[docs] Restructure doxygen oneD documentation

doc/doxygen/mainpage.md

@@ -13,7 +13,7 @@ A topical overview is provided as follows:
 * @ref chemkinetics (reactions, rates of progress, reaction path analysis, ...)
 * @ref tranprops (diffusion, viscosity, thermal conductivity, ...)
 * @ref zerodGroup (reactors, walls, flow devices, ...)
-* @ref onedim (flames, flow domains, boundaries, ...)
+* @ref onedGroup (flames, flow domains, boundaries, ...)
 * @ref physConstants (universal constants, built into %Cantera for convenience)
 
 For fundamental scientific theory used for the implementation of %Cantera, refer to the

include/cantera/oneD/Boundary1D.h

@@ -21,6 +21,11 @@ namespace Cantera
 const int LeftInlet = 1;
 const int RightInlet = -1;
 
+//! @defgroup bdryGroup Boundaries
+//! Boundaries of one-dimensional flow domains.
+//! @ingroup onedGroup
+//! @{
+
 /**
  * The base class for boundaries between one-dimensional spatial domains. The
  * boundary may have its own internal variables, such as surface species
@@ -30,7 +35,6 @@ const int RightInlet = -1;
  *
  * The public methods are all virtual, and the base class implementations throw
  * exceptions.
- * @ingroup onedim
  */
 class Boundary1D : public Domain1D
 {
@@ -126,7 +130,6 @@ class Boundary1D : public Domain1D
 
 /**
  * An inlet.
- * @ingroup onedim
  */
 class Inlet1D : public Boundary1D
 {
@@ -173,7 +176,6 @@ class Inlet1D : public Boundary1D
 
 /**
  * A terminator that does nothing.
- * @ingroup onedim
  */
 class Empty1D : public Boundary1D
 {
@@ -205,7 +207,6 @@ class Empty1D : public Boundary1D
 /**
  * A symmetry plane. The axial velocity u = 0, and all other components have
  * zero axial gradients.
- * @ingroup onedim
  */
 class Symm1D : public Boundary1D
 {
@@ -235,7 +236,6 @@ class Symm1D : public Boundary1D
 
 /**
  * An outlet.
- * @ingroup onedim
  */
 class Outlet1D : public Boundary1D
 {
@@ -265,7 +265,6 @@ class Outlet1D : public Boundary1D
 
 /**
  * An outlet with specified composition.
- * @ingroup onedim
  */
 class OutletRes1D : public Boundary1D
 {
@@ -306,7 +305,6 @@ class OutletRes1D : public Boundary1D
  * A non-reacting surface. The axial velocity is zero (impermeable), as is the
  * transverse velocity (no slip). The temperature is specified, and a zero flux
  * condition is imposed for the species.
- * @ingroup onedim
  */
 class Surf1D : public Boundary1D
 {
@@ -339,7 +337,6 @@ class Surf1D : public Boundary1D
 
 /**
  * A reacting surface.
- * @ingroup onedim
  */
 class ReactingSurf1D : public Boundary1D
 {
@@ -395,6 +392,8 @@ class ReactingSurf1D : public Boundary1D
     vector_fp m_fixed_cov;
 };
 
+//! @} End of bdryGroup
+
 }
 
 #endif

include/cantera/oneD/Domain1D.h

@@ -35,7 +35,7 @@ class SolutionArray;
 
