source: src/atom.hpp@ a0064e

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 a0064e was a0064e, checked in by Frederik Heber <heber@…>, 14 years ago

Moved stuff in src/Helpers and src/Patterns out to stand-alone project CodePatterns.

Makefile.am's:

  • CodePatterns added to AM_LDFLAGS and AM_CFLAGS
  • libMoleCuilderHelpers removed

Helpers/...

  • defs.hpp include prefixed with Helpers/
  • helpers.?pp removed lots of old, unused functions: bound, ask_value, ...
  • fast_functions.hpp has lots of functions removed as well.
  • all other files and unit tests moved to project CodePatterns.

Patterns/...

  • added ax_codepatterns.m4 containing AM_PATH_CODEPATTERNS to configure.ac
  • Property mode set to 100644
File size: 4.1 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 "atom_trajectoryparticle.hpp"
30#include "TesselPoint.hpp"
31#include "types.hpp"
32
33#include "Helpers/enumeration.hpp"
34
35/****************************************** forward declarations *****************************/
36
37class Vector;
38class World;
39class molecule;
40class Shape;
41
42/********************************************** declarations *******************************/
43
44/** Single atom.
45 * Class incorporates position, type
46 */
47class atom : public TrajectoryParticle, public GraphNode, public BondedParticle, public TesselPoint {
48 friend atom* NewAtom(atomId_t);
49 friend void DeleteAtom(atom*);
50 public:
51 atom *father; //!< In many-body bond order fragmentations points to originating atom
52 int *sort; //!< sort criteria
53
54 virtual atom *clone();
55
56 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
57 bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
58 bool OutputXYZLine(ofstream *out) const;
59 bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
60 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
61 void OutputMPQCLine(ostream * const out, const Vector *center) const;
62
63 void InitComponentNr();
64 void resetGraphNr();
65
66 void EqualsFather ( const atom *ptr, const atom **res ) const;
67 bool isFather(const atom *ptr);
68 void CorrectFather();
69 atom *GetTrueFather();
70 bool Compare(const atom &ptr) const;
71
72 double DistanceToVector(const Vector &origin) const;
73 double DistanceSquaredToVector(const Vector &origin) const;
74 bool IsInShape(const Shape&) const;
75
76 // getter and setter
77
78 /**
79 * returns the World that contains this atom.
80 * Use this if you need to get the world without locking
81 * the singleton for example.
82 *
83 */
84 World *getWorld();
85 void setWorld(World*);
86
87 virtual atomId_t getId() const;
88 virtual bool changeId(atomId_t newId);
89
90 /**
91 * this function sets the Id without notifying the world. Only use it, if the world has already
92 * gotten an ID for this Atom.
93 */
94 virtual void setId(atomId_t);
95
96 void setMolecule(molecule*);
97 molecule* getMolecule() const;
98 void removeFromMolecule();
99
100 double getMass() const;
101 int getNr() const;
102
103 // Output operator
104 std::ostream & operator << (std::ostream &ost) const;
105
106 protected:
107
108 /**
109 * Protected constructor to ensure construction of atoms through the world.
110 * see World::createAtom()
111 */
112 atom();
113
114 /**
115 * Protected copy-constructor to ensure construction of atoms by cloning.
116 * see atom::clone()
117 */
118 atom(class atom *pointer);
119
120 /**
121 * Protected destructor to ensure destruction of atoms through the world.
122 * see World::destroyAtom()
123 */
124 virtual ~atom();
125 private:
126 molecule *mol; // !< the molecule this atom belongs to
127 World* world;
128 atomId_t id;
129};
130
131/**
132 * Global output operator for class atom.
133 */
134std::ostream & operator << (std::ostream &ost, const atom &_atom);
135
136/**
137 * internal method used by the world. Do not use if you don't know what you are doing.
138 * You might get burned...
139 * Use World::createAtom() instead.
140 */
141atom* NewAtom(atomId_t _id);
142
143/**
144* internal method used by the world. Do not use if you don't know what you are doing.
145 * You might get burned...
146 * Use World::destroyAtom() instead.
147 */
148void DeleteAtom(atom*);
149
150/**
151 * Simple function to compare atoms by their elements to allow sorting of atoms by this criteria
152 */
153bool compareAtomElements(atom* atom1,atom* atom2);
154
155
156#endif /* ATOM_HPP_ */
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