[14de469] | 1 | /** \file vector.cpp
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| 2 | *
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| 3 | * Function implementations for the class vector.
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| 4 | *
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| 5 | */
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| 6 |
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| 7 | #include "molecules.hpp"
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| 8 |
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| 9 |
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| 10 | /************************************ Functions for class vector ************************************/
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| 11 |
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| 12 | /** Constructor of class vector.
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| 13 | */
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[e9b8bb] | 14 | Vector::Vector() { x[0] = x[1] = x[2] = 0.; };
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[14de469] | 15 |
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[498a9f] | 16 | /** Constructor of class vector.
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| 17 | */
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[e9b8bb] | 18 | Vector::Vector(double x1, double x2, double x3) { x[0] = x1; x[1] = x2; x[2] = x3; };
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[498a9f] | 19 |
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[14de469] | 20 | /** Desctructor of class vector.
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| 21 | */
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[e9b8bb] | 22 | Vector::~Vector() {};
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[14de469] | 23 |
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| 24 | /** Calculates distance between this and another vector.
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| 25 | * \param *y array to second vector
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| 26 | * \return \f$| x - y |^2\f$
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| 27 | */
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[e9b8bb] | 28 | double Vector::Distance(const Vector *y) const
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[14de469] | 29 | {
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| 30 | double res = 0.;
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[7f3b9d] | 31 | for (int i=NDIM;i--;)
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[14de469] | 32 | res += (x[i]-y->x[i])*(x[i]-y->x[i]);
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| 33 | return (res);
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| 34 | };
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| 35 |
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| 36 | /** Calculates distance between this and another vector in a periodic cell.
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| 37 | * \param *y array to second vector
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| 38 | * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
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| 39 | * \return \f$| x - y |^2\f$
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| 40 | */
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[e9b8bb] | 41 | double Vector::PeriodicDistance(const Vector *y, const double *cell_size) const
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[14de469] | 42 | {
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| 43 | double res = Distance(y), tmp, matrix[NDIM*NDIM];
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[e9b8bb] | 44 | Vector Shiftedy, TranslationVector;
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[14de469] | 45 | int N[NDIM];
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| 46 | matrix[0] = cell_size[0];
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| 47 | matrix[1] = cell_size[1];
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| 48 | matrix[2] = cell_size[3];
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| 49 | matrix[3] = cell_size[1];
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| 50 | matrix[4] = cell_size[2];
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| 51 | matrix[5] = cell_size[4];
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| 52 | matrix[6] = cell_size[3];
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| 53 | matrix[7] = cell_size[4];
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| 54 | matrix[8] = cell_size[5];
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| 55 | // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
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| 56 | for (N[0]=-1;N[0]<=1;N[0]++)
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| 57 | for (N[1]=-1;N[1]<=1;N[1]++)
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| 58 | for (N[2]=-1;N[2]<=1;N[2]++) {
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| 59 | // create the translation vector
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| 60 | TranslationVector.Zero();
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[7f3b9d] | 61 | for (int i=NDIM;i--;)
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[14de469] | 62 | TranslationVector.x[i] = (double)N[i];
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| 63 | TranslationVector.MatrixMultiplication(matrix);
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| 64 | // add onto the original vector to compare with
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| 65 | Shiftedy.CopyVector(y);
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| 66 | Shiftedy.AddVector(&TranslationVector);
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| 67 | // get distance and compare with minimum so far
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| 68 | tmp = Distance(&Shiftedy);
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| 69 | if (tmp < res) res = tmp;
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| 70 | }
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| 71 | return (res);
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| 72 | };
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| 73 |
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| 74 | /** Keeps the vector in a periodic cell, defined by the symmetric \a *matrix.
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| 75 | * \param *out ofstream for debugging messages
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| 76 | * Tries to translate a vector into each adjacent neighbouring cell.
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| 77 | */
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[e9b8bb] | 78 | void Vector::KeepPeriodic(ofstream *out, double *matrix)
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[14de469] | 79 | {
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| 80 | // int N[NDIM];
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| 81 | // bool flag = false;
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| 82 | //vector Shifted, TranslationVector;
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[e9b8bb] | 83 | Vector TestVector;
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[db942e] | 84 | // *out << Verbose(1) << "Begin of KeepPeriodic." << endl;
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| 85 | // *out << Verbose(2) << "Vector is: ";
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| 86 | // Output(out);
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| 87 | // *out << endl;
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[14de469] | 88 | TestVector.CopyVector(this);
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| 89 | TestVector.InverseMatrixMultiplication(matrix);
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[7f3b9d] | 90 | for(int i=NDIM;i--;) { // correct periodically
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[14de469] | 91 | if (TestVector.x[i] < 0) { // get every coefficient into the interval [0,1)
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| 92 | TestVector.x[i] += ceil(TestVector.x[i]);
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| 93 | } else {
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| 94 | TestVector.x[i] -= floor(TestVector.x[i]);
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| 95 | }
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| 96 | }
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| 97 | TestVector.MatrixMultiplication(matrix);
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| 98 | CopyVector(&TestVector);
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[db942e] | 99 | // *out << Verbose(2) << "New corrected vector is: ";
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| 100 | // Output(out);
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| 101 | // *out << endl;
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| 102 | // *out << Verbose(1) << "End of KeepPeriodic." << endl;
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[14de469] | 103 | };
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| 104 |
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| 105 | /** Calculates scalar product between this and another vector.
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| 106 | * \param *y array to second vector
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| 107 | * \return \f$\langle x, y \rangle\f$
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| 108 | */
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[e9b8bb] | 109 | double Vector::ScalarProduct(const Vector *y) const
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[14de469] | 110 | {
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| 111 | double res = 0.;
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[7f3b9d] | 112 | for (int i=NDIM;i--;)
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[14de469] | 113 | res += x[i]*y->x[i];
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| 114 | return (res);
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| 115 | };
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| 116 |
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[498a9f] | 117 | /** projects this vector onto plane defined by \a *y.
