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).
 */
  
/**
 * @file Stats.hpp
 * @author tlin
 * @date 11/04/2004
 * @time 23:56am
 * @version 1.0
 */

#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,
      SHORT_RANGE_POTENTIAL,
      BOND_POTENTIAL,
      BEND_POTENTIAL,
      DIHEDRAL_POTENTIAL,
      INVERSION_POTENTIAL,
      RAW_POTENTIAL,
      RESTRAINT_POTENTIAL,
      PRESSURE_TENSOR,
      SYSTEM_DIPOLE,
      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);
    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:	1859
Committed:	Thu Apr 4 19:42:59 2013 UTC (12 years, 1 month ago) by gezelter
File size:	4409 byte(s)
Log Message:	Adding a few new statsFileFormat options: COM, COM_VELOCITY, ANGULAR_MOMENTUM
#	Content
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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	/**
44	* @file Stats.hpp
45	* @author tlin
46	* @date 11/04/2004
47	* @time 23:56am
48	* @version 1.0
49	*/
50
51	#ifndef BRAINS_STATS_HPP
52	#define BRAINS_STATS_HPP
53
54	#include <string>
55	#include <map>
56	#include <bitset>
57
58	#include "math/SquareMatrix3.hpp"
59	#include "utils/Accumulator.hpp"
60	#include "brains/SimInfo.hpp"
61
62	using namespace std;
63	namespace OpenMD {
64
65	class Stats{
66	public:
67	enum StatsIndex {
68	BEGININDEX = 0, //internal use
69	TIME = BEGININDEX,
70	TOTAL_ENERGY,
71	POTENTIAL_ENERGY,
72	KINETIC_ENERGY,
73	TEMPERATURE,
74	PRESSURE,
75	VOLUME,
76	HULLVOLUME,
77	GYRVOLUME,
78	CONSERVED_QUANTITY,
79	TRANSLATIONAL_KINETIC,
80	ROTATIONAL_KINETIC,
81	LONG_RANGE_POTENTIAL,
82	VANDERWAALS_POTENTIAL,
83	ELECTROSTATIC_POTENTIAL,
84	METALLIC_POTENTIAL,
85	HYDROGENBONDING_POTENTIAL,
86	SHORT_RANGE_POTENTIAL,
87	BOND_POTENTIAL,
88	BEND_POTENTIAL,
89	DIHEDRAL_POTENTIAL,
90	INVERSION_POTENTIAL,
91	RAW_POTENTIAL,
92	RESTRAINT_POTENTIAL,
93	PRESSURE_TENSOR,
94	SYSTEM_DIPOLE,
95	TAGGED_PAIR_DISTANCE,
96	SHADOWH,
97	HELFANDMOMENT,
98	HEATFLUX,
99	ELECTRONIC_TEMPERATURE,
100	COM,
101	COM_VELOCITY,
102	ANGULAR_MOMENTUM,
103	ENDINDEX //internal use
104	};
105
106	struct StatsData {
107	string title;
108	string units;
109	string dataType;
110	BaseAccumulator* accumulator;
111	};
112
113	typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
114	typedef map<string, StatsIndex> StatsMapType;
115
116	Stats(SimInfo* info);
117	void parseStatFileFormat(const std::string& format);
118	void collectStats();
119
120	StatsBitSet getStatsMask();
121	StatsMapType getStatsMap();
122	void setStatsMask(StatsBitSet mask);
123
124	string getTitle(int index);
125	string getUnits(int index);
126	string getDataType(int index);
127
128	int getIntData(int index);
129	RealType getRealData(int index);
130	Vector3d getVectorData(int index);
131	Mat3x3d getMatrixData(int index);
132
133	private:
134	SimInfo* info_;
135	void init();
136	bool isInit_;
137	vector<StatsData> data_;
138	StatsBitSet statsMask_;
139	StatsMapType statsMap_;
140	};
141	} //end namespace OpenMD
142	#endif //BRAINS_STATS_HPP