source: src/Atom/AtomicInfo.cpp@ d53902

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Last change on this file since d53902 was b3d687, checked in by Frederik Heber <heber@…>, 13 years ago

FIX: Filler::operator() did not create a molecule for each cloned cluster.

  • so far we assume (in AtomicInfo) that each atoms always belongs to a molecule. However, the CopyAtomsInterface copies without creating new molecules or associating copied ones with the old molecules.
  • AtomicInfo asserts that atom is associated to a molecule.
  • CopyAtoms_withBonds now associates cloned atoms with molecule of original atom.
  • Filler::operator() creates a molecule for each cloned cluster and associates all atoms in the cluster with it.
  • This [closes #180].
  • Property mode set to 100644
File size: 2.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * AtomicInfo.cpp
10 *
11 * Created on: Aug 10, 2010
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include "CodePatterns/MemDebug.hpp"
21
22#include "atom.hpp"
23#include "AtomicInfo.hpp"
24#include "CodePatterns/Assert.hpp"
25#include "Descriptors/AtomIdDescriptor.hpp"
26#include "Descriptors/MoleculeIdDescriptor.hpp"
27#include "Element/element.hpp"
28#include "LinearAlgebra/Vector.hpp"
29#include "molecule.hpp"
30#include "World.hpp"
31
32/********************************** Functions for class AtomicInfo **********************************/
33
34AtomicInfo::AtomicInfo() :
35 Type(NULL),
36 charge(0.),
37 FatherId(0),
38 MolId(0),
39 Id(0),
40 Nr(0)
41{}
42AtomicInfo::AtomicInfo(const atom &_atom) :
43 Position(_atom.getPosition()),
44 Type(_atom.getType()),
45 charge(_atom.getCharge()),
46 Velocity(_atom.getAtomicVelocity()),
47 FatherId(_atom.father->getId()),
48 MolId(0),
49 Id(_atom.getId()),
50 Nr(_atom.getNr())
51{
52 const molecule * const mol = _atom.getMolecule();
53 ASSERT(mol != NULL,
54 "Atom "+toString(_atom.getId())+" is not associated with any molecule.");
55 MolId = mol->getId();
56}
57
58AtomicInfo::~AtomicInfo()
59{}
60
61
62bool AtomicInfo::setAtom(atom &_atom) const
63{
64 _atom.setPosition(Position);
65 _atom.setType(Type);
66 _atom.setCharge(charge);
67 _atom.setAtomicVelocity(Velocity);
68
69 // set old id
70 bool status = true;
71 if (_atom.getId() != Id)
72 status = _atom.changeId(Id);
73
74 // set its father
75 atom * const _father = World::getInstance().getAtom(AtomById(FatherId));
76 if (_father == NULL)
77 _atom.father = &_atom;
78 else
79 _atom.father = _father;
80
81 // setting molecule
82 molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId));
83 if (_mol != NULL)
84 _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
85 _atom.changeNr(Nr);
86
87 return status;
88}
89
90atomId_t AtomicInfo::getId() const {
91 return Id;
92}
93
94AtomicInfo& AtomicInfo::operator=(const AtomicInfo& AI)
95{
96 if (&AI == this) // check self-assignment
97 return *this;
98 Position = AI.Position;
99 Type = AI.Type;
100 FatherId = AI.FatherId;
101 MolId = AI.MolId;
102 Velocity = AI.Velocity;
103 Id = AI.Id;
104 Nr = AI.Nr;
105 return *this;
106}
107
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