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 "UseTheForce/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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	3086 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	483	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	483	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	483	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	483	*/
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 "UseTheForce/ForceField.hpp"
56	gezelter	1390	namespace OpenMD {
57	gezelter	507	//convert lattice vector to rotation matrix
58	tim	963	RealType getAtomMass(const std::string& at, ForceField* myFF);
59			RealType getMolMass(MoleculeStamp molStamp, ForceField myFF);
60	gezelter	507	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	gezelter	483
69	gezelter	507	ForceField* myFF;
70			std::vector<Vector3d> refCoords;
71			int nIntegrableObjects;
72	gezelter	483
73	gezelter	507	};
74	gezelter	483
75			}
76			#endif
77