Changes in / [23e09b:6d4a76]

Location:

src

Files:

• #border.cpp# (deleted)
• #makefile# (deleted)
• #molecules.hpp# (deleted)
• boundary.cpp (modified) (10 diffs)
• boundary.hpp (modified) (2 diffs)
• builder.cpp (modified) (2 diffs)

src/boundary.cpp

@@ -2 +2 @@
 #include "boundary.hpp"
 
-#define DEBUG 0
+#define DEBUG 1
+#define DoTecplotOutput 0
+#define DoRaster3DOutput 1
+#define TecplotSuffix ".dat"
+#define Raster3DSuffix ".r3d"
 
 // ======================================== Points on Boundary =================================
@@ -564 +568 @@
 }
 ;
+
+/** Creates the objects in a raster3d file (renderable with a header.r3d)
+ * \param *out output stream for debugging
+ * \param *tecplot output stream for tecplot data
+ * \param *Tess Tesselation structure with constructed triangles
+ * \param *mol molecule structure with atom positions
+ */
+void write_raster3d_file(ofstream *out, ofstream *rasterfile, class Tesselation *Tess, class molecule *mol)
+{
+  atom *Walker = mol->start;
+  bond *Binder = mol->first;
+  int i;
+  Vector *center = mol->DetermineCenterOfAll(out);
+  if (rasterfile != NULL) {
+    //cout << Verbose(1) << "Writing Raster3D file ... ";
+    *rasterfile << "# Raster3D object description, created by MoleCuilder" << endl;
+    *rasterfile << "@header.r3d" << endl;
+    *rasterfile << "# All atoms as spheres" << endl;
+    while (Walker->next != mol->end) {
+      Walker = Walker->next;
+      *rasterfile << "2" << endl << "  "; // 2 is sphere type
+      for (i=0;i<NDIM;i++)
+        *rasterfile << Walker->x.x[i]+center->x[i] << " ";
+      *rasterfile << "\t0.1\t1. 1. 1." << endl; // radius 0.05 and white as colour
+    }
+
+    *rasterfile << "# All bonds as vertices" << endl;
+    while (Binder->next != mol->last) {
+      Binder = Binder->next;
+      *rasterfile << "3" << endl << "  "; // 2 is round-ended cylinder type
+      for (i=0;i<NDIM;i++)
+        *rasterfile << Binder->leftatom->x.x[i]+center->x[i] << " ";
+      *rasterfile << "\t0.03\t";
+      for (i=0;i<NDIM;i++)
+        *rasterfile << Binder->rightatom->x.x[i]+center->x[i] << " ";
+      *rasterfile << "\t0.03\t0. 0. 1." << endl; // radius 0.05 and blue as colour
+    }
+
+    *rasterfile << "# All tesselation triangles" << endl;
+    for (TriangleMap::iterator TriangleRunner = Tess->TrianglesOnBoundary.begin(); TriangleRunner != Tess->TrianglesOnBoundary.end(); TriangleRunner++) {
+      *rasterfile << "1" << endl << "  "; // 1 is triangle type
+      for (i=0;i<3;i++) { // print each node
+        for (int j=0;j<NDIM;j++)  // and for each node all NDIM coordinates
+          *rasterfile << TriangleRunner->second->endpoints[i]->node->x.x[j]+center->x[j] << " ";
+        *rasterfile << "\t";
+      }
+      *rasterfile << "1. 0. 0." << endl;  // red as colour
+      *rasterfile << "18" << endl << "  0.5 0.5 0.5" << endl; // 18 is transparency type for previous object
+    }
+  } else {
+    cerr << "ERROR: Given rasterfile is " << rasterfile << "." << endl;
+  }
+  delete(center);
+};
 
 /*
@@ -1923 +1981 @@
 /** This function finds a triangle to a line, adjacent to an existing one.
  * @param out   output stream for debugging
- * @param tecplot output stream for writing found triangles in TecPlot format
  * @param mol molecule structure with all atoms and bonds
  * @param Line current baseline to search from
@@ -1930 +1987 @@
  * @param N number of found triangles
  */
-void Tesselation::Find_next_suitable_triangle(ofstream *out, ofstream *tecplot,
+void Tesselation::Find_next_suitable_triangle(ofstream *out,
     molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T,
-    const double& RADIUS, int N)
+    const double& RADIUS, int N, const char *tempbasename)
 {
   cout << Verbose(1) << "Looking for next suitable triangle \n";
@@ -1939 +1996 @@
   Vector Chord;
   ofstream *tempstream = NULL;
-  char filename[255];
+  char NumberName[255];
+  double tmp;
+  //atom* Walker;
   atom* OldThirdPoint;
 
@@ -2008 +2067 @@
       cout << "Letzter Winkel bei " << TrianglesOnBoundaryCount << " Winkel ist " << Storage[2] << endl;
 
