| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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 |
|
#ifndef SELECTION_DISTANCEFINDER_HPP |
| 43 |
|
#define SELECTION_DISTANCEFINDER_HPP |
| 44 |
|
#include "brains/SimInfo.hpp" |
| 45 |
< |
#include "utils/OpenMDBitSet.hpp" |
| 45 |
> |
#include "selection/SelectionSet.hpp" |
| 46 |
|
#include "primitives/StuntDouble.hpp" |
| 47 |
+ |
#include "primitives/Bond.hpp" |
| 48 |
+ |
#include "primitives/Bend.hpp" |
| 49 |
+ |
#include "primitives/Torsion.hpp" |
| 50 |
+ |
#include "primitives/Inversion.hpp" |
| 51 |
|
namespace OpenMD { |
| 52 |
|
|
| 53 |
|
class DistanceFinder { |
| 54 |
|
public: |
| 55 |
|
DistanceFinder(SimInfo* si); |
| 56 |
|
|
| 57 |
< |
OpenMDBitSet find(const OpenMDBitSet& bs, RealType distance); |
| 57 |
> |
SelectionSet find(const SelectionSet& bs, RealType distance); |
| 58 |
> |
SelectionSet find(const SelectionSet& bs, RealType distance, int frame); |
| 59 |
|
|
| 60 |
|
SimInfo* info_; |
| 61 |
|
std::vector<StuntDouble*> stuntdoubles_; |
| 62 |
< |
int nStuntDoubles_; |
| 62 |
> |
std::vector<Bond*> bonds_; |
| 63 |
> |
std::vector<Bend*> bends_; |
| 64 |
> |
std::vector<Torsion*> torsions_; |
| 65 |
> |
std::vector<Inversion*> inversions_; |
| 66 |
> |
std::vector<Molecule*> molecules_; |
| 67 |
> |
vector<int> nObjects_; |
| 68 |
|
|
| 69 |
|
}; |
| 70 |
|
|
