applications/staticProps/SCDOrderParameter.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]  Vardeman & Gezelter, in progress (2009).                        
 */
#ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "utils/Tuple.hpp"
namespace OpenMD {
  class SCDElem {
  public:
    SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
    
    std::string getSelection1() const {return sele1_;}
    std::string getSelection2() const {return sele2_;}
    std::string getSelection3() const {return sele3_;}
    RealType calcSCD(Snapshot* snapshot);
            
  private:
            
    std::string sele1_;                
    std::string sele2_;
    std::string sele3_;
    bool usePeriodicBoundaryConditions_;
      
    typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3;
        
    std::vector<SDTuple3> tuples_;
  };


  class SCDOrderParameter : public StaticAnalyser{
  public:
    SCDOrderParameter(SimInfo* info, const std::string& filename, 
                      const std::string& sele1, const std::string& sele2, const std::string& sele3);

    SCDOrderParameter(SimInfo* info, const std::string& filename, 
                      const std::string& molname, int beginIndex, int endIndex);
    virtual void process();

  private:
    void writeSCD();

    std::vector<SCDElem> scdElems_;
    std::vector<RealType> scdParam_;
            
    Snapshot* currentSnapshot_;

            
  };
}

#endif


Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/SCDOrderParameter.hpp*
File size:	3640 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	545	/*
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	545	* 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	545	* 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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	545	*/
41			#ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
42			#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
43			#include "selection/SelectionEvaluator.hpp"
44			#include "selection/SelectionManager.hpp"
45			#include "applications/staticProps/StaticAnalyser.hpp"
46			#include "utils/Tuple.hpp"
47	gezelter	1390	namespace OpenMD {
48	gezelter	1078	class SCDElem {
49			public:
50			SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
51	tim	545
52	gezelter	1078	std::string getSelection1() const {return sele1_;}
53			std::string getSelection2() const {return sele2_;}
54			std::string getSelection3() const {return sele3_;}
55			RealType calcSCD(Snapshot* snapshot);
56	tim	545
57	gezelter	1078	private:
58	tim	545
59	gezelter	1078	std::string sele1_;
60			std::string sele2_;
61			std::string sele3_;
62			bool usePeriodicBoundaryConditions_;
63
64			typedef tuple3<StuntDouble, StuntDouble, StuntDouble*> SDTuple3;
65	tim	545
66	gezelter	1078	std::vector<SDTuple3> tuples_;
67			};
68	tim	545
69
70	gezelter	1078	class SCDOrderParameter : public StaticAnalyser{
71			public:
72			SCDOrderParameter(SimInfo* info, const std::string& filename,
73			const std::string& sele1, const std::string& sele2, const std::string& sele3);
74	tim	545
75	gezelter	1078	SCDOrderParameter(SimInfo* info, const std::string& filename,
76			const std::string& molname, int beginIndex, int endIndex);
77			virtual void process();
78	tim	545
79	gezelter	1078	private:
80			void writeSCD();
81	tim	545
82	gezelter	1078	std::vector<SCDElem> scdElems_;
83			std::vector<RealType> scdParam_;
84	tim	545
85	gezelter	1078	Snapshot* currentSnapshot_;
86	tim	545
87
88	gezelter	1078	};
89	tim	545	}
90
91			#endif
92
93