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| 118 | * \param *y array to normal vector of plane
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| 119 | * \return \f$\langle x, y \rangle\f$
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| 120 | */
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[e9b8bb] | 121 | void Vector::ProjectOntoPlane(const Vector *y)
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[498a9f] | 122 | {
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[e9b8bb] | 123 | Vector tmp;
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[498a9f] | 124 | tmp.CopyVector(y);
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| 125 | tmp.Scale(Projection(y));
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| 126 | this->SubtractVector(&tmp);
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| 127 | };
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| 128 |
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[14de469] | 129 | /** Calculates the projection of a vector onto another \a *y.
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| 130 | * \param *y array to second vector
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| 131 | * \return \f$\langle x, y \rangle\f$
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| 132 | */
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[e9b8bb] | 133 | double Vector::Projection(const Vector *y) const
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[14de469] | 134 | {
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[498a9f] | 135 | return (ScalarProduct(y));
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[14de469] | 136 | };
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| 137 |
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| 138 | /** Calculates norm of this vector.
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| 139 | * \return \f$|x|\f$
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| 140 | */
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[e9b8bb] | 141 | double Vector::Norm() const
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[14de469] | 142 | {
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| 143 | double res = 0.;
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[7f3b9d] | 144 | for (int i=NDIM;i--;)
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[14de469] | 145 | res += this->x[i]*this->x[i];
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| 146 | return (sqrt(res));
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| 147 | };
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| 148 |
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| 149 | /** Normalizes this vector.
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| 150 | */
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[e9b8bb] | 151 | void Vector::Normalize()
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[14de469] | 152 | {
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| 153 | double res = 0.;
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[7f3b9d] | 154 | for (int i=NDIM;i--;)
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[14de469] | 155 | res += this->x[i]*this->x[i];
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| 156 | res = 1./sqrt(res);
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| 157 | Scale(&res);
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| 158 | };
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| 159 |
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| 160 | /** Zeros all components of this vector.
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| 161 | */
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[e9b8bb] | 162 | void Vector::Zero()
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[14de469] | 163 | {
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[7f3b9d] | 164 | for (int i=NDIM;i--;)
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[14de469] | 165 | this->x[i] = 0.;
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| 166 | };
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| 167 |
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[498a9f] | 168 | /** Zeros all components of this vector.
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| 169 | */
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[e9b8bb] | 170 | void Vector::One(double one)
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[498a9f] | 171 | {
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| 172 | for (int i=NDIM;i--;)
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| 173 | this->x[i] = one;
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| 174 | };
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| 175 |
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| 176 | /** Initialises all components of this vector.
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| 177 | */
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[e9b8bb] | 178 | void Vector::Init(double x1, double x2, double x3)
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[498a9f] | 179 | {
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| 180 | x[0] = x1;
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| 181 | x[1] = x2;
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| 182 | x[2] = x3;
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| 183 | };
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| 184 |
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[14de469] | 185 | /** Calculates the angle between this and another vector.
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| 186 | * \param *y array to second vector
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[498a9f] | 187 | * \return \f$\acos\bigl(frac{\langle x, y \rangle}{|x||y|}\bigr)\f$
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[14de469] | 188 | */
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[e9b8bb] | 189 | double Vector::Angle(Vector *y) const
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[14de469] | 190 | {
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[498a9f] | 191 | return acos(this->ScalarProduct(y)/Norm()/y->Norm());
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[14de469] | 192 | };
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| 193 |
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| 194 | /** Rotates the vector around the axis given by \a *axis by an angle of \a alpha.
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| 195 | * \param *axis rotation axis
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| 196 | * \param alpha rotation angle in radian
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| 197 | */
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[e9b8bb] | 198 | void Vector::RotateVector(const Vector *axis, const double alpha)
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[14de469] | 199 | {
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[e9b8bb] | 200 | Vector a,y;
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[14de469] | 201 | // normalise this vector with respect to axis
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| 202 | a.CopyVector(this);
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| 203 | a.Scale(Projection(axis));
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| 204 | SubtractVector(&a);
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| 205 | // construct normal vector
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| 206 | y.MakeNormalVector(axis,this);
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| 207 | y.Scale(Norm());
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| 208 | // scale normal vector by sine and this vector by cosine
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| 209 | y.Scale(sin(alpha));
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| 210 | Scale(cos(alpha));
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| 211 | // add scaled normal vector onto this vector
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| 212 | AddVector(&y);
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| 213 | // add part in axis direction
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| 214 | AddVector(&a);
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| 215 | };
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| 216 |
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[342f33f] | 217 | /** Sums vector \a to this lhs component-wise.
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| 218 | * \param a base vector
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| 219 | * \param b vector components to add
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| 220 | * \return lhs + a
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| 221 | */
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[e9b8bb] | 222 | Vector& operator+=(Vector& a, const Vector& b)
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[342f33f] | 223 | {
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| 224 | a.AddVector(&b);
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| 225 | return a;
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| 226 | };
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| 227 | /** factor each component of \a a times a double \a m.
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| 228 | * \param a base vector
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| 229 | * \param m factor
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| 230 | * \return lhs.x[i] * m
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| 231 | */
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[e9b8bb] | 232 | Vector& operator*=(Vector& a, const double m)
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[342f33f] | 233 | {
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| 234 | a.Scale(m);
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| 235 | return a;
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| 236 | };
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| 237 |
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| 238 | /** Sums two vectors \a and \b component-wise.
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| 239 | * \param a first vector
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| 240 | * \param b second vector
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| 241 | * \return a + b
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| 242 | */
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[e9b8bb] | 243 | Vector& operator+(const Vector& a, const Vector& b)
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[342f33f] | 244 | {
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[e9b8bb] | 245 | Vector *x = new Vector;
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[342f33f] | 246 | x->CopyVector(&a);
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| 247 | x->AddVector(&b);
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| 248 | return *x;
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| 249 | };
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| 250 |
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| 251 | /** Factors given vector \a a times \a m.
