| 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 |
|
* 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, 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 |
|
/** |
| 50 |
|
#define MATH_SQUAREMATRIX_HPP |
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|
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|
#include "math/RectMatrix.hpp" |
| 53 |
+ |
#include "utils/NumericConstant.hpp" |
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|
|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
| 57 |
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/** |
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* @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp" |
| 140 |
|
bool isSymmetric() const { |
| 141 |
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for (unsigned int i = 0; i < Dim - 1; i++) |
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|
for (unsigned int j = i; j < Dim; j++) |
| 143 |
< |
if (fabs(this->data_[i][j] - this->data_[j][i]) > oopse::epsilon) |
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> |
if (fabs(this->data_[i][j] - this->data_[j][i]) > epsilon) |
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return false; |
| 145 |
|
|
| 146 |
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return true; |
| 159 |
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bool isDiagonal() const { |
| 160 |
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for (unsigned int i = 0; i < Dim ; i++) |
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|
for (unsigned int j = 0; j < Dim; j++) |
| 162 |
< |
if (i !=j && fabs(this->data_[i][j]) > oopse::epsilon) |
| 162 |
> |
if (i !=j && fabs(this->data_[i][j]) > epsilon) |
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return false; |
| 164 |
|
|
| 165 |
|
return true; |
| 171 |
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return false; |
| 172 |
|
|
| 173 |
|
for (unsigned int i = 0; i < Dim ; i++) |
| 174 |
< |
if (fabs(this->data_[i][i] - 1) > oopse::epsilon) |
| 174 |
> |
if (fabs(this->data_[i][i] - 1) > epsilon) |
| 175 |
|
return false; |
| 176 |
|
|
| 177 |
|
return true; |
| 373 |
|
numPos++; |
| 374 |
|
} |
| 375 |
|
} |
| 376 |
< |
// if ( numPos < ceil(double(n)/double(2.0)) ) |
| 376 |
> |
// if ( numPos < ceil(RealType(n)/RealType(2.0)) ) |
| 377 |
|
if ( numPos < ceil_half_n) { |
| 378 |
|
for (i=0; i<n; i++) { |
| 379 |
|
v(i, j) *= -1.0; |
| 389 |
|
} |
| 390 |
|
|
| 391 |
|
|
| 392 |
+ |
typedef SquareMatrix<RealType, 6> Mat6x6d; |
| 393 |
|
} |
| 394 |
|
#endif //MATH_SQUAREMATRIX_HPP |
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|
