| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 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 |
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#ifndef UTILS_MOLOCATOR_HPP |
| 43 |
– |
|
| 44 |
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#define UTILS_MOLOCATOR_HPP |
| 45 |
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|
| 46 |
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#include <vector> |
| 51 |
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#include "primitives/Molecule.hpp" |
| 52 |
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#include "math/SquareMatrix3.hpp" |
| 53 |
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#include "math/Vector3.hpp" |
| 54 |
< |
#include "UseTheForce/ForceField.hpp" |
| 54 |
> |
#include "brains/ForceField.hpp" |
| 55 |
> |
|
| 56 |
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namespace OpenMD { |
| 57 |
< |
//convert lattice vector to rotation matrix |
| 57 |
< |
RealType getAtomMass(const std::string& at, ForceField* myFF); |
| 58 |
< |
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF); |
| 59 |
< |
RotMat3x3d latVec2RotMat(const Vector3d& lv); |
| 57 |
> |
|
| 58 |
|
class MoLocator{ |
| 59 |
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public: |
| 60 |
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MoLocator( MoleculeStamp* theStamp, ForceField* theFF); |
| 61 |
|
void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol); |
| 62 |
+ |
static RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF); |
| 63 |
+ |
|
| 64 |
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private: |
| 65 |
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void calcRef( void ); |
| 66 |
+ |
static RealType getAtomMass(const std::string& at, ForceField* myFF); |
| 67 |
+ |
RotMat3x3d latVec2RotMat(const Vector3d& lv); ///< convert lattice vector to rotation matrix |
| 68 |
+ |
|
| 69 |
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MoleculeStamp* myStamp; |
| 70 |
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|
| 71 |
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ForceField* myFF; |
| 72 |
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std::vector<Vector3d> refCoords; |
| 73 |
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int nIntegrableObjects; |
| 71 |
– |
|
| 74 |
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}; |
| 73 |
– |
|
| 75 |
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} |
| 76 |
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#endif |
| 77 |
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|
