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 41da13 was c538d1, checked in by Tillmann Crueger <crueger@…>, 15 years ago |
Added a method that allows producing a Shape from a box
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Property mode
set to
100644
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File size:
2.1 KB
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[83c09a] | 1 | /*
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| 2 | * Box.hpp
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| 3 | *
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| 4 | * Created on: Jun 30, 2010
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| 5 | * Author: crueger
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| 6 | */
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| 7 |
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| 8 | #ifndef BOX_HPP_
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| 9 | #define BOX_HPP_
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| 10 |
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[3dcb1f] | 11 | class Matrix;
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| 12 | class Vector;
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[c538d1] | 13 | class Shape;
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[83c09a] | 14 |
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[89e820] | 15 | #include <list>
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| 16 | #include "VectorSet.hpp"
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| 17 |
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[abd8f7] | 18 | /**
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| 19 | * A simple class that can be used to store periodic Boxes
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| 20 | * in the form of a parallelepiped.
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| 21 | *
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| 22 | * Stores a matrix that can be used to translate from periodic
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| 23 | * [0,1) space as well as the inverse that is needed to
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| 24 | * translate back to that space.
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| 25 | */
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[83c09a] | 26 | class Box
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| 27 | {
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| 28 | public:
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| 29 | Box();
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[7579a4b] | 30 | Box(const Box&);
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[83c09a] | 31 | virtual ~Box();
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| 32 |
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[abd8f7] | 33 | /**
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| 34 | * Get the matrix describing the form of the parallelepiped
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| 35 | */
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[7579a4b] | 36 | const Matrix &getM() const;
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[abd8f7] | 37 |
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| 38 | /**
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| 39 | * Get the inverse of the matrix M (see above).
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| 40 | */
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[7579a4b] | 41 | const Matrix &getMinv() const;
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[abd8f7] | 42 |
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| 43 | /**
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| 44 | * Set the form of the parallelepiped.
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| 45 | */
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[83c09a] | 46 | void setM(Matrix);
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[7579a4b] | 47 |
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| 48 | Box &operator=(const Box&);
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| 49 | Box &operator=(const Matrix&);
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| 50 |
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[abd8f7] | 51 | /**
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| 52 | * Translate a point from [0,1) to the boxed space.
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| 53 | */
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[014475] | 54 | Vector translateIn(const Vector &point) const;
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[abd8f7] | 55 |
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| 56 | /**
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| 57 | * Translate a point from the boxed space to the [0,1) space.
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| 58 | */
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[014475] | 59 | Vector translateOut(const Vector &point) const;
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[3dcb1f] | 60 |
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[abd8f7] | 61 | /**
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| 62 | * Wrap a point so that it will lie within the space defined by the box.
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| 63 | */
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[014475] | 64 | Vector WrapPeriodically(const Vector &point) const;
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[abd8f7] | 65 |
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| 66 | /**
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| 67 | * Produce corresponding points in several adjacent boxes.
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[a630fd] | 68 | *
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| 69 | * n specifies the number of times the point is expanded.
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| 70 | * Carefull, needs O(n^3) time and produces as many vectors.
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[abd8f7] | 71 | */
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[7ac4af] | 72 | VECTORSET(std::list) explode(const Vector &point,int n) const;
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| 73 | VECTORSET(std::list) explode(const Vector &point) const;
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[527de2] | 74 |
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[abd8f7] | 75 | /**
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| 76 | * Calculate the distance of two points in the periodic space
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| 77 | * defined by this box
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| 78 | */
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[014475] | 79 | double periodicDistanceSquared(const Vector &point1,const Vector &point2) const;
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[abd8f7] | 80 |
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| 81 | /**
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| 82 | * Calculate the distance of two points in the periodic space
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| 83 | * defined by this box
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| 84 | */
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[014475] | 85 | double periodicDistance(const Vector &point1,const Vector &point2) const;
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[f429d7] | 86 |
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[c538d1] | 87 | Shape getShape() const;
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| 88 |
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[83c09a] | 89 | private:
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| 90 | Matrix *M; //!< Defines the layout of the box
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| 91 | Matrix *Minv; //!< Inverse of M to avoid recomputation
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| 92 | };
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| 93 |
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| 94 | #endif /* BOX_HPP_ */
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