source: src/atom.hpp@ 0d9546

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Last change on this file since 0d9546 was 0d9546, checked in by Frederik Heber <heber@…>, 14 years ago

new function atom::unsetMolecule().

  • is meant along with setMolecule() to be used by molecule only to allow for (un)setting mol reference.
  • atom::(un)setMolecule() is private.
  • AtomicInfo added also as friend to atom::setMolecule().
  • Property mode set to 100644
File size: 8.2 KB
Line 
1/*
2 * atom.hpp
3 *
4 * Created on: Aug 3, 2009
5 * Author: heber
6 */
7
8#ifndef ATOM_HPP_
9#define ATOM_HPP_
10
11using namespace std;
12
13/*********************************************** includes ***********************************/
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <iosfwd>
21#include <list>
22#include <vector>
23
24#include "Helpers/helpers.hpp"
25#include "atom_atominfo.hpp"
26#include "atom_bondedparticle.hpp"
27#include "atom_graphnode.hpp"
28#include "atom_particleinfo.hpp"
29#include "TesselPoint.hpp"
30#include "types.hpp"
31
32#include "CodePatterns/enumeration.hpp"
33
34/****************************************** forward declarations *****************************/
35
36class AtomicInfo;
37class Vector;
38class World;
39class molecule;
40class Shape;
41
42/********************************************** declarations *******************************/
43
44/** Single atom.
45 * Class incorporates position, type
46 */
47class atom : public GraphNode, public BondedParticle, public TesselPoint {
48 friend atom* NewAtom(atomId_t);
49 friend void DeleteAtom(atom*);
50public:
51 atom *father; //!< In many-body bond order fragmentations points to originating atom
52 int *sort; //!< sort criteria
53
54 /** Clones this atom.
55 *
56 * Does not clone the bonds!
57 *
58 * @return reference to atom
59 */
60 virtual atom *clone();
61
62 /** Pushes back another step in all trajectory vectors.
63 *
64 * This allows to extend all trajectories contained in different classes
65 * consistently. This is implemented by the topmost class which calls the
66 * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
67 */
68 virtual void UpdateSteps();
69
70 /** Output of a single atom with given numbering.
71 * \param ElementNo cardinal number of the element
72 * \param AtomNo cardinal number among these atoms of the same element
73 * \param *out stream to output to
74 * \param *comment commentary after '#' sign
75 * \return true - \a *out present, false - \a *out is NULL
76 */
77 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
78
79 /** Output of a single atom with numbering from array according to atom::type.
80 * \param *ElementNo cardinal number of the element
81 * \param *AtomNo cardinal number among these atoms of the same element
82 * \param *out stream to output to
83 * \param *comment commentary after '#' sign
84 * \return true - \a *out present, false - \a *out is NULL
85 */
86 bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
87
88 /** Output of a single atom as one line in xyz file.
89 * \param *out stream to output to
90 * \return true - \a *out present, false - \a *out is NULL
91 */
92 bool OutputXYZLine(ofstream *out) const;
93
94 /** Output of a single atom as one line in xyz file.
95 * \param *out stream to output to
96 * \param *ElementNo array with ion type number in the config file this atom's element shall have
97 * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
98 * \param step Trajectory time step to output
99 * \return true - \a *out present, false - \a *out is NULL
100 */
101 bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
102
103 /** Output of a single atom as one lin in xyz file.
104 * \param *out stream to output to
105 * \param step Trajectory time step to output
106 * \return true - \a *out present, false - \a *out is NULL
107 */
108 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
109
110 /** Outputs the MPQC configuration line for this atom.
111 * \param *out output stream
112 * \param *center center of molecule subtracted from position
113 * \param *AtomNo pointer to atom counter that is increased by one
114 */
115 void OutputMPQCLine(ostream * const out, const Vector *center) const;
116
117 /** Initialises the component number array.
118 * Size is set to atom::ListOfBonds.size()+1 (last is th encode end by -1)
119 */
120 void InitComponentNr();
121
122 /** Resets GraphNr to -1.
123 *
124 */
125 void resetGraphNr();
