Changeset 834ff3 for molecuilder/src/molecules.hpp

Timestamp:

Aug 3, 2009, 2:48:42 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

d8fce3, e78824

Parents:

4e4940

Message:

Huge refactoring of Tesselation routines, but not finished yet.

• new file tesselation.cpp with all of classes tesselation, Boundary..Set and CandidatesForTesselationOB
• new file tesselationhelper.cpp with all auxiliary functions.
• boundary.cpp just contains super functions, combininb molecule and Tesselation pointers
• new pointer molecule::TesselStruct
• PointMap, LineMap, TriangleMap DistanceMap have been moved from molecules.hpp to tesselation.hpp
• new abstract class PointCloud and TesselPoint
• atom inherits TesselPoint
• molecule inherits PointCloud (i.e. a set of TesselPoints) and implements all virtual functions for the chained list
• TriangleFilesWritten is thrown out, intermediate steps are written in find_nonconvex_border and not in find_next_triangle()
• LinkedCell class uses TesselPoint as its nodes, i.e. as long as any class inherits TesselPoint, it may make use of LinkedCell as well and a PointCloud is used to initialize
• class atom and bond definitions have been moved to own header files

NOTE: This is not bugfree yet. Tesselation of heptan produces way too many triangles, but runs without faults or leaks.

File:

• molecuilder/src/molecules.hpp (modified) (8 diffs)

molecuilder/src/molecules.hpp

@@ -25 +25 @@
 #include <vector>
 
+#include "atom.hpp"
+#include "bond.hpp"
 #include "helpers.hpp"
+#include "linkedcell.hpp"
 #include "parser.hpp"
 #include "periodentafel.hpp"
 #include "stackclass.hpp"
+#include "tesselation.hpp"
 #include "vector.hpp"
 
-class atom;
-class bond;
 class config;
 class molecule;
@@ -38 +40 @@
 class MoleculeListClass;
 class Verbose;
-class Tesselation;
 
 /******************************** Some definitions for easier reading **********************************/
@@ -58 +59 @@
 #define BoundariesTestPair pair< Boundaries::iterator, bool>
 
-#define PointMap map < int, class BoundaryPointSet * >
-#define PointPair pair < int, class BoundaryPointSet * >
-#define PointTestPair pair < PointMap::iterator, bool >
-#define CandidateList list <class CandidateForTesselation *>
-
-#define LineMap multimap < int, class BoundaryLineSet * >
-#define LinePair pair < int, class BoundaryLineSet * >
-#define LineTestPair pair < LineMap::iterator, bool >
-
-#define TriangleMap map < int, class BoundaryTriangleSet * >
-#define TrianglePair pair < int, class BoundaryTriangleSet * >
-#define TriangleTestPair pair < TrianglePair::iterator, bool >
-
-#define DistanceMultiMap multimap <double, pair < PointMap::iterator, PointMap::iterator> >
-#define DistanceMultiMapPair pair <double, pair < PointMap::iterator, PointMap::iterator> >
-
 #define MoleculeList list <molecule *>
 #define MoleculeListTest pair <MoleculeList::iterator, bool>
@@ -125 +110 @@
 };
 
-/** Single atom.
- * Class incoporates position, type
- */
-class atom {
-  public:
-    Vector x;       //!< coordinate array of atom, giving position within cell
-    Vector v;       //!< velocity array of atom
-    element *type;  //!< pointing to element
-    atom *previous; //!< previous atom in molecule list
-    atom *next;     //!< next atom in molecule list
-    atom *father;   //!< In many-body bond order fragmentations points to originating atom
-    atom *Ancestor; //!< "Father" in Depth-First-Search
-    char *Name;      //!< unique name used during many-body bond-order fragmentation
-    int FixedIon;   //!< config variable that states whether forces act on the ion or not
-    int *sort;      //!< sort criteria
-    int nr;         //!< continuous, unique number
-    int GraphNr;      //!< unique number, given in DepthFirstSearchAnalysis()
-    int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
-    int LowpointNr; //!< needed in DepthFirstSearchAnalysis() to detect nonseparable components, is the lowest possible number of an atom to reach via tree edges only followed by at most one back edge.
-    bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
-    bool IsCyclic;        //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
-    unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
-    bool MaxOrder;  //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
-
-  atom();
-  atom(class atom *pointer);
-  ~atom();
-
-  bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
-  bool OutputXYZLine(ofstream *out) const;
-  atom *GetTrueFather();
-  bool Compare(atom &ptr);
-
-  private:
-};
-
-ostream & operator << (ostream &ost, const atom &a);
-
-/** Bonds between atoms.
- * Class incorporates bonds between atoms in a molecule,
- * used to derive tge fragments in many-body bond order
- * calculations.
- */
-class bond {
-  public:
-    atom *leftatom;    //!< first bond partner
-    atom *rightatom;  //!< second bond partner
-    bond *previous; //!< previous atom in molecule list
-    bond *next;     //!< next atom in molecule list
-    int HydrogenBond;  //!< Number of hydrogen atoms in the bond
-    int BondDegree;    //!< single, double, triple, ... bond
-    int nr;           //!< unique number in a molecule, updated by molecule::CreateAdjacencyList()
-    bool Cyclic;      //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
-    enum EdgeType Type;//!< whether this is a tree or back edge
-
-  atom * GetOtherAtom(atom *Atom) const;
-  bond * GetFirstBond();
-  bond * GetLastBond();
-
-  bool MarkUsed(enum Shading color);
-  enum Shading IsUsed();
-  void ResetUsed();
-  bool Contains(const atom *ptr);
-  bool Contains(const int nr);
-
-  bond();
-  bond(atom *left, atom *right);
-  bond(atom *left, atom *right, int degree);
-  bond(atom *left, atom *right, int degree, int number);
-  ~bond();
-
-  private:
-    enum Shading Used;        //!< marker in depth-first search, DepthFirstSearchAnalysis()
-};
-
-
-ostream & operator << (ostream &ost, const bond &b);
 
 #define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
@@ -210 +118 @@
  * Class incorporates number of types
  */
-class molecule {
+class molecule : public PointCloud {
   public:
     double cell_size[6];//!< cell size
@@ -234 +142 @@
     char name[MAXSTRINGSIZE];         //!< arbitrary name
     int IndexNr;        //!< index of molecule in a MoleculeListClass
+    class Tesselation *TesselStruct;
 
   molecule(periodentafel *teil);
   ~molecule();
+
+  // re-definition of virtual functions from PointCloud
+  Vector *GetCenter(ofstream *out);
+  TesselPoint *GetPoint();
+  TesselPoint *GetTerminalPoint();
+  void GoToNext();
+  void GoToPrevious();
+  void GoToFirst();
+  void GoToLast();
+  bool IsEmpty();
+  bool IsLast();
 
   /// remove atoms from molecule.
@@ -350 +270 @@
   private:
   int last_atom;      //!< number given to last atom
+  atom *InternalPointer;  //!< internal pointer for PointCloud
 };
 
@@ -524 +445 @@
   char *GetDefaultPath() const;
   void SetDefaultPath(const char *path);
-  void InitThermostats(ifstream *source);
+  void InitThermostats(class ConfigFileBuffer *fb);
 };