Merge remote-tracking branch 'origin/master' into boundarylayer_fixes_cleanup

libsrc/general/CMakeLists.txt

@@ -2,7 +2,6 @@ target_sources(nglib PRIVATE
     gzstream.cpp
     hashtabl.cpp
     mystring.cpp
-    ngarray.cpp
     ngbitarray.cpp
     optmem.cpp
     parthreads.cpp

libsrc/general/ngarray.cpp

@@ -1,75 +0,0 @@
-#ifndef FILE_NGSTD_NgArrayCPP
-#define FILE_NGSTD_NgArrayCPP
-// necessary for SGI ????
-
-/**************************************************************************/
-/* File:   array.cpp                                                       */
-/* Author: Joachim Schoeberl                                              */
-/* Date:   01. Jun. 95                                                    */
-/**************************************************************************/
-
-/* 
-   Abstract data type NgArray
-*/
-
-#include <mystdlib.h>
-#include <myadt.hpp>
-#include <assert.h>
-
-
-namespace netgen
-{
-  //using namespace netgen;
-
-#ifdef NONE  
-  void BASE_Array :: ReSize (int minsize, int elementsize)
-  {
-    cout << "resize, minsize = " << minsize << endl;
-
-    if (inc == -1)
-      throw Exception ("Try to resize fixed size array");
-
-    
-    void * p;
-    int nsize = (inc) ? allocsize + inc : 2 * allocsize;
-    if (nsize < minsize) nsize = minsize;
-
-    if (data)
-      {
-	p = new char [nsize * elementsize];
-	
-	int mins = (nsize < actsize) ? nsize : actsize; 
-	memcpy (p, data, mins * elementsize);
-	
-	delete [] static_cast<char*> (data);
-	data = p;
-      }
-    else
-      {
-	data = new char[nsize * elementsize];
-      }
-    
-    allocsize = nsize;
-    cout << "resize done" << endl;
-  }
-  
-  
-  
-  void BASE_Array :: RangeCheck (int i) const
-  {
-    if (i < 0 || i >= actsize)
-      throw ArrayRangeException ();
-  }
-  
-  void BASE_Array :: CheckNonEmpty () const
-  {
-    if (!actsize)
-      {
-	throw Exception ("NgArray should not be empty");
-	//      cerr << "NgArray shouldn't be empty";
-      }
-  }
-#endif
-}
-#endif // FILE_NGSTD_NgArrayCPP
-

libsrc/general/ngarray.hpp

@@ -11,6 +11,7 @@
 
 namespace netgen
 {
+  using namespace ngcore;
 
   // template <class T, int B1, int B2> class IndirectArray;
   template <class TA1, class TA2> class NgIndirectArray;
@@ -111,11 +112,7 @@ namespace netgen
     /// Access array. BASE-based
     T & operator[] (TIND i) const
     {
-#ifdef DEBUG
-      if (i-BASE < 0 || i-BASE >= size)
-	cout << "array<" << typeid(T).name() << "> out of range, i = " << i << ", s = " << size << endl;
-#endif
-
+      NETGEN_CHECK_RANGE(i,BASE,size+BASE);
       return data[i-BASE]; 
     }
 
@@ -130,13 +127,7 @@ namespace netgen
     /// Access array, one-based  (old fashioned)
     T & Elem (int i)
     {
-#ifdef DEBUG
-      if (i < 1 || i > size)
-	cout << "NgArray<" << typeid(T).name() 
-	     << ">::Elem out of range, i = " << i
-	     << ", s = " << size << endl;
-#endif
-
+      NETGEN_CHECK_RANGE(i,1,size+1);
       return ((T*)data)[i-1]; 
     }
   
@@ -144,30 +135,21 @@ namespace netgen
     // [[deprecated("Use operator[] instead")]]    
     const T & Get (int i) const 
     {
-#ifdef DEBUG
-      if (i < 1 || i > size)
-	cout << "NgArray<" << typeid(T).name() << ">::Get out of range, i = " << i
-	     << ", s = " << size << endl;
-#endif
-
+      NETGEN_CHECK_RANGE(i,1,size+1);
       return ((const T*)data)[i-1]; 
     }
 
     /// Access array, one-based  (old fashioned)
     void Set (int i, const T & el)
     { 
-#ifdef DEBUG
-      if (i < 1 || i > size)
-	cout << "NgArray<" << typeid(T).name() << ">::Set out of range, i = " << i
-	     << ", s = " << size << endl;
-#endif
-
+      NETGEN_CHECK_RANGE(i,1,size+1);
       ((T*)data)[i-1] = el; 
     }
 
     /// access first element
     T & First () const
     {
+      NETGEN_CHECK_RANGE(0,0,size);
       return data[0];
     }
 
