Changeset f39735 for molecuilder/src/molecules.hpp

Timestamp:

Jul 23, 2009, 1:45:24 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

47548d

Parents:

560995 (diff), 1b2aa1 (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.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• molecuilder/src/molecules.hpp (modified) (11 diffs)

molecuilder/src/molecules.hpp

@@ -71 +71 @@
 #define DistanceMultiMapPair pair <double, pair < PointMap::iterator, PointMap::iterator> >
 
+#define MoleculeList list <molecule *>
+#define MoleculeListTest pair <MoleculeList::iterator, bool>
+
 /******************************** Some small functions and/or structures **********************************/
 
@@ -116 +119 @@
   element *type;
 };
-
-
 
 /** Single atom.
@@ -131 +132 @@
     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
+    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
@@ -146 +147 @@
   ~atom();
 
-  bool Output(int ElementNo, int AtomNo, ofstream *out) const;
+  bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
   bool OutputXYZLine(ofstream *out) const;
   atom *GetTrueFather();
@@ -163 +164 @@
 class bond {
   public:
-        atom *leftatom;         //!< first bond partner
-        atom *rightatom;        //!< second bond partner
+    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 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()
@@ -218 +219 @@
     int MDSteps;        //!< The number of MD steps in Trajectories
     int *NumberOfBondsPerAtom;  //!< Number of Bonds each atom has
-    int AtomCount;                                      //!< number of atoms, brought up-to-date by CountAtoms()
-    int BondCount;                                      //!< number of atoms, brought up-to-date by CountBonds()
+    int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
+    int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
     int ElementCount;       //!< how many unique elements are therein
     int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
-    int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
+    int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
     int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
     int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
     double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
+    bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
+    Vector Center;      //!< Center of molecule in a global box
+    char name[MAXSTRINGSIZE];         //!< arbitrary name
+    int IndexNr;        //!< index of molecule in a MoleculeListClass
 
   molecule(periodentafel *teil);
@@ -233 +238 @@
   bool AddAtom(atom *pointer);
   bool RemoveAtom(atom *pointer);
+  bool UnlinkAtom(atom *pointer);
   bool CleanupMolecule();
 
@@ -253 +259 @@
   bool CenterInBox(ofstream *out, Vector *BoxLengths);
   void CenterEdge(ofstream *out, Vector *max);
-  void CenterOrigin(ofstream *out, Vector *max);
-  void CenterGravity(ofstream *out, Vector *max);
+  void CenterOrigin(ofstream *out);
+  void CenterPeriodic(ofstream *out);
+  void CenterAtVector(ofstream *out, Vector *newcenter);
   void Translate(const Vector *x);
   void Mirror(const Vector *x);
   void Align(Vector *n);
   void Scale(double **factor);
-  void DetermineCenter(Vector &center);
+  void DeterminePeriodicCenter(Vector &center);
   Vector * DetermineCenterOfGravity(ofstream *out);
   Vector * DetermineCenterOfAll(ofstream *out);
+  void SetNameFromFilename(const char *filename);
   void SetBoxDimension(Vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);
   void ScanForPeriodicCorrection(ofstream *out);
-        void PrincipalAxisSystem(ofstream *out, bool DoRotate);
-        double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
-        
   bool VerletForceIntegration(ofstream *out, char *file, config &configuration);
   void Thermostats(config &configuration, double ActualTemp, int Thermostat);
+  void PrincipalAxisSystem(ofstream *out, bool DoRotate);
+  double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
+  Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
+
 
   double ConstrainedPotential(ofstream *out, atom **permutation, int start, int end, double *constants, bool IsAngstroem);
@@ -315 +324 @@
   /// -# BOSSANOVA
   void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
-        int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
+  int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
   bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
   molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
@@ -343 +352 @@
 class MoleculeListClass {
   public:
-    molecule **ListOfMolecules;   //!< pointer list of fragment molecules to check for equality
-    int NumberOfMolecules;        //!< Number of entries in \a **FragmentList and of to be returned one.
-    int NumberOfTopAtoms;         //!< Number of atoms in the molecule from which all fragments originate
+    MoleculeList ListOfMolecules; //!< List of the contained molecules
+    int MaxIndex;
 
   MoleculeListClass();
-  MoleculeListClass(int Num, int NumAtoms);
   ~MoleculeListClass();
 
-  /// Output configs.
   bool AddHydrogenCorrection(ofstream *out, char *path);
   bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
-  bool OutputConfigForListOfFragments(ofstream *out, const char *fragmentprefix, config *configuration, int *SortIndex, bool DoPeriodic, bool DoCentering);
+  void insert(molecule *mol);
+  molecule * ReturnIndex(int index);
+  bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
+  int NumberOfActiveMolecules();
+  void Enumerate(ofstream *out);
   void Output(ofstream *out);
+
+  // merging of molecules
+  bool SimpleMerge(molecule *mol, molecule *srcmol);
+  bool SimpleAdd(molecule *mol, molecule *srcmol);
+  bool SimpleMultiMerge(molecule *mol, int *src, int N);
+  bool SimpleMultiAdd(molecule *mol, int *src, int N);
+  bool ScatterMerge(molecule *mol, int *src, int N);
+  bool EmbedMerge(molecule *mol, molecule *srcmol);
 
   private:
@@ -479 +497 @@
   bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
   bool SaveMPQC(const char *filename, molecule *mol) const;
-  void Edit(molecule *mol);
+  void Edit();
   bool GetIsAngstroem() const;
   char *GetDefaultPath() const;