src/gromacs/math/coordinatetransformation.cpp

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  35 /*! \internal \file
  36  * \brief Implements coordinate transformation routines.
  37  *
  38  * \author Christian Blau <blau@kth.se>
  39  */
  40 #include "gmxpre.h"
  41
  42 #include "coordinatetransformation.h"
  43
  44 #include <vector>
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/mdspan/extensions.h"
  48 #include "gromacs/utility/arrayref.h"
  49
  50 #include "matrix.h"
  51
  52 namespace gmx
  53 {
  54
  55 /********************************************************************
  56  * ScaleCoordinates::Impl
  57  */
  58
  59 class ScaleCoordinates::Impl
  60 {
  61 public:
  62     Impl(const RVec& scale);
  63     void inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const;
  64     void scale(ArrayRef<RVec> coordinates) const;
  65
  66 private:
  67     RVec scale_;
  68 };
  69 ScaleCoordinates::Impl::Impl(const RVec& scale) : scale_{ scale } {}
  70 void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
  71 {
  72     for (auto& coordinate : coordinates)
  73     {
  74         coordinate[XX] *= scale_[XX];
  75         coordinate[YY] *= scale_[YY];
  76         coordinate[ZZ] *= scale_[ZZ];
  77     }
  78 }
  79
  80 void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
  81 {
  82     RVec inverseScale;
  83     for (int dimension = XX; dimension <= ZZ; ++dimension)
  84     {
  85         inverseScale[dimension] = scale_[dimension] != 0 ? 1. / scale_[dimension] : 1.;
  86     }
  87
  88     for (auto& coordinate : coordinates)
  89     {
  90         coordinate[XX] *= inverseScale[XX];
  91         coordinate[YY] *= inverseScale[YY];
  92         coordinate[ZZ] *= inverseScale[ZZ];
  93     }
  94 }
  95
  96 /********************************************************************
  97  * ScaleCoordinates
  98  */
  99
 100 ScaleCoordinates::ScaleCoordinates(const RVec& scale) : impl_{ new Impl(scale) } {}
 101
 102 void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
 103 {
 104     impl_->scale(coordinates);
 105 }
 106
 107 void ScaleCoordinates::operator()(RVec* coordinate) const
 108 {
 109     impl_->scale({ coordinate, coordinate + 1 });
 110 }
 111
 112 void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
 113 {
 114     impl_->inverseIgnoringZeroScale(coordinates);
 115 }
 116
 117 void ScaleCoordinates::inverseIgnoringZeroScale(RVec* coordinate) const
 118 {
 119     impl_->inverseIgnoringZeroScale({ coordinate, coordinate + 1 });
 120 }
 121
 122 ScaleCoordinates::~ScaleCoordinates() = default;
 123
 124 ScaleCoordinates::ScaleCoordinates(const ScaleCoordinates& other) : impl_(new Impl(*other.impl_)) {}
 125
 126 ScaleCoordinates& ScaleCoordinates::operator=(const ScaleCoordinates& other)
 127 {
 128     *impl_ = *other.impl_;
 129     return *this;
 130 }
 131
 132 ScaleCoordinates::ScaleCoordinates(ScaleCoordinates&&) noexcept = default;
 133
 134 ScaleCoordinates& ScaleCoordinates::operator=(ScaleCoordinates&&) noexcept = default;
 135
 136 /********************************************************************
 137  * TranslateAndScale::Impl
 138  */
 139
 140 class TranslateAndScale::Impl
 141 {
 142 public:
 143     Impl(const RVec& scale, const RVec& translation);
 144     void transform(ArrayRef<RVec> coordinates) const;
 145     RVec scale_;
 146     RVec translation_;
 147 };
 148
 149 TranslateAndScale::Impl::Impl(const RVec& scale, const RVec& translation) :
 150     scale_{ scale },
 151     translation_{ translation }
 152 {
 153 }
 154
 155 void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
 156 {
 157     for (auto& coordinate : coordinates)
 158     {
 159         coordinate += translation_;
 160         coordinate[XX] *= scale_[XX];
 161         coordinate[YY] *= scale_[YY];
 162         coordinate[ZZ] *= scale_[ZZ];
 163     }
 164 }
 165
 166
 167 /********************************************************************
 168  * TranslateAndScale
 169  */
 170
 171 TranslateAndScale::TranslateAndScale(const RVec& scale, const RVec& translation) :
 172     impl_(new Impl(scale, translation))
 173 {
 174 }
 175
 176 void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
 177 {
 178     impl_->transform(coordinates);
 179 }
 180
 181 void TranslateAndScale::operator()(RVec* coordinate) const
 182 {
 183     impl_->transform({ coordinate, coordinate + 1 });
 184 }
 185
 186 ScaleCoordinates TranslateAndScale::scaleOperationOnly() const
 187 {
 188     return ScaleCoordinates{ impl_->scale_ };
 189 }
 190
 191 TranslateAndScale::~TranslateAndScale() = default;
 192
 193 TranslateAndScale::TranslateAndScale(const TranslateAndScale& other) : impl_(new Impl(*other.impl_))
 194 {
 195 }
 196
 197 TranslateAndScale& TranslateAndScale::operator=(const TranslateAndScale& other)
 198 {
 199     *impl_ = *other.impl_;
 200     return *this;
 201 }
 202
 203 TranslateAndScale::TranslateAndScale(TranslateAndScale&&) noexcept = default;
 204
 205 TranslateAndScale& TranslateAndScale::operator=(TranslateAndScale&&) noexcept = default;
 206
 207 /********************************************************************
 208  * AffineTransformation
 209  */
 210
 211 AffineTransformation::AffineTransformation(Matrix3x3ConstSpan matrix, const RVec& translation) :
 212     translation_{ translation }
 213 {
 214     std::copy(begin(matrix), end(matrix), begin(matrix_));
 215 }
 216
 217 void AffineTransformation::operator()(ArrayRef<RVec> vectors) const
 218 {
 219     for (RVec& vector : vectors)
 220     {
 221         matrixVectorMultiply(matrix_.asConstView(), &vector);
 222         vector += translation_;
 223     }
 224 }
 225
 226 void AffineTransformation::operator()(RVec* vector) const
 227 {
 228     (*this)({ vector, vector + 1 });
 229 }
 230
 231 } // namespace gmx