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  • src/molecules.hpp

    r437922 rca2587  
    7676struct KeyCompare
    7777{
    78   bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
     78        bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
    7979};
    8080
    8181struct Trajectory
    8282{
    83   vector<Vector> R;  //!< position vector
    84   vector<Vector> U;  //!< velocity vector
    85   vector<Vector> F;  //!< last force vector
    86   atom *ptr;        //!< pointer to atom whose trajectory we contain
    87 };
    88 
    89 //bool operator < (KeySet SubgraphA, KeySet SubgraphB);  //note: this declaration is important, otherwise normal < is used (producing wrong order)
     83        vector<Vector> R;       //!< position vector
     84        vector<Vector> U;       //!< velocity vector
     85        vector<Vector> F;       //!< last force vector
     86        atom *ptr;                              //!< pointer to atom whose trajectory we contain
     87};
     88
     89//bool operator < (KeySet SubgraphA, KeySet SubgraphB);  //note: this declaration is important, otherwise normal < is used (producing wrong order)
    9090inline void InsertFragmentIntoGraph(ofstream *out, struct UniqueFragments *Fragment); // Insert a KeySet into a Graph
    91 inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter);  // Insert all KeySet's in a Graph into another Graph
     91inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter);    // Insert all KeySet's in a Graph into another Graph
    9292int CompareDoubles (const void * a, const void * b);
    9393
    … …  
    9797
    9898// some algebraic matrix stuff
    99 #define RDET3(a) ((a)[0]*(a)[4]*(a)[8] + (a)[3]*(a)[7]*(a)[2] + (a)[6]*(a)[1]*(a)[5] - (a)[2]*(a)[4]*(a)[6] - (a)[5]*(a)[7]*(a)[0] - (a)[8]*(a)[1]*(a)[3])  //!< hard-coded determinant of a 3x3 matrix
    100 #define RDET2(a0,a1,a2,a3) ((a0)*(a3)-(a1)*(a2))                      //!< hard-coded determinant of a 2x2 matrix
     99#define RDET3(a) ((a)[0]*(a)[4]*(a)[8] + (a)[3]*(a)[7]*(a)[2] + (a)[6]*(a)[1]*(a)[5] - (a)[2]*(a)[4]*(a)[6] - (a)[5]*(a)[7]*(a)[0] - (a)[8]*(a)[1]*(a)[3])      //!< hard-coded determinant of a 3x3 matrix
     100#define RDET2(a0,a1,a2,a3) ((a0)*(a3)-(a1)*(a2))                                                                                        //!< hard-coded determinant of a 2x2 matrix
    101101
    102102
    … …  
    104104 */
    105105struct LSQ_params {
    106   Vector **vectors;
    107   int num;
     106        Vector **vectors;
     107        int num;
    108108};
    109109
    … …  
    113113 */
    114114struct lsq_params {
    115   gsl_vector *x;
    116   const molecule *mol;
    117   element *type;
     115        gsl_vector *x;
     116        const molecule *mol;
     117        element *type;
    118118};
    119119
    … …  
    122122 */
    123123class atom {
    124   public:
    125     Vector x;      //!< coordinate array of atom, giving position within cell
    126     Vector v;      //!< velocity array of atom
    127     element *type;  //!< pointing to element
    128     atom *previous; //!< previous atom in molecule list
    129     atom *next;    //!< next atom in molecule list
    130     atom *father;  //!< In many-body bond order fragmentations points to originating atom
    131     atom *Ancestor; //!< "Father" in Depth-First-Search
    132     char *Name;      //!< unique name used during many-body bond-order fragmentation
    133     int FixedIon;  //!< config variable that states whether forces act on the ion or not
    134     int *sort;      //!< sort criteria
    135     int nr;        //!< continuous, unique number
    136     int GraphNr;      //!< unique number, given in DepthFirstSearchAnalysis()
    137     int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
    138     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.
