# | Line 6 | Line 6 | |
---|---|---|
6 | * redistribute this software in source and binary code form, provided | |
7 | * 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. | |
# | Line 37 | Line 28 | |
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] Vardeman & Gezelter, in progress (2009). |
40 | */ | |
41 | ||
42 | /** | |
# | Line 49 | Line 49 | |
49 | #define MATH_SQUAREMATRIX_HPP | |
50 | ||
51 | #include "math/RectMatrix.hpp" | |
52 | + | #include "utils/NumericConstant.hpp" |
53 | ||
54 | < | namespace oopse { |
54 | > | namespace OpenMD { |
55 | ||
56 | /** | |
57 | * @class SquareMatrix SquareMatrix.hpp "math/SquareMatrix.hpp" | |
# | Line 138 | Line 139 | namespace oopse { | |
139 | bool isSymmetric() const { | |
140 | for (unsigned int i = 0; i < Dim - 1; i++) | |
141 | for (unsigned int j = i; j < Dim; j++) | |
142 | < | if (fabs(this->data_[i][j] - this->data_[j][i]) > oopse::epsilon) |
142 | > | if (fabs(this->data_[i][j] - this->data_[j][i]) > epsilon) |
143 | return false; | |
144 | ||
145 | return true; | |
# | Line 157 | Line 158 | namespace oopse { | |
158 | bool isDiagonal() const { | |
159 | for (unsigned int i = 0; i < Dim ; i++) | |
160 | for (unsigned int j = 0; j < Dim; j++) | |
161 | < | if (i !=j && fabs(this->data_[i][j]) > oopse::epsilon) |
161 | > | if (i !=j && fabs(this->data_[i][j]) > epsilon) |
162 | return false; | |
163 | ||
164 | return true; | |
# | Line 169 | Line 170 | namespace oopse { | |
170 | return false; | |
171 | ||
172 | for (unsigned int i = 0; i < Dim ; i++) | |
173 | < | if (fabs(this->data_[i][i] - 1) > oopse::epsilon) |
173 | > | if (fabs(this->data_[i][i] - 1) > epsilon) |
174 | return false; | |
175 | ||
176 | return true; | |
# | Line 371 | Line 372 | namespace oopse { | |
372 | numPos++; | |
373 | } | |
374 | } | |
375 | < | // if ( numPos < ceil(double(n)/double(2.0)) ) |
375 | > | // if ( numPos < ceil(RealType(n)/RealType(2.0)) ) |
376 | if ( numPos < ceil_half_n) { | |
377 | for (i=0; i<n; i++) { | |
378 | v(i, j) *= -1.0; | |
# | Line 387 | Line 388 | namespace oopse { | |
388 | } | |
389 | ||
390 | ||
391 | + | typedef SquareMatrix<RealType, 6> Mat6x6d; |
392 | } | |
393 | #endif //MATH_SQUAREMATRIX_HPP | |
394 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |