applications/staticProps/NanoVolume.hpp

/* Copyright (c) 2006 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.
 *
 *
 *  NanoVolume.hpp
 *
 *  Purpose: To calculate convexhull, hull volume and radius
 *  using the CGAL library.
 *
 *  Created by Charles F. Vardeman II on 14 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: NanoVolume.hpp,v 1.5 2008-09-14 01:32:23 chuckv Exp $
 *
 */
#ifndef APPLICATIONS_STATICPROPS_NANOVOLUME_HPP_
#define APPLICATIONS_STATICPROPS_NANOVOLUME_HPP_
#include <vector>
#include "config.h"
#include "math/Vector3.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"

#if defined(HAVE_QHULL) || defined(HAVE_CGAL)
#ifdef HAVE_QHULL
#include "math/ConvexHull.hpp"
#endif

#ifdef HAVE_CGAL
#include "math/AlphaShape.hpp"
#endif
#endif

namespace oopse {
  class NanoVolume : public StaticAnalyser {
  public:
    NanoVolume(SimInfo* info, const std::string& filename, const std::string& sele);
    virtual void process();
    
  private:    
    Snapshot* currentSnapshot_;
    std::string selectionScript_;
    SelectionManager seleMan_;
    SelectionEvaluator evaluator_;
    std::vector<Atom*> theAtoms_;
    int frameCounter_;
    RealType totalVolume_;
    
  };
}
#endif /*NANOVOLUME_HPP_*/
Revision:	1293
Committed:	Sun Sep 14 01:32:26 2008 UTC (16 years, 7 months ago) by chuckv
Original Path:	*trunk/src/applications/staticProps/NanoVolume.hpp*
File size:	3289 byte(s)
Log Message:	Added large quantities of code for convex hull and constant pressure langevin dynamics.
#	User	Rev	Content
1	chuckv	1181	/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
2			*
3			* The University of Notre Dame grants you ("Licensee") a
4			* non-exclusive, royalty free, license to use, modify and
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8			* 1. Acknowledgement of the program authors must be made in any
9			* publication of scientific results based in part on use of the
10			* program. An acceptable form of acknowledgement is citation of
11			* the article in which the program was described (Matthew
12			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14			* Parallel Simulation Engine for Molecular Dynamics,"
15			* J. Comput. Chem. 26, pp. 252-271 (2005))
16			*
17			* 2. Redistributions of source code must retain the above copyright
18			* notice, this list of conditions and the following disclaimer.
19			*
20			* 3. Redistributions in binary form must reproduce the above copyright
21			* notice, this list of conditions and the following disclaimer in the
22			* documentation and/or other materials provided with the
23			* distribution.
24			*
25			* This software is provided "AS IS," without a warranty of any
26			* kind. All express or implied conditions, representations and
27			* warranties, including any implied warranty of merchantability,
28			* fitness for a particular purpose or non-infringement, are hereby
29			* excluded. The University of Notre Dame and its licensors shall not
30			* be liable for any damages suffered by licensee as a result of
31			* using, modifying or distributing the software or its
32			* derivatives. In no event will the University of Notre Dame or its
33			* licensors be liable for any lost revenue, profit or data, or for
34			* direct, indirect, special, consequential, incidental or punitive
35			* damages, however caused and regardless of the theory of liability,
36			* arising out of the use of or inability to use software, even if the
37			* University of Notre Dame has been advised of the possibility of
38			* such damages.
39			*
40			*
41			* NanoVolume.hpp
42			*
43			* Purpose: To calculate convexhull, hull volume and radius
44			* using the CGAL library.
45			*
46			* Created by Charles F. Vardeman II on 14 Dec 2006.
47			* @author Charles F. Vardeman II
48	chuckv	1293	* @version $Id: NanoVolume.hpp,v 1.5 2008-09-14 01:32:23 chuckv Exp $
49	chuckv	1181	*
50			*/
51			#ifndef APPLICATIONS_STATICPROPS_NANOVOLUME_HPP_
52			#define APPLICATIONS_STATICPROPS_NANOVOLUME_HPP_
53			#include <vector>
54	chuckv	1199	#include "config.h"
55	chuckv	1182	#include "math/Vector3.hpp"
56	chuckv	1181	#include "selection/SelectionEvaluator.hpp"
57			#include "selection/SelectionManager.hpp"
58			#include "applications/staticProps/StaticAnalyser.hpp"
59
60	chuckv	1199	#if defined(HAVE_QHULL) \|\| defined(HAVE_CGAL)
61			#ifdef HAVE_QHULL
62			#include "math/ConvexHull.hpp"
63			#endif
64	chuckv	1181
65	chuckv	1199	#ifdef HAVE_CGAL
66			#include "math/AlphaShape.hpp"
67			#endif
68			#endif
69
70	chuckv	1181	namespace oopse {
71			class NanoVolume : public StaticAnalyser {
72			public:
73			NanoVolume(SimInfo* info, const std::string& filename, const std::string& sele);
74			virtual void process();
75
76			private:
77			Snapshot* currentSnapshot_;
78			std::string selectionScript_;
79			SelectionManager seleMan_;
80			SelectionEvaluator evaluator_;
81	chuckv	1293	std::vector<Atom*> theAtoms_;
82	chuckv	1181	int frameCounter_;
83	chuckv	1188	RealType totalVolume_;
84	chuckv	1181
85			};
86			}
87			#endif /NANOVOLUME_HPP_/