src/visitors/LipidTransVisitor.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifndef VISITORS_LIPIDTRANSVISITOR_HPP
#define VISITORS_LIPIDTRANSVISITOR_HPP

#include "visitors/BaseVisitor.hpp"
#include "primitives/StuntDouble.hpp"
#include "visitors/AtomData.hpp"
#include "primitives/Molecule.hpp"
#include "brains/SimInfo.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
namespace OpenMD {

  class LipidTransVisitor : public BaseVisitor {
  public:
    LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript); 
        
    virtual void visit(Atom* atom) { internalVisit(atom); }
    virtual void visit(DirectionalAtom* datom) { internalVisit(datom);}
    virtual void visit(RigidBody* rb) { internalVisit(rb);}

    virtual const std::string toString();

    void update();
        
  protected:
    void internalVisit(StuntDouble* sd);
    SimInfo* info_;
    SelectionEvaluator originEvaluator_;
    SelectionManager originSeleMan_;
    DirectionalAtom* originDatom_;
    SelectionEvaluator refEvaluator_;
    SelectionManager refSeleMan_;
    StuntDouble* refSd_;
    RotMat3x3d rotMat_;
    Vector3d origin_;
  };
}
#endif
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	3326 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	gezelter	507	/*
2	tim	369	* 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	tim	369	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	369	* 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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	tim	369	*/
42
43			#ifndef VISITORS_LIPIDTRANSVISITOR_HPP
44			#define VISITORS_LIPIDTRANSVISITOR_HPP
45
46			#include "visitors/BaseVisitor.hpp"
47			#include "primitives/StuntDouble.hpp"
48			#include "visitors/AtomData.hpp"
49			#include "primitives/Molecule.hpp"
50			#include "brains/SimInfo.hpp"
51			#include "selection/SelectionEvaluator.hpp"
52			#include "selection/SelectionManager.hpp"
53	gezelter	1390	namespace OpenMD {
54	tim	369
55	gezelter	507	class LipidTransVisitor : public BaseVisitor {
56			public:
57			LipidTransVisitor(SimInfo* info, const std::string& originSeleScript, const std::string& refSeleScript);
58	tim	369
59	gezelter	507	virtual void visit(Atom* atom) { internalVisit(atom); }
60			virtual void visit(DirectionalAtom* datom) { internalVisit(datom);}
61			virtual void visit(RigidBody* rb) { internalVisit(rb);}
62	tim	369
63	gezelter	507	virtual const std::string toString();
64	tim	369
65	gezelter	507	void update();
66	tim	369
67	gezelter	507	protected:
68			void internalVisit(StuntDouble* sd);
69			SimInfo* info_;
70			SelectionEvaluator originEvaluator_;
71			SelectionManager originSeleMan_;
72			DirectionalAtom* originDatom_;
73			SelectionEvaluator refEvaluator_;
74			SelectionManager refSeleMan_;
75			StuntDouble* refSd_;
76			RotMat3x3d rotMat_;
77			Vector3d origin_;
78			};
79	tim	369	}
80			#endif