source: src/molecules.hpp@ cdee6b

/** \file molecules.hpp
 *
 * Class definitions of atom and molecule, element and periodentafel 
 */

#ifndef MOLECULES_HPP_
#define MOLECULES_HPP_

using namespace std;

// GSL headers
#include <gsl/gsl_multimin.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_eigen.h>
#include <gsl/gsl_heapsort.h>

// STL headers
#include <map>
#include <set>
#include <deque>

#include "helpers.hpp"
#include "stackclass.hpp"
#include "vector.hpp"

class atom;
class bond;
class config;
class element;
class molecule;
class MoleculeListClass;
class periodentafel;
class vector;
class Verbose;

/******************************** Some definitions for easier reading **********************************/

#define KeyStack deque<int>
#define KeySet set<int>
#define NumberValuePair pair<int, double>
#define Graph map <KeySet, NumberValuePair, KeyCompare >
#define GraphPair pair <KeySet, NumberValuePair >
#define KeySetTestPair pair<KeySet::iterator, bool>
#define GraphTestPair pair<Graph::iterator, bool>

#define DistanceNrPair pair < double, atom* >
#define DistanceMap multimap < double, atom* >
#define DistanceTestPair pair < DistanceMap::iterator, bool>

#define Boundaries map <double, DistanceNrPair >
#define BoundariesPair pair<double, DistanceNrPair >
#define BoundariesTestPair pair< Boundaries::iterator, bool>

#define LinesMap map <int, int>
#define LinesPair pair <int, int>
#define LinesTestPair pair < LinesMap::iterator, bool>

#define LinetoAtomMap map < int, atom * > 
#define LinetoAtomPair pair < int, atom * > 
#define LinetoAtomTestPair pair < LinetoAtomMap::iterator, bool> 

struct KeyCompare
{
  bool operator() (const KeySet SubgraphA, const KeySet SubgraphB) const;
};

//bool operator < (KeySet SubgraphA, KeySet SubgraphB);   //note: this declaration is important, otherwise normal < is used (producing wrong order)
inline void InsertFragmentIntoGraph(ofstream *out, struct UniqueFragments *Fragment); // Insert a KeySet into a Graph
inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter);  // Insert all KeySet's in a Graph into another Graph 
int CompareDoubles (const void * a, const void * b);


/************************************* Class definitions ****************************************/

/** Chemical element.
 * Class incorporates data for a certain chemical element to be referenced from atom class.
 */
class element {
  public:
    double mass;    //!< mass in g/mol
    double CovalentRadius;  //!< covalent radius
    double VanDerWaalsRadius;  //!< can-der-Waals radius
    int Z;          //!< atomic number
    char name[64];  //!< atom name, i.e. "Hydrogren"
    char symbol[3]; //!< short form of the atom, i.e. "H"
    char period[8];    //!< period: n quantum number
    char group[8];    //!< group: l quantum number
    char block[8];    //!< block: l quantum number
    element *previous;  //!< previous item in list
    element *next;  //!< next element in list
    int *sort;      //!< sorc criteria
    int No;         //!< number of element set on periodentafel::Output()
    double Valence;             //!< number of valence electrons for this element
    int NoValenceOrbitals;  //!< number of valence orbitals, used for determining bond degree in molecule::CreateConnectmatrix()
    double HBondDistance[NDIM]; //!< distance in Angstrom of this element to hydrogen  (for single, double and triple bonds)
    double HBondAngle[NDIM];     //!< typical angle for one, two, three bonded hydrogen (in degrees)

  element();
  ~element();

  //> print element entries to screen
  bool Output(ofstream *out) const;
  bool Checkout(ofstream *out, const int No, const int NoOfAtoms) const;
  
  private:
};

/** Periodentafel is a list of all elements sorted by their atomic number.
 */
class periodentafel {
  public:
    element *start; //!< start of element list
    element *end;   //!< end of element list
    char header1[MAXSTRINGSIZE]; //!< store first header line
    char header2[MAXSTRINGSIZE]; //!< store second header line
  
  periodentafel();
  ~periodentafel(); 
  
  bool AddElement(element *pointer);
  bool RemoveElement(element *pointer);
  bool CleanupPeriodtable();
  element * FindElement(int Z);
  element * FindElement(char *shorthand) const;
  element * AskElement(); 
  bool Output(ofstream *output) const;
  bool Checkout(ofstream *output, const int *checkliste) const;
  bool LoadPeriodentafel(char *filename = NULL);
  bool StorePeriodentafel(char *filename = NULL) const;
  
  private:
};

// some algebraic matrix stuff
#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
#define RDET2(a0,a1,a2,a3) ((a0)*(a3)-(a1)*(a2))                      //!< hard-coded determinant of a 2x2 matrix


/** Parameter structure for least square minimsation.
 */
struct LSQ_params {
  vector **vectors;
  int num;
};

double LSQ(const gsl_vector * x, void * params);

/** Parameter structure for least square minimsation.
 */
struct lsq_params {
  gsl_vector *x;
  const molecule *mol;
  element *type;
};