    139     bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
    140     bool IsCyclic;        //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
    141     unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
    142     bool MaxOrder;  //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
    143 
    144   atom();
    145   ~atom();
    146 
    147   bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
    148   bool OutputXYZLine(ofstream *out) const;
    149   atom *GetTrueFather();
    150   bool Compare(atom &ptr);
    151 
    152   private:
     124        public:
     125                Vector x;                        //!< coordinate array of atom, giving position within cell
     126                Vector v;                        //!< velocity array of atom
     127                element *type;  //!< pointing to element
     128                atom *previous; //!< previous atom in molecule list
     129                atom *next;              //!< next atom in molecule list
     130                atom *father;    //!< In many-body bond order fragmentations points to originating atom
     131                atom *Ancestor; //!< "Father" in Depth-First-Search
     132                char *Name;                     //!< unique name used during many-body bond-order fragmentation
     133                int FixedIon;    //!< config variable that states whether forces act on the ion or not
     134                int *sort;                      //!< sort criteria
     135                int nr;                          //!< continuous, unique number
     136                int GraphNr;                    //!< unique number, given in DepthFirstSearchAnalysis()
     137                int *ComponentNr;//!< belongs to this nonseparable components, given in DepthFirstSearchAnalysis() (if more than one, then is SeparationVertex)
     138                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.
     139                bool SeparationVertex; //!< whether this atom separates off subsets of atoms or not, determined in DepthFirstSearchAnalysis()
     140                bool IsCyclic;                          //!< whether atom belong to as cycle or not, determined in DepthFirstSearchAnalysis()
     141                unsigned char AdaptiveOrder;    //!< current present bond order at site (0 means "not set")
     142                bool MaxOrder;  //!< whether this atom as a root in fragmentation still creates more fragments on higher orders or not
     143
     144        atom();
     145        ~atom();
     146
     147        bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
     148        bool OutputXYZLine(ofstream *out) const;
     149        atom *GetTrueFather();
     150        bool Compare(atom &ptr);
     151
     152        private:
    153153};
    154154
    … …  
    161161 */
    162162class bond {
    163   public:
    164     atom *leftatom;    //!< first bond partner
    165     atom *rightatom;  //!< second bond partner
    166     bond *previous; //!< previous atom in molecule list
    167     bond *next;    //!< next atom in molecule list
    168     int HydrogenBond;  //!< Number of hydrogen atoms in the bond
    169     int BondDegree;    //!< single, double, triple, ... bond
    170     int nr;          //!< unique number in a molecule, updated by molecule::CreateAdjacencyList()
    171     bool Cyclic;      //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
    172     enum EdgeType Type;//!< whether this is a tree or back edge
    173 
    174   atom * GetOtherAtom(atom *Atom) const;
    175   bond * GetFirstBond();
    176   bond * GetLastBond();
    177 
    178   bool MarkUsed(enum Shading color);
    179   enum Shading IsUsed();
    180   void ResetUsed();
    181   bool Contains(const atom *ptr);
    182   bool Contains(const int nr);
    183 
    184   bond();
    185   bond(atom *left, atom *right);
    186   bond(atom *left, atom *right, int degree);
    187   bond(atom *left, atom *right, int degree, int number);
    188   ~bond();
    189 
    190   private:
    191     enum Shading Used;        //!< marker in depth-first search, DepthFirstSearchAnalysis()
     163        public:
     164                atom *leftatom;         //!< first bond partner
     165                atom *rightatom;        //!< second bond partner
     166                bond *previous; //!< previous atom in molecule list
     167                bond *next;              //!< next atom in molecule list
     168                int HydrogenBond;       //!< Number of hydrogen atoms in the bond
     169                int BondDegree;         //!< single, double, triple, ... bond
     170                int nr;                                  //!< unique number in a molecule, updated by molecule::CreateAdjacencyList()
     171                bool Cyclic;                    //!< flag whether bond is part of a cycle or not, given in DepthFirstSearchAnalysis()
     172                enum EdgeType Type;//!< whether this is a tree or back edge
     173
     174        atom * GetOtherAtom(atom *Atom) const;
     175        bond * GetFirstBond();
