src/utils/MoLocator.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#ifndef UTILS_MOLOCATOR_HPP

#define UTILS_MOLOCATOR_HPP

#include <vector>

#include "primitives/Atom.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "types/MoleculeStamp.hpp"
#include "primitives/Molecule.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "brains/ForceField.hpp"
namespace OpenMD {
  //convert lattice vector to rotation matrix
  RealType getAtomMass(const std::string& at, ForceField* myFF);
  RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF);
  RotMat3x3d latVec2RotMat(const Vector3d& lv);
  class MoLocator{
  public:
    MoLocator( MoleculeStamp* theStamp, ForceField* theFF);
    void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol);
  private:
    void calcRef( void );
    MoleculeStamp* myStamp;

    ForceField* myFF;
    std::vector<Vector3d> refCoords;
    int nIntegrableObjects;

  };

}
#endif

Revision:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	3081 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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	#ifndef UTILS_MOLOCATOR_HPP
44
45	#define UTILS_MOLOCATOR_HPP
46
47	#include <vector>
48
49	#include "primitives/Atom.hpp"
50	#include "primitives/DirectionalAtom.hpp"
51	#include "types/MoleculeStamp.hpp"
52	#include "primitives/Molecule.hpp"
53	#include "math/SquareMatrix3.hpp"
54	#include "math/Vector3.hpp"
55	#include "brains/ForceField.hpp"
56	namespace OpenMD {
57	//convert lattice vector to rotation matrix
58	RealType getAtomMass(const std::string& at, ForceField* myFF);
59	RealType getMolMass(MoleculeStamp molStamp, ForceField myFF);
60	RotMat3x3d latVec2RotMat(const Vector3d& lv);
61	class MoLocator{
62	public:
63	MoLocator( MoleculeStamp* theStamp, ForceField* theFF);
64	void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol);
65	private:
66	void calcRef( void );
67	MoleculeStamp* myStamp;
68
69	ForceField* myFF;
70	std::vector<Vector3d> refCoords;
71	int nIntegrableObjects;
72
73	};
74
75	}
76	#endif
77