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| 252 | * \param a vector
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| 253 | * \param m factor
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| 254 | * \return a + b
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| 255 | */
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[e9b8bb] | 256 | Vector& operator*(const Vector& a, const double m)
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[342f33f] | 257 | {
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[e9b8bb] | 258 | Vector *x = new Vector;
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[342f33f] | 259 | x->CopyVector(&a);
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| 260 | x->Scale(m);
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| 261 | return *x;
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| 262 | };
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| 263 |
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[14de469] | 264 | /** Prints a 3dim vector.
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| 265 | * prints no end of line.
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| 266 | * \param *out output stream
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| 267 | */
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[e9b8bb] | 268 | bool Vector::Output(ofstream *out) const
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[14de469] | 269 | {
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| 270 | if (out != NULL) {
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| 271 | *out << "(";
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| 272 | for (int i=0;i<NDIM;i++) {
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| 273 | *out << x[i];
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| 274 | if (i != 2)
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| 275 | *out << ",";
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| 276 | }
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| 277 | *out << ")";
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| 278 | return true;
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| 279 | } else
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| 280 | return false;
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| 281 | };
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| 282 |
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[e9b8bb] | 283 | ofstream& operator<<(ofstream& ost,Vector& m)
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[14de469] | 284 | {
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| 285 | m.Output(&ost);
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| 286 | return ost;
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| 287 | };
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| 288 |
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| 289 | /** Scales each atom coordinate by an individual \a factor.
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| 290 | * \param *factor pointer to scaling factor
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| 291 | */
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[e9b8bb] | 292 | void Vector::Scale(double **factor)
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[14de469] | 293 | {
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[7f3b9d] | 294 | for (int i=NDIM;i--;)
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[342f33f] | 295 | x[i] *= (*factor)[i];
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[14de469] | 296 | };
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| 297 |
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[e9b8bb] | 298 | void Vector::Scale(double *factor)
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[14de469] | 299 | {
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[7f3b9d] | 300 | for (int i=NDIM;i--;)
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[342f33f] | 301 | x[i] *= *factor;
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[14de469] | 302 | };
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| 303 |
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[e9b8bb] | 304 | void Vector::Scale(double factor)
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[14de469] | 305 | {
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[7f3b9d] | 306 | for (int i=NDIM;i--;)
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[342f33f] | 307 | x[i] *= factor;
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[14de469] | 308 | };
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| 309 |
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| 310 | /** Translate atom by given vector.
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| 311 | * \param trans[] translation vector.
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| 312 | */
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[e9b8bb] | 313 | void Vector::Translate(const Vector *trans)
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[14de469] | 314 | {
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[7f3b9d] | 315 | for (int i=NDIM;i--;)
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[14de469] | 316 | x[i] += trans->x[i];
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| 317 | };
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| 318 |
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| 319 | /** Do a matrix multiplication.
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| 320 | * \param *matrix NDIM_NDIM array
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| 321 | */
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[e9b8bb] | 322 | void Vector::MatrixMultiplication(double *M)
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[14de469] | 323 | {
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[e9b8bb] | 324 | Vector C;
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[14de469] | 325 | // do the matrix multiplication
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| 326 | C.x[0] = M[0]*x[0]+M[3]*x[1]+M[6]*x[2];
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| 327 | C.x[1] = M[1]*x[0]+M[4]*x[1]+M[7]*x[2];
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| 328 | C.x[2] = M[2]*x[0]+M[5]*x[1]+M[8]*x[2];
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| 329 | // transfer the result into this
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[7f3b9d] | 330 | for (int i=NDIM;i--;)
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[14de469] | 331 | x[i] = C.x[i];
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| 332 | };
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| 333 |
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| 334 | /** Do a matrix multiplication with \a *matrix' inverse.
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| 335 | * \param *matrix NDIM_NDIM array
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| 336 | */
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[e9b8bb] | 337 | void Vector::InverseMatrixMultiplication(double *A)
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[14de469] | 338 | {
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[e9b8bb] | 339 | Vector C;
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[14de469] | 340 | double B[NDIM*NDIM];
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| 341 | double detA = RDET3(A);
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| 342 | double detAReci;
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| 343 |
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| 344 | // calculate the inverse B
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| 345 | if (fabs(detA) > MYEPSILON) {; // RDET3(A) yields precisely zero if A irregular
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| 346 | detAReci = 1./detA;
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| 347 | B[0] = detAReci*RDET2(A[4],A[5],A[7],A[8]); // A_11
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| 348 | B[1] = -detAReci*RDET2(A[1],A[2],A[7],A[8]); // A_12
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| 349 | B[2] = detAReci*RDET2(A[1],A[2],A[4],A[5]); // A_13
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| 350 | B[3] = -detAReci*RDET2(A[3],A[5],A[6],A[8]); // A_21
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| 351 | B[4] = detAReci*RDET2(A[0],A[2],A[6],A[8]); // A_22
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| 352 | B[5] = -detAReci*RDET2(A[0],A[2],A[3],A[5]); // A_23
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| 353 | B[6] = detAReci*RDET2(A[3],A[4],A[6],A[7]); // A_31
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| 354 | B[7] = -detAReci*RDET2(A[0],A[1],A[6],A[7]); // A_32
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| 355 | B[8] = detAReci*RDET2(A[0],A[1],A[3],A[4]); // A_33
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| 356 |
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| 357 | // do the matrix multiplication
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| 358 | C.x[0] = B[0]*x[0]+B[3]*x[1]+B[6]*x[2];
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| 359 | C.x[1] = B[1]*x[0]+B[4]*x[1]+B[7]*x[2];
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| 360 | C.x[2] = B[2]*x[0]+B[5]*x[1]+B[8]*x[2];
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| 361 | // transfer the result into this
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[7f3b9d] | 362 | for (int i=NDIM;i--;)
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[14de469] | 363 | x[i] = C.x[i];
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| 364 | } else {
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| 365 | cerr << "ERROR: inverse of matrix does not exists!" << endl;
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| 366 | }
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| 367 | };
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| 368 |
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| 369 |
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| 370 | /** Creates this vector as the b y *factors' components scaled linear combination of the given three.
