WIP: extend nglib api

.gitignore

@@ -5,7 +5,7 @@ build
 *.vol
 *.ini
 __pycache__
-*.json
 *.zip
 .cache
 *.patch
+.vscode/

CMakeLists.txt

@@ -25,12 +25,12 @@ option( USE_GEOM2D     "build 2d geometry kernels" ON)
 option( USE_JPEG    "enable snapshots using library libjpeg" OFF )
 option( USE_MPEG    "enable video recording with FFmpeg, uses libavcodec" OFF )
 option( USE_CGNS    "enable CGNS file read/write support" OFF )
-option( USE_NUMA         "compile with NUMA-aware code")
-option( INTEL_MIC        "cross compile for intel xeon phi")
+option( USE_NUMA         "compile with NUMA-aware code" OFF)
+option( INTEL_MIC        "cross compile for intel xeon phi" OFF)
 option( INSTALL_PROFILES "install environment variable settings to /etc/profile.d" OFF )
-option( USE_CCACHE       "use ccache")
+option( USE_CCACHE       "use ccache" OFF)
 option( USE_INTERNAL_TCL "Compile tcl files into the code and don't install them" ON)
-option( ENABLE_UNIT_TESTS "Enable Catch unit tests")
+option( ENABLE_UNIT_TESTS "Enable Catch unit tests" OFF)
 option( ENABLE_CPP_CORE_GUIDELINES_CHECK "Enable cpp core guideline checks on ngcore" OFF)
 option( DEBUG_LOG "Enable more debug output (may increase computation time) - only works with USE_SPDLOG=ON" OFF)
 option( CHECK_RANGE "Check array range access, automatically enabled if built in debug mode" OFF)

libsrc/core/bitarray.hpp

@@ -226,7 +226,7 @@ class BitArray
 
     bool operator[] (IndexType i) const { return Test(i); } 
     T_Range<IndexType> Range() const { return { IndexBASE<IndexType>(), IndexBASE<IndexType>()+Size() }; }
-    NGCORE_API TBitArray & Or (const TBitArray & ba2)
+    inline TBitArray & Or (const TBitArray & ba2)
     {
       BitArray::Or(ba2);
       return *this;

libsrc/core/utils.cpp

@@ -26,6 +26,7 @@ namespace ngcore
 {
     namespace detail
     {
+      /*
         // see https://github.com/RobotLocomotion/drake/blob/master/common/nice_type_name.cc
         static const auto demangle_regexes =
             std::array<std::pair<std::regex, std::string>, 8>{
@@ -48,10 +49,11 @@ namespace ngcore
                 {std::regex("\\bstd::basic_string<char,std::char_traits<char>,"
                         "std::allocator<char>>"), "std::string"}
             };
+        */
         std::string CleanupDemangledName( std::string s )
         {
-            for(const auto & [r, sub] : demangle_regexes)
-                s = std::regex_replace (s,r,sub);
+            // for(const auto & [r, sub] : demangle_regexes)
+            //     s = std::regex_replace (s,r,sub);
 #ifdef EMSCRIPTEN
             // for some reason regex_replace is not working at all
             std::string temp = s;

libsrc/core/version.cpp

@@ -23,7 +23,7 @@ namespace ngcore
   }
 
   static bool dummy = [](){
-    SetLibraryVersion("netgen", NETGEN_VERSION);
+    SetLibraryVersion("netgen", VersionInfo(NETGEN_VERSION));
     return true;
   }();
 } // namespace ngcore

libsrc/core/version.hpp

@@ -18,37 +18,41 @@ namespace ngcore
     VersionInfo() = default;
     VersionInfo(std::string vstring)
     {
+      try {
       minor_ = release = patch = 0;
       git_hash = "";
       if(vstring.substr(0,1) == "v")
         vstring = vstring.substr(1,vstring.size()-1);
       auto dot = vstring.find('.');
       mayor_ = std::stoi(vstring.substr(0,dot));
-      if(dot == size_t(-1)) vstring = "";
+      if(dot == std::string::npos) vstring = "";
       else vstring = vstring.substr(dot+1, vstring.size()-dot-1);
       if(!vstring.empty())
         {
           dot = vstring.find('.');
           minor_ = std::stoi(vstring.substr(0,dot));
-          if (dot == size_t(-1)) vstring = "";
+          if (dot == std::string::npos) vstring = "";
           else vstring = vstring.substr(dot+1, vstring.size()-dot-1);
           if(!vstring.empty())
             {
               dot = vstring.find('-');
               release = std::stoi(vstring.substr(0,dot));
-              if(dot == size_t(-1)) vstring = "";
+              if(dot == std::string::npos) vstring = "";
               else vstring = vstring.substr(dot+1,vstring.size()-dot-1);
               if(!vstring.empty())
                 {
                   dot = vstring.find('-');
                   patch = std::stoi(vstring.substr(0,dot));
-                  if(dot == size_t(-1)) vstring = "";
+                  if(dot == std::string::npos) vstring = "";
                   else vstring = vstring.substr(dot+1, vstring.size()-dot-1);
                   if(!vstring.empty())
                     git_hash = vstring;
                 }
             }
         }
+      }
+      catch (const std::invalid_argument&)
+      {}
     }
     VersionInfo(const char* cstr) : VersionInfo(std::string(cstr)) { }
 

