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Comparing trunk/src/brains/Stats.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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
43		/**
#	Line 51 | Line 52
52		#define BRAINS_STATS_HPP
53
54		#include <string>
55	+	#include <map>
56	+	#include <bitset>
57
58		#include "math/SquareMatrix3.hpp"
59	<	namespace oopse {
59	>	#include "utils/Accumulator.hpp"
60	>	#include "brains/SimInfo.hpp"
61
62	<	/**
63	<	* @class Stats Stats.hpp "brains/Stats.hpp"
64	<	*/
62	>	using namespace std;
63	>	namespace OpenMD {
64	>
65		class Stats{
66		public:
67		enum StatsIndex {
#	Line 69 | Line 73 | namespace oopse {
73		TEMPERATURE,
74		PRESSURE,
75		VOLUME,
76	+	HULLVOLUME,
77	+	GYRVOLUME,
78		CONSERVED_QUANTITY,
79		TRANSLATIONAL_KINETIC,
80		ROTATIONAL_KINETIC,
81		LONG_RANGE_POTENTIAL,
76	–	SHORT_RANGE_POTENTIAL,
82		VANDERWAALS_POTENTIAL,
83	<	ELECTROSTATIC_POTENTIAL,
83	>	ELECTROSTATIC_POTENTIAL,
84	>	METALLIC_POTENTIAL,
85	>	HYDROGENBONDING_POTENTIAL,
86	>	RECIPROCAL_POTENTIAL,
87	>	SHORT_RANGE_POTENTIAL,
88		BOND_POTENTIAL,
89		BEND_POTENTIAL,
90		DIHEDRAL_POTENTIAL,
91	<	IMPROPER_POTENTIAL,
92	<	VRAW,
93	<	VHARM,
91	>	INVERSION_POTENTIAL,
92	>	RAW_POTENTIAL,
93	>	RESTRAINT_POTENTIAL,
94	>	PRESSURE_TENSOR,
95	>	SYSTEM_DIPOLE,
96	>	TAGGED_PAIR_DISTANCE,
97	>	SHADOWH,
98	>	HELFANDMOMENT,
99	>	HEATFLUX,
100	>	ELECTRONIC_TEMPERATURE,
101	>	COM,
102	>	COM_VELOCITY,
103	>	ANGULAR_MOMENTUM,
104		ENDINDEX  //internal use
105		};
106
107	<	Stats();
108	<	const double& operator [](int index) const {
109	<	assert(index >=0 && index < ENDINDEX);
110	<	return data_[index];
111	<	}
107	>	struct StatsData {
108	>	string title;
109	>	string units;
110	>	string dataType;
111	>	BaseAccumulator* accumulator;
112	>	};
113	>
114	>	typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
115	>	typedef map<string, StatsIndex> StatsMapType;
116
117	<	double& operator [](int index){
118	<	assert(index >=0 && index < ENDINDEX);
119	<	return data_[index];
120	<	}
98	<
99	<	static std::string getTitle(int index) {
100	<	assert(index >=0 && index < ENDINDEX);
101	<	return title_[index];
102	<	}
117	>	Stats(SimInfo* info);
118	>	virtual ~Stats();
119	>	void parseStatFileFormat(const std::string& format);
120	>	void collectStats();
121
122	<	static std::string getUnits(int index) {
123	<	assert(index >=0 && index < ENDINDEX);
124	<	return units_[index];
107	<	}
122	>	StatsBitSet  getStatsMask();
123	>	StatsMapType getStatsMap();
124	>	void         setStatsMask(StatsBitSet mask);
125
126	<	Mat3x3d getTau() {
127	<	return tau_;
128	<	}
129	<
130	<	void setTau(const Mat3x3d& tau) {
131	<	tau_ = tau;
132	<	}
133	<
126	>	string    getTitle(int index);
127	>	string    getUnits(int index);
128	>	string    getDataType(int index);
129	>
130	>	int       getIntData(int index);
131	>	RealType  getRealData(int index);
132	>	Vector3d  getVectorData(int index);
133	>	Mat3x3d   getMatrixData(int index);
134	>
135		private:
136	<	static void init();
137	<	static bool isInit_;
138	<	double data_[ENDINDEX - BEGININDEX];
139	<	static std::string title_[ENDINDEX - BEGININDEX];
140	<	static std::string units_[ENDINDEX - BEGININDEX];
141	<	Mat3x3d tau_;
136	>	SimInfo* info_;
137	>	void init();
138	>	bool isInit_;
139	>	vector<StatsData> data_;
140	>	StatsBitSet statsMask_;
141	>	StatsMapType statsMap_;
142		};
143	<
126	<	} //end namespace oopse
143	>	} //end namespace OpenMD
144		#endif //BRAINS_STATS_HPP

Comparing trunk/src/brains/Stats.hpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

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