     176        bond * GetLastBond();
     177
     178        bool MarkUsed(enum Shading color);
     179        enum Shading IsUsed();
     180        void ResetUsed();
     181        bool Contains(const atom *ptr);
     182        bool Contains(const int nr);
     183
     184        bond();
     185        bond(atom *left, atom *right);
     186        bond(atom *left, atom *right, int degree);
     187        bond(atom *left, atom *right, int degree, int number);
     188        ~bond();
     189
     190        private:
     191                enum Shading Used;                              //!< marker in depth-first search, DepthFirstSearchAnalysis()
    192192};
    193193
    … …  
    200200 */
    201201class molecule {
    202   public:
    203     double cell_size[6];//!< cell size
    204     periodentafel *elemente; //!< periodic table with each element
    205     atom *start;        //!< start of atom list
    206     atom *end;          //!< end of atom list
    207     bond *first;        //!< start of bond list
    208     bond *last;         //!< end of bond list
    209     bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
    210     map<atom *, struct Trajectory> Trajectories; //!< contains old trajectory points
    211     int MDSteps;        //!< The number of MD steps in Trajectories
    212     int *NumberOfBondsPerAtom;  //!< Number of Bonds each atom has
    213     int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
    214     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
    215     int ElementCount;       //!< how many unique elements are therein
    216     int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
    217     int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
    218     int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
    219     int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
    220     double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
    221     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
    222     Vector Center;      //!< Center of molecule in a global box
    223     char name[MAXSTRINGSIZE];         //!< arbitrary name
    224     int IndexNr;        //!< index of molecule in a MoleculeListClass
    225 
    226   molecule(periodentafel *teil);
    227   ~molecule();
    228 
    229   /// remove atoms from molecule.
    230   bool AddAtom(atom *pointer);
    231   bool RemoveAtom(atom *pointer);
    232   bool UnlinkAtom(atom *pointer);
    233   bool CleanupMolecule();
    234 
    235   /// Add/remove atoms to/from molecule.
    236   atom * AddCopyAtom(atom *pointer);
    237   bool AddXYZFile(string filename);
    238   bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
    239   bond * AddBond(atom *first, atom *second, int degree);
    240   bool RemoveBond(bond *pointer);
    241   bool RemoveBonds(atom *BondPartner);
    242 
    243   /// Find atoms.
    244   atom * FindAtom(int Nr) const;
    245   atom * AskAtom(string text);
    246 
    247   /// Count and change present atoms' coordination.
    248   void CountAtoms(ofstream *out);
    249   void CountElements();
    250   void CalculateOrbitals(class config &configuration);
    251   bool CenterInBox(ofstream *out, Vector *BoxLengths);
    252   void CenterEdge(ofstream *out, Vector *max);
    253   void CenterOrigin(ofstream *out);
    254   void CenterPeriodic(ofstream *out);
    255   void CenterAtVector(ofstream *out, Vector *newcenter);
    256   void Translate(const Vector *x);
    257   void Mirror(const Vector *x);
    258   void Align(Vector *n);
    259   void Scale(double **factor);
    260   void DeterminePeriodicCenter(Vector &center);
    261   Vector * DetermineCenterOfGravity(ofstream *out);
    262   Vector * DetermineCenterOfAll(ofstream *out);
    263   void SetNameFromFilename(const char *filename);
    264   void SetBoxDimension(Vector *dim);
    265   double * ReturnFullMatrixforSymmetric(double *cell_size);
    266   void ScanForPeriodicCorrection(ofstream *out);
    267   void PrincipalAxisSystem(ofstream *out, bool DoRotate);
    268   double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
    269   Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
    270 
    271   bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
    272 
    273   bool CheckBounds(const Vector *x) const;
    274   void GetAlignvector(struct lsq_params * par) const;
    275 
    276   /// Initialising routines in fragmentation
    277   void CreateAdjacencyList2(ofstream *out, ifstream *output);
    278   void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
    279   void CreateListOfBondsPerAtom(ofstream *out);
    280 
    281   // Graph analysis
    282   MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
    283   void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
    284   bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
    285   bond * FindNextUnused(atom *vertex);
    286   void SetNextComponentNumber(atom *vertex, int nr);
    287   void InitComponentNumbers();
    288   void OutputComponentNumber(ofstream *out, atom *vertex);
    289   void ResetAllBondsToUnused();
