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Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 309 by tim, Thu Feb 10 14:15:52 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 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, 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_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,
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
59	<	private:
59	>	int getNRBins() {
60	>	return nRBins_;
61	>	}
62
63	<	virtual void preProcess();
64	<	virtual void initalizeHistogram();
65	<	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
57	<	virtual void processHistogram();
63	>	RealType getLength() {
64	>	return len_;
65	>	}
66
67	<	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
60	<
61	<	virtual void writeRdf();
67	>	int getNAngleBins() {return nAngleBins_;}
68
69	<	std::vector<std::vector<int> > histogram_;
64	<	std::vector<std::vector<double> > avgGofr_;
65	<	int npairs_;
66	<	};
69	>	private:
70
71	+	virtual void preProcess();
72	+	virtual void processNonOverlapping( SelectionManager& sman1,
73	+	SelectionManager& sman2);
74	+	virtual void processOverlapping( SelectionManager& sman );
75
76	<	class GofRTheta : GofRAngle {
77	<	public:
78	<	GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len);
76	>	virtual void initializeHistogram();
77	>	virtual void processHistogram();
78	>	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
79	>	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2,
80	>	StuntDouble* sd3);
81	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
82	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
83	>	StuntDouble* sd3) = 0;
84	>	virtual void writeRdf();
85
73	–	private:
86
87	<	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
88	<	};
87	>	RealType deltaCosAngle_;
88	>	int nAngleBins_;
89	>	RealType len_;
90	>	int nRBins_;
91	>	RealType deltaR_;
92
93	+	bool doSele3_;
94	+	std::string selectionScript3_;
95	+	SelectionManager seleMan3_;
96	+	SelectionEvaluator evaluator3_;
97	+
98	+	std::vector<std::vector<int> > histogram_;
99	+	std::vector<std::vector<RealType> > avgGofr_;
100	+	int npairs_;
101	+	};
102
79	–	class GofROmega : GofRAngle {
80	–	public:
81	–	GofROmega(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len);
103
104	<	private:
104	>	class GofRTheta : public GofRAngle {
105	>	public:
106	>	GofRTheta(SimInfo* info, const std::string& filename,
107	>	const std::string& sele1, const std::string& sele2,
108	>	RealType len, int nrbins, int nangleBins)
109	>	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
110	>	setOutputName(getPrefix(filename) + ".gofrt");
111	>	}
112	>	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	>
121	>	private:
122
123	<	virtual double evaluateAngel(StuntDouble* sd1, StuntDouble* sd2) = 0;
124	<	};
123	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
124	>	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
125	>	StuntDouble* sd3);
126	>	};
127
128	+
129	+	class GofROmega : public GofRAngle {
130	+	public:
131	+	GofROmega(SimInfo* info, const std::string& filename,
132	+	const std::string& sele1, const std::string& sele2,
133	+	RealType len, int nrbins, int nangleBins)
134	+	: GofRAngle (info, filename, sele1, sele2, len, nrbins, nangleBins) {
135	+	setOutputName(getPrefix(filename) + ".gofro");
136	+	}
137	+	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	+
146	+	private:
147	+	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
148	+	virtual RealType evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
149	+	StuntDouble* sd3);
150	+
151	+	};
152	+
153		}
154		#endif
155

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 309 by tim, Thu Feb 10 14:15:52 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

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