| 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: |
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* |
| 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 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* 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, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
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|
| 43 |
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/** |
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*/ |
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#ifndef MATH_SQUAREMATRIX3_HPP |
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#define MATH_SQUAREMATRIX3_HPP |
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+ |
#include "config.h" |
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+ |
#include <cmath> |
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#include <vector> |
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#include "Quaternion.hpp" |
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#include "SquareMatrix.hpp" |
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#include "Vector3.hpp" |
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#include "utils/NumericConstant.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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template<typename Real> |
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class SquareMatrix3 : public SquareMatrix<Real, 3> { |
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return *this; |
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} |
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|
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+ |
|
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/** |
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* Sets this matrix to a rotation matrix by three euler angles |
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* @ param euler |
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* Sets this matrix to a rotation matrix by three euler angles |
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* @param phi |
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* @param theta |
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< |
* @psi theta |
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> |
* @param psi |
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*/ |
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void setupRotMat(Real phi, Real theta, Real psi) { |
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Real sphi, stheta, spsi; |
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} |
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|
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|
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– |
|
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/** |
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* Returns the quaternion from this rotation matrix |
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* @return the quaternion from this rotation matrix |
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SquareMatrix3<Real> inverse() const { |
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SquareMatrix3<Real> m; |
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RealType det = determinant(); |
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< |
if (fabs(det) <= oopse::epsilon) { |
| 327 |
> |
if (fabs(det) <= OpenMD::epsilon) { |
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|
//"The method was called on a matrix with |determinant| <= 1e-6.", |
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//"This is a runtime or a programming error in your application."); |
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std::vector<int> zeroDiagElementIndex; |
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for (int i =0; i < 3; ++i) { |
| 332 |
< |
if (fabs(this->data_[i][i]) <= oopse::epsilon) { |
| 332 |
> |
if (fabs(this->data_[i][i]) <= OpenMD::epsilon) { |
| 333 |
|
zeroDiagElementIndex.push_back(i); |
| 334 |
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} |
| 335 |
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} |
| 352 |
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|
| 353 |
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/* |
| 354 |
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for(std::vector<int>::iterator iter = zeroDiagElementIndex.begin(); iter != zeroDiagElementIndex.end() ++iter) { |
| 355 |
< |
if (this->data_[*iter][0] > oopse::epsilon || this->data_[*iter][1] ||this->data_[*iter][2] || |
| 356 |
< |
this->data_[0][*iter] > oopse::epsilon || this->data_[1][*iter] ||this->data_[2][*iter] ) { |
| 355 |
> |
if (this->data_[*iter][0] > OpenMD::epsilon || this->data_[*iter][1] ||this->data_[*iter][2] || |
| 356 |
> |
this->data_[0][*iter] > OpenMD::epsilon || this->data_[1][*iter] ||this->data_[2][*iter] ) { |
| 357 |
|
std::cout << "can not inverse matrix" << std::endl; |
| 358 |
|
} |
| 359 |
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} |
| 420 |
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Vector3<Real> v_maxI, v_k, v_j; |
| 421 |
|
|
| 422 |
|
// diagonalize using Jacobi |
| 423 |
< |
jacobi(a, w, v); |
| 423 |
> |
SquareMatrix3<Real>::jacobi(a, w, v); |
| 424 |
|
// if all the eigenvalues are the same, return identity matrix |
| 425 |
|
if (w[0] == w[1] && w[0] == w[2] ) { |
| 426 |
|
v = SquareMatrix3<Real>::identity(); |
| 569 |
|
typedef SquareMatrix3<RealType> Mat3x3d; |
| 570 |
|
typedef SquareMatrix3<RealType> RotMat3x3d; |
| 571 |
|
|
| 572 |
< |
} //namespace oopse |
| 572 |
> |
} //namespace OpenMD |
| 573 |
|
#endif // MATH_SQUAREMATRIX_HPP |
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|
|