    290   void ResetAllAtomNumbers();
    291   int CountCyclicBonds(ofstream *out);
    292   bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
    293   string GetColor(enum Shading color);
    294 
    295   molecule *CopyMolecule();
    296 
    297   /// Fragment molecule by two different approaches:
    298   int FragmentMolecule(ofstream *out, int Order, config *configuration);
    299   bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
    300   bool StoreAdjacencyToFile(ofstream *out, char *path);
    301   bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
    302   bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
    303   bool StoreOrderAtSiteFile(ofstream *out, char *path);
    304   bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
    305   bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
    306   bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
    307   bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
    308   bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
    309   void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
    310   /// -# BOSSANOVA
    311   void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
    312   int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
    313   bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
    314   molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
    315   void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
    316   int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
    317   int GuesstimateFragmentCount(ofstream *out, int order);
    318 
    319   // Recognize doubly appearing molecules in a list of them
    320   int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
    321   int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
    322 
    323   // Output routines.
    324   bool Output(ofstream *out);
    325   bool OutputTrajectories(ofstream *out);
    326   void OutputListOfBonds(ofstream *out) const;
    327   bool OutputXYZ(ofstream *out) const;
    328   bool OutputTrajectoriesXYZ(ofstream *out);
    329   bool Checkout(ofstream *out) const;
    330   bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
    331 
    332   private:
    333   int last_atom;      //!< number given to last atom
     202        public:
     203                double cell_size[6];//!< cell size
     204                periodentafel *elemente; //!< periodic table with each element
     205                atom *start;                            //!< start of atom list
     206                atom *end;                                      //!< end of atom list
     207                bond *first;                            //!< start of bond list
     208                bond *last;                              //!< end of bond list
     209                bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
     210                map<atom *, struct Trajectory> Trajectories; //!< contains old trajectory points
     211                int MDSteps;                            //!< The number of MD steps in Trajectories
     212                int *NumberOfBondsPerAtom;      //!< Number of Bonds each atom has
     213                int AtomCount;                                  //!< number of atoms, brought up-to-date by CountAtoms()
     214                int BondCount;                                  //!< number of atoms, brought up-to-date by CountBonds()
     215                int ElementCount;                        //!< how many unique elements are therein
     216                int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
     217                int NoNonHydrogen;      //!< number of non-hydrogen atoms in molecule
     218                int NoNonBonds;          //!< number of non-hydrogen bonds in molecule
     219                int NoCyclicBonds;      //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
     220                double BondDistance;    //!< typical bond distance used in CreateAdjacencyList() and furtheron
     221                bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
     222                Vector Center;      //!< Center of molecule in a global box
     223                char name[MAXSTRINGSIZE];         //!< arbitrary name
     224                int IndexNr;        //!< index of molecule in a MoleculeListClass
     225
     226        molecule(periodentafel *teil);
     227        ~molecule();
     228
     229        /// remove atoms from molecule.
     230        bool AddAtom(atom *pointer);
     231        bool RemoveAtom(atom *pointer);
     232        bool UnlinkAtom(atom *pointer);
     233        bool CleanupMolecule();
     234
     235        /// Add/remove atoms to/from molecule.
     236        atom * AddCopyAtom(atom *pointer);
     237        bool AddXYZFile(string filename);
     238        bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
     239        bond * AddBond(atom *first, atom *second, int degree);
     240        bool RemoveBond(bond *pointer);
     241        bool RemoveBonds(atom *BondPartner);
     242
     243        /// Find atoms.