@@ -175,6 +157,7 @@ namespace netgen
     /// access last element. check by macro CHECK_RANGE
     T & Last () const
     {
+      NETGEN_CHECK_RANGE(size-1,0,size);
       return data[size-1];
     }
 
@@ -345,10 +328,7 @@ namespace netgen
     /// Delete element i (0-based). Move last element to position i.
     void Delete (TIND i)
     {
-#ifdef CHECK_Array_RANGE
-      RangeCheck (i+1);
-#endif
-
+      NETGEN_CHECK_RANGE(i,0,size);
       data[i] = std::move(data[size-1]);
       size--;
       //    DeleteElement (i+1);
@@ -358,10 +338,7 @@ namespace netgen
     /// Delete element i (1-based). Move last element to position i.
     void DeleteElement (TIND i)
     {
-#ifdef CHECK_Array_RANGE
-      RangeCheck (i);
-#endif
-
+      NETGEN_CHECK_RANGE(i,1,size+1);
       data[i-1] = std::move(data[size-1]);
       size--;
     }

libsrc/general/table.hpp

@@ -120,7 +120,7 @@ public:
   
   /// Creates fixed maximal element size table
   inline TABLE (const NgFlatArray<int,BASE> & entrysizes)
-    : BASE_TABLE (NgFlatArray<int> (entrysizes.Size(), const_cast<int*>(&entrysizes[BASE])), 
+    : BASE_TABLE (NgFlatArray<int> (entrysizes.Size(), entrysizes.Size() ? const_cast<int*>(&entrysizes[BASE]) : nullptr), 
 		  sizeof(T))
   { ; }
 

libsrc/meshing/basegeom.cpp

@@ -1245,8 +1245,7 @@ namespace netgen
 
   void NetgenGeometry :: FinalizeMesh(Mesh& mesh) const
   {
-    if(solids.Size())
-      for (int i = 0; i < mesh.GetNDomains(); i++)
+      for (int i = 0; i < std::min(solids.Size(), (size_t)mesh.GetNDomains()); i++)
         if (auto name = solids[i]->properties.name)
           mesh.SetMaterial (i+1, *name);
 

libsrc/meshing/python_mesh.cpp

@@ -1783,6 +1783,18 @@ project_boundaries : Optional[str] = None
   layer-ending should be projected to that boundary.
 
 )delimiter")
+    .def(py::init([]( const py::dict & d ) {
+      try {
+        // Call other constructor with named arguments by unpacking the dictionary
+        py::object cls = py::type::of<BoundaryLayerParameters>();
+        return cls(**d).cast<BoundaryLayerParameters>();
+      }
+      catch (py::error_already_set & e) {
+        cerr << "Error creating BoundaryLayerParameters from dict:" << endl;
+        cerr << e.what() << endl;
+        throw;
+      }
+    }))
     .def_readwrite("boundary", &BoundaryLayerParameters::boundary)
     .def_readwrite("thickness", &BoundaryLayerParameters::thickness)
     .def_readwrite("new_material", &BoundaryLayerParameters::new_material)
@@ -1795,6 +1807,7 @@ project_boundaries : Optional[str] = None
     .def_readwrite("keep_surfaceindex", &BoundaryLayerParameters::keep_surfaceindex)
     .def_readwrite("limit_safety", &BoundaryLayerParameters::limit_safety)
     ;
+  py::implicitly_convertible<py::dict, BoundaryLayerParameters>();
 
 #ifdef NG_CGNS
   m.def("ReadCGNSFile", &ReadCGNSFile, py::arg("filename"), py::arg("base")=1, "Read mesh and solution vectors from CGNS file");

libsrc/meshing/smoothing3.cpp

@@ -335,8 +335,8 @@ namespace netgen
   {
     static Timer tim("PointFunction - build elementsonpoint table"); RegionTimer reg(tim);
 
-    Array<bool, PointIndex> bad_point(points.Size());
-    bad_point = false;
+    Array<bool, PointIndex> non_tet_points(points.Size());
+    non_tet_points = false;
     // Don't optimize if point is adjacent to a non-tet element
     ParallelForRange(elements.Range(), [&] (auto myrange)
         {
@@ -345,7 +345,7 @@ namespace netgen
               const auto & el = elements[ei];
               if(el.NP()!=4)
                 for(auto pi : el.PNums())
-                  bad_point[pi] = true;
+                  non_tet_points[pi] = true;
             }
        });
 
@@ -358,7 +358,7 @@ namespace netgen
                    return;
 
                  for (PointIndex pi : el.PNums())
-                   if(!bad_point[pi])
+                   if(!non_tet_points[pi])
                      table.Add (pi, ei);
                }, points.Size());
   }