| 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. |
| 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 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 53 |
|
#include <cmath> |
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|
#include "Vector.hpp" |
| 55 |
|
|
| 56 |
< |
namespace oopse { |
| 56 |
> |
namespace OpenMD { |
| 57 |
|
|
| 58 |
|
/** |
| 59 |
|
* @class RectMatrix RectMatrix.hpp "math/RectMatrix.hpp" |
| 152 |
|
Vector<Real, Row> getRow(unsigned int row) { |
| 153 |
|
Vector<Real, Row> v; |
| 154 |
|
|
| 155 |
< |
for (unsigned int i = 0; i < Row; i++) |
| 155 |
> |
for (unsigned int i = 0; i < Col; i++) |
| 156 |
|
v[i] = this->data_[row][i]; |
| 157 |
|
|
| 158 |
|
return v; |
| 165 |
|
*/ |
| 166 |
|
void setRow(unsigned int row, const Vector<Real, Row>& v) { |
| 167 |
|
|
| 168 |
< |
for (unsigned int i = 0; i < Row; i++) |
| 168 |
> |
for (unsigned int i = 0; i < Col; i++) |
| 169 |
|
this->data_[row][i] = v[i]; |
| 170 |
|
} |
| 171 |
|
|
| 177 |
|
Vector<Real, Col> getColumn(unsigned int col) { |
| 178 |
|
Vector<Real, Col> v; |
| 179 |
|
|
| 180 |
< |
for (unsigned int j = 0; j < Col; j++) |
| 180 |
> |
for (unsigned int j = 0; j < Row; j++) |
| 181 |
|
v[j] = this->data_[j][col]; |
| 182 |
|
|
| 183 |
|
return v; |
| 190 |
|
*/ |
| 191 |
|
void setColumn(unsigned int col, const Vector<Real, Col>& v){ |
| 192 |
|
|
| 193 |
< |
for (unsigned int j = 0; j < Col; j++) |
| 193 |
> |
for (unsigned int j = 0; j < Row; j++) |
| 194 |
|
this->data_[j][col] = v[j]; |
| 195 |
|
} |
| 196 |
|
|
| 221 |
|
/** |
| 222 |
|
* Tests if this matrix is identical to matrix m |
| 223 |
|
* @return true if this matrix is equal to the matrix m, return false otherwise |
| 224 |
< |
* @m matrix to be compared |
| 224 |
> |
* @param m matrix to be compared |
| 225 |
|
* |
| 226 |
|
* @todo replace operator == by template function equal |
| 227 |
|
*/ |
| 237 |
|
/** |
| 238 |
|
* Tests if this matrix is not equal to matrix m |
| 239 |
|
* @return true if this matrix is not equal to the matrix m, return false otherwise |
| 240 |
< |
* @m matrix to be compared |
| 240 |
> |
* @param m matrix to be compared |
| 241 |
|
*/ |
| 242 |
|
bool operator !=(const RectMatrix<Real, Row, Col>& m) { |
| 243 |
|
return !(*this == m); |
| 390 |
|
|
| 391 |
|
return result; |
| 392 |
|
} |
| 393 |
< |
|
| 393 |
> |
|
| 394 |
> |
template<class MatrixType> |
| 395 |
> |
void setSubMatrix(unsigned int beginRow, unsigned int beginCol, const MatrixType& m) { |
| 396 |
> |
assert(beginRow + m.getNRow() -1 <= getNRow()); |
| 397 |
> |
assert(beginCol + m.getNCol() -1 <= getNCol()); |
| 398 |
> |
|
| 399 |
> |
for (unsigned int i = 0; i < m.getNRow(); ++i) |
| 400 |
> |
for (unsigned int j = 0; j < m.getNCol(); ++j) |
| 401 |
> |
this->data_[beginRow+i][beginCol+j] = m(i, j); |
| 402 |
> |
} |
| 403 |
> |
|
| 404 |
> |
template<class MatrixType> |
| 405 |
> |
void getSubMatrix(unsigned int beginRow, unsigned int beginCol, MatrixType& m) { |
| 406 |
> |
assert(beginRow + m.getNRow() -1 <= getNRow()); |
| 407 |
> |
assert(beginCol + m.getNCol() - 1 <= getNCol()); |
| 408 |
> |
|
| 409 |
> |
for (unsigned int i = 0; i < m.getNRow(); ++i) |
| 410 |
> |
for (unsigned int j = 0; j < m.getNCol(); ++j) |
| 411 |
> |
m(i, j) = this->data_[beginRow+i][beginCol+j]; |
| 412 |
> |