     244        atom * FindAtom(int Nr) const;
     245        atom * AskAtom(string text);
     246
     247        /// Count and change present atoms' coordination.
     248        void CountAtoms(ofstream *out);
     249        void CountElements();
     250        void CalculateOrbitals(class config &configuration);
     251        bool CenterInBox(ofstream *out, Vector *BoxLengths);
     252        void CenterEdge(ofstream *out, Vector *max);
     253        void CenterOrigin(ofstream *out, Vector *max);
     254        void CenterGravity(ofstream *out, Vector *max);
     255        void Translate(const Vector *x);
     256        void Mirror(const Vector *x);
     257        void Align(Vector *n);
     258        void Scale(double **factor);
     259        void DetermineCenter(Vector &center);
     260        Vector * DetermineCenterOfGravity(ofstream *out);
     261        Vector * DetermineCenterOfAll(ofstream *out);
     262        void SetNameFromFilename(char *filename);
     263        void SetBoxDimension(Vector *dim);
     264        double * ReturnFullMatrixforSymmetric(double *cell_size);
     265        void ScanForPeriodicCorrection(ofstream *out);
     266        void PrincipalAxisSystem(ofstream *out, bool DoRotate);
     267        double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
     268        Vector* FindEmbeddingHole(ofstream *out, molecule *srcmol);
     269
     270        bool VerletForceIntegration(char *file, double delta_t, bool IsAngstroem);
     271
     272        bool CheckBounds(const Vector *x) const;
     273        void GetAlignvector(struct lsq_params * par) const;
     274
     275        /// Initialising routines in fragmentation
     276        void CreateAdjacencyList2(ofstream *out, ifstream *output);
     277        void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
     278        void CreateListOfBondsPerAtom(ofstream *out);
     279
     280        // Graph analysis
     281        MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
     282        void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
     283        bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
     284        bond * FindNextUnused(atom *vertex);
     285        void SetNextComponentNumber(atom *vertex, int nr);
     286        void InitComponentNumbers();
     287        void OutputComponentNumber(ofstream *out, atom *vertex);
     288        void ResetAllBondsToUnused();
     289        void ResetAllAtomNumbers();
     290        int CountCyclicBonds(ofstream *out);
     291        bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
     292        string GetColor(enum Shading color);
     293
     294        molecule *CopyMolecule();
     295
     296        /// Fragment molecule by two different approaches:
     297        int FragmentMolecule(ofstream *out, int Order, config *configuration);
     298        bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
     299        bool StoreAdjacencyToFile(ofstream *out, char *path);
     300        bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
     301        bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
     302        bool StoreOrderAtSiteFile(ofstream *out, char *path);
     303        bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
     304        bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
     305        bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
     306        bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
     307        bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
     308        void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
     309        /// -# BOSSANOVA
     310        void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
     311        int PowerSetGenerator(ofstream *out, int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
     312        bool BuildInducedSubgraph(ofstream *out, const molecule *Father);
     313        molecule * StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem);
     314        void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
     315        int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
     316        int GuesstimateFragmentCount(ofstream *out, int order);
     317
     318        // Recognize doubly appearing molecules in a list of them
     319        int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
     320        int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
     321
     322        // Output routines.
