| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 52 |
|
#include "math/RectMatrix.hpp" |
| 53 |
|
#include "utils/NumericConstant.hpp" |
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|
|
| 55 |
< |
namespace oopse { |
| 55 |
> |
namespace OpenMD { |
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|
|
| 57 |
|
/** |
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|
* @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp" |
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|
* @brief A square matrix class |
| 60 |
< |
* @template Real the element type |
| 61 |
< |
* @template Dim the dimension of the square matrix |
| 60 |
> |
* \tparam Real the element type |
| 61 |
> |
* \tparam Dim the dimension of the square matrix |
| 62 |
|
*/ |
| 63 |
|
template<typename Real, int Dim> |
| 64 |
|
class SquareMatrix : public RectMatrix<Real, Dim, Dim> { |
| 125 |
|
Real det; |
| 126 |
|
return det; |
| 127 |
|
} |
| 128 |
< |
|
| 128 |
> |
|
| 129 |
|
/** Returns the trace of this matrix. */ |
| 130 |
|
Real trace() const { |
| 131 |
|
Real tmp = 0; |
| 135 |
|
|
| 136 |
|
return tmp; |
| 137 |
|
} |
| 138 |
+ |
|
| 139 |
+ |
/** |
| 140 |
+ |
* Returns the tensor contraction (double dot product) of two rank 2 |
| 141 |
+ |
* tensors (or Matrices) |
| 142 |
+ |
* @param t1 first tensor |
| 143 |
+ |
* @param t2 second tensor |
| 144 |
+ |
* @return the tensor contraction (double dot product) of t1 and t2 |
| 145 |
+ |
*/ |
| 146 |
+ |
Real doubleDot( const SquareMatrix<Real, Dim>& t1, const SquareMatrix<Real, Dim>& t2 ) { |
| 147 |
+ |
Real tmp; |
| 148 |
+ |
tmp = 0; |
| 149 |
+ |
|
| 150 |
+ |
for (unsigned int i = 0; i < Dim; i++) |
| 151 |
+ |
for (unsigned int j =0; j < Dim; j++) |
| 152 |
+ |
tmp += t1[i][j] * t2[i][j]; |
| 153 |
+ |
|
| 154 |
+ |
return tmp; |
| 155 |
+ |
} |
| 156 |
|
|
| 157 |
+ |
|
| 158 |
|
/** Tests if this matrix is symmetrix. */ |
| 159 |
|
bool isSymmetric() const { |
| 160 |
|
for (unsigned int i = 0; i < Dim - 1; i++) |
| 182 |
|
return false; |
| 183 |
|
|
| 184 |
|
return true; |
| 185 |
+ |
} |
| 186 |
+ |
|
| 187 |
+ |
/** |
| 188 |
+ |
* Returns a column vector that contains the elements from the |
| 189 |
+ |
* diagonal of m in the order R(0) = m(0,0), R(1) = m(1,1), and so |
| 190 |
+ |
* on. |
| 191 |
+ |
*/ |
| 192 |
+ |
Vector<Real, Dim> diagonals() const { |
| 193 |
+ |
Vector<Real, Dim> result; |
| 194 |
+ |
for (unsigned int i = 0; i < Dim; i++) { |
| 195 |
+ |
result(i) = this->data_[i][i]; |
| 196 |
+ |
} |
| 197 |
+ |
return result; |
| 198 |
|
} |
| 199 |
|
|
| 200 |
|
/** Tests if this matrix is the unit matrix. */ |
| 232 |
|
* @return true if success, otherwise return false |
| 233 |
|
* @param a symmetric matrix whose eigenvectors are to be computed. On return, the matrix is |
| 234 |
|
* overwritten |
| 235 |
< |
* @param w will contain the eigenvalues of the matrix On return of this function |
| 235 |
> |
* @param d will contain the eigenvalues of the matrix On return of this function |
| 236 |
|
* @param v the columns of this matrix will contain the eigenvectors. The eigenvectors are |
| 237 |
|
* normalized and mutually orthogonal. |
| 238 |
|
*/ |
| 371 |
|
//// this is NEVER called |
| 372 |
|
if ( i >= VTK_MAX_ROTATIONS ) { |
| 373 |
|
std::cout << "vtkMath::Jacobi: Error extracting eigenfunctions" << std::endl; |
| 374 |
+ |
if (n > 4) { |
| 375 |
+ |
delete[] b; |
| 376 |
+ |
delete[] z; |
| 377 |
+ |
} |
| 378 |
|
return 0; |
| 379 |
|
} |
| 380 |
|
|
| 409 |
|
numPos++; |
| 410 |
|
} |
| 411 |
|
} |
| 412 |
< |
// if ( numPos < ceil(double(n)/double(2.0)) ) |
| 412 |
> |
// if ( numPos < ceil(RealType(n)/RealType(2.0)) ) |
| 413 |
|
if ( numPos < ceil_half_n) { |
| 414 |
|
for (i=0; i<n; i++) { |
| 415 |
|
v(i, j) *= -1.0; |
| 425 |
|
} |
| 426 |
|
|
| 427 |
|
|
| 428 |
< |
typedef SquareMatrix<double, 6> Mat6x6d; |
| 428 |
> |
typedef SquareMatrix<RealType, 6> Mat6x6d; |
| 429 |
|
} |
| 430 |
|
#endif //MATH_SQUAREMATRIX_HPP |
| 431 |
|
|
