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. 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_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 oopse {
  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:	3054
Committed:	Wed Oct 18 21:58:48 2006 UTC (17 years, 10 months ago) by gezelter
File size:	3598 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	tim	2242	/*
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			#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			namespace oopse {
48	gezelter	3054	class SCDElem {
49			public:
50			SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
51	tim	2242
52	gezelter	3054	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	2242
57	gezelter	3054	private:
58	tim	2242
59	gezelter	3054	std::string sele1_;
60			std::string sele2_;
61			std::string sele3_;
62			bool usePeriodicBoundaryConditions_;
63
64			typedef tuple3<StuntDouble, StuntDouble, StuntDouble*> SDTuple3;
65	tim	2242
66	gezelter	3054	std::vector<SDTuple3> tuples_;
67			};
68	tim	2242
69
70	gezelter	3054	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	2242
75	gezelter	3054	SCDOrderParameter(SimInfo* info, const std::string& filename,
76			const std::string& molname, int beginIndex, int endIndex);
77			virtual void process();
78	tim	2242
79	gezelter	3054	private:
80			void writeSCD();
81	tim	2242
82	gezelter	3054	std::vector<SCDElem> scdElems_;
83			std::vector<RealType> scdParam_;
84	tim	2242
85	gezelter	3054	Snapshot* currentSnapshot_;
86	tim	2242
87
88	gezelter	3054	};
89	tim	2242	}
90
91			#endif
92
93