     323        bool Output(ofstream *out);
     324        bool OutputTrajectories(ofstream *out);
     325        void OutputListOfBonds(ofstream *out) const;
     326        bool OutputXYZ(ofstream *out) const;
     327        bool OutputTrajectoriesXYZ(ofstream *out);
     328        bool Checkout(ofstream *out) const;
     329        bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
     330
     331        private:
     332        int last_atom;                  //!< number given to last atom
    334333};
    335334
    … …  
    337336 */
    338337class MoleculeListClass {
    339   public:
    340     MoleculeList ListOfMolecules; //!< List of the contained molecules
    341     int MaxIndex;
    342 
    343   MoleculeListClass();
    344   ~MoleculeListClass();
    345 
    346   bool AddHydrogenCorrection(ofstream *out, char *path);
    347   bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
    348   void insert(molecule *mol);
    349   molecule * ReturnIndex(int index);
    350   bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
    351   int NumberOfActiveMolecules();
    352   void Enumerate(ofstream *out);
    353   void Output(ofstream *out);
    354 
    355   // merging of molecules
     338        public:
     339          MoleculeList ListOfMolecules; //!< List of the contained molecules
     340          int MaxIndex;
     341
     342        MoleculeListClass();
     343        ~MoleculeListClass();
     344
     345        bool AddHydrogenCorrection(ofstream *out, char *path);
     346        bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
     347        bool insert(molecule *mol);
     348        molecule * ReturnIndex(int index);
     349        bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
     350        int NumberOfActiveMolecules();
     351        void Enumerate(ofstream *out);
     352        void Output(ofstream *out);
     353
     354        // merging of molecules
    356355  bool SimpleMerge(molecule *mol, molecule *srcmol);
    357356  bool SimpleAdd(molecule *mol, molecule *srcmol);
    … …  
    361360  bool EmbedMerge(molecule *mol, molecule *srcmol);
    362361
    363   private:
     362        private:
    364363};
    365364
    … …  
    369368 */
    370369class MoleculeLeafClass {
    371   public:
    372     molecule *Leaf;                  //!< molecule of this leaf
    373     //MoleculeLeafClass *UpLeaf;        //!< Leaf one level up
    374     //MoleculeLeafClass *DownLeaf;      //!< First leaf one level down
    375     MoleculeLeafClass *previous;  //!< Previous leaf on this level
    376     MoleculeLeafClass *next;      //!< Next leaf on this level
    377 
    378   //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
    379   MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
    380   ~MoleculeLeafClass();
    381 
    382   bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
    383   bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
    384   bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
    385   bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
    386   bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
    387   void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
    388   int Count() const;
     370        public:
     371                molecule *Leaf;                                                                  //!< molecule of this leaf
     372                //MoleculeLeafClass *UpLeaf;                            //!< Leaf one level up
     373                //MoleculeLeafClass *DownLeaf;                  //!< First leaf one level down
     374                MoleculeLeafClass *previous;    //!< Previous leaf on this level
     375                MoleculeLeafClass *next;                        //!< Next leaf on this level
     376
     377        //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
     378        MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
     379        ~MoleculeLeafClass();
     380
     381        bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
     382        bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
     383        bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
     384        bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
     385        bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
     386        void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
     387        int Count() const;
    389388};
    390389
    … …  
    393392 */
    394393class config {
    395   public:
    396     int PsiType;
    397     int MaxPsiDouble;
    398     int PsiMaxNoUp;
    399     int PsiMaxNoDown;
    400     int MaxMinStopStep;
    401     int InitMaxMinStopStep;
    402     int ProcPEGamma;
    403     int ProcPEPsi;
    404     char *configpath;
    405     char *configname;
    406     bool FastParsing;
    407     double Deltat;
    408     string basis;
    409 
    410     private:
    411     char *mainname;
    412     char *defaultpath;
    413     char *pseudopotpath;
    414 
    415     int DoOutVis;
    416     int DoOutMes;
    417     int DoOutNICS;
    418     int DoOutOrbitals;
    419     int DoOutCurrent;
    420     int DoFullCurrent;
    421     int DoPerturbation;
    422     int DoWannier;
    423     int CommonWannier;
