applications/simpleBuilder/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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#ifndef APPLICATIONS_SIMPLEBUILDER_MOLOCATOR_HPP

#define APPLICATIONS_SIMPLEBUILDER_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 oopse {
//convert lattice vector to rotation matrix
double getAtomMass(const std::string& at, ForceField* myFF);
double 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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 6 months ago) by gezelter
File size:	3037 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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. 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#ifndef APPLICATIONS_SIMPLEBUILDER_MOLOCATOR_HPP
43	tim	1501
44	gezelter	1930	#define APPLICATIONS_SIMPLEBUILDER_MOLOCATOR_HPP
45
46	tim	1501	#include <vector>
47	gezelter	1930
48	tim	1501	#include "primitives/Atom.hpp"
49			#include "primitives/DirectionalAtom.hpp"
50			#include "types/MoleculeStamp.hpp"
51			#include "primitives/Molecule.hpp"
52	gezelter	1930	#include "math/SquareMatrix3.hpp"
53	tim	1674	#include "math/Vector3.hpp"
54	gezelter	1930	#include "UseTheForce/ForceField.hpp"
55			namespace oopse {
56	tim	1501	//convert lattice vector to rotation matrix
57	gezelter	1930	double getAtomMass(const std::string& at, ForceField* myFF);
58			double getMolMass(MoleculeStamp molStamp, ForceField myFF);
59			RotMat3x3d latVec2RotMat(const Vector3d& lv);
60	tim	1501	class MoLocator{
61	gezelter	1930	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	tim	1501
68	gezelter	1930	ForceField* myFF;
69			std::vector<Vector3d> refCoords;
70			int nIntegrableObjects;
71	tim	1501
72			};
73
74	gezelter	1930	}
75	tim	1501	#endif
76	gezelter	1930