} |
| 413 |
> |
|
| 414 |
> |
unsigned int getNRow() const {return Row;} |
| 415 |
> |
unsigned int getNCol() const {return Col;} |
| 416 |
> |
|
| 417 |
|
protected: |
| 418 |
|
Real data_[Row][Col]; |
| 419 |
|
}; |
| 507 |
|
} |
| 508 |
|
|
| 509 |
|
/** |
| 510 |
< |
* Return the multiplication of a matrix and a vector (m * v). |
| 510 |
> |
* Returns the multiplication of a matrix and a vector (m * v). |
| 511 |
|
* @return the multiplication of a matrix and a vector |
| 512 |
|
* @param m the matrix |
| 513 |
|
* @param v the vector |
| 524 |
|
} |
| 525 |
|
|
| 526 |
|
/** |
| 527 |
+ |
* Returns the multiplication of a vector transpose and a matrix (v^T * m). |
| 528 |
+ |
* @return the multiplication of a vector transpose and a matrix |
| 529 |
+ |
* @param v the vector |
| 530 |
+ |
* @param m the matrix |
| 531 |
+ |
*/ |
| 532 |
+ |
template<typename Real, unsigned int Row, unsigned int Col> |
| 533 |
+ |
inline Vector<Real, Col> operator *(const Vector<Real, Row>& v, const RectMatrix<Real, Row, Col>& m) { |
| 534 |
+ |
Vector<Real, Row> result; |
| 535 |
+ |
|
| 536 |
+ |
for (unsigned int i = 0; i < Col ; i++) |
| 537 |
+ |
for (unsigned int j = 0; j < Row ; j++) |
| 538 |
+ |
result[i] += v[j] * m(j, i); |
| 539 |
+ |
|
| 540 |
+ |
return result; |
| 541 |
+ |
} |
| 542 |
+ |
|
| 543 |
+ |
/** |
| 544 |
|
* Return the scalar division of matrix (m / s). |
| 545 |
|
* @return the scalar division of matrix |
| 546 |
|
* @param m the matrix |
| 555 |
|
return result; |
| 556 |
|
} |
| 557 |
|
|
| 558 |
+ |
|
| 559 |
|
/** |
| 560 |
+ |
* Returns the vector (cross) product of two matrices. This |
| 561 |
+ |
* operation is defined in: |
| 562 |
+ |
* |
| 563 |
+ |
* W. Smith, "Point Multipoles in the Ewald Summation (Revisited)," |
| 564 |
+ |
* CCP5 Newsletter No 46., pp. 18-30. |
| 565 |
+ |
* |
| 566 |
+ |
* Equation 21 defines: |
| 567 |
+ |
* \f[ |
| 568 |
+ |
* V_alpha = \sum_\beta \left[ A_{\alpha+1,\beta} * B_{\alpha+2,\beta} |
| 569 |
+ |
-A_{\alpha+2,\beta} * B_{\alpha+2,\beta} \right] |
| 570 |
+ |
* \f] |
| 571 |
+ |
|
| 572 |
+ |
* where \f[\alpha+1\f] and \f[\alpha+2\f] are regarded as cyclic |
| 573 |
+ |
* permuations of the matrix indices (i.e. for a 3x3 matrix, when |
| 574 |
+ |
* \f[\alpha = 2\f], \f[\alpha + 1 = 3 \f], and \f[\alpha + 2 = 1 \f] ). |
| 575 |
+ |
* |
| 576 |
+ |
* @param t1 first matrix |
| 577 |
+ |
* @param t2 second matrix |
| 578 |
+ |
* @return the cross product (vector product) of t1 and t2 |
| 579 |
+ |
*/ |
| 580 |
+ |
template<typename Real, unsigned int Row, unsigned int Col> |
| 581 |
+ |
inline Vector<Real, Row> cross( const RectMatrix<Real, Row, Col>& t1, |
| 582 |
+ |
const RectMatrix<Real, Row, Col>& t2 ) { |
| 583 |
+ |
Vector<Real, Row> result; |
| 584 |
+ |
unsigned int i1; |
| 585 |
+ |
unsigned int i2; |
| 586 |
+ |
|
| 587 |
+ |
for (unsigned int i = 0; i < Row; i++) { |
| 588 |
+ |
i1 = (i+1)%Row; |
| 589 |
+ |
i2 = (i+2)%Row; |
| 590 |
+ |
for (unsigned int j = 0; j < Col; j++) { |
| 591 |
+ |
result[i] += t1(i1,j) * t2(i2,j) - t1(i2,j) * t2(i1,j); |
| 592 |
+ |
} |
| 593 |
+ |
} |
| 594 |
+ |
return result; |
| 595 |
+ |
} |
| 596 |
+ |
|
| 597 |
+ |
|
| 598 |
+ |
/** |
| 599 |
|
* Write to an output stream |
| 600 |
|
*/ |
| 601 |
|
template<typename Real, unsigned int Row, unsigned int Col> |