    424     double SawtoothStart;
    425     int VectorPlane;
    426     double VectorCut;
    427     int UseAddGramSch;
    428     int Seed;
    429 
    430     int MaxOuterStep;
    431     int OutVisStep;
    432     int OutSrcStep;
    433     double TargetTemp;
    434     int ScaleTempStep;
    435     int MaxPsiStep;
    436     double EpsWannier;
    437 
    438     int MaxMinStep;
    439     double RelEpsTotalEnergy;
    440     double RelEpsKineticEnergy;
    441     int MaxMinGapStopStep;
    442     int MaxInitMinStep;
    443     double InitRelEpsTotalEnergy;
    444     double InitRelEpsKineticEnergy;
    445     int InitMaxMinGapStopStep;
    446 
    447     //double BoxLength[NDIM*NDIM];
    448 
    449     double ECut;
    450     int MaxLevel;
    451     int RiemannTensor;
    452     int LevRFactor;
    453     int RiemannLevel;
    454     int Lev0Factor;
    455     int RTActualUse;
    456     int AddPsis;
    457 
    458     double RCut;
    459     int StructOpt;
    460     int IsAngstroem;
    461     int RelativeCoord;
    462     int MaxTypes;
    463 
    464 
    465   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);
    466 
    467   public:
    468   config();
    469   ~config();
    470 
    471   int TestSyntax(char *filename, periodentafel *periode, molecule *mol);
    472   void Load(char *filename, periodentafel *periode, molecule *mol);
    473   void LoadOld(char *filename, periodentafel *periode, molecule *mol);
    474   void RetrieveConfigPathAndName(string filename);
    475   bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
    476   bool SaveMPQC(const char *filename, molecule *mol) const;
    477   void Edit();
    478   bool GetIsAngstroem() const;
    479   char *GetDefaultPath() const;
    480   void SetDefaultPath(const char *path);
     394        public:
     395                int PsiType;
     396                int MaxPsiDouble;
     397                int PsiMaxNoUp;
     398                int PsiMaxNoDown;
     399                int MaxMinStopStep;
     400                int InitMaxMinStopStep;
     401                int ProcPEGamma;
     402                int ProcPEPsi;
     403                char *configpath;
     404                char *configname;
     405                bool FastParsing;
     406                double Deltat;
     407                string basis;
     408
     409                private:
     410                char *mainname;
     411                char *defaultpath;
     412                char *pseudopotpath;
     413
     414                int DoOutVis;
     415                int DoOutMes;
     416                int DoOutNICS;
     417                int DoOutOrbitals;
     418                int DoOutCurrent;
     419                int DoFullCurrent;
     420                int DoPerturbation;
     421                int DoWannier;
     422                int CommonWannier;
     423                double SawtoothStart;
     424                int VectorPlane;
     425                double VectorCut;
     426                int UseAddGramSch;
     427                int Seed;
     428
     429                int MaxOuterStep;
     430                int OutVisStep;
     431                int OutSrcStep;
     432                double TargetTemp;
     433                int ScaleTempStep;
     434                int MaxPsiStep;
     435                double EpsWannier;
     436
     437                int MaxMinStep;
     438                double RelEpsTotalEnergy;
     439                double RelEpsKineticEnergy;
     440                int MaxMinGapStopStep;
     441                int MaxInitMinStep;
     442                double InitRelEpsTotalEnergy;
     443                double InitRelEpsKineticEnergy;
     444                int InitMaxMinGapStopStep;
     445
     446                //double BoxLength[NDIM*NDIM];
     447
     448                double ECut;
     449                int MaxLevel;
     450                int RiemannTensor;
     451                int LevRFactor;
     452                int RiemannLevel;
     453                int Lev0Factor;
     454                int RTActualUse;
     455                int AddPsis;
     456
     457                double RCut;
     458                int StructOpt;
     459                int IsAngstroem;
     460                int RelativeCoord;
     461                int MaxTypes;
     462
     463
     464        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);
     465
     466        public:
     467        config();
     468        ~config();
     469
     470        int TestSyntax(char *filename, periodentafel *periode, molecule *mol);
     471        void Load(char *filename, periodentafel *periode, molecule *mol);
     472        void LoadOld(char *filename, periodentafel *periode, molecule *mol);
     473        void RetrieveConfigPathAndName(string filename);
     474        bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
     475        bool SaveMPQC(const char *filename, molecule *mol) const;
     476        void Edit();
     477        bool GetIsAngstroem() const;
     478        char *GetDefaultPath() const;
     479        void SetDefaultPath(const char *path);
    481480};
    482481
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