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| 371 | * this vector = x1*factors[0] + x2* factors[1] + x3*factors[2]
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| 372 | * \param *x1 first vector
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| 373 | * \param *x2 second vector
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| 374 | * \param *x3 third vector
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| 375 | * \param *factors three-component vector with the factor for each given vector
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| 376 | */
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[e9b8bb] | 377 | void Vector::LinearCombinationOfVectors(const Vector *x1, const Vector *x2, const Vector *x3, double *factors)
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[14de469] | 378 | {
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[7f3b9d] | 379 | for(int i=NDIM;i--;)
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[14de469] | 380 | x[i] = factors[0]*x1->x[i] + factors[1]*x2->x[i] + factors[2]*x3->x[i];
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| 381 | };
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| 382 |
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| 383 | /** Mirrors atom against a given plane.
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| 384 | * \param n[] normal vector of mirror plane.
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| 385 | */
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[e9b8bb] | 386 | void Vector::Mirror(const Vector *n)
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[14de469] | 387 | {
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| 388 | double projection;
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[65684f] | 389 | projection = ScalarProduct(n)/n->ScalarProduct(n); // remove constancy from n (keep as logical one)
|
---|
[14de469] | 390 | // withdraw projected vector twice from original one
|
---|
| 391 | cout << Verbose(1) << "Vector: ";
|
---|
| 392 | Output((ofstream *)&cout);
|
---|
| 393 | cout << "\t";
|
---|
[7f3b9d] | 394 | for (int i=NDIM;i--;)
|
---|
[14de469] | 395 | x[i] -= 2.*projection*n->x[i];
|
---|
| 396 | cout << "Projected vector: ";
|
---|
| 397 | Output((ofstream *)&cout);
|
---|
| 398 | cout << endl;
|
---|
| 399 | };
|
---|
| 400 |
|
---|
| 401 | /** Calculates normal vector for three given vectors (being three points in space).
|
---|
| 402 | * Makes this vector orthonormal to the three given points, making up a place in 3d space.
|
---|
| 403 | * \param *y1 first vector
|
---|
| 404 | * \param *y2 second vector
|
---|
| 405 | * \param *y3 third vector
|
---|
| 406 | * \return true - success, vectors are linear independent, false - failure due to linear dependency
|
---|
| 407 | */
|
---|
[e9b8bb] | 408 | bool Vector::MakeNormalVector(const Vector *y1, const Vector *y2, const Vector *y3)
|
---|
[14de469] | 409 | {
|
---|
[e9b8bb] | 410 | Vector x1, x2;
|
---|
[14de469] | 411 |
|
---|
| 412 | x1.CopyVector(y1);
|
---|
| 413 | x1.SubtractVector(y2);
|
---|
| 414 | x2.CopyVector(y3);
|
---|
| 415 | x2.SubtractVector(y2);
|
---|
| 416 | if ((x1.Norm()==0) || (x2.Norm()==0)) {
|
---|
| 417 | cout << Verbose(4) << "Given vectors are linear dependent." << endl;
|
---|
| 418 | return false;
|
---|
| 419 | }
|
---|
[110ceb] | 420 | // cout << Verbose(4) << "relative, first plane coordinates:";
|
---|
| 421 | // x1.Output((ofstream *)&cout);
|
---|
| 422 | // cout << endl;
|
---|
| 423 | // cout << Verbose(4) << "second plane coordinates:";
|
---|
| 424 | // x2.Output((ofstream *)&cout);
|
---|
| 425 | // cout << endl;
|
---|
[14de469] | 426 |
|
---|
| 427 | this->x[0] = (x1.x[1]*x2.x[2] - x1.x[2]*x2.x[1]);
|
---|
| 428 | this->x[1] = (x1.x[2]*x2.x[0] - x1.x[0]*x2.x[2]);
|
---|
| 429 | this->x[2] = (x1.x[0]*x2.x[1] - x1.x[1]*x2.x[0]);
|
---|
| 430 | Normalize();
|
---|
| 431 |
|
---|
| 432 | return true;
|
---|
| 433 | };
|
---|
| 434 |
|
---|
| 435 |
|
---|
| 436 | /** Calculates orthonormal vector to two given vectors.
|
---|
| 437 | * Makes this vector orthonormal to two given vectors. This is very similar to the other
|
---|
| 438 | * vector::MakeNormalVector(), only there three points whereas here two difference
|
---|
| 439 | * vectors are given.
|
---|
| 440 | * \param *x1 first vector
|
---|
| 441 | * \param *x2 second vector
|
---|
| 442 | * \return true - success, vectors are linear independent, false - failure due to linear dependency
|
---|
| 443 | */
|
---|
[e9b8bb] | 444 | bool Vector::MakeNormalVector(const Vector *y1, const Vector *y2)
|
---|
[14de469] | 445 | {
|
---|
[e9b8bb] | 446 | Vector x1,x2;
|
---|
[14de469] | 447 | x1.CopyVector(y1);
|
---|
| 448 | x2.CopyVector(y2);
|
---|
| 449 | Zero();
|
---|
| 450 | if ((x1.Norm()==0) || (x2.Norm()==0)) {
|
---|
| 451 | cout << Verbose(4) << "Given vectors are linear dependent." << endl;
|
---|
| 452 | return false;
|
---|
| 453 | }
|
---|
[110ceb] | 454 | // cout << Verbose(4) << "relative, first plane coordinates:";
|
---|
| 455 | // x1.Output((ofstream *)&cout);
|
---|
| 456 | // cout << endl;
|
---|
| 457 | // cout << Verbose(4) << "second plane coordinates:";
|
---|
| 458 | // x2.Output((ofstream *)&cout);
|
---|
| 459 | // cout << endl;
|
---|
[14de469] | 460 |
|
---|
| 461 | this->x[0] = (x1.x[1]*x2.x[2] - x1.x[2]*x2.x[1]);
|
---|
| 462 | this->x[1] = (x1.x[2]*x2.x[0] - x1.x[0]*x2.x[2]);
|
---|
| 463 | this->x[2] = (x1.x[0]*x2.x[1] - x1.x[1]*x2.x[0]);
|
---|
| 464 | Normalize();
|
---|
| 465 |
|
---|
| 466 | return true;
|
---|
| 467 | };
|
---|
| 468 |
|
---|
| 469 | /** Calculates orthonormal vector to one given vectors.
