applications/staticProps/GofRAngle.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_GOFRANGLE_HPP
#define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP

#include "applications/staticProps/RadialDistrFunc.hpp"
namespace OpenMD {

  class GofRAngle : public RadialDistrFunc {
    
  public:
    GofRAngle(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2, 
              RealType len, int nrbins, int nangleBins);
    GofRAngle(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2, 
              const std::string& sele3, 
              RealType len, int nrbins, int nangleBins);

    int getNRBins() {
      return nRBins_; 
    }

    RealType getLength() {
      return len_;
    }

    int getNAngleBins() {return nAngleBins_;}
        
  private:

    virtual void preProcess();
    virtual void processNonOverlapping( SelectionManager& sman1,
                                        SelectionManager& sman2);
    virtual void processOverlapping( SelectionManager& sman );

    virtual void initializeHistogram();
    virtual void processHistogram();
    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
    virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2, 
                                  StuntDouble* sd3);
    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, 
                                   StuntDouble* sd3) = 0;
    virtual void writeRdf();


    RealType deltaCosAngle_;
    int nAngleBins_;
    RealType len_;
    int nRBins_;
    RealType deltaR_;

    bool doSele3_;
    std::string selectionScript3_;
    SelectionManager seleMan3_;
    SelectionEvaluator evaluator3_;
        
    std::vector<std::vector<int> > histogram_;
    std::vector<std::vector<RealType> > avgGofr_;
    int npairs_;
  };


  class GofRTheta : public GofRAngle {
  public:
    GofRTheta(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2, 
              RealType len, int nrbins, int nangleBins)
      : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
        setOutputName(getPrefix(filename) + ".gofrt");
      }
    GofRTheta(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2,
              const std::string& sele3,
              RealType len, int nrbins, int nangleBins)
      : GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins, 
                   nangleBins) {
        setOutputName(getPrefix(filename) + ".gofrt");
      }
        
  private:

    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);        
    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, 
                                   StuntDouble* sd3);        
  };


  class GofROmega : public GofRAngle {
  public:
    GofROmega(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2, 
              RealType len, int nrbins, int nangleBins)
      : GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
        setOutputName(getPrefix(filename) + ".gofro");
      }
    GofROmega(SimInfo* info, const std::string& filename, 
              const std::string& sele1, const std::string& sele2,
              const std::string& sele3,
              RealType len, int nrbins, int nangleBins)
      : GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins, 
                   nangleBins) {
        setOutputName(getPrefix(filename) + ".gofro");
      }
    
  private:
    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);     
    virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, 
                                   StuntDouble* sd3);        
   
  };

}
#endif

Revision:	2023
Committed:	Thu Oct 2 14:35:14 2014 UTC (10 years, 7 months ago) by gezelter
File size:	6064 byte(s)
Log Message:	Added 3rd selection option for the 2d g(r) analyzers
#	User	Rev	Content
1	tim	309	/*
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	309	* 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	309	* 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	309	*/
42	tim	311	#ifndef APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
43			#define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
44	tim	309
45	tim	311	#include "applications/staticProps/RadialDistrFunc.hpp"
46	gezelter	1390	namespace OpenMD {
47	tim	309
48	gezelter	507	class GofRAngle : public RadialDistrFunc {
49	tim	309
50	gezelter	507	public:
51	gezelter	2023	GofRAngle(SimInfo* info, const std::string& filename,
52			const std::string& sele1, const std::string& sele2,
53			RealType len, int nrbins, int nangleBins);
54			GofRAngle(SimInfo* info, const std::string& filename,
55			const std::string& sele1, const std::string& sele2,
56			const std::string& sele3,
57			RealType len, int nrbins, int nangleBins);
58	tim	309
59	gezelter	507	int getNRBins() {
60			return nRBins_;
61			}
62	tim	311
63	tim	963	RealType getLength() {
64	gezelter	507	return len_;
65			}
66	tim	354
67	gezelter	507	int getNAngleBins() {return nAngleBins_;}
68	tim	310
69	gezelter	507	private:
70	tim	309
71	gezelter	507	virtual void preProcess();
72	gezelter	2023	virtual void processNonOverlapping( SelectionManager& sman1,
73			SelectionManager& sman2);
74			virtual void processOverlapping( SelectionManager& sman );
75
76	jmichalk	1785	virtual void initializeHistogram();
77	xsun	1213	virtual void processHistogram();
78	gezelter	507	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
79	gezelter	2023	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
80			StuntDouble* sd3);
81	tim	963	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
82	gezelter	2023	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
83			StuntDouble* sd3) = 0;
84	gezelter	507	virtual void writeRdf();
85	tim	310
86	gezelter	2023
87	tim	963	RealType deltaCosAngle_;
88	gezelter	507	int nAngleBins_;
89	tim	963	RealType len_;
90	gezelter	507	int nRBins_;
91	tim	963	RealType deltaR_;
92	gezelter	2023
93			bool doSele3_;
94			std::string selectionScript3_;
95			SelectionManager seleMan3_;
96			SelectionEvaluator evaluator3_;
97	tim	309
98	gezelter	507	std::vector<std::vector<int> > histogram_;
99	tim	963	std::vector<std::vector<RealType> > avgGofr_;
100	gezelter	507	int npairs_;
101			};
102	tim	309
103
104	gezelter	507	class GofRTheta : public GofRAngle {
105			public:
106	gezelter	2023	GofRTheta(SimInfo* info, const std::string& filename,
107			const std::string& sele1, const std::string& sele2,
108			RealType len, int nrbins, int nangleBins)
109	gezelter	507	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
110			setOutputName(getPrefix(filename) + ".gofrt");
111			}
112	gezelter	2023	GofRTheta(SimInfo* info, const std::string& filename,
113			const std::string& sele1, const std::string& sele2,
114			const std::string& sele3,
115			RealType len, int nrbins, int nangleBins)
116			: GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins,
117			nangleBins) {
118			setOutputName(getPrefix(filename) + ".gofrt");
119			}
120	tim	311
121	gezelter	507	private:
122	tim	309
123	tim	963	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
124	gezelter	2023	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
125			StuntDouble* sd3);
126	gezelter	507	};
127	tim	309
128
129	gezelter	507	class GofROmega : public GofRAngle {
130			public:
131	gezelter	2023	GofROmega(SimInfo* info, const std::string& filename,
132			const std::string& sele1, const std::string& sele2,
133			RealType len, int nrbins, int nangleBins)
134	gezelter	507	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
135			setOutputName(getPrefix(filename) + ".gofro");
136			}
137	gezelter	2023	GofROmega(SimInfo* info, const std::string& filename,
138			const std::string& sele1, const std::string& sele2,
139			const std::string& sele3,
140			RealType len, int nrbins, int nangleBins)
141			: GofRAngle (info, filename, sele1, sele2, sele3, len, nrbins,
142			nangleBins) {
143			setOutputName(getPrefix(filename) + ".gofro");
144			}
145	tim	311
146	gezelter	507	private:
147	gezelter	2023	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
148			virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
149			StuntDouble* sd3);
150
151	gezelter	507	};
152	tim	309
153			}
154			#endif
155