| 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 |
|
* 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 |
|
/** |
| 57 |
|
#include <algorithm> |
| 58 |
|
#include <vector> |
| 59 |
|
|
| 60 |
< |
namespace oopse { |
| 60 |
> |
namespace OpenMD { |
| 61 |
|
|
| 62 |
|
/** |
| 63 |
|
* @class DynamicVector DynamicVector.hpp "math/DynamicVector.hpp" |
| 127 |
|
DynamicVector(_InputIterator first, _InputIterator last, |
| 128 |
|
const allocator_type& alloc = allocator_type()) |
| 129 |
|
: std::vector<Real, Alloc>(first, last, alloc) {} |
| 130 |
< |
|
| 130 |
> |
|
| 131 |
> |
inline Real operator()(unsigned int i) const{ |
| 132 |
> |
return (*this)[i]; |
| 133 |
> |
} |
| 134 |
> |
|
| 135 |
> |
inline Real& operator()(unsigned int i){ |
| 136 |
> |
return (*this)[i]; |
| 137 |
> |
} |
| 138 |
|
/** |
| 139 |
|
* Tests if this vetor is equal to other vector |
| 140 |
|
* @return true if equal, otherwise return false |
| 295 |
|
|
| 296 |
|
len = length(); |
| 297 |
|
|
| 298 |
< |
//if (len < oopse:epsilon) |
| 298 |
> |
//if (len < OpenMD::NumericConstant::epsilon) |
| 299 |
|
// throw(); |
| 300 |
|
|
| 301 |
|
*this /= len; |
| 308 |
|
inline bool isNormalized() { |
| 309 |
|
return equal(lengthSquare(), 1.0); |
| 310 |
|
} |
| 311 |
+ |
|
| 312 |
+ |
template<class VectorType> |
| 313 |
+ |
void getSubVector(unsigned int beginning, VectorType& v) { |
| 314 |
+ |
assert(beginning + v.size() -1 <= this->size()); |
| 315 |
+ |
|
| 316 |
+ |
for (unsigned int i = 0; i < v.size(); ++i) |
| 317 |
+ |
v(i) = (*this)[beginning+i]; |
| 318 |
+ |
} |
| 319 |
+ |
|
| 320 |
|
|
| 321 |
|
}; |
| 322 |
|
|
