* NL: Added low-level access to matrix in OpenNL

* periodic.h: added access to nb_vertices_non_periodic()
* cleanup

src/lib/geogram/NL/nl.h

@@ -1476,6 +1476,32 @@ extern "C" {
      */
     NLAPI void NLAPIENTRY nlPrintfFuncs(NLprintfFunc f1, NLfprintfFunc f2);
 
+/**
+ * @}
+ * \name Low-level access
+ * @{
+ */
+
+    /**
+     * \brief Forward declaration of Matrix structure
+     * \details Standard usage does not need to access the
+     *  structure. For advanced users, it is declared in
+     *  nl_matrix.h.
+     */
+    struct NLMatrixStruct;
+
+    /**
+     * \brief Opaque handle to a matrix
+     */
+    typedef struct NLMatrixStruct* NLMatrix;
+
+    /**
+     * \brief Gets the current matrix
+     * \details for advanced low-level matrix manipulation
+     * \return a pointer to the current matrix, can be a NLSparseMatrix
+     *  or a NLCRSMatrix depending on whether pattern was pre-created.
+     */
+    NLAPI NLMatrix NLAPIENTRY nlGetCurrentMatrix(void);
 
 /**
  * @}

src/lib/geogram/NL/nl_api.c

@@ -92,6 +92,14 @@ static NLCRSMatrix* nlGetCurrentCRSMatrix(void) {
 
 /*****************************************************************************/
 
+NLMatrix nlGetCurrentMatrix(void) {
+    return nlCurrentContext->has_matrix_pattern ?
+	(NLMatrix) nlGetCurrentCRSMatrix() :
+	(NLMatrix) nlGetCurrentSparseMatrix() ;
+}
+
+/*****************************************************************************/
+
 NLboolean nlInitExtension(const char* extension) {
     if(!strcmp(extension, "SUPERLU")) {
         return nlInitExtension_SUPERLU();

src/lib/geogram/basic/geofile.cpp

@@ -294,11 +294,18 @@ namespace GEO {
         if(ascii_) {
             if(comment == nullptr) {
                 if(fprintf(ascii_file_, "\"%s\"\n", encode(str).c_str()) == 0) {
-                    throw GeoFileException("Could not write string data to file");
+                    throw GeoFileException(
+			"Could not write string data to file"
+		    );
                 }
             } else {
-                if(fprintf(ascii_file_, "\"%s\" # this is %s\n", encode(str).c_str(), comment) == 0) {
-                    throw GeoFileException("Could not write string data to file");
+                if(fprintf(
+		       ascii_file_, "\"%s\" # this is %s\n",
+		       encode(str).c_str(), comment) == 0
+		  ) {
+                    throw GeoFileException(
+			"Could not write string data to file"
+		    );
                 }
             }
             return;

src/lib/geogram/basic/stopwatch.cpp

@@ -77,18 +77,20 @@ namespace GEO {
     double Stopwatch::elapsed_time() const {
         auto now(std::chrono::system_clock::now());
         auto elapsed = now-start_;
-        auto elapsed_milliseconds = std::chrono::duration_cast<std::chrono::milliseconds>(
-            elapsed
-        );
+        auto elapsed_milliseconds =
+	    std::chrono::duration_cast<std::chrono::milliseconds>(
+		elapsed
+	    );
         return 0.001 * double(elapsed_milliseconds.count());
     }
 
     double Stopwatch::now() {
         auto now(std::chrono::system_clock::now());
         auto elapsed = now.time_since_epoch();
-        auto elapsed_milliseconds = std::chrono::duration_cast<std::chrono::milliseconds>(
-            elapsed
-        );
+        auto elapsed_milliseconds =
+	    std::chrono::duration_cast<std::chrono::milliseconds>(
+		elapsed
+	    );
         return 0.001 * double(elapsed_milliseconds.count());
     }
 

src/lib/geogram/delaunay/parallel_delaunay_3d.cpp

@@ -279,9 +279,7 @@ namespace GEO {
          * \return a poiner to the \p t th thread
          */
         Delaunay3dThread* thread(index_t t) {
-            return static_cast<Delaunay3dThread*>(
-                master_->threads_[t].get()
-            );
+            return static_cast<Delaunay3dThread*>(master_->threads_[t].get());
         }
 
         /**

src/lib/geogram/delaunay/periodic.h

@@ -57,6 +57,18 @@ namespace GEO {
     class GEOGRAM_API Periodic {
     public:
 
+    /**
+     * \brief Gets the number of non-periodic vertices
+     * \details in periodic mode, nb_vertices() returns
+     *  the total number of vertices, real ones and
+     *  periodic instances. This function gets the number
+     *  of real vertices.
+     * \return the number of non-periodic vertices
+     */
+    index_t nb_vertices_non_periodic() const {
+	return nb_vertices_non_periodic_;
+    }
+
     /**
      * \brief Gets the instance from a periodic vertex.
      * \return the instance in 0..26

src/lib/geogram/delaunay/periodic_delaunay_3d.cpp

@@ -789,8 +789,7 @@ namespace GEO {
 
 
         /**
-         * \brief Creates a star of tetrahedra filling the conflict
-         *  zone.
+         * \brief Creates a star of tetrahedra filling the conflict zone.
          * \param[in] v the index of the point to be inserted
          * \details This function is used when the Cavity computed
          *  when traversing the conflict zone is OK, that is to say
@@ -949,7 +948,7 @@ namespace GEO {
                 )
             );
 
-            //   At this point, this threads owns all the tets in conflict and
+            //   At this point, this thread owns all the tets in conflict and
             // their neighbors, therefore no other thread can interfere, and
             // we can update the triangulation.
 
@@ -3423,11 +3422,13 @@ namespace GEO {
 
         // Create periodic_v_to_cell_ structure in compressed row
         // storage format.
+
 	// It was used in previous version for handling periodic boundary
 	// conditions based on ConvexCell, it is no longer the case, new
 	// code solely uses tetrahedra. It is kept here for reference for
 	// implementing the distributed version (using ConvexCell can save
 	// points tranfers).
+
         if(update_periodic_v_to_cell_) {
             periodic_v_to_cell_rowptr_.resize(nb_vertices_non_periodic_ + 1);
             periodic_v_to_cell_rowptr_[0] = 0;
@@ -3943,6 +3944,8 @@ namespace GEO {
 
         // Local tet vertex indices from facet and vertex in facet indices.
 	// Carefully chosen in such a way that f[(lv+1)%3][2] == lv
+	// This is used in the code block below, that handles tets with
+	// a vertex at infinity
         static GEO::index_t fv[4][3] = {
             {1,2,3},
             {3,2,0},
@@ -4181,7 +4184,7 @@ namespace GEO {
 		    std::abs(Ty2 - Ty1) >= 2 ||
 		    std::abs(Tz2 - Tz1) >= 2
 		) {
-		    // Here we could use -1 to encore large displacements,
+		    // Here we could use -1 to encode large displacements,
 		    // and issue an error message (for now they are ignored)
 		    continue;
 		}