[357fba] | 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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[f66195] | 13 | /*********************************************** includes ***********************************/
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| 14 |
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[cd4ccc] | 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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[986ed3] | 20 | #include <iosfwd>
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[266237] | 21 | #include <list>
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[fcd7b6] | 22 | #include <vector>
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[cd4ccc] | 23 |
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[8f4df1] | 24 | #include "Helpers/helpers.hpp"
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[6b919f8] | 25 | #include "atom_atominfo.hpp"
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| 26 | #include "atom_bondedparticle.hpp"
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| 27 | #include "atom_graphnode.hpp"
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| 28 | #include "atom_particleinfo.hpp"
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[d74077] | 29 | #include "TesselPoint.hpp"
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[ead4e6] | 30 | #include "types.hpp"
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[f66195] | 31 |
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[ad011c] | 32 | #include "CodePatterns/enumeration.hpp"
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[a0064e] | 33 |
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[f66195] | 34 | /****************************************** forward declarations *****************************/
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[357fba] | 35 |
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[f66195] | 36 | class Vector;
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[46d958] | 37 | class World;
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[6cfa36] | 38 | class molecule;
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[c550dd] | 39 | class Shape;
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[f66195] | 40 |
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| 41 | /********************************************** declarations *******************************/
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[e41951] | 42 |
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[357fba] | 43 | /** Single atom.
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| 44 | * Class incorporates position, type
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| 45 | */
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[6625c3] | 46 | class atom : public GraphNode, public BondedParticle, public TesselPoint {
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[88d586] | 47 | friend atom* NewAtom(atomId_t);
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[46d958] | 48 | friend void DeleteAtom(atom*);
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[357fba] | 49 | public:
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| 50 | atom *father; //!< In many-body bond order fragmentations points to originating atom
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| 51 | int *sort; //!< sort criteria
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| 52 |
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[46d958] | 53 | virtual atom *clone();
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[357fba] | 54 |
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[e2373df] | 55 | /** Pushes back another step in all trajectory vectors.
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| 56 | *
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| 57 | * This allows to extend all trajectories contained in different classes
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| 58 | * consistently. This is implemented by the topmost class which calls the
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| 59 | * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
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| 60 | */
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| 61 | virtual void UpdateSteps();
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| 62 |
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[e138de] | 63 | bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
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[0ba410] | 64 | bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
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[357fba] | 65 | bool OutputXYZLine(ofstream *out) const;
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[882a8a] | 66 | bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
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[e138de] | 67 | bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
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[0dc86e2] | 68 | void OutputMPQCLine(ostream * const out, const Vector *center) const;
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[266237] | 69 |
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[4455f4] | 70 | void InitComponentNr();
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[14b65e] | 71 | void resetGraphNr();
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[681a8a] | 72 |
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[b453f9] | 73 | void EqualsFather ( const atom *ptr, const atom **res ) const;
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[00abfc] | 74 | bool isFather(const atom *ptr);
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[e65246] | 75 | void CorrectFather();
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[357fba] | 76 | atom *GetTrueFather();
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[b453f9] | 77 | bool Compare(const atom &ptr) const;
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[357fba] | 78 |
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[b453f9] | 79 | double DistanceToVector(const Vector &origin) const;
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| 80 | double DistanceSquaredToVector(const Vector &origin) const;
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[c550dd] | 81 | bool IsInShape(const Shape&) const;
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[4a7776a] | 82 |
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[46d958] | 83 | // getter and setter
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| 84 |
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| 85 | /**
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| 86 | * returns the World that contains this atom.
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| 87 | * Use this if you need to get the world without locking
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| 88 | * the singleton for example.
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| 89 | *
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| 90 | */
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| 91 | World *getWorld();
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| 92 | void setWorld(World*);
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| 93 |
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[ad2b411] | 94 | virtual atomId_t getId() const;
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[88d586] | 95 | virtual bool changeId(atomId_t newId);
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| 96 |
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| 97 | /**
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| 98 | * this function sets the Id without notifying the world. Only use it, if the world has already
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| 99 | * gotten an ID for this Atom.
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| 100 | */
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| 101 | virtual void setId(atomId_t);
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| 102 |
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[6cfa36] | 103 | void setMolecule(molecule*);
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[e41c48] | 104 | molecule* getMolecule() const;
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[6cfa36] | 105 | void removeFromMolecule();
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| 106 |
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[e8a21f] | 107 | int getNr() const;
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[1f8337] | 108 |
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[d74077] | 109 | // Output operator
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| 110 | std::ostream & operator << (std::ostream &ost) const;
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| 111 |
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[46d958] | 112 | protected:
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[6cfa36] | 113 |
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[46d958] | 114 | /**
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| 115 | * Protected constructor to ensure construction of atoms through the world.
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| 116 | * see World::createAtom()
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| 117 | */
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| 118 | atom();
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| 119 |
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| 120 | /**
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| 121 | * Protected copy-constructor to ensure construction of atoms by cloning.
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| 122 | * see atom::clone()
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| 123 | */
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| 124 | atom(class atom *pointer);
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| 125 |
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| 126 | /**
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| 127 | * Protected destructor to ensure destruction of atoms through the world.
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| 128 | * see World::destroyAtom()
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| 129 | */
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| 130 | virtual ~atom();
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[357fba] | 131 | private:
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[6cfa36] | 132 | molecule *mol; // !< the molecule this atom belongs to
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[46d958] | 133 | World* world;
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[88d586] | 134 | atomId_t id;
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[357fba] | 135 | };
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| 136 |
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[d74077] | 137 | /**
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| 138 | * Global output operator for class atom.
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| 139 | */
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| 140 | std::ostream & operator << (std::ostream &ost, const atom &_atom);
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| 141 |
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[46d958] | 142 | /**
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| 143 | * internal method used by the world. Do not use if you don't know what you are doing.
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| 144 | * You might get burned...
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| 145 | * Use World::createAtom() instead.
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| 146 | */
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[88d586] | 147 | atom* NewAtom(atomId_t _id);
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[46d958] | 148 |
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| 149 | /**
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| 150 | * internal method used by the world. Do not use if you don't know what you are doing.
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| 151 | * You might get burned...
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| 152 | * Use World::destroyAtom() instead.
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| 153 | */
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| 154 | void DeleteAtom(atom*);
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| 155 |
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[e5f64de] | 156 | /**
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| 157 | * Simple function to compare atoms by their elements to allow sorting of atoms by this criteria
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| 158 | */
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| 159 | bool compareAtomElements(atom* atom1,atom* atom2);
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| 160 |
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[46d958] | 161 |
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[357fba] | 162 | #endif /* ATOM_HPP_ */
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