-
-  if ((TrianglesOnBoundaryCount % 1) == 0)
-    {
-    sprintf(filename, "testEnvelope-%d.dat", TriangleFilesWritten);
-    tempstream = new ofstream(filename, ios::trunc);
-    write_tecplot_file(out, tempstream, this, mol, TriangleFilesWritten++);
-    tempstream->close();
-    tempstream->flush();
-    delete(tempstream);
+  if ((TrianglesOnBoundaryCount % 10) == 0) {
+    sprintf(NumberName, "-%d", TriangleFilesWritten);
+    if (DoTecplotOutput) {
+      string NameofTempFile(tempbasename);
+      NameofTempFile.append(NumberName);
+      NameofTempFile.append(TecplotSuffix);
+      cout << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
+      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
+      write_tecplot_file(out, tempstream, this, mol, TriangleFilesWritten);
+      tempstream->close();
+      tempstream->flush();
+      delete(tempstream);
+    }
+    if (DoRaster3DOutput) {
+      string NameofTempFile(tempbasename);
+      NameofTempFile.append(NumberName);
+      NameofTempFile.append(Raster3DSuffix);
+      cout << Verbose(1) << "Writing temporary non convex hull to file " << NameofTempFile << ".\n";
+      tempstream = new ofstream(NameofTempFile.c_str(), ios::trunc);
+      write_raster3d_file(out, tempstream, this, mol);
+      tempstream->close();
+      tempstream->flush();
+      delete(tempstream);
+    }
+    if (DoTecplotOutput || DoRaster3DOutput)
+      TriangleFilesWritten++;
   }
 
-  if (TrianglesOnBoundaryCount >189 and TrianglesOnBoundaryCount < 200 )
-    {
-      cout << Verbose(1)
-          << "No new Atom found, triangle construction will crash" << endl;
-      write_tecplot_file(out, tecplot, this, mol, TriangleFilesWritten);
-      cout << "This is currently added candidate" << Opt_Candidate << endl;
-    }
-  // Konstruiere nun neues Dreieck am Ende der Liste der Dreiecke
+      // Konstruiere nun neues Dreieck am Ende der Liste der Dreiecke
 
   cout << " Optimal candidate is " << *Opt_Candidate << endl;
@@ -2229 +2298 @@
 ;
 
-void Find_non_convex_border(ofstream *out, ofstream *tecplot, molecule* mol)
+void Find_non_convex_border(ofstream *out, const char *filename, molecule* mol)
 {
   int N = 0;
@@ -2237 +2306 @@
   const double RADIUS = 6.;
   LineMap::iterator baseline;
+  cout << Verbose(0) << "Begin of Find_non_convex_border\n";
+  bool flag = false;  // marks whether we went once through all baselines without finding any without two triangles
   Tess->Find_starting_triangle(mol, RADIUS);
 
@@ -2245 +2316 @@
         {
           cout << Verbose(1) << "Begin of Tesselation ... " << endl;
-          Tess->Find_next_suitable_triangle(out, tecplot, mol,
+          Tess->Find_next_suitable_triangle(out, mol,
               *(baseline->second),
-              *(((baseline->second->triangles.begin()))->second), RADIUS, N); //the line is there, so there is a triangle, but only one.
+              *(((baseline->second->triangles.begin()))->second), RADIUS, N, filename); //the line is there, so there is a triangle, but only one.
+          flag = true;
           cout << Verbose(1) << "End of Tesselation ... " << endl;
         }
@@ -2259 +2331 @@
       baseline++;
     }
-  write_tecplot_file(out, tecplot, Tess, mol, -1);
-
-}
-;
+  cout << Verbose(1) << "Writing final tecplot file\n";
+  if (DoTecplotOutput) {
+    string Name(filename);
+    Name.append(TecplotSuffix);
+    ofstream tecplot(Name.c_str(), ios::trunc);
+    write_tecplot_file(out, &tecplot, Tess, mol, -1);
+    tecplot.close();
+  }
+  if (DoRaster3DOutput) {
+    string Name(filename);
+    Name.append(Raster3DSuffix);
+    ofstream raster(Name.c_str(), ios::trunc);
+    write_raster3d_file(out, &raster, Tess, mol);
+    raster.close();
+  }
+}
+;

src/boundary.hpp

@@ -86 +86 @@
     void AddTriangleToLines();
     void Find_starting_triangle(molecule* mol, const double RADIUS);
-    void Find_next_suitable_triangle(ofstream *out, ofstream *tecplot, molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, int N);
+    void Find_next_suitable_triangle(ofstream *out, molecule* mol, BoundaryLineSet &Line, BoundaryTriangleSet &T, const double& RADIUS, int N, const char *tempbasename);
 
     PointMap PointsOnBoundary;
@@ -111 +111 @@
 void PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol, double ClusterVolume, double celldensity);
 void Find_next_suitable_point(atom a, atom b, atom Candidate, int n, Vector *d1, Vector *d2, atom*& Opt_Candidate, double *Storage, const double RADIUS, molecule *mol, bool problem);
-void Find_non_convex_border(ofstream *out, ofstream *tecplot, molecule* mol);
+void Find_non_convex_border(ofstream *out, const char *filename, molecule* mol);
 
 

src/builder.cpp

@@ -1025 +1025 @@
                 else {
                         cout << Verbose(0) << "Evaluating npn-convex envelope.";
-                        ofstream *output = new ofstream(argv[argptr], ios::trunc);
                         cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
-                        Find_non_convex_border((ofstream *)&cout, output, mol);
-                        output->close();
-                        delete(output);
+                        Find_non_convex_border((ofstream *)&cout, argv[argptr], mol);
                         argptr+=1;
                         }
@@ -1037 +1034 @@
               if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag = 255;
-                cerr << "Not enough or invalid arguments given for storing tempature: -T <temperature file>" << endl;
+                cerr << "Not enough or invalid arguments given for storing temperature: -T <temperature file>" << endl;
               } else {
                 cout << Verbose(1) << "Storing temperatures in " << argv[argptr] << "." << endl;