source: src/atom.hpp@ 1363de

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 1363de was 1363de, checked in by Frederik Heber <heber@…>, 14 years ago

DOCUFIX: atom - Moved all doxygen documentation to header file.

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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*);
49public:
50 atom *father; //!< In many-body bond order fragmentations points to originating atom
51 int *sort; //!< sort criteria
52
53 /** Clones this atom.
54 *
55 * Does not clone the bonds!
56 *
57 * @return reference to atom
58 */
59 virtual atom *clone();
60
61 /** Pushes back another step in all trajectory vectors.
62 *
63 * This allows to extend all trajectories contained in different classes
64 * consistently. This is implemented by the topmost class which calls the
65 * real functions, \sa AppendTrajectoryStep(), by all necessary subclasses.
66 */
67 virtual void UpdateSteps();
68
69 /** Output of a single atom with given numbering.
70 * \param ElementNo cardinal number of the element
71 * \param AtomNo cardinal number among these atoms of the same element
72 * \param *out stream to output to
73 * \param *comment commentary after '#' sign
74 * \return true - \a *out present, false - \a *out is NULL
75 */
76 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
77
78 /** Output of a single atom with numbering from array according to atom::type.
79 * \param *ElementNo cardinal number of the element
80 * \param *AtomNo cardinal number among these atoms of the same element
81 * \param *out stream to output to
82 * \param *comment commentary after '#' sign
83 * \return true - \a *out present, false - \a *out is NULL
84 */
85 bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
86
87 /** Output of a single atom as one line in xyz file.
88 * \param *out stream to output to
89 * \return true - \a *out present, false - \a *out is NULL
90 */
91 bool OutputXYZLine(ofstream *out) const;
92
93 /** Output of a single atom as one line in xyz file.
94 * \param *out stream to output to
95 * \param *ElementNo array with ion type number in the config file this atom's element shall have
96 * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
97 * \param step Trajectory time step to output
98 * \return true - \a *out present, false - \a *out is NULL
99 */
100 bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
101
102 /** Output of a single atom as one lin in xyz file.
103 * \param *out stream to output to
104 * \param step Trajectory time step to output
105 * \return true - \a *out present, false - \a *out is NULL
106 */
107 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
108
109 /** Outputs the MPQC configuration line for this atom.
110 * \param *out output stream
111 * \param *center center of molecule subtracted from position
112 * \param *AtomNo pointer to atom counter that is increased by one
113 */
114 void OutputMPQCLine(ostream * const out, const Vector *center) const;
115
116 /** Initialises the component number array.
117 * Size is set to atom::ListOfBonds.size()+1 (last is th encode end by -1)
118 */
119 void InitComponentNr();
120
121 /** Resets GraphNr to -1.
122 *
123 */
124 void resetGraphNr();
125
126 /** Check whether father is equal to given atom.
127 * \param *ptr atom to compare father to
128 * \param **res return value (only set if atom::father is equal to \a *ptr)
129 */
130 void EqualsFather ( const atom *ptr, const atom **res ) const;
131
132 /** States whether the given \a *ptr is our father.
133 *
134 * @param ptr atom to compare atom::Father with
135 * @return true - \a *ptr is father, false - not
136 */
137 bool isFather(const atom *ptr);
138
139 /** If we are copy of copy, we are linked to be just a copy.
140 *
141 */
142 void CorrectFather();
143
144 /** Climbs up the father list until NULL, last is returned.
145 * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
146 */
147 atom *GetTrueFather();
148
149 /** Compares the indices of \a this atom with a given \a ptr.
150 * \param ptr atom to compare index against
151 * \return true - this one's is smaller, false - not
152 */
153 bool Compare(const atom &ptr) const;
154
155 /** Returns distance to a given vector.
156 * \param origin vector to calculate distance to
157 * \return distance
158 */
159 double DistanceToVector(const Vector &origin) const;
160
161 /** Returns squared distance to a given vector.
162 * \param origin vector to calculate distance to
163 * \return distance squared
164 */
165 double DistanceSquaredToVector(const Vector &origin) const;
166 /** Checks whether atom is within the given box.
167 * \param offset offset to box origin
168 * \param *parallelepiped box matrix
169 * \return true - is inside, false - is not
170 */
171 bool IsInShape(const Shape&) const;
172
173 // getter and setter
174
175 /**
176 * returns the World that contains this atom.
177 * Use this if you need to get the world without locking
178 * the singleton for example.
179 *
180 */
181 World *getWorld();
182 void setWorld(World*);
183
184 virtual atomId_t getId() const;
185 virtual bool changeId(atomId_t newId);
186
187 /**
188 * this function sets the Id without notifying the world. Only use it, if the world has already
189 * gotten an ID for this Atom.
190 */
191 virtual void setId(atomId_t);
192
193 /** Makes the atom be contained in the new molecule \a *_mol.
194 * Uses atom::removeFromMolecule() to delist from old molecule.
195 * \param *_mol pointer to new molecule
196 */
197 void setMolecule(molecule*);
198
199 /** Returns pointer to the molecule which atom belongs to.
200 * \return containing molecule
201 */
202 molecule* getMolecule() const;
203
204 /** Erases the atom in atom::mol's list of atoms and sets it to zero.
205 */
206 void removeFromMolecule();
207
208 /** Getter for ParticleInfo::Nr of the atom.
209 *
210 * @return index
211 */
212 int getNr() const;
213
214 // Output operator
215 std::ostream & operator << (std::ostream &ost) const;
216
217 protected:
218
219 /**
220 * Protected constructor to ensure construction of atoms through the world.
221 * see World::createAtom()
222 */
223 atom();
224
225 /**
226 * Protected copy-constructor to ensure construction of atoms by cloning.
227 * see atom::clone()
228 */
229 atom(class atom *pointer);
230
231 /**
232 * Protected destructor to ensure destruction of atoms through the world.
233 * see World::destroyAtom()
234 */
235 virtual ~atom();
236 private:
237 molecule *mol; // !< the molecule this atom belongs to
238 World* world;
239 atomId_t id;
240};
241
242/**
243 * Global output operator for class atom.
244 */
245std::ostream & operator << (std::ostream &ost, const atom &_atom);
246
247/**
248 * internal method used by the world. Do not use if you don't know what you are doing.
249 * You might get burned...
250 * Use World::createAtom() instead.
251 */
252atom* NewAtom(atomId_t _id);
253
254/**
255* internal method used by the world. Do not use if you don't know what you are doing.
256 * You might get burned...
257 * Use World::destroyAtom() instead.
258 */
259void DeleteAtom(atom*);
260
261/**
262 * Simple function to compare atoms by their elements to allow sorting of atoms by this criteria
263 */
264bool compareAtomElements(atom* atom1,atom* atom2);
265
266
267#endif /* ATOM_HPP_ */
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