source: src/atom.hpp@ fb0b62

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 fb0b62 was 6625c3, checked in by Frederik Heber <heber@…>, 14 years ago

Removed atom_trajectoryparticle*, replaced by AtomInfo class now having std::vector<> for trajectories.

AtomInfo:

Other changes:

  • gsl_rng_gaussian() exchanged by boost::random specific type.
  • Property mode set to 100644
File size: 4.0 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 Vector;
37class World;
38class molecule;
39class Shape;
40
41/********************************************** declarations *******************************/
42
43/** Single atom.
44 * Class incorporates position, type
45 */
46class atom : public GraphNode, public BondedParticle, public TesselPoint {
47 friend atom* NewAtom(atomId_t);
48 friend void DeleteAtom(atom*);
49 public:
50 atom *father; //!< In many-body bond order fragmentations points to originating atom
51 int *sort; //!< sort criteria
52
53 virtual atom *clone();
54
55 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
56 bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
57 bool OutputXYZLine(ofstream *out) const;
58 bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
59 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
60 void OutputMPQCLine(ostream * const out, const Vector *center) const;
61
62 void InitComponentNr();
63 void resetGraphNr();
64
65 void EqualsFather ( const atom *ptr, const atom **res ) const;
66 bool isFather(const atom *ptr);
67 void CorrectFather();
68 atom *GetTrueFather();
69 bool Compare(const atom &ptr) const;
70
71 double DistanceToVector(const Vector &origin) const;
72 double DistanceSquaredToVector(const Vector &origin) const;
73 bool IsInShape(const Shape&) const;
74
75 // getter and setter
76
77 /**
78 * returns the World that contains this atom.
79 * Use this if you need to get the world without locking
80 * the singleton for example.
81 *
82 */
83 World *getWorld();
84 void setWorld(World*);
85
86 virtual atomId_t getId() const;
87 virtual bool changeId(atomId_t newId);
88
89 /**
90 * this function sets the Id without notifying the world. Only use it, if the world has already
91 * gotten an ID for this Atom.
92 */
93 virtual void setId(atomId_t);
94
95 void setMolecule(molecule*);
96 molecule* getMolecule() const;
97 void removeFromMolecule();
98
99 int getNr() const;
100
101 // Output operator
102 std::ostream & operator << (std::ostream &ost) const;
103
104 protected:
105
106 /**
107 * Protected constructor to ensure construction of atoms through the world.
108 * see World::createAtom()
109 */
110 atom();
111
112 /**
113 * Protected copy-constructor to ensure construction of atoms by cloning.
114 * see atom::clone()
115 */
116 atom(class atom *pointer);
117
118 /**
119 * Protected destructor to ensure destruction of atoms through the world.
120 * see World::destroyAtom()
121 */
122 virtual ~atom();
123 private:
124 molecule *mol; // !< the molecule this atom belongs to
125 World* world;
126 atomId_t id;
127};
128
129/**
130 * Global output operator for class atom.
131 */
132std::ostream & operator << (std::ostream &ost, const atom &_atom);
133
134/**
135 * internal method used by the world. Do not use if you don't know what you are doing.
136 * You might get burned...
137 * Use World::createAtom() instead.
138 */
139atom* NewAtom(atomId_t _id);
140
141/**
142* internal method used by the world. Do not use if you don't know what you are doing.
143 * You might get burned...
144 * Use World::destroyAtom() instead.
145 */
146void DeleteAtom(atom*);
147
148/**
149 * Simple function to compare atoms by their elements to allow sorting of atoms by this criteria
150 */
151bool compareAtomElements(atom* atom1,atom* atom2);
152
153
154#endif /* ATOM_HPP_ */
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