source: src/Fragmentation/Exporters/SphericalPointDistribution.hpp@ c4abf2

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Last change on this file since c4abf2 was 3dadd5, checked in by Frederik Heber <heber@…>, 9 years ago

Revert "Removing SphericalPointDistribution::getSimplePolygon() to allow for easy rebasing of very old branch on top."

This reverts commit c8fd68b29755db45c6c61c8b73eba4c88480c5bf.

Conflicts:

src/Fragmentation/Exporters/SphericalPointDistribution.cpp
src/Fragmentation/Exporters/SphericalPointDistribution.hpp

  • needed to reattach SphericalPointDistribution::getSimplifiedPolygon() that was removed in order to ease rebasing a very old branch on top.
  • SaturateAction changed to use WeightedPolygon_t and getRemainingPoints().
  • Property mode set to 100644
File size: 8.9 KB
RevLine 
[e895f7]1/*
2 * SphericalPointDistribution.hpp
3 *
4 * Created on: May 29, 2014
5 * Author: heber
6 */
7
8
9#ifndef SPHERICALPOINTDISTRIBUTION_HPP_
10#define SPHERICALPOINTDISTRIBUTION_HPP_
11
12// include config.h
13#ifdef HAVE_CONFIG_H
14#include <config.h>
15#endif
16
17#include "CodePatterns/Assert.hpp"
18
19#include <cmath>
20#include <list>
[6393ff]21#include <map>
22#include <set>
23#include <vector>
[e895f7]24
25#include "LinearAlgebra/Vector.hpp"
26
[450adf]27class SphericalPointDistributionTest;
28
[e895f7]29/** contains getters for the VSEPR model for specific number of electrons.
30 *
31 * This struct contains specialized functions returning a list of Vectors
32 * (points in space) to match the VSEPR model for the given number of electrons.
33 *
34 * This is implemented via template specialization of the function get().
35 *
36 * These specializations are taken from the python script \b CreateVspeShapes.py
37 * by Christian Neuen, 07th May 2009.
38 */
39struct SphericalPointDistribution
40{
41 /** Cstor for SphericalPointDistribution, allows setting radius of sphere
42 *
43 * \param _BondLength desired radius of sphere
44 */
45 SphericalPointDistribution(const double _Bondlength = 1.) :
[0c42f2]46 Bondlength(_Bondlength)
[e895f7]47 {}
48
49 //!> typedef for the list of points
50 typedef std::list<Vector> Polygon_t;
[2199c2]51 //!> typedef for the list of points with integral weights
52 typedef std::list<std::pair<Vector, int> > WeightedPolygon_t;
[6393ff]53 //!> typedef for a sorted list of indices
54 typedef std::set<unsigned int> IndexSet_t;
55 //!> typedef for the adjacency list of a polygon
56 typedef std::map<unsigned int, IndexSet_t > adjacency_t;
[e895f7]57
58 /** General getter function for the distribution of points on the surface.
59 *
60 * \warn this function needs to be specialized!
61 *
62 * \return Polygon_t with points on the surface centered at (0,0,0)
63 */
[0c42f2]64 template <int N> Polygon_t get() const
[e895f7]65 {
66 ASSERT(0, "SphericalPointDistribution::get() - not specialized for "+toString(N)+".");
[0c42f2]67 return Polygon_t();
[e895f7]68 }
69
[6393ff]70 template <int N> adjacency_t getConnections()
71 {
72 ASSERT(0, "SphericalPointDistribution::getConnections() - not specialized for "+toString(N)+".");
73 return Polygon_t();
74 }
75
[3dadd5]76 /** Initializes the polygon with the given \a _NumberOfPoints.
77 *
78 * \param _NumberOfPoints number of points
79 */
80 Polygon_t getSimplePolygon(const int _NumberOfPoints) const;
81
[fe90ab]82 /** Returns vacant spots to fill to get a complete spherical point distribution from
83 * given points \a _polygon, containing then \a _N in total.
[64cafb2]84 *
85 * This is a helper to determine points where to best insert saturation
86 * hydrogens.
[e895f7]87 *
[fe90ab]88 * \param _polygon already filled places to match
89 * \param _N desired total number fo points
[e895f7]90 */
[fe90ab]91 Polygon_t getRemainingPoints(const WeightedPolygon_t &_polygon, const int _N);
[64cafb2]92
[e895f7]93 //!> default radius of the spherical distribution
94 const double Bondlength;
95 //!> precalculated value for root of 3
[0c42f2]96 static const double SQRT_3;
[653cea]97 //!> threshold for L1 error below which matching is immediately acceptable
98 static const double L1THRESHOLD;
99 //!> threshold for L2 error below which matching is acceptable
100 static const double L2THRESHOLD;
[b67d89]101
[450adf]102 //!> typedef for a full rotation specification consisting of axis and angle.
[b67d89]103 typedef std::pair<Vector, double> Rotation_t;
104
[450adf]105 //!> typedef for a list of indices (of points in a polygon)
[b67d89]106 typedef std::list<unsigned int> IndexList_t;
[450adf]107 //!> typedef enumerating possibly multiple points accumulated as one point
108 typedef std::list< IndexList_t > IndexTupleList_t;
109 //!> typedef for a vector of indices
[b67d89]110 typedef std::vector<unsigned int> IndexArray_t;
[450adf]111 //!> typedef for a Vector of positions
[b67d89]112 typedef std::vector<Vector> VectorArray_t;
[450adf]113 //!> typedef for a Vector of positions with weights
114 typedef std::vector< std::pair<Vector, int> > WeightedVectorArray_t;
[653cea]115 //!> typedef for a vector of degrees (or integral weights)