|
---|
| 470 | * Just subtracts the projection onto the given vector from this vector.
|
---|
| 471 | * \param *x1 vector
|
---|
| 472 | * \return true - success, false - vector is zero
|
---|
| 473 | */
|
---|
[e9b8bb] | 474 | bool Vector::MakeNormalVector(const Vector *y1)
|
---|
[14de469] | 475 | {
|
---|
| 476 | bool result = false;
|
---|
[e9b8bb] | 477 | Vector x1;
|
---|
[14de469] | 478 | x1.CopyVector(y1);
|
---|
| 479 | x1.Scale(x1.Projection(this));
|
---|
| 480 | SubtractVector(&x1);
|
---|
[7f3b9d] | 481 | for (int i=NDIM;i--;)
|
---|
[14de469] | 482 | result = result || (fabs(x[i]) > MYEPSILON);
|
---|
| 483 |
|
---|
| 484 | return result;
|
---|
| 485 | };
|
---|
| 486 |
|
---|
| 487 | /** Creates this vector as one of the possible orthonormal ones to the given one.
|
---|
| 488 | * Just scan how many components of given *vector are unequal to zero and
|
---|
| 489 | * try to get the skp of both to be zero accordingly.
|
---|
| 490 | * \param *vector given vector
|
---|
| 491 | * \return true - success, false - failure (null vector given)
|
---|
| 492 | */
|
---|
[e9b8bb] | 493 | bool Vector::GetOneNormalVector(const Vector *GivenVector)
|
---|
[14de469] | 494 | {
|
---|
| 495 | int Components[NDIM]; // contains indices of non-zero components
|
---|
| 496 | int Last = 0; // count the number of non-zero entries in vector
|
---|
| 497 | int j; // loop variables
|
---|
| 498 | double norm;
|
---|
| 499 |
|
---|
| 500 | cout << Verbose(4);
|
---|
[65684f] | 501 | GivenVector->Output((ofstream *)&cout);
|
---|
[14de469] | 502 | cout << endl;
|
---|
[7f3b9d] | 503 | for (j=NDIM;j--;)
|
---|
[14de469] | 504 | Components[j] = -1;
|
---|
| 505 | // find two components != 0
|
---|
| 506 | for (j=0;j<NDIM;j++)
|
---|
[65684f] | 507 | if (fabs(GivenVector->x[j]) > MYEPSILON)
|
---|
[14de469] | 508 | Components[Last++] = j;
|
---|
| 509 | cout << Verbose(4) << Last << " Components != 0: (" << Components[0] << "," << Components[1] << "," << Components[2] << ")" << endl;
|
---|
| 510 |
|
---|
| 511 | switch(Last) {
|
---|
| 512 | case 3: // threecomponent system
|
---|
| 513 | case 2: // two component system
|
---|
[65684f] | 514 | norm = sqrt(1./(GivenVector->x[Components[1]]*GivenVector->x[Components[1]]) + 1./(GivenVector->x[Components[0]]*GivenVector->x[Components[0]]));
|
---|
[14de469] | 515 | x[Components[2]] = 0.;
|
---|
| 516 | // in skp both remaining parts shall become zero but with opposite sign and third is zero
|
---|
[65684f] | 517 | x[Components[1]] = -1./GivenVector->x[Components[1]] / norm;
|
---|
| 518 | x[Components[0]] = 1./GivenVector->x[Components[0]] / norm;
|
---|
[14de469] | 519 | return true;
|
---|
| 520 | break;
|
---|
| 521 | case 1: // one component system
|
---|
| 522 | // set sole non-zero component to 0, and one of the other zero component pendants to 1
|
---|
| 523 | x[(Components[0]+2)%NDIM] = 0.;
|
---|
| 524 | x[(Components[0]+1)%NDIM] = 1.;
|
---|
| 525 | x[Components[0]] = 0.;
|
---|
| 526 | return true;
|
---|
| 527 | break;
|
---|
| 528 | default:
|
---|
| 529 | return false;
|
---|
| 530 | }
|
---|
| 531 | };
|
---|
| 532 |
|
---|
[110ceb] | 533 | /** Determines paramter needed to multiply this vector to obtain intersection point with plane defined by \a *A, \a *B and \a *C.
|
---|
| 534 | * \param *A first plane vector
|
---|
| 535 | * \param *B second plane vector
|
---|
| 536 | * \param *C third plane vector
|
---|
| 537 | * \return scaling parameter for this vector
|
---|
| 538 | */
|
---|
[e9b8bb] | 539 | double Vector::CutsPlaneAt(Vector *A, Vector *B, Vector *C)
|
---|
[110ceb] | 540 | {
|
---|
| 541 | // cout << Verbose(3) << "For comparison: ";
|
---|
| 542 | // cout << "A " << A->Projection(this) << "\t";
|
---|
| 543 | // cout << "B " << B->Projection(this) << "\t";
|
---|
| 544 | // cout << "C " << C->Projection(this) << "\t";
|
---|
| 545 | // cout << endl;
|
---|
| 546 | return A->Projection(this);
|
---|
| 547 | };
|
---|
| 548 |
|
---|
[14de469] | 549 | /** Creates a new vector as the one with least square distance to a given set of \a vectors.
