src/brains/Stats.hpp

/*
 * Copyright (c) 2005, 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
#ifndef BRAINS_STATS_HPP
#define BRAINS_STATS_HPP

#include <string>
#include <map>
#include <bitset>

#include "math/SquareMatrix3.hpp"
#include "utils/Accumulator.hpp"
#include "brains/SimInfo.hpp"

using namespace std;
namespace OpenMD {

  class Stats{
  public:
    enum StatsIndex {
      BEGININDEX = 0,  //internal use
      TIME = BEGININDEX,            
      TOTAL_ENERGY,
      POTENTIAL_ENERGY,
      KINETIC_ENERGY,
      TEMPERATURE,
      PRESSURE,
      VOLUME,
      HULLVOLUME,
      GYRVOLUME,
      CONSERVED_QUANTITY,             
      TRANSLATIONAL_KINETIC,
      ROTATIONAL_KINETIC,
      LONG_RANGE_POTENTIAL,   
      VANDERWAALS_POTENTIAL,
      ELECTROSTATIC_POTENTIAL,      
      METALLIC_POTENTIAL,
      HYDROGENBONDING_POTENTIAL,
      RECIPROCAL_POTENTIAL,
      SHORT_RANGE_POTENTIAL,
      BOND_POTENTIAL,
      BEND_POTENTIAL,
      DIHEDRAL_POTENTIAL,
      INVERSION_POTENTIAL,
      RAW_POTENTIAL,
      RESTRAINT_POTENTIAL,
      PRESSURE_TENSOR,
      SYSTEM_DIPOLE,
      SYSTEM_QUADRUPOLE,
      TAGGED_PAIR_DISTANCE,
      SHADOWH,
      HELFANDMOMENT,
      HEATFLUX,  
      ELECTRONIC_TEMPERATURE,
      COM,
      COM_VELOCITY,
      ANGULAR_MOMENTUM,
      ENDINDEX  //internal use
    };

    struct StatsData {
      string title;
      string units;
      string dataType;
      BaseAccumulator* accumulator;
    };
    
    typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
    typedef map<string, StatsIndex> StatsMapType;

    Stats(SimInfo* info);
    virtual ~Stats();
    void parseStatFileFormat(const std::string& format);
    void collectStats();

    StatsBitSet  getStatsMask();
    StatsMapType getStatsMap();
    void         setStatsMask(StatsBitSet mask);

    string    getTitle(int index); 
    string    getUnits(int index);
    string    getDataType(int index);

    int       getIntData(int index);
    RealType  getRealData(int index);
    Vector3d  getVectorData(int index);
    Mat3x3d   getMatrixData(int index);
    
  private:
    SimInfo* info_;
    void init();
    bool isInit_;
    vector<StatsData> data_;
    StatsBitSet statsMask_;
    StatsMapType statsMap_;
  };
} //end namespace OpenMD
#endif //BRAINS_STATS_HPP
Revision:	2046
Committed:	Tue Dec 2 22:11:04 2014 UTC (10 years, 7 months ago) by gezelter
File size:	4393 byte(s)
Log Message:	Fixed some broken comments for use with Doxygen. Made changes to allow topology-based force-field overrides in include files. Fixed a calculation of box quadrupole moments for molecules with point dipoles.
#	User	Rev	Content
1	gezelter	507	/*
2	chuckv	1402	* Copyright (c) 2005, 2009 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef BRAINS_STATS_HPP
44			#define BRAINS_STATS_HPP
45
46			#include <string>
47	tim	681	#include <map>
48	gezelter	1782	#include <bitset>
49	gezelter	246
50			#include "math/SquareMatrix3.hpp"
51	gezelter	1782	#include "utils/Accumulator.hpp"
52			#include "brains/SimInfo.hpp"
53
54			using namespace std;
55	gezelter	1390	namespace OpenMD {
56	gezelter	246
57	gezelter	507	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	gezelter	1291	HULLVOLUME,
69			GYRVOLUME,
70	gezelter	507	CONSERVED_QUANTITY,
71			TRANSLATIONAL_KINETIC,
72			ROTATIONAL_KINETIC,
73			LONG_RANGE_POTENTIAL,
74			VANDERWAALS_POTENTIAL,
75	gezelter	1925	ELECTROSTATIC_POTENTIAL,
76	gezelter	1782	METALLIC_POTENTIAL,
77			HYDROGENBONDING_POTENTIAL,
78	gezelter	1925	RECIPROCAL_POTENTIAL,
79	gezelter	1782	SHORT_RANGE_POTENTIAL,
80	gezelter	507	BOND_POTENTIAL,
81			BEND_POTENTIAL,
82			DIHEDRAL_POTENTIAL,
83	cli2	1275	INVERSION_POTENTIAL,
84	gezelter	1782	RAW_POTENTIAL,
85			RESTRAINT_POTENTIAL,
86			PRESSURE_TENSOR,
87			SYSTEM_DIPOLE,
88	gezelter	2022	SYSTEM_QUADRUPOLE,
89	gezelter	1291	TAGGED_PAIR_DISTANCE,
90	chuckv	1402	SHADOWH,
91	gezelter	1782	HELFANDMOMENT,
92			HEATFLUX,
93			ELECTRONIC_TEMPERATURE,
94	gezelter	1879	COM,
95			COM_VELOCITY,
96			ANGULAR_MOMENTUM,
97	gezelter	507	ENDINDEX //internal use
98			};
99	gezelter	246
100	gezelter	1782	struct StatsData {
101			string title;
102			string units;
103			string dataType;
104	gezelter	1791	BaseAccumulator* accumulator;
105	gezelter	1782	};
106
107			typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
108			typedef map<string, StatsIndex> StatsMapType;
109	gezelter	246
110	gezelter	1782	Stats(SimInfo* info);
111	gezelter	1879	virtual ~Stats();
112	gezelter	1782	void parseStatFileFormat(const std::string& format);
113			void collectStats();
114	gezelter	246
115	gezelter	1782	StatsBitSet getStatsMask();
116			StatsMapType getStatsMap();
117			void setStatsMask(StatsBitSet mask);
118	gezelter	246
119	gezelter	1782	string getTitle(int index);
120			string getUnits(int index);
121			string getDataType(int index);
122	tim	681
123	gezelter	1782	int getIntData(int index);
124			RealType getRealData(int index);
125			Vector3d getVectorData(int index);
126			Mat3x3d getMatrixData(int index);
127
128	gezelter	507	private:
129	gezelter	1782	SimInfo* info_;
130			void init();
131			bool isInit_;
132			vector<StatsData> data_;
133			StatsBitSet statsMask_;
134			StatsMapType statsMap_;
135	gezelter	507	};
136	gezelter	1390	} //end namespace OpenMD
137	gezelter	246	#endif //BRAINS_STATS_HPP