source: src/Box.hpp@ d66cb7

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 d66cb7 was d66cb7, checked in by Frederik Heber <heber@…>, 13 years ago

Replaced Conditions_t by BoundaryConditions::BCContainer in class Box.

  • Property mode set to 100644
File size: 3.9 KB
Line 
1/*
2 * Box.hpp
3 *
4 * Created on: Jun 30, 2010
5 * Author: crueger
6 */
7
8#ifndef BOX_HPP_
9#define BOX_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16
17class RealSpaceMatrix;
18class Vector;
19class Shape;
20class Plane;
21
22#include <list>
23#include <vector>
24#include "CodePatterns/Observer/Observable.hpp"
25#include "LinearAlgebra/VectorSet.hpp"
26
27#include "Box_BoundaryConditions.hpp"
28
29/**
30 * A simple class that can be used to store periodic Boxes
31 * in the form of a parallelepiped.
32 *
33 * Stores a matrix that can be used to translate from periodic
34 * [0,1) space as well as the inverse that is needed to
35 * translate back to that space.
36 */
37class Box : public Observable
38{
39public:
40 enum NotificationType {
41 BoundaryConditionsChanged,
42 MatrixChanged,
43 NotificationType_MAX // denotes the maximum of available notification types
44 };
45
46 Box();
47 Box(const Box&);
48 Box(RealSpaceMatrix _M);
49 virtual ~Box();
50
51 /**
52 * Get the matrix describing the form of the parallelepiped
53 */
54 const RealSpaceMatrix &getM() const;
55
56 /**
57 * Get the inverse of the matrix M (see above).
58 */
59 const RealSpaceMatrix &getMinv() const;
60
61 /**
62 * Set the form of the parallelepiped.
63 */
64 void setM(RealSpaceMatrix);
65
66 Box &operator=(const Box&);
67 Box &operator=(const RealSpaceMatrix&);
68
69 /**
70 * Translate a point from [0,1) to the boxed space.
71 */
72 Vector translateIn(const Vector &point) const;
73
74 /**
75 * Translate a point from the boxed space to the [0,1) space.
76 */
77 Vector translateOut(const Vector &point) const;
78
79 /**
80 * Wrap a point so that it will lie within the space defined by the box.
81 */
82 Vector WrapPeriodically(const Vector &point) const;
83
84 /**
85 * Checks whether a given vector is inside the box.
86 */
87 bool isInside(const Vector &point) const;
88
89 /**
90 * Produce corresponding points in several adjacent boxes.
91 *
92 * n specifies the number of times the point is expanded.
93 * Carefull, needs O(n^3) time and produces as many vectors.
94 */
95 VECTORSET(std::vector) explode(const Vector &point,int n) const;
96 VECTORSET(std::vector) explode(const Vector &point) const;
97
98 /**
99 * Calculate the distance of two points in the periodic space
100 * defined by this box
101 */
102 double periodicDistanceSquared(const Vector &point1,const Vector &point2) const;
103
104 /**
105 * Calculate the distance of two points in the periodic space
106 * defined by this box
107 */
108 double periodicDistance(const Vector &point1,const Vector &point2) const;
109
110 /**
111 * Calculates the minimum distance to the boundary of the periodic
112 * space defined by this box.
113 */
114 double DistanceToBoundary(const Vector &point) const;
115
116 Shape getShape() const;
117
118 const BoundaryConditions::Conditions_t getConditions() const;
119 void setCondition(size_t i,const BoundaryConditions::BoundaryCondition_t condition);
120
121 const std::vector<std::pair<Plane,Plane> > getBoundingPlanes() const;
122
123 void setCuboid(const Vector&);
124
125private:
126 /** Internal explode function that works on the staticly present internal_list
127 *
128 * \todo Note that is not thread-safe!
129 *
130 * Most of the time of explode is consumed by memory allocation if it is called
131 * repeatedly.
132 *
133 * @param point point to explode
134 * @param n neighbour shells to explode
135 */
136 void internal_explode(const Vector &point,int n) const;
137
138 //!> Internal vector list for exploding vectors used in Box::internal_explode().
139 mutable VECTORSET(std::vector) internal_list;
140
141 //!> Internal vector for coordinates used in Box::internal_explode()
142 mutable std::vector<int> coords;
143 //!> Internal vector for indices used in Box::internal_explode()
144 mutable std::vector<int> index;
145
146 BoundaryConditions::BCContainer conditions;
147 RealSpaceMatrix *M; //!< Defines the layout of the box
148 RealSpaceMatrix *Minv; //!< Inverse of M to avoid recomputation
149};
150
151std::ostream & operator << (std::ostream& ost, const Box &m);
152
153#endif /* BOX_HPP_ */
Note: See TracBrowser for help on using the repository browser.