source: src/atom.hpp@ f16a4b

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since f16a4b was 46d958, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Made the world solely responsible for creating and destroying atoms.
  • Property mode set to 100644
File size: 3.3 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 <iostream>
21#include <list>
22#include <vector>
23
24#include "atom_atominfo.hpp"
25#include "atom_bondedparticle.hpp"
26#include "atom_graphnode.hpp"
27#include "atom_particleinfo.hpp"
28#include "atom_trajectoryparticle.hpp"
29#include "tesselation.hpp"
30
31/****************************************** forward declarations *****************************/
32
33class Vector;
34class World;
35
36/********************************************** declarations *******************************/
37
38/** Single atom.
39 * Class incorporates position, type
40 */
41class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
42 friend atom* NewAtom();
43 friend void DeleteAtom(atom*);
44 public:
45 atom *previous; //!< previous atom in molecule list
46 atom *next; //!< next atom in molecule list
47 atom *father; //!< In many-body bond order fragmentations points to originating atom
48 int *sort; //!< sort criteria
49
50 virtual atom *clone();
51
52 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
53 bool OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
54 bool OutputXYZLine(ofstream *out) const;
55 bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
56 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
57 void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;
58
59 void InitComponentNr();
60
61 void EqualsFather ( const atom *ptr, const atom **res ) const;
62 void CorrectFather();
63 atom *GetTrueFather();
64 bool Compare(const atom &ptr) const;
65
66 double DistanceToVector(const Vector &origin) const;
67 double DistanceSquaredToVector(const Vector &origin) const;
68 bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;
69
70 // getter and setter
71
72 /**
73 * returns the World that contains this atom.
74 * Use this if you need to get the world without locking
75 * the singleton for example.
76 *
77 */
78 World *getWorld();
79 void setWorld(World*);
80
81 virtual int getId();
82 virtual void setId(int);
83 protected:
84 /**
85 * Protected constructor to ensure construction of atoms through the world.
86 * see World::createAtom()
87 */
88 atom();
89
90 /**
91 * Protected copy-constructor to ensure construction of atoms by cloning.
92 * see atom::clone()
93 */
94 atom(class atom *pointer);
95
96 /**
97 * Protected destructor to ensure destruction of atoms through the world.
98 * see World::destroyAtom()
99 */
100 virtual ~atom();
101 private:
102 World* world;
103 int id;
104};
105
106/**
107 * internal method used by the world. Do not use if you don't know what you are doing.
108 * You might get burned...
109 * Use World::createAtom() instead.
110 */
111atom* NewAtom();
112
113/**
114* internal method used by the world. Do not use if you don't know what you are doing.
115 * You might get burned...
116 * Use World::destroyAtom() instead.
117 */
118void DeleteAtom(atom*);
119
120
121#endif /* ATOM_HPP_ */
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