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

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (file contents):
Revision 353 by tim, Wed Feb 16 19:36:30 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_GOFRANGLE_HPP
43		#define APPLICATIONS_STATICPROPS_GOFRANGLE_HPP
44
45		#include "applications/staticProps/RadialDistrFunc.hpp"
46	<	namespace oopse {
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);
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	<	void setNRBins(int nbins) {
60	<	assert(nbins > 0);
61	<	nRBins_ = nbins;
55	<	deltaR_ = len_ / nRBins_;
56	<	for (int i = 0 ; i < nRBins_; ++i) {
57	<	histogram_[i].resize(nAngleBins_);
58	<	avgGofr_[i].resize(nAngleBins_);
59	<	}
60	<	}
59	>	int getNRBins() {
60	>	return nRBins_;
61	>	}
62
63	<	int getNRBins() {
64	<	return nRBins_;
65	<	}
63	>	RealType getLength() {
64	>	return len_;
65	>	}
66
67	<	void setLength(double len) {
67	<	len_ = len;
68	<	deltaR_ = len_ /nRBins_;
69	<	}
70	<
71	<	double getLength() {
72	<	return len_;
73	<	}
67	>	int getNAngleBins() {return nAngleBins_;}
68
69	<	void setNAngleBins(int nbins) {
76	<	assert(nbins >0);
77	<	nAngleBins_ = nbins;
78	<	deltaCosAngle_ = 2.0 / nAngleBins_;
79	<	for (int i = 0 ; i < nRBins_; ++i) {
80	<	histogram_[i].resize(nAngleBins_);
81	<	avgGofr_[i].resize(nAngleBins_);
82	<	}
83	<	}
84	<
85	<	int getNAngleBins() {return nAngleBins_;}
86	<
87	<	private:
69	>	private:
70
71	<	virtual void preProcess();
72	<	virtual void initalizeHistogram();
73	<	virtual void collectHistogram(StuntDouble* sd1, StuntDouble* sd2);
74	<	virtual void processHistogram();
71	>	virtual void preProcess();
72	>	virtual void processNonOverlapping( SelectionManager& sman1,
73	>	SelectionManager& sman2);
74	>	virtual void processOverlapping( SelectionManager& sman );
75
76	<	virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) = 0;
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
96	–	virtual void writeRdf();
86
87	<	double deltaCosAngle_;
88	<	int nAngleBins_;
89	<	double len_;
90	<	int nRBins_;
91	<	double deltaR_;
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<double> > avgGofr_;
100	<	int npairs_;
101	<	};
98	>	std::vector<std::vector<int> > histogram_;
99	>	std::vector<std::vector<RealType> > avgGofr_;
100	>	int npairs_;
101	>	};
102
103
104	<	class GofRTheta : public GofRAngle {
105	<	public:
106	<	GofRTheta(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
107	<	: GofRAngle (info, filename, sele1, sele2) {
108	<	setOutputName(getPrefix(filename) + ".gofrt");
109	<	}
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:
121	>	private:
122
123	<	virtual double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
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, const std::string& sele1, const std::string& sele2)
132	<	: GofRAngle (info, filename, sele1, sele2) {
133	<	setOutputName(getPrefix(filename) + ".gofrw");
134	<	}
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 double evaluateAngle(StuntDouble* sd1, StuntDouble* sd2);
148	<	};
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

Comparing trunk/src/applications/staticProps/GofRAngle.hpp (property svn:keywords):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 2023 by gezelter, Thu Oct 2 14:35:14 2014 UTC

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