126
127 /** Check whether father is equal to given atom.
128 * \param *ptr atom to compare father to
129 * \param **res return value (only set if atom::father is equal to \a *ptr)
130 */
131 void EqualsFather ( const atom *ptr, const atom **res ) const;
132
133 /** States whether the given \a *ptr is our father.
134 *
135 * @param ptr atom to compare atom::Father with
136 * @return true - \a *ptr is father, false - not
137 */
138 bool isFather(const atom *ptr);
139
140 /** If we are copy of copy, we are linked to be just a copy.
141 *
142 */
143 void CorrectFather();
144
145 /** Climbs up the father list until NULL, last is returned.
146 * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
147 */
148 atom *GetTrueFather();
149
150 /** Compares the indices of \a this atom with a given \a ptr.
151 * \param ptr atom to compare index against
152 * \return true - this one's is smaller, false - not
153 */
154 bool Compare(const atom &ptr) const;
155
156 /** Returns distance to a given vector.
157 * \param origin vector to calculate distance to
158 * \return distance
159 */
160 double DistanceToVector(const Vector &origin) const;
161
162 /** Returns squared distance to a given vector.
163 * \param origin vector to calculate distance to
164 * \return distance squared
165 */
166 double DistanceSquaredToVector(const Vector &origin) const;
167 /** Checks whether atom is within the given box.
168 * \param offset offset to box origin
169 * \param *parallelepiped box matrix
170 * \return true - is inside, false - is not
171 */
172 bool IsInShape(const Shape&) const;
173
174 // getter and setter
175
176 /**
177 * returns the World that contains this atom.
178 * Use this if you need to get the world without locking
179 * the singleton for example.
180 *
181 */
182 World *getWorld();
183 void setWorld(World*);
184
185 virtual atomId_t getId() const;
186 virtual bool changeId(atomId_t newId);
187
188 /**
189 * this function sets the Id without notifying the world. Only use it, if the world has already
190 * gotten an ID for this Atom.
191 */
192 virtual void setId(atomId_t);
193
194 /** Returns pointer to the molecule which atom belongs to.
195 * \return containing molecule
196 */
197 molecule* getMolecule() const;
198
199 /** Erases the atom in atom::mol's list of atoms and sets it to zero.
200 */
201 void removeFromMolecule();
202
203 /** Getter for ParticleInfo::Nr of the atom.
204 *
205 * @return index
206 */
207 int getNr() const;
208
209 // Output operator
210 std::ostream & operator << (std::ostream &ost) const;
211
212 protected:
213
214 /**
215 * Protected constructor to ensure construction of atoms through the world.
216 * see World::createAtom()
217 */
218 atom();
219
220 /**
221 * Protected copy-constructor to ensure construction of atoms by cloning.
222 * see atom::clone()
223 */
224 atom(class atom *pointer);
225
226 /**
227 * Protected destructor to ensure destruction of atoms through the world.
228 * see World::destroyAtom()
229 */
230 virtual ~atom();
231 private:
232 friend class molecule;
233 friend class AtomicInfo;
234 /** Makes the atom be contained in the new molecule \a *_mol.
235 * Uses atom::removeFromMolecule() to delist from old molecule.
236 * \param *_mol pointer to new molecule
237 */
238 void setMolecule(molecule*);
239
240 /** Makes the atom be contained in the no molecule.
241 * Use atom::removeFromMolecule() to delist from old molecule,
242 * this assume that the molecule already knows about it.
243 */
244 void unsetMolecule();
245
246
247 private:
248 molecule *mol; // !< the molecule this atom belongs to
249 World* world;
250 atomId_t id;
251};
252
253/**
254 * Global output operator for class atom.
255 */
256std::ostream & operator << (std::ostream &ost, const atom &_atom);
257
258/**
259 * internal method used by the world. Do not use if you don't know what you are doing.
260 * You might get burned...
261 * Use World::createAtom() instead.
262 */
263atom* NewAtom(atomId_t _id);
264
265/**
266* internal method used by the world. Do not use if you don't know what you are doing.
267 * You might get burned...
268 * Use World::destroyAtom() instead.
269 */
270void DeleteAtom(atom*);
271
272/**
273 * Simple function to compare atoms by their elements to allow sorting of atoms by this criteria
274 */
275bool compareAtomElements(atom* atom1,atom* atom2);
276
277
278#endif /* ATOM_HPP_ */
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