|
---|
| 550 | * \param *vectors set of vectors
|
---|
| 551 | * \param num number of vectors
|
---|
| 552 | * \return true if success, false if failed due to linear dependency
|
---|
| 553 | */
|
---|
[e9b8bb] | 554 | bool Vector::LSQdistance(Vector **vectors, int num)
|
---|
[14de469] | 555 | {
|
---|
| 556 | int j;
|
---|
| 557 |
|
---|
| 558 | for (j=0;j<num;j++) {
|
---|
| 559 | cout << Verbose(1) << j << "th atom's vector: ";
|
---|
| 560 | (vectors[j])->Output((ofstream *)&cout);
|
---|
| 561 | cout << endl;
|
---|
| 562 | }
|
---|
| 563 |
|
---|
| 564 | int np = 3;
|
---|
| 565 | struct LSQ_params par;
|
---|
| 566 |
|
---|
| 567 | const gsl_multimin_fminimizer_type *T =
|
---|
| 568 | gsl_multimin_fminimizer_nmsimplex;
|
---|
| 569 | gsl_multimin_fminimizer *s = NULL;
|
---|
[65684f] | 570 | gsl_vector *ss, *y;
|
---|
[14de469] | 571 | gsl_multimin_function minex_func;
|
---|
| 572 |
|
---|
| 573 | size_t iter = 0, i;
|
---|
| 574 | int status;
|
---|
| 575 | double size;
|
---|
| 576 |
|
---|
| 577 | /* Initial vertex size vector */
|
---|
| 578 | ss = gsl_vector_alloc (np);
|
---|
[65684f] | 579 | y = gsl_vector_alloc (np);
|
---|
[14de469] | 580 |
|
---|
| 581 | /* Set all step sizes to 1 */
|
---|
| 582 | gsl_vector_set_all (ss, 1.0);
|
---|
| 583 |
|
---|
| 584 | /* Starting point */
|
---|
| 585 | par.vectors = vectors;
|
---|
| 586 | par.num = num;
|
---|
| 587 |
|
---|
[7f3b9d] | 588 | for (i=NDIM;i--;)
|
---|
[65684f] | 589 | gsl_vector_set(y, i, (vectors[0]->x[i] - vectors[1]->x[i])/2.);
|
---|
[14de469] | 590 |
|
---|
| 591 | /* Initialize method and iterate */
|
---|
| 592 | minex_func.f = &LSQ;
|
---|
| 593 | minex_func.n = np;
|
---|
| 594 | minex_func.params = (void *)∥
|
---|
| 595 |
|
---|
| 596 | s = gsl_multimin_fminimizer_alloc (T, np);
|
---|
[65684f] | 597 | gsl_multimin_fminimizer_set (s, &minex_func, y, ss);
|
---|
[14de469] | 598 |
|
---|
| 599 | do
|
---|
| 600 | {
|
---|
| 601 | iter++;
|
---|
| 602 | status = gsl_multimin_fminimizer_iterate(s);
|
---|
| 603 |
|
---|
| 604 | if (status)
|
---|
| 605 | break;
|
---|
| 606 |
|
---|
| 607 | size = gsl_multimin_fminimizer_size (s);
|
---|
| 608 | status = gsl_multimin_test_size (size, 1e-2);
|
---|
| 609 |
|
---|
| 610 | if (status == GSL_SUCCESS)
|
---|
| 611 | {
|
---|
| 612 | printf ("converged to minimum at\n");
|
---|
| 613 | }
|
---|
| 614 |
|
---|
| 615 | printf ("%5d ", (int)iter);
|
---|
| 616 | for (i = 0; i < (size_t)np; i++)
|
---|
| 617 | {
|
---|
| 618 | printf ("%10.3e ", gsl_vector_get (s->x, i));
|
---|
| 619 | }
|
---|
| 620 | printf ("f() = %7.3f size = %.3f\n", s->fval, size);
|
---|
| 621 | }
|
---|
| 622 | while (status == GSL_CONTINUE && iter < 100);
|
---|
| 623 |
|
---|
[7f3b9d] | 624 | for (i=(size_t)np;i--;)
|
---|
[14de469] | 625 | this->x[i] = gsl_vector_get(s->x, i);
|
---|
[65684f] | 626 | gsl_vector_free(y);
|
---|
[14de469] | 627 | gsl_vector_free(ss);
|
---|
| 628 | gsl_multimin_fminimizer_free (s);
|
---|
| 629 |
|
---|
| 630 | return true;
|
---|
| 631 | };
|
---|
| 632 |
|
---|
| 633 | /** Adds vector \a *y componentwise.
|
---|
| 634 | * \param *y vector
|
---|
| 635 | */
|
---|
[e9b8bb] | 636 | void Vector::AddVector(const Vector *y)
|
---|
[14de469] | 637 | {
|
---|
[7f3b9d] | 638 | for (int i=NDIM;i--;)
|
---|
[14de469] | 639 | this->x[i] += y->x[i];
|
---|
| 640 | }
|
---|
| 641 |
|
---|
| 642 | /** Adds vector \a *y componentwise.
|
---|
| 643 | * \param *y vector
|
---|
| 644 | */
|
---|
[e9b8bb] | 645 | void Vector::SubtractVector(const Vector *y)
|
---|
[14de469] | 646 | {
|
---|
[7f3b9d] | 647 | for (int i=NDIM;i--;)
|
---|
[14de469] | 648 | this->x[i] -= y->x[i];
|
---|
| 649 | }
|
---|
| 650 |
|
---|
| 651 | /** Copy vector \a *y componentwise.
|
---|
| 652 | * \param *y vector
|
---|
| 653 | */
|
---|
[e9b8bb] | 654 | void Vector::CopyVector(const Vector *y)
|
---|
[14de469] | 655 | {
|
---|
[7f3b9d] | 656 | for (int i=NDIM;i--;)
|
---|
[14de469] | 657 | this->x[i] = y->x[i];
|
---|
| 658 | }
|
---|
| 659 |
|
---|
| 660 |
|
---|
| 661 | /** Asks for position, checks for boundary.
|
---|
| 662 | * \param cell_size unitary size of cubic cell, coordinates must be within 0...cell_size
|
---|
| 663 | * \param check whether bounds shall be checked (true) or not (false)
|
---|
| 664 | */
|
---|
[e9b8bb] | 665 | void Vector::AskPosition(double *cell_size, bool check)
|
---|
[14de469] | 666 | {
|
---|
| 667 | char coords[3] = {'x','y','z'};
|
---|
| 668 | int j = -1;
|
---|
| 669 | for (int i=0;i<3;i++) {
|
---|
| 670 | j += i+1;
|
---|
| 671 | do {
|
---|
| 672 | cout << Verbose(0) << coords[i] << "[0.." << cell_size[j] << "]: ";
|
---|
| 673 | cin >> x[i];
|
---|
| 674 | } while (((x[i] < 0) || (x[i] >= cell_size[j])) && (check));
|
---|
| 675 | }
|
---|
| 676 | };
|
---|
| 677 |
|
---|
| 678 | /** Solves a vectorial system consisting of two orthogonal statements and a norm statement.
