Changeset f4a346 for molecuilder/src/molecules.hpp

Timestamp:

Aug 3, 2009, 8:21:05 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

04dcc0

Parents:

0e2190 (diff), eb167d (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'TesselationRefactoring' into ConcaveHull

Conflicts:

molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/linkedcell.cpp
molecuilder/src/linkedcell.hpp
molecuilder/src/molecules.hpp

All of Saskia Metzler's new function were transfered from boundary.cpp to tesselation.cpp and the changes due to TesselPoint, LinkedCell and so on incorporated.

File:

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

molecuilder/src/molecules.hpp

@@ -18 +18 @@
 #include <gsl/gsl_randist.h>
 
-// STL headers
+//// STL headers
 #include <map>
 #include <set>
@@ -25 +25 @@
 #include <vector>
 
-#include "helpers.hpp"
+#include "atom.hpp"
+#include "bond.hpp"
+#include "element.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;
 class MoleculeLeafClass;
 class MoleculeListClass;
-class Verbose;
-class Tesselation;
 
 /******************************** Some definitions for easier reading **********************************/
@@ -50 +49 @@
 #define GraphTestPair pair<Graph::iterator, bool>
 
+#define MoleculeList list <molecule *>
+#define MoleculeListTest pair <MoleculeList::iterator, bool>
+
 #define DistancePair pair < double, atom* >
 #define DistanceMap multimap < double, atom* >
 #define DistanceTestPair pair < DistanceMap::iterator, bool>
 
-#define Boundaries map <double, DistancePair >
-#define BoundariesPair pair<double, DistancePair >
-#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>
-
-#define LinkedAtoms list <atom *>
+
+//#define LinkedAtoms list <atom *>
 
 /******************************** Some small functions and/or structures **********************************/
@@ -125 +105 @@
 };
 
-/** 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(const 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 
 enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover };   //!< Thermostat names for output
@@ -210 +112 @@
  * Class incorporates number of types
  */
-class molecule {
+class molecule : public PointCloud {
   public:
     double cell_size[6];//!< cell size
@@ -234 +136 @@
     char name[MAXSTRINGSIZE];         //!< arbitrary name
     int IndexNr;        //!< index of molecule in a MoleculeListClass
+    class Tesselation *TesselStruct;
 
   molecule(periodentafel *teil);
-  ~molecule();
+  virtual ~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 +264 @@
   private:
   int last_atom;      //!< number given to last atom
+  atom *InternalPointer;  //!< internal pointer for PointCloud
 };
 
@@ -423 +338 @@
 
 
-/** The config file.
- * The class contains all parameters that control a dft run also functions to load and save.
- */
-class config {
-  public:
-    int PsiType;
-    int MaxPsiDouble;
-    int PsiMaxNoUp;
-    int PsiMaxNoDown;
-    int MaxMinStopStep;
-    int InitMaxMinStopStep;
-    int ProcPEGamma;
-    int ProcPEPsi;
-    char *configpath;
-    char *configname;
-    bool FastParsing;
-    double Deltat;
-    string basis;
-
-    char *databasepath;
-
-    int DoConstrainedMD;
-    int MaxOuterStep;
-    int Thermostat;
-    int *ThermostatImplemented;
-    char **ThermostatNames;
-    double TempFrequency;
-    double alpha;
-    double HooverMass;
-    double TargetTemp;
-    int ScaleTempStep;
-    
-  private:
-    char *mainname;
-    char *defaultpath;
-    char *pseudopotpath;
-
-    int DoOutVis;
-    int DoOutMes;
-    int DoOutNICS;
-    int DoOutOrbitals;
-    int DoOutCurrent;
-    int DoFullCurrent;
-    int DoPerturbation;
-    int DoWannier;
-    int CommonWannier;
-    double SawtoothStart;
-    int VectorPlane;
-    double VectorCut;
-    int UseAddGramSch;
-    int Seed;
-
-    int OutVisStep;
-    int OutSrcStep;
-    int MaxPsiStep;
-    double EpsWannier;
-
-    int MaxMinStep;
-    double RelEpsTotalEnergy;
-    double RelEpsKineticEnergy;
-    int MaxMinGapStopStep;
-    int MaxInitMinStep;
-    double InitRelEpsTotalEnergy;
-    double InitRelEpsKineticEnergy;
-    int InitMaxMinGapStopStep;
-
-    //double BoxLength[NDIM*NDIM];
-
-    double ECut;
-    int MaxLevel;
-    int RiemannTensor;
-    int LevRFactor;
-    int RiemannLevel;
-    int Lev0Factor;
-    int RTActualUse;
-    int AddPsis;
-
-    double RCut;
-    int StructOpt;
-    int IsAngstroem;
-    int RelativeCoord;
-    int MaxTypes;
-
-
-  int ParseForParameter(int verbose, ifstream *file, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
-  int ParseForParameter(int verbose, struct ConfigFileBuffer *FileBuffer, const char *name, int sequential, int const xth, int const yth, int type, void *value, int repetition, int critical);
-
-  public:
-  config();
-  ~config();
-
-  int TestSyntax(char *filename, periodentafel *periode, molecule *mol);
-  void Load(char *filename, periodentafel *periode, molecule *mol);
-  void LoadOld(char *filename, periodentafel *periode, molecule *mol);
-  void RetrieveConfigPathAndName(string filename);
-  bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
-  bool SaveMPQC(const char *filename, molecule *mol) const;
-  void Edit();
-  bool GetIsAngstroem() const;
-  char *GetDefaultPath() const;
-  void SetDefaultPath(const char *path);
-  void InitThermostats(ifstream *source);
-};
-
 #endif /*MOLECULES_HPP_*/