| 1 | /*
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| 2 | * atom.hpp
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| 3 | *
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| 4 | * Created on: Aug 3, 2009
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef ATOM_HPP_
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| 9 | #define ATOM_HPP_
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| 10 |
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| 11 | using namespace std;
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| 12 |
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| 13 | /*********************************************** includes ***********************************/
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| 14 |
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| 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 |
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| 20 | #include <iostream>
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| 21 | #include <list>
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| 22 | #include <vector>
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| 23 |
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| 24 | #include "atom_atominfo.hpp"
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| 25 | #include "atom_bondedparticle.hpp"
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| 26 | #include "atom_graphnode.hpp"
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| 27 | #include "atom_particleinfo.hpp"
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| 28 | #include "atom_trajectoryparticle.hpp"
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| 29 | #include "tesselation.hpp"
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| 30 |
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| 31 | /****************************************** forward declarations *****************************/
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| 32 |
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| 33 | class Vector;
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| 34 |
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| 35 | /********************************************** declarations *******************************/
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| 36 |
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| 37 | /** Single atom.
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| 38 | * Class incorporates position, type
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| 39 | */
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| 40 | class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
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| 41 | public:
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| 42 | atom *previous; //!< previous atom in molecule list
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| 43 | atom *next; //!< next atom in molecule list
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| 44 | atom *father; //!< In many-body bond order fragmentations points to originating atom
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| 45 | int *sort; //!< sort criteria
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| 46 |
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| 47 | atom();
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| 48 | atom(class atom *pointer);
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| 49 | virtual ~atom();
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| 50 |
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| 51 | bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
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| 52 | bool OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
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| 53 | bool OutputXYZLine(ofstream *out) const;
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| 54 | bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
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| 55 | bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
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| 56 | void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;
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| 57 |
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| 58 | void InitComponentNr();
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| 59 |
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| 60 | void EqualsFather ( const atom *ptr, const atom **res ) const;
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| 61 | void CorrectFather();
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| 62 | atom *GetTrueFather();
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| 63 | bool Compare(const atom &ptr) const;
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| 64 |
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| 65 | double DistanceToVector(const Vector &origin) const;
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| 66 | double DistanceSquaredToVector(const Vector &origin) const;
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| 67 | bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;
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| 68 |
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| 69 | private:
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| 70 | };
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| 71 |
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| 72 | #endif /* ATOM_HPP_ */
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