src/selection/DistanceFinder.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 SELECTION_DISTANCEFINDER_HPP
#define SELECTION_DISTANCEFINDER_HPP
#include "brains/SimInfo.hpp"
#include "selection/SelectionSet.hpp"
#include "primitives/StuntDouble.hpp"
#include "primitives/Bond.hpp"
#include "primitives/Bend.hpp"
#include "primitives/Torsion.hpp"
#include "primitives/Inversion.hpp"
namespace OpenMD {

  class DistanceFinder {
  public:
    DistanceFinder(SimInfo* si);

    SelectionSet find(const SelectionSet& bs, RealType distance);
    SelectionSet find(const SelectionSet& bs, RealType distance, int frame);

    SimInfo* info_;
    std::vector<StuntDouble*> stuntdoubles_;
    std::vector<Bond*> bonds_;
    std::vector<Bend*> bends_;
    std::vector<Torsion*> torsions_;
    std::vector<Inversion*> inversions_;
    vector<int> nObjects_;
        
  };

}
#endif 
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	2984 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	User	Rev	Content
1	tim	295	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	295	* 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	295	* 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	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	295	*/
42			#ifndef SELECTION_DISTANCEFINDER_HPP
43			#define SELECTION_DISTANCEFINDER_HPP
44			#include "brains/SimInfo.hpp"
45	gezelter	1953	#include "selection/SelectionSet.hpp"
46	tim	315	#include "primitives/StuntDouble.hpp"
47	gezelter	1953	#include "primitives/Bond.hpp"
48			#include "primitives/Bend.hpp"
49			#include "primitives/Torsion.hpp"
50			#include "primitives/Inversion.hpp"
51	gezelter	1390	namespace OpenMD {
52	tim	295
53	gezelter	507	class DistanceFinder {
54			public:
55			DistanceFinder(SimInfo* si);
56	tim	295
57	gezelter	1953	SelectionSet find(const SelectionSet& bs, RealType distance);
58			SelectionSet find(const SelectionSet& bs, RealType distance, int frame);
59	tim	295
60	gezelter	507	SimInfo* info_;
61			std::vector<StuntDouble*> stuntdoubles_;
62	gezelter	1953	std::vector<Bond*> bonds_;
63			std::vector<Bend*> bends_;
64			std::vector<Torsion*> torsions_;
65			std::vector<Inversion*> inversions_;
66			vector<int> nObjects_;
67	tim	295
68	gezelter	507	};
69	tim	295
70			}
71			#endif