|
---|
| 679 | * This is linear system of equations to be solved, however of the three given (skp of this vector\
|
---|
| 680 | * with either of the three hast to be zero) only two are linear independent. The third equation
|
---|
| 681 | * is that the vector should be of magnitude 1 (orthonormal). This all leads to a case-based solution
|
---|
| 682 | * where very often it has to be checked whether a certain value is zero or not and thus forked into
|
---|
| 683 | * another case.
|
---|
| 684 | * \param *x1 first vector
|
---|
| 685 | * \param *x2 second vector
|
---|
| 686 | * \param *y third vector
|
---|
| 687 | * \param alpha first angle
|
---|
| 688 | * \param beta second angle
|
---|
| 689 | * \param c norm of final vector
|
---|
| 690 | * \return a vector with \f$\langle x1,x2 \rangle=A\f$, \f$\langle x1,y \rangle = B\f$ and with norm \a c.
|
---|
| 691 | * \bug this is not yet working properly
|
---|
| 692 | */
|
---|
[e9b8bb] | 693 | bool Vector::SolveSystem(Vector *x1, Vector *x2, Vector *y, double alpha, double beta, double c)
|
---|
[14de469] | 694 | {
|
---|
| 695 | double D1,D2,D3,E1,E2,F1,F2,F3,p,q=0., A, B1, B2, C;
|
---|
| 696 | double ang; // angle on testing
|
---|
| 697 | double sign[3];
|
---|
| 698 | int i,j,k;
|
---|
| 699 | A = cos(alpha) * x1->Norm() * c;
|
---|
| 700 | B1 = cos(beta + M_PI/2.) * y->Norm() * c;
|
---|
| 701 | B2 = cos(beta) * x2->Norm() * c;
|
---|
| 702 | C = c * c;
|
---|
| 703 | cout << Verbose(2) << "A " << A << "\tB " << B1 << "\tC " << C << endl;
|
---|
| 704 | int flag = 0;
|
---|
| 705 | if (fabs(x1->x[0]) < MYEPSILON) { // check for zero components for the later flipping and back-flipping
|
---|
| 706 | if (fabs(x1->x[1]) > MYEPSILON) {
|
---|
| 707 | flag = 1;
|
---|
| 708 | } else if (fabs(x1->x[2]) > MYEPSILON) {
|
---|
| 709 | flag = 2;
|
---|
| 710 | } else {
|
---|
| 711 | return false;
|
---|
| 712 | }
|
---|
| 713 | }
|
---|
| 714 | switch (flag) {
|
---|
| 715 | default:
|
---|
| 716 | case 0:
|
---|
| 717 | break;
|
---|
| 718 | case 2:
|
---|
| 719 | flip(&x1->x[0],&x1->x[1]);
|
---|
| 720 | flip(&x2->x[0],&x2->x[1]);
|
---|
| 721 | flip(&y->x[0],&y->x[1]);
|
---|
| 722 | //flip(&x[0],&x[1]);
|
---|
| 723 | flip(&x1->x[1],&x1->x[2]);
|
---|
| 724 | flip(&x2->x[1],&x2->x[2]);
|
---|
| 725 | flip(&y->x[1],&y->x[2]);
|
---|
| 726 | //flip(&x[1],&x[2]);
|
---|
| 727 | case 1:
|
---|
| 728 | flip(&x1->x[0],&x1->x[1]);
|
---|
| 729 | flip(&x2->x[0],&x2->x[1]);
|
---|
| 730 | flip(&y->x[0],&y->x[1]);
|
---|
| 731 | //flip(&x[0],&x[1]);
|
---|
| 732 | flip(&x1->x[1],&x1->x[2]);
|
---|
| 733 | flip(&x2->x[1],&x2->x[2]);
|
---|
| 734 | flip(&y->x[1],&y->x[2]);
|
---|
| 735 | //flip(&x[1],&x[2]);
|
---|
| 736 | break;
|
---|
| 737 | }
|
---|
| 738 | // now comes the case system
|
---|
| 739 | D1 = -y->x[0]/x1->x[0]*x1->x[1]+y->x[1];
|
---|
| 740 | D2 = -y->x[0]/x1->x[0]*x1->x[2]+y->x[2];
|
---|
| 741 | D3 = y->x[0]/x1->x[0]*A-B1;
|
---|
| 742 | cout << Verbose(2) << "D1 " << D1 << "\tD2 " << D2 << "\tD3 " << D3 << "\n";
|
---|
| 743 | if (fabs(D1) < MYEPSILON) {
|
---|
| 744 | cout << Verbose(2) << "D1 == 0!\n";
|
---|
| 745 | if (fabs(D2) > MYEPSILON) {
|
---|
| 746 | cout << Verbose(3) << "D2 != 0!\n";
|
---|
| 747 | x[2] = -D3/D2;
|
---|
| 748 | E1 = A/x1->x[0] + x1->x[2]/x1->x[0]*D3/D2;
|
---|
| 749 | E2 = -x1->x[1]/x1->x[0];
|
---|
| 750 | cout << Verbose(3) << "E1 " << E1 << "\tE2 " << E2 << "\n";
|
---|
| 751 | F1 = E1*E1 + 1.;
|
---|
| 752 | F2 = -E1*E2;
|
---|
| 753 | F3 = E1*E1 + D3*D3/(D2*D2) - C;
|
---|
| 754 | cout << Verbose(3) << "F1 " << F1 << "\tF2 " << F2 << "\tF3 " << F3 << "\n";
|
---|
| 755 | if (fabs(F1) < MYEPSILON) {
|
---|
| 756 | cout << Verbose(4) << "F1 == 0!\n";
|
---|
| 757 | cout << Verbose(4) << "Gleichungssystem linear\n";
