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root/OpenMD/trunk/src/applications/staticProps/GofRAngle.hpp

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 309 by tim, Thu Feb 10 14:15:52 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 24107 (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_GOFANGLE_HPP
43	<	#define APPLICATIONS_STATICPROPS_GOFANGLE_HPP
42	>	#ifndef APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
43	>	#define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
44
45	<	#include "application/staticProps/RadialDistrFunc.hpp"
46	<	namespace oopse {
45	>	#include "applications/staticProps/RadialDistrFunc.hpp"
46	>	namespace OpenMD {
47
48	<	class GofRAngle : public RadialDistrFunc {
48	>	class GofRAngle : public RadialDistrFunc {
49
50	<	public:
51	<	GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len);
50	>	public:
51	>	GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins);
52
53	<	private:
53	>	int getNRBins() {
54	>	return nRBins_;
55	>	}
56
57	<	virtual void preProcess();
58	<	virtual void initalizeHistogram();
59	<	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
57	<	virtual void processHistogram();
57	>	RealType getLength() {
58	>	return len_;
59	>	}
60
61	<	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
60	<
61	<	virtual void writeRdf();
61	>	int getNAngleBins() {return nAngleBins_;}
62
63	<	std::vector<std::vector<int> > histogram_;
64	<	std::vector<std::vector<double> > avgGofr_;
65	<	int npairs_;
66	<	};
63	>	private:
64
65	+	virtual void preProcess();
66	+	virtual void initializeHistogram();
67	+	virtual void processHistogram();
68	+	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
69
70	<	class GofRTheta : GofRAngle {
70	<	public:
71	<	GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len);
70	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
71
72	<	private:
72	>	virtual void writeRdf();
73
74	<	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
75	<	};
74	>	RealType deltaCosAngle_;
75	>	int nAngleBins_;
76	>	RealType len_;
77	>	int nRBins_;
78	>	RealType deltaR_;
79	>
80	>	std::vector<std::vector<int> > histogram_;
81	>	std::vector<std::vector<RealType> > avgGofr_;
82	>	int npairs_;
83	>	};
84
85
86	<	class GofROmega : GofRAngle {
87	<	public:
88	<	GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len);
86	>	class GofRTheta : public GofRAngle {
87	>	public:
88	>	GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
89	>	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
90	>	setOutputName(getPrefix(filename) + ".gofrt");
91	>	}
92	>
93	>	private:
94
95	<	private:
95	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
96	>	};
97
85	–	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
86	–	};
98
99	+	class GofROmega : public GofRAngle {
100	+	public:
101	+	GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins, int nangleBins)
102	+	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
103	+	setOutputName(getPrefix(filename) + ".gofro");
104	+	}
105	+
106	+	private:
107	+	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
108	+	};
109	+
110		}
111		#endif
112

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 309 by tim, Thu Feb 10 14:15:52 2005 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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