source: src/Box.hpp@ 1d5a871

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Last change on this file since 1d5a871 was 66fd49, checked in by Frederik Heber <heber@…>, 14 years ago

Rewrite of FillVoidWithMoleculeAction.

FillVoidWithMoleculeAction:

  • new parameter MinDistance and default value of 0.
  • BUGFIX: filler is already created when parsing file, removed useless creation of it initially (also caused lots of confusion due to an "extra" molecule).
  • Undo implemented, regression test inserted.
  • Redo is somewhat hard to implement, as one would use performCall() if it only it would not retrieve its values from ValueStorage ...

FillVoidWithMolecule():

  • filler is now the zeroth not the last molecule, marked by firstInsertion and firstInserter. Filler is removed if no molecules are filled.
  • outsourced stuff into smaller functions
  • removed FillIt to through every atom despite only CurrentPosition, indepedent of atom position, is checked.

TESTFIXES:

  • Analysis/3: test.xyz changed because boundary is now 1.5 instead of 2.1 as 2.1 is not enough of molecules get filled in (and the filler already is).
  • Analysis/3: tensid.data was actually lacking water at (0,0,0) which is after the rewrite present.
  • Property mode set to 100644
File size: 2.8 KB
RevLine 
[83c09a]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
[56f73b]11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16
[cca9ef]17class RealSpaceMatrix;
[3dcb1f]18class Vector;
[c538d1]19class Shape;
[29ac78]20class Plane;
[83c09a]21
[89e820]22#include <list>
[77374e]23#include <vector>
[57f243]24#include "LinearAlgebra/VectorSet.hpp"
[89e820]25
[abd8f7]26/**
27 * A simple class that can be used to store periodic Boxes
28 * in the form of a parallelepiped.
29 *
30 * Stores a matrix that can be used to translate from periodic
31 * [0,1) space as well as the inverse that is needed to
32 * translate back to that space.
33 */
[83c09a]34class Box
35{
36public:
[77374e]37 typedef enum{
38 Wrap,
39 Bounce,
40 Ignore
41 } BoundaryCondition_t;
42
43 typedef vector<BoundaryCondition_t> Conditions_t;
44
[83c09a]45 Box();
[7579a4b]46 Box(const Box&);
[83c09a]47 virtual ~Box();
48
[abd8f7]49 /**
50 * Get the matrix describing the form of the parallelepiped
51 */
[cca9ef]52 const RealSpaceMatrix &getM() const;
[abd8f7]53
54 /**
55 * Get the inverse of the matrix M (see above).
56 */
[cca9ef]57 const RealSpaceMatrix &getMinv() const;
[abd8f7]58
59 /**
60 * Set the form of the parallelepiped.
61 */
[cca9ef]62 void setM(RealSpaceMatrix);
[7579a4b]63
64 Box &operator=(const Box&);
[cca9ef]65 Box &operator=(const RealSpaceMatrix&);
[7579a4b]66
[abd8f7]67 /**
68 * Translate a point from [0,1) to the boxed space.
69 */
[014475]70 Vector translateIn(const Vector &point) const;
[abd8f7]71
72 /**
73 * Translate a point from the boxed space to the [0,1) space.
74 */
[014475]75 Vector translateOut(const Vector &point) const;
[3dcb1f]76
[abd8f7]77 /**
78 * Wrap a point so that it will lie within the space defined by the box.
79 */
[014475]80 Vector WrapPeriodically(const Vector &point) const;
[abd8f7]81
[0ff6b5]82 /**
83 * Checks whether a given vector is inside the box.
84 */
85 bool isInside(const Vector &point) const;
86
[abd8f7]87 /**
88 * Produce corresponding points in several adjacent boxes.
[a630fd]89 *
90 * n specifies the number of times the point is expanded.
91 * Carefull, needs O(n^3) time and produces as many vectors.
[abd8f7]92 */
[7ac4af]93 VECTORSET(std::list) explode(const Vector &point,int n) const;
94 VECTORSET(std::list) explode(const Vector &point) const;
[527de2]95
[abd8f7]96 /**
97 * Calculate the distance of two points in the periodic space
98 * defined by this box
99 */
[014475]100 double periodicDistanceSquared(const Vector &point1,const Vector &point2) const;
[abd8f7]101
102 /**
103 * Calculate the distance of two points in the periodic space
104 * defined by this box
105 */
[014475]106 double periodicDistance(const Vector &point1,const Vector &point2) const;
[f429d7]107
[66fd49]108 /**
109 * Calculates the minimum distance to the boundary of the periodic
110 * space defined by this box.
111 */
112 double DistanceToBoundary(const Vector &point) const;
113
[c538d1]114 Shape getShape() const;
[66fd49]115 const Conditions_t getConditions() const;
[77374e]116 void setCondition(int,BoundaryCondition_t);
117
[66fd49]118 const vector<pair<Plane,Plane> > getBoundingPlanes() const;
[29ac78]119
[e1ab97]120 void setCuboid(const Vector&);
[c538d1]121
[83c09a]122private:
[77374e]123 Conditions_t conditions;
[cca9ef]124 RealSpaceMatrix *M; //!< Defines the layout of the box
125 RealSpaceMatrix *Minv; //!< Inverse of M to avoid recomputation
[83c09a]126};
127
128#endif /* BOX_HPP_ */
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