libsrc/interface/writevtk.cpp

@@ -0,0 +1,136 @@
+/*************************************
+ * Write Gmsh file
+ * First issue the 04/26/2004 by Paul CARRICO ([email protected])
+ * At the moment, the GMSH format is available for
+ * linear tetrahedron elements i.e. in 3D
+ * (based on Neutral Format)
+ *
+ * Second issue the 05/05/2004 by Paul CARRICO
+ * Thanks to Joachim Schoeberl for the correction of a minor bug
+ * the 2 initial Gmsh Format (i.e. volume format and surface format) are group together)
+ * in only one file
+ **************************************/
+
+#include <mystdlib.h>
+
+#include <myadt.hpp>
+#include <linalg.hpp>
+#include <csg.hpp>
+#include <meshing.hpp>
+
+namespace netgen
+{
+#include "writeuser.hpp"
+
+  extern MeshingParameters mparam;
+
+
+/*
+ *  VTK mesh format
+ *  points, elements, surface elements
+ */
+
+void WriteVtkFormat (const Mesh & mesh,
+                      const string & filename)
+{
+  ofstream outfile (filename.c_str());
+  outfile.precision(6);
+  outfile.setf (ios::fixed, ios::floatfield);
+  outfile.setf (ios::showpoint);
+
+  int np = mesh.GetNP();  /// number of point
+  int ne = mesh.GetNE();  /// number of element
+  int nse = mesh.GetNSE();  /// number of surface element (BC)
+
+  outfile << "# vtk DataFile Version 2.0\n";
+  outfile << "Created with netgen\n";
+  outfile << "ASCII\n";
+  outfile << "DATASET UNSTRUCTURED_GRID\n";
+
+  outfile << "POINTS " << np << " double\n";
+  for (int i=0; i<np; i++)
+  {
+  auto & p = mesh.Point(i+1);
+    outfile << p[0] << " " << p[1] << " " << p[2] << "\n";
+  }
+
+  std::vector<int> types;
+  std::vector<int> domains;
+  if (ne > 0)
+  {
+    unsigned int size = 0;
+    for (int i=0; i<ne; i++)
+      size += mesh.VolumeElement(i+1).GetNV() + 1; // only save "linear" corners
+
+    outfile << "CELLS " << ne << " " << size << "\n";
+    for (int i=0; i<ne; i++)
+    {
+      auto& el = mesh.VolumeElement(i+1);
+      domains.push_back(el.GetIndex());
+      switch (el.GetType())
+      {
+      case TET:
+      case TET10: // reorder to follow VTK convention & zero based indices
+        outfile << 4 << " " << el[0]-1 << " " << el[1]-1 << " " << el[3]-1 << " " << el[2]-1 << "\n";
+        types.push_back(10);
+        break;
+      case PRISM: // reorder to follow VTK convention & zero based indices
+        outfile << 6 << " "
+          << el[0]-1 << " " << el[2]-1 << " " << el[1]-1 << " " 
+          << el[3]-1 << " " << el[5]-1 << " " << el[4]-1 << "\n";
+        types.push_back(13);
+        break;
+      default:
+        throw ngcore::Exception("Unexpected element type");
+        break;
+      }
+    }
+  }
+  else
+  {
+    unsigned int size = 0;
+    for (int i=0; i<nse; i++)
+      size += mesh.SurfaceElement(i+1).GetNV() + 1;
+
+    outfile << "CELLS " << nse << " " << size << "\n";
+    for (int i=0; i<nse; i++)
+    {
+      auto& el = mesh.SurfaceElement(i+1);
+      domains.push_back(el.GetIndex());
+      switch (el.GetType())
+      {
+      case TRIG:
+      case TRIG6:
+        outfile << 3 << " " << el[0]-1 << " " << el[1]-1 << " " << el[2]-1 << "\n";
+        types.push_back(5);
+        break;
+      case QUAD:
+        outfile << 4 << " " << el[0]-1 << " " << el[1]-1 << " " << el[2]-1 << " " << el[3]-1 << "\n";
+        types.push_back(9);
+        break;
+      default:
+        throw ngcore::Exception("Unexpected element type");
+      break;
+      }
+    }
+  }
+
+  outfile << "CELL_TYPES " << types.size() << "\n";
+  for (auto type_id: types)
+  {
+    outfile << type_id << "\n";
+  }
+
+  outfile << "CELL_DATA " << domains.size() << "\n";
+  outfile << "SCALARS scalars int 1\n";
+  outfile << "LOOKUP_TABLE default\n";
+  for (auto id: domains)
+  {
+    outfile << id << "\n";
+  }
+
+  outfile.close();
+}
+}
+
+