|
---|
| 758 | x[1] = F3/(2.*F2);
|
---|
| 759 | } else {
|
---|
| 760 | p = F2/F1;
|
---|
| 761 | q = p*p - F3/F1;
|
---|
| 762 | cout << Verbose(4) << "p " << p << "\tq " << q << endl;
|
---|
| 763 | if (q < 0) {
|
---|
| 764 | cout << Verbose(4) << "q < 0" << endl;
|
---|
| 765 | return false;
|
---|
| 766 | }
|
---|
| 767 | x[1] = p + sqrt(q);
|
---|
| 768 | }
|
---|
| 769 | x[0] = A/x1->x[0] - x1->x[1]/x1->x[0]*x[1] + x1->x[2]/x1->x[0]*x[2];
|
---|
| 770 | } else {
|
---|
| 771 | cout << Verbose(2) << "Gleichungssystem unterbestimmt\n";
|
---|
| 772 | return false;
|
---|
| 773 | }
|
---|
| 774 | } else {
|
---|
| 775 | E1 = A/x1->x[0]+x1->x[1]/x1->x[0]*D3/D1;
|
---|
| 776 | E2 = x1->x[1]/x1->x[0]*D2/D1 - x1->x[2];
|
---|
| 777 | cout << Verbose(2) << "E1 " << E1 << "\tE2 " << E2 << "\n";
|
---|
| 778 | F1 = E2*E2 + D2*D2/(D1*D1) + 1.;
|
---|
| 779 | F2 = -(E1*E2 + D2*D3/(D1*D1));
|
---|
| 780 | F3 = E1*E1 + D3*D3/(D1*D1) - C;
|
---|
| 781 | cout << Verbose(2) << "F1 " << F1 << "\tF2 " << F2 << "\tF3 " << F3 << "\n";
|
---|
| 782 | if (fabs(F1) < MYEPSILON) {
|
---|
| 783 | cout << Verbose(3) << "F1 == 0!\n";
|
---|
| 784 | cout << Verbose(3) << "Gleichungssystem linear\n";
|
---|
| 785 | x[2] = F3/(2.*F2);
|
---|
| 786 | } else {
|
---|
| 787 | p = F2/F1;
|
---|
| 788 | q = p*p - F3/F1;
|
---|
| 789 | cout << Verbose(3) << "p " << p << "\tq " << q << endl;
|
---|
| 790 | if (q < 0) {
|
---|
| 791 | cout << Verbose(3) << "q < 0" << endl;
|
---|
| 792 | return false;
|
---|
| 793 | }
|
---|
| 794 | x[2] = p + sqrt(q);
|
---|
| 795 | }
|
---|
| 796 | x[1] = (-D2 * x[2] - D3)/D1;
|
---|
| 797 | x[0] = A/x1->x[0] - x1->x[1]/x1->x[0]*x[1] + x1->x[2]/x1->x[0]*x[2];
|
---|
| 798 | }
|
---|
| 799 | switch (flag) { // back-flipping
|
---|
| 800 | default:
|
---|
| 801 | case 0:
|
---|
| 802 | break;
|
---|
| 803 | case 2:
|
---|
| 804 | flip(&x1->x[0],&x1->x[1]);
|
---|
| 805 | flip(&x2->x[0],&x2->x[1]);
|
---|
| 806 | flip(&y->x[0],&y->x[1]);
|
---|
| 807 | flip(&x[0],&x[1]);
|
---|
| 808 | flip(&x1->x[1],&x1->x[2]);
|
---|
| 809 | flip(&x2->x[1],&x2->x[2]);
|
---|
| 810 | flip(&y->x[1],&y->x[2]);
|
---|
| 811 | flip(&x[1],&x[2]);
|
---|
| 812 | case 1:
|
---|
| 813 | flip(&x1->x[0],&x1->x[1]);
|
---|
| 814 | flip(&x2->x[0],&x2->x[1]);
|
---|
| 815 | flip(&y->x[0],&y->x[1]);
|
---|
| 816 | //flip(&x[0],&x[1]);
|
---|
| 817 | flip(&x1->x[1],&x1->x[2]);
|
---|
| 818 | flip(&x2->x[1],&x2->x[2]);
|
---|
| 819 | flip(&y->x[1],&y->x[2]);
|
---|
| 820 | flip(&x[1],&x[2]);
|
---|
| 821 | break;
|
---|
| 822 | }
|
---|
| 823 | // one z component is only determined by its radius (without sign)
|
---|
| 824 | // thus check eight possible sign flips and determine by checking angle with second vector
|
---|
| 825 | for (i=0;i<8;i++) {
|
---|
| 826 | // set sign vector accordingly
|
---|
| 827 | for (j=2;j>=0;j--) {
|
---|
| 828 | k = (i & pot(2,j)) << j;
|
---|
| 829 | cout << Verbose(2) << "k " << k << "\tpot(2,j) " << pot(2,j) << endl;
|
---|
| 830 | sign[j] = (k == 0) ? 1. : -1.;
|
---|
| 831 | }
|
---|
| 832 | cout << Verbose(2) << i << ": sign matrix is " << sign[0] << "\t" << sign[1] << "\t" << sign[2] << "\n";
|
---|
| 833 | // apply sign matrix
|
---|
[7f3b9d] | 834 | for (j=NDIM;j--;)
|
---|
[14de469] | 835 | x[j] *= sign[j];
|
---|
| 836 | // calculate angle and check
|
---|
| 837 | ang = x2->Angle (this);
|
---|
| 838 | cout << Verbose(1) << i << "th angle " << ang << "\tbeta " << cos(beta) << " :\t";
|
---|
| 839 | if (fabs(ang - cos(beta)) < MYEPSILON) {
|
---|
| 840 | break;
|
---|
| 841 | }
|
---|
| 842 | // unapply sign matrix (is its own inverse)
|
---|
[7f3b9d] | 843 | for (j=NDIM;j--;)
|
---|
[14de469] | 844 | x[j] *= sign[j];
|
---|
| 845 | }
|
---|
| 846 | return true;
|
---|
| 847 | };
|
---|