Changes in src/molecules.hpp [2746be:437922]

File:

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

src/molecules.hpp

@@ -69 +69 @@
 #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 **********************************/
 
@@ -114 +117 @@
   element *type;
 };
-
-
 
 /** Single atom.
@@ -129 +130 @@
     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
@@ -144 +145 @@
   ~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();
@@ -161 +162 @@
 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()
@@ -210 +211 @@
     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);
@@ -225 +230 @@
   bool AddAtom(atom *pointer);
   bool RemoveAtom(atom *pointer);
+  bool UnlinkAtom(atom *pointer);
   bool CleanupMolecule();
 
@@ -245 +251 @@
   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(char *file, double delta_t, bool IsAngstroem);
+  void PrincipalAxisSystem(ofstream *out, bool DoRotate);
+  double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
+  Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
+
+  bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
 
   bool CheckBounds(const Vector *x) const;
@@ -300 +310 @@
   /// -# 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);
@@ -328 +338 @@
 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);
+  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:
@@ -456 +475 @@
   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;