| 1 |
< |
/* |
| 1 |
> |
/* |
| 2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#ifndef UTILS_MOLOCATOR_HPP |
| 52 |
|
#include "math/SquareMatrix3.hpp" |
| 53 |
|
#include "math/Vector3.hpp" |
| 54 |
|
#include "UseTheForce/ForceField.hpp" |
| 55 |
< |
namespace oopse { |
| 56 |
< |
//convert lattice vector to rotation matrix |
| 57 |
< |
double getAtomMass(const std::string& at, ForceField* myFF); |
| 58 |
< |
double getMolMass(MoleculeStamp *molStamp, ForceField *myFF); |
| 59 |
< |
RotMat3x3d latVec2RotMat(const Vector3d& lv); |
| 60 |
< |
class MoLocator{ |
| 61 |
< |
public: |
| 62 |
< |
MoLocator( MoleculeStamp* theStamp, ForceField* theFF); |
| 63 |
< |
void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol); |
| 64 |
< |
private: |
| 65 |
< |
void calcRef( void ); |
| 66 |
< |
MoleculeStamp* myStamp; |
| 55 |
> |
namespace OpenMD { |
| 56 |
> |
//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); |
| 60 |
> |
class MoLocator{ |
| 61 |
> |
public: |
| 62 |
> |
MoLocator( MoleculeStamp* theStamp, ForceField* theFF); |
| 63 |
> |
void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol); |
| 64 |
> |
private: |
| 65 |
> |
void calcRef( void ); |
| 66 |
> |
MoleculeStamp* myStamp; |
| 67 |
|
|
| 68 |
< |
ForceField* myFF; |
| 69 |
< |
std::vector<Vector3d> refCoords; |
| 70 |
< |
int nIntegrableObjects; |
| 68 |
> |
ForceField* myFF; |
| 69 |
> |
std::vector<Vector3d> refCoords; |
| 70 |
> |
int nIntegrableObjects; |
| 71 |
|
|
| 72 |
< |
}; |
| 72 |
> |
}; |
| 73 |
|
|
| 74 |
|
} |
| 75 |
|
#endif |
