| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* distribution. |
| 28 |
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* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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|
#ifndef UTILS_MOLOCATOR_HPP |
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– |
|
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#define UTILS_MOLOCATOR_HPP |
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|
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#include <vector> |
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#include "primitives/Molecule.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/Vector3.hpp" |
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< |
#include "UseTheForce/ForceField.hpp" |
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< |
namespace oopse { |
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< |
//convert lattice vector to rotation matrix |
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< |
RealType getAtomMass(const std::string& at, ForceField* myFF); |
| 58 |
< |
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF); |
| 59 |
< |
RotMat3x3d latVec2RotMat(const Vector3d& lv); |
| 54 |
> |
#include "brains/ForceField.hpp" |
| 55 |
> |
|
| 56 |
> |
namespace OpenMD { |
| 57 |
> |
|
| 58 |
|
class MoLocator{ |
| 59 |
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public: |
| 60 |
|
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 |
|
private: |
| 65 |
|
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 |
|
MoleculeStamp* myStamp; |
| 70 |
|
|
| 71 |
|
ForceField* myFF; |
| 72 |
|
std::vector<Vector3d> refCoords; |
| 73 |
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int nIntegrableObjects; |
| 71 |
– |
|
| 74 |
|
}; |
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– |
|
| 75 |
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} |
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#endif |
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|
