState(doublereal* y);
+    virtual void getState(double* y);
 
     //! Return k-th derivative at the current time
     virtual void getDerivative(int k, double* dky);
-    virtual void getState(doublereal* y, doublereal* ydot);
+    virtual void getState(double* y, double* ydot);
 
-    virtual void getConstraints(doublereal* constraints);
+    virtual void getConstraints(double* constraints);
 
     virtual size_t nparams() {
         return m_sens_params.size();

interfaces/cython/cantera/reactor.pxd

@@ -59,10 +59,10 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
         double area() except +translate_exception
         void setSurfaceAreaToVolumeRatio(double) except +translate_exception
         double surfaceAreaToVolumeRatio() except +translate_exception
-        void setSteadyStateAtol(double) except +translate_exception
-        void setSteadyStateRtol(double) except +translate_exception
-        void setSteadyStateMaxSteps(int) except +translate_exception
-        void setSteadyStateMaxErrorFailures(int) except +translate_exception
+        void setInletSurfaceAtol(double) except +translate_exception
+        void setInletSurfaceRtol(double) except +translate_exception
+        void setInletSurfaceMaxSteps(int) except +translate_exception
+        void setInletSurfaceMaxErrorFailures(int) except +translate_exception
 
     # walls
     cdef cppclass CxxWallBase "Cantera::WallBase":

interfaces/cython/cantera/reactor.pyx

@@ -478,29 +478,29 @@ cdef class FlowReactor(Reactor):
         def __set__(self, area):
             (<CxxFlowReactor*>self.reactor).setArea(area)
 
-    property steady_state_atol:
+    property inlet_surface_atol:
         """ Set the steady-state tolerances used to determine the initial surface
             species coverages"""
         def __set__(self, atol):
-            (<CxxFlowReactor*>self.reactor).setSteadyStateAtol(atol)
+            (<CxxFlowReactor*>self.reactor).setInletSurfaceAtol(atol)
 
-    property steady_state_rtol:
+    property inlet_surface_rtol:
         """ Set the steady-state tolerances used to determine the initial surface
             species coverages"""
         def __set__(self, rtol):
-            (<CxxFlowReactor*>self.reactor).setSteadyStateRtol(rtol)
+            (<CxxFlowReactor*>self.reactor).setInletSurfaceRtol(rtol)
 
-    property steady_state_max_steps:
+    property inlet_surface_max_steps:
         """ Set the maximum number of integrator steps used to determine the initial surface
             species coverages"""
         def __set__(self, nsteps):
-            (<CxxFlowReactor*>self.reactor).setSteadyStateMaxSteps(nsteps)
+            (<CxxFlowReactor*>self.reactor).setInletSurfaceMaxSteps(nsteps)
 
-    property steady_state_max_error_failures:
+    property inlet_surface_max_error_failures:
         """ Set the maximum number of integrator error failures allowed when determining
             the initial surface species coverages"""
         def __set__(self, nsteps):
-            (<CxxFlowReactor*>self.reactor).setSteadyStateMaxErrorFailures(nsteps)
+            (<CxxFlowReactor*>self.reactor).setInletSurfaceMaxErrorFailures(nsteps)
 
     property surface_area_to_volume_ratio:
         """ Get/set the surface area to volume ratio of the reactor [m^-1] """