116 typedef std::vector<unsigned int> WeightsArray_t;
[b67d89]117
118 //!> amplitude up to which deviations in checks of rotations are tolerated
119 static const double warn_amplitude;
120
[0983e6]121 struct PolygonWithIndices
122 {
123 //!> array with points
124 VectorArray_t polygon;
125 //!> list with indices for the above points, defining subset
126 IndexList_t indices;
127 };
128
[3678eb]129 static Vector calculateCenterOfMinimumDistance(
130 const SphericalPointDistribution::VectorArray_t &_positions,
131 const SphericalPointDistribution::IndexList_t &_indices);
132
[fe90ab]133private:
134 //!> points for the ideal distribution
135 Polygon_t points;
136 //!> connection information between these ideal points
137 adjacency_t adjacency;
138
139 /** Initialize inner status (points and adjacency) to desired number of
140 * points.
141 *
142 * \param _N number of points
143 */
144 void initSelf(const int _N);
145
[b67d89]146private:
[450adf]147 //!> grant unit tests access to private parts
148 friend class SphericalPointDistributionTest;
149
[b67d89]150 static std::pair<double, double> calculateErrorOfMatching(
[653cea]151 const VectorArray_t &_old,
152 const VectorArray_t &_new,
153 const IndexTupleList_t &_Matching);
[b67d89]154
155 static Polygon_t removeMatchingPoints(
[0983e6]156 const PolygonWithIndices &_points);
[b67d89]157
158 struct MatchingControlStructure {
[fe90ab]159 MatchingControlStructure(
160 const adjacency_t &_adjacency,
161 const VectorArray_t &_oldpoints,
162 const VectorArray_t &_newpoints,
163 const WeightsArray_t &_weights
164 );
[b67d89]165 bool foundflag;
166 double bestL2;
[fe90ab]167 const adjacency_t &adjacency;
168 const VectorArray_t oldpoints;
169 const VectorArray_t newpoints;
170 const WeightsArray_t weights;
[653cea]171 IndexTupleList_t bestmatching;
[b67d89]172 };
173
174 static void recurseMatchings(
175 MatchingControlStructure &_MCS,
[653cea]176 IndexTupleList_t &_matching,
[b67d89]177 IndexList_t _indices,
[653cea]178 WeightsArray_t &_remainingweights,
179 WeightsArray_t::iterator _remainiter,
180 const unsigned int _matchingsize
181 );
[b67d89]182
[fe90ab]183 IndexList_t findBestMatching(const WeightedPolygon_t &_polygon);
[450adf]184
185 static IndexList_t joinPoints(
186 Polygon_t &_newpolygon,
187 const VectorArray_t &_newpoints,
188 const IndexTupleList_t &_bestmatching
[b67d89]189 );
190
191 static Rotation_t findPlaneAligningRotation(
[0983e6]192 const PolygonWithIndices &_referencepositions,
193 const PolygonWithIndices &_currentpositions
[b67d89]194 );
195
196 static Rotation_t findPointAligningRotation(
[0983e6]197 const PolygonWithIndices &remainingold,
198 const PolygonWithIndices &remainingnew);
[e895f7]199};
200
[f54930]201// declare specializations
202
[0c42f2]203template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<0>() const;
204template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<1>() const;
205template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<2>() const;
206template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<3>() const;
207template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<4>() const;
208template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<5>() const;
209template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<6>() const;
210template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<7>() const;
211template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<8>() const;
212template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<9>() const;
213template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<10>() const;
214template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<11>() const;
215template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<12>() const;
216template <> SphericalPointDistribution::Polygon_t SphericalPointDistribution::get<14>() const;
[e895f7]217
[6393ff]218template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<0>();
219template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<1>();
220template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<2>();
221template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<3>();
222template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<4>();
223template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<5>();
224template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<6>();
225template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<7>();
226template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<8>();
227template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<9>();
228template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<10>();
229template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<11>();
230template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<12>();
231template <> SphericalPointDistribution::adjacency_t SphericalPointDistribution::getConnections<14>();
232
[e895f7]233#endif /* SPHERICALPOINTDISTRIBUTION_HPP_ */
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