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Comparing trunk/src/brains/Stats.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2005, 2009 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. 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
42	–	/**
43	–	* @file Stats.hpp
44	–	* @author tlin
45	–	* @date 11/04/2004
46	–	* @time 23:56am
47	–	* @version 1.0
48	–	*/
49	–
43		#ifndef BRAINS_STATS_HPP
44		#define BRAINS_STATS_HPP
45
46		#include <string>
47	+	#include <map>
48	+	#include <bitset>
49
50		#include "math/SquareMatrix3.hpp"
51	<	namespace oopse {
51	>	#include "utils/Accumulator.hpp"
52	>	#include "brains/SimInfo.hpp"
53
54	<	/**
55	<	* @class Stats Stats.hpp "brains/Stats.hpp"
60	<	*/
61	<	class Stats{
62	<	public:
63	<	enum StatsIndex {
64	<	BEGININDEX = 0,  //internal use
65	<	TIME = BEGININDEX,
66	<	TOTAL_ENERGY,
67	<	POTENTIAL_ENERGY,
68	<	KINETIC_ENERGY,
69	<	TEMPERATURE,
70	<	PRESSURE,
71	<	VOLUME,
72	<	CONSERVED_QUANTITY,
73	<	TRANSLATIONAL_KINETIC,
74	<	ROTATIONAL_KINETIC,
75	<	LONG_RANGE_POTENTIAL,
76	<	SHORT_RANGE_POTENTIAL,
77	<	VANDERWAALS_POTENTIAL,
78	<	ELECTROSTATIC_POTENTIAL,
79	<	BOND_POTENTIAL,
80	<	BEND_POTENTIAL,
81	<	DIHEDRAL_POTENTIAL,
82	<	IMPROPER_POTENTIAL,
83	<	VRAW,
84	<	VHARM,
85	<	ENDINDEX  //internal use
86	<	};
54	>	using namespace std;
55	>	namespace OpenMD {
56
57	<	Stats();
58	<	const double& operator [](int index) const {
59	<	assert(index >=0 && index < ENDINDEX);
60	<	return data_[index];
61	<	}
57	>	class Stats{
58	>	public:
59	>	enum StatsIndex {
60	>	BEGININDEX = 0,  //internal use
61	>	TIME = BEGININDEX,
62	>	TOTAL_ENERGY,
63	>	POTENTIAL_ENERGY,
64	>	KINETIC_ENERGY,
65	>	TEMPERATURE,
66	>	PRESSURE,
67	>	VOLUME,
68	>	HULLVOLUME,
69	>	GYRVOLUME,
70	>	CONSERVED_QUANTITY,
71	>	TRANSLATIONAL_KINETIC,
72	>	ROTATIONAL_KINETIC,
73	>	LONG_RANGE_POTENTIAL,
74	>	VANDERWAALS_POTENTIAL,
75	>	ELECTROSTATIC_POTENTIAL,
76	>	METALLIC_POTENTIAL,
77	>	HYDROGENBONDING_POTENTIAL,
78	>	RECIPROCAL_POTENTIAL,
79	>	SHORT_RANGE_POTENTIAL,
80	>	BOND_POTENTIAL,
81	>	BEND_POTENTIAL,
82	>	DIHEDRAL_POTENTIAL,
83	>	INVERSION_POTENTIAL,
84	>	RAW_POTENTIAL,
85	>	RESTRAINT_POTENTIAL,
86	>	PRESSURE_TENSOR,
87	>	SYSTEM_DIPOLE,
88	>	SYSTEM_QUADRUPOLE,
89	>	TAGGED_PAIR_DISTANCE,
90	>	SHADOWH,
91	>	HELFANDMOMENT,
92	>	HEATFLUX,
93	>	ELECTRONIC_TEMPERATURE,
94	>	COM,
95	>	COM_VELOCITY,
96	>	ANGULAR_MOMENTUM,
97	>	ENDINDEX  //internal use
98	>	};
99
100	<	double& operator [](int index){
101	<	assert(index >=0 && index < ENDINDEX);
102	<	return data_[index];
103	<	}
104	<
105	<	static std::string getTitle(int index) {
106	<	assert(index >=0 && index < ENDINDEX);
107	<	return title_[index];
108	<	}
100	>	struct StatsData {
101	>	string title;
102	>	string units;
103	>	string dataType;
104	>	BaseAccumulator* accumulator;
105	>	};
106	>
107	>	typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
108	>	typedef map<string, StatsIndex> StatsMapType;
109
110	<	static std::string getUnits(int index) {
111	<	assert(index >=0 && index < ENDINDEX);
112	<	return units_[index];
113	<	}
110	>	Stats(SimInfo* info);
111	>	virtual ~Stats();
112	>	void parseStatFileFormat(const std::string& format);
113	>	void collectStats();
114
115	<	Mat3x3d getTau() {
116	<	return tau_;
117	<	}
112	<
113	<	void setTau(const Mat3x3d& tau) {
114	<	tau_ = tau;
115	<	}
116	<
117	<	private:
118	<	static void init();
119	<	static bool isInit_;
120	<	double data_[ENDINDEX - BEGININDEX];
121	<	static std::string title_[ENDINDEX - BEGININDEX];
122	<	static std::string units_[ENDINDEX - BEGININDEX];
123	<	Mat3x3d tau_;
124	<	};
115	>	StatsBitSet  getStatsMask();
116	>	StatsMapType getStatsMap();
117	>	void         setStatsMask(StatsBitSet mask);
118
119	<	} //end namespace oopse
119	>	string    getTitle(int index);
120	>	string    getUnits(int index);
121	>	string    getDataType(int index);
122	>
123	>	int       getIntData(int index);
124	>	RealType  getRealData(int index);
125	>	Vector3d  getVectorData(int index);
126	>	Mat3x3d   getMatrixData(int index);
127	>
128	>	private:
129	>	SimInfo* info_;
130	>	void init();
131	>	bool isInit_;
132	>	vector<StatsData> data_;
133	>	StatsBitSet statsMask_;
134	>	StatsMapType statsMap_;
135	>	};
136	>	} //end namespace OpenMD
137		#endif //BRAINS_STATS_HPP

Comparing trunk/src/brains/Stats.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 UTC

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