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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	3707 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
43	#define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
44	#include "selection/SelectionEvaluator.hpp"
45	#include "selection/SelectionManager.hpp"
46	#include "applications/staticProps/StaticAnalyser.hpp"
47	#include "utils/Tuple.hpp"
48	namespace OpenMD {
49	class SCDElem {
50	public:
51	SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
52
53	std::string getSelection1() const {return sele1_;}
54	std::string getSelection2() const {return sele2_;}
55	std::string getSelection3() const {return sele3_;}
56	RealType calcSCD(Snapshot* snapshot);
57
58	private:
59
60	std::string sele1_;
61	std::string sele2_;
62	std::string sele3_;
63	bool usePeriodicBoundaryConditions_;
64
65	typedef tuple3<StuntDouble, StuntDouble, StuntDouble*> SDTuple3;
66
67	std::vector<SDTuple3> tuples_;
68	};
69
70
71	class SCDOrderParameter : public StaticAnalyser{
72	public:
73	SCDOrderParameter(SimInfo* info, const std::string& filename,
74	const std::string& sele1, const std::string& sele2, const std::string& sele3);
75
76	SCDOrderParameter(SimInfo* info, const std::string& filename,
77	const std::string& molname, int beginIndex, int endIndex);
78	virtual void process();
79
80	private:
81	void writeSCD();
82
83	std::vector<SCDElem> scdElems_;
84	std::vector<RealType> scdParam_;
85
86	Snapshot* currentSnapshot_;
87
88
89	};
90	}
91
92	#endif
93
94