/** 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, given in DepthFirstSearchAnalysis()
    unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
  
  atom();
  ~atom();
  
  bool Output(int ElementNo, int AtomNo, ofstream *out) const;
  bool OutputXYZLine(ofstream *out) const;
  atom *GetTrueFather();
  bool Compare(atom &ptr);
  
  private:
};

ostream & operator << (ostream &ost, 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, bond &b);

class MoleculeLeafClass;

/** The complete molecule.
 * Class incorporates number of types
 */
class molecule {
  public:
    double cell_size[6];//!< cell size
    periodentafel *elemente; //!< periodic table with each element
    atom *start;        //!< start of atom list
    atom *end;          //!< end of atom list
    bond *first;        //!< start of bond list
    bond *last;         //!< end of bond list
    bond ***ListOfBondsPerAtom; //!< pointer list for each atom and each bond it has
    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 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 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
  
  molecule(periodentafel *teil);
  ~molecule();
  
  /// remove atoms from molecule.
  bool AddAtom(atom *pointer);
  bool RemoveAtom(atom *pointer);
  bool CleanupMolecule();

  /// Add/remove atoms to/from molecule.
  atom * AddCopyAtom(atom *pointer);
  bool AddXYZFile(string filename);
  bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);  
  bond * AddBond(atom *first, atom *second, int degree);
  bool RemoveBond(bond *pointer);
  bool RemoveBonds(atom *BondPartner);
    
  /// Find atoms.
  atom * FindAtom(int Nr) const; 
  atom * AskAtom(string text);

  /// Count and change present atoms' coordination.
  void CountAtoms(ofstream *out);
  void CountElements();
  void CalculateOrbitals(class config &configuration);
  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 Translate(const vector *x);
  void Mirror(const vector *x);
  void Align(vector *n);
  void Scale(double **factor);
  void DetermineCenter(vector &center);
  vector * DetermineCenterOfGravity(ofstream *out);
  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 CheckBounds(const vector *x) const;
  void GetAlignVector(struct lsq_params * par) const;

  /// Initialising routines in fragmentation  
  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
  void CreateListOfBondsPerAtom(ofstream *out);
  
  // Graph analysis
  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, int *&MinimumRingSize);
  void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
  bond * FindNextUnused(atom *vertex);
  void SetNextComponentNumber(atom *vertex, int nr);
  void InitComponentNumbers();
  void OutputComponentNumber(ofstream *out, atom *vertex);
  void ResetAllBondsToUnused();
  void ResetAllAtomNumbers();
  int CountCyclicBonds(ofstream *out);
  string GetColor(enum Shading color);

  molecule *CopyMolecule();
  
  /// Fragment molecule by two different approaches:
  void FragmentMolecule(ofstream *out, int Order, config *configuration);
  bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, char *path = NULL);
  bool StoreAdjacencyToFile(ofstream *out, char *path);
  bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);
  bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
  bool StoreOrderAtSiteFile(ofstream *out, char *path);
  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
  bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
  bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
  bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
  bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
  void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
  /// -# BOSSANOVA
  void FragmentBOSSANOVA(ofstream *out, Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
        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);
  void SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
  int LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList);
  int GuesstimateFragmentCount(ofstream *out, int order);
          
  // Recognize doubly appearing molecules in a list of them   
  int * IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold);
  int * GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule);
        
  // Output routines.
  bool Output(ofstream *out);
  void OutputListOfBonds(ofstream *out) const;
  bool OutputXYZ(ofstream *out) const;
  bool Checkout(ofstream *out) const;

  private:
  int last_atom;      //!< number given to last atom
};

/** A list of \a molecule classes.
 */
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
    
  MoleculeListClass();
  MoleculeListClass(int Num, int NumAtoms);
  ~MoleculeListClass();

  /// Output configs.
  bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
  bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
  void Output(ofstream *out);
  
  private:
};


/** A leaf for a tree of \a molecule class
 * Wraps molecules in a tree structure
 */
class MoleculeLeafClass {
  public:
    molecule *Leaf;                   //!< molecule of this leaf 
    //MoleculeLeafClass *UpLeaf;        //!< Leaf one level up
    //MoleculeLeafClass *DownLeaf;      //!< First leaf one level down
    MoleculeLeafClass *previous;  //!< Previous leaf on this level
    MoleculeLeafClass *next;      //!< Next leaf on this level

  //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
  MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
  ~MoleculeLeafClass();

  bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
  bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
  bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
  bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
  bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList);
  void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
  int Count() const;
};

/** 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;
    
    private:
    char *mainname;
    char *defaultpath;
    char *pseudopotpath;
    
    int DoOutVis;
    int DoOutMes;
    int DoOutNICS;
    int DoOutOrbitals;
    int DoOutCurrent;
    int DoFullCurrent;
    int DoPerturbation;
    int CommonWannier;
    double SawtoothStart;
    int VectorPlane;
    double VectorCut;
    int UseAddGramSch;
    int Seed;
    
    int MaxOuterStep;
    double Deltat;
    int OutVisStep;
    int OutSrcStep;
    double TargetTemp;
    int ScaleTempStep;
    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);
  
  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(ofstream *file, periodentafel *periode, molecule *mol) const;
  void Edit(molecule *mol);
  bool GetIsAngstroem() const;
  char *GetDefaultPath() const;
  void SetDefaultPath(const char *path);
};

#endif /*MOLECULES_HPP_*/