| 6 |
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* 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. |
| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 52 |
|
#include <cmath> |
| 53 |
|
#include "Vector.hpp" |
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|
|
| 55 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
| 57 |
|
/** |
| 58 |
|
* @class RectMatrix RectMatrix.hpp "math/RectMatrix.hpp" |
| 151 |
|
Vector<Real, Row> getRow(unsigned int row) { |
| 152 |
|
Vector<Real, Row> v; |
| 153 |
|
|
| 154 |
< |
for (unsigned int i = 0; i < Row; i++) |
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> |
for (unsigned int i = 0; i < Col; i++) |
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|
v[i] = this->data_[row][i]; |
| 156 |
|
|
| 157 |
|
return v; |
| 164 |
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*/ |
| 165 |
|
void setRow(unsigned int row, const Vector<Real, Row>& v) { |
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|
|
| 167 |
< |
for (unsigned int i = 0; i < Row; i++) |
| 167 |
> |
for (unsigned int i = 0; i < Col; i++) |
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|
this->data_[row][i] = v[i]; |
| 169 |
|
} |
| 170 |
|
|
| 176 |
|
Vector<Real, Col> getColumn(unsigned int col) { |
| 177 |
|
Vector<Real, Col> v; |
| 178 |
|
|
| 179 |
< |
for (unsigned int j = 0; j < Col; j++) |
| 179 |
> |
for (unsigned int j = 0; j < Row; j++) |
| 180 |
|
v[j] = this->data_[j][col]; |
| 181 |
|
|
| 182 |
|
return v; |
| 189 |
|
*/ |
| 190 |
|
void setColumn(unsigned int col, const Vector<Real, Col>& v){ |
| 191 |
|
|
| 192 |
< |
for (unsigned int j = 0; j < Col; j++) |
| 192 |
> |
for (unsigned int j = 0; j < Row; j++) |
| 193 |
|
this->data_[j][col] = v[j]; |
| 194 |
|
} |
| 195 |
|
|
| 389 |
|
|
| 390 |
|
return result; |
| 391 |
|
} |
| 392 |
< |
|
| 392 |
> |
|
| 393 |
> |
template<class MatrixType> |
| 394 |
> |
void setSubMatrix(unsigned int beginRow, unsigned int beginCol, const MatrixType& m) { |
| 395 |
> |
assert(beginRow + m.getNRow() -1 <= getNRow()); |
| 396 |
> |
assert(beginCol + m.getNCol() -1 <= getNCol()); |
| 397 |
> |
|
| 398 |
> |
for (unsigned int i = 0; i < m.getNRow(); ++i) |
| 399 |
> |
for (unsigned int j = 0; j < m.getNCol(); ++j) |
| 400 |
> |
this->data_[beginRow+i][beginCol+j] = m(i, j); |
| 401 |
> |
} |
| 402 |
> |
|
| 403 |
> |
template<class MatrixType> |
| 404 |
> |
void getSubMatrix(unsigned int beginRow, unsigned int beginCol, MatrixType& m) { |
| 405 |
> |
assert(beginRow + m.getNRow() -1 <= getNRow()); |
| 406 |
> |
assert(beginCol + m.getNCol() - 1 <= getNCol()); |
| 407 |
> |
|
| 408 |
> |
for (unsigned int i = 0; i < m.getNRow(); ++i) |
| 409 |
> |
for (unsigned int j = 0; j < m.getNCol(); ++j) |
| 410 |
> |
m(i, j) = this->data_[beginRow+i][beginCol+j]; |
| 411 |
> |
} |
| 412 |
> |
|
| 413 |
> |
unsigned int getNRow() const {return Row;} |
| 414 |
> |
unsigned int getNCol() const {return Col;} |
| 415 |
> |
|
| 416 |
|
protected: |
| 417 |
|
Real data_[Row][Col]; |
| 418 |
|
}; |
