extend doxygen support

analysis/ElectroChemistry.cpp

@@ -1,5 +1,6 @@
 #include "analysis/ElectroChemistry.h"
 
+
 ElectroChemistryAnalyzer::ElectroChemistryAnalyzer(std::shared_ptr <Domain> dm):
 	Dm(dm)
 {

analysis/FreeEnergy.h

@@ -19,6 +19,14 @@
 #include "IO/Writer.h"
 #include "models/FreeLeeModel.h"
 
+/**
+ * \class FreeEnergyAnalyzer
+ *
+ * @brief 
+ * The FreeEnergyAnalyzer class is constructed to analyze the LBPM free energy model for liquid-gas systems
+ * 
+ */
+
 class FreeEnergyAnalyzer{
 public:
 	std::shared_ptr <Domain> Dm;

analysis/GreyPhase.h

@@ -15,6 +15,14 @@
 #include "IO/Reader.h"
 #include "IO/Writer.h"
 
+
+/**
+ * \class GreyPhase
+ *
+ * @brief 
+ * The GreyPhase class tracks pressure, mass and momentum within a grey phase 
+ * 
+ */
 class GreyPhase{
  public:
   double p;
@@ -26,6 +34,14 @@ class GreyPhase{
  private:
 };
 
+
+/**
+ * \class GreyPhaseAnalysis
+ *
+ * @brief 
+ * The GreyPhaseAnalysis class is constructed to analyze the LBPM greyscale model
+ * 
+ */
 class GreyPhaseAnalysis{
 public:
 	std::shared_ptr <Domain> Dm;

analysis/Minkowski.cpp

@@ -50,7 +50,7 @@ void Minkowski::ComputeScalar(const DoubleArray& Field, const double isovalue)
 {
     PROFILE_START("ComputeScalar");
 	Xi = Ji = Ai = 0.0;
-	DECL object;
+	DCEL object;
 	int e1,e2,e3;
 	double s,s1,s2,s3;
 	double a1,a2,a3;

analysis/Minkowski.h

@@ -18,6 +18,14 @@
 #include "IO/Reader.h"
 #include "IO/Writer.h"
 
+/**
+ * \class Minkowski
+ *
+ * @brief 
+ * The Minkowski class is constructed to analyze the geometric properties of structures based on the Minkowski functionals
+ * 
+ */
+
 
 class Minkowski{
 	//...........................................................................
@@ -45,6 +53,7 @@ public:
 	int n_connected_components;
 	//...........................................................................
 	int Nx,Ny,Nz;
+
 	double V(){
 		return Vi;
 	}
@@ -59,15 +68,56 @@ public:
 	}
 		
 	//..........................................................................
+    /**
+    * \brief   Null constructor
+    */
 	Minkowski(){};//NULL CONSTRUCTOR
+	
+    /**
+    * \brief   Constructor based on an existing Domain
+    * @param Dm    - Domain structure 
+    */
 	Minkowski(std::shared_ptr <Domain> Dm);
 	~Minkowski();
+	
+    /**
+    * \brief   Compute scalar minkowski functionals	
+	 *  step 1. compute the distance to an object 
+	 *  step 2. construct dcel to represent the isosurface 
+	 *  step 3. compute the scalar Minkowski functionals
+	 * THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
+	 *    0 - labels the object
+	 *    1 - labels everything else
+	 */    
 	void MeasureObject();
+	
 	void MeasureObject(double factor, const DoubleArray &Phi);
+	
+    /**
+    * \details   Compute scalar minkowski functionals for connected part of a structure
+    *   step 1. compute connected components and extract largest region by volume
+    *  step 2. compute the distance to the connected part of the structure 
+    *  step 3. construct dcel to represent the isosurface 
+    *  step 4. compute the scalar Minkowski functionals
+    * THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
+    *    0 - labels the object
+    *    1 - labels everything else
+    */    
 	int MeasureConnectedPathway();
+
 	int MeasureConnectedPathway(double factor, const DoubleArray &Phi);
+	
+    /**
+    * \brief   Compute scalar minkowski functionals
+    * \details Construct an isosurface and return the geometric invariants based on the triangulated list
+    * @param isovalue        - threshold value to use to determine iso-surface
+    * @param Field           - DoubleArray containing the field to threshold
+    */
 	void ComputeScalar(const DoubleArray& Field, const double isovalue);
 
+    /**
+    * \brief   print the scalar invariants
+    */
 	void PrintAll();
 
 };

doxygen/DoxygenMainpage.h

@@ -1,12 +1,17 @@
 /** \mainpage LBPM
  *
- * This is the documentation for LBPM
+ * C/C++ routines 
  *
  *   - \ref IO "IO routines"
  *   - \ref analysis "Analysis routines"
- *   - \ref FlowAdaptor "Flow adaptor"
+ *       - \ref FlowAdaptor "FlowAdaptor"
+ *       - \ref DCEL "Doubly connected edge list"
+ *       - \ref Minkowski "Minkowski functionals"
  *   - \ref models "Lattice Boltzmann models"
- *   - \ref ScaLBL "Lattice Boltzmann building blocks"
+ *   - \ref ScaLBL "Scalable Lattice Boltzmann Library (ScaLBL)"
+ *   - \ref cpu "cpu implementation for library routines"
+ *   - \ref cuda "CUDA implementation for library routines"
+ *   - \ref hip "HIP implementation for library routines"
  *   - \ref tests "Unit tests"
  *   - \ref Utilities "Utility routines"
  *

tests/test_dcel_tri_normal.cpp

@@ -54,7 +54,7 @@ int main(int argc, char **argv)
 		}
 		pmmc_MeshGradient(SDs,SDs_x,SDs_y,SDs_z,Nx,Ny,Nz);
 
-		DECL object;
+		DCEL object;
 		Point P1,P2,P3;
 		Point U,V,W;
 		int e1,e2,e3;