 /**
  * Base class for one-dimensional domains.
- * @ingroup onedim
+ * @ingroup flowGroup
  */
 class Domain1D
 {

include/cantera/oneD/DomainFactory.h

@@ -19,8 +19,6 @@ namespace Cantera
 //! ```cpp
 //!     shared_ptr<Domain1D> d1 = newDomain("Inlet", sol, "reactants");
 //! ```
-//!
-//! @ingroup onedim
 class DomainFactory : public Factory<Domain1D, shared_ptr<Solution>, const string&>
 {
 public:
@@ -50,7 +48,7 @@ class DomainFactory : public Factory<Domain1D, shared_ptr<Solution>, const strin
 //! @param solution  Solution holding ThermoPhase, Kinetics and Transport objects.
 //! @param id  string identifier describing domain. If omitted, id defaults to the
 //!     domain type identifier.
-//! @ingroup onedim
+//! @ingroup onedGroup
 template <class T=Domain1D>
 shared_ptr<T> newDomain(
     const string& domainType, shared_ptr<Solution> solution, const string& id="")

include/cantera/oneD/IonFlow.h

@@ -26,7 +26,7 @@ namespace Cantera
  * Pederson, Timothy, and R. C. Brown.
  * "Simulation of electric field effects in premixed methane flames."
  * Combustion and Flames 94.4(1993): 433-448.
- * @ingroup onedim
+ * @ingroup flowGroup
  */
 class IonFlow : public StFlow
 {

include/cantera/oneD/MultiJac.h

@@ -17,8 +17,8 @@ namespace Cantera
  * residual function supplied by an instance of class OneDim. The residual
  * function may consist of several linked 1D domains, with different variables
  * in each domain.
- * @ingroup onedim
- */
+* @ingroup onedUtilsGroup
+  */
 class MultiJac : public BandMatrix
 {
 public:

include/cantera/oneD/MultiNewton.h

@@ -11,10 +11,14 @@
 namespace Cantera
 {
 
+//! @defgroup onedUtilsGroup Utilities
+//! Utility classes and functions for one-dimensional problems.
+//! @ingroup onedGroup
+
 /**
  * Newton iterator for multi-domain, one-dimensional problems.
  * Used by class OneDim.
- * @ingroup onedim
+ * @ingroup onedUtilsGroup
  */
 class MultiNewton
 {

include/cantera/oneD/OneDim.h

@@ -21,7 +21,7 @@ class AnyMap;
 /**
  * Container class for multiple-domain 1D problems. Each domain is
  * represented by an instance of Domain1D.
- * @ingroup onedim
+ * @ingroup onedGroup
  */
 class OneDim
 {

include/cantera/oneD/Sim1D.h

@@ -16,7 +16,7 @@ namespace Cantera
 /**
  * One-dimensional simulations. Class Sim1D extends class OneDim by storing
  * the solution vector, and by adding a hybrid Newton/time-stepping solver.
- * @ingroup onedim
+ * @ingroup onedGroup
  */
 class Sim1D : public OneDim
 {

include/cantera/oneD/StFlow.h

@@ -32,10 +32,14 @@ enum offset
 
 class Transport;
 
+//! @defgroup flowGroup Flow Domains
+//! One-dimensional flow domains.
+//! @ingroup onedGroup
+
 /**
  *  This class represents 1D flow domains that satisfy the one-dimensional
  *  similarity solution for chemically-reacting, axisymmetric flows.
- *  @ingroup onedim
+ *  @ingroup flowGroup
  */
 class StFlow : public Domain1D
 {

include/cantera/oneD/refine.h

@@ -12,8 +12,8 @@ namespace Cantera
 class Domain1D;
 
 //! Refine Domain1D grids so that profiles satisfy adaptation tolerances
-//! @ingroup onedim
-class Refiner
+//! @ingroup onedUtilsGroup
+ class Refiner
 {
 public:
     Refiner(Domain1D& domain);

include/cantera/onedim.h

@@ -1,10 +1,10 @@
 //! @file onedim.h
 
 /*!
- * @defgroup onedim One-Dimensional Reacting Flows
+ * @defgroup onedGroup One-Dimensional Reacting Flows
  *
- * These classes comprise Cantera's ability to solve steady-state one-
- * dimensional reacting flow problems, such as laminar flames, opposed flow
+ * @details These classes comprise %Cantera's ability to solve steady-state
+ * one-dimensional reacting flow problems, such as laminar flames, opposed flow
  * diffusion flames, and stagnation flow chemical vapor deposition.
  */