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, 24107 (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,
      ENDINDEX  //internal use
    };

    struct StatsData {
      string title;
      string units;
      string dataType;
      Accumulator* 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:	1777
Committed:	Thu Aug 9 18:35:09 2012 UTC (12 years, 8 months ago) by gezelter
File size:	4349 byte(s)
Log Message:	Various fixes for the RNEMD output.
#	User	Rev	Content
1	gezelter	1710	/*
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, 24107 (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	gezelter	1764	#include <bitset>
57	gezelter	1710
58			#include "math/SquareMatrix3.hpp"
59	gezelter	1764	#include "utils/Accumulator.hpp"
60			#include "brains/SimInfo.hpp"
61
62			using namespace std;
63	gezelter	1710	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	gezelter	1760	METALLIC_POTENTIAL,
85			HYDROGENBONDING_POTENTIAL,
86			SHORT_RANGE_POTENTIAL,
87	gezelter	1710	BOND_POTENTIAL,
88			BEND_POTENTIAL,
89			DIHEDRAL_POTENTIAL,
90			INVERSION_POTENTIAL,
91	gezelter	1760	RAW_POTENTIAL,
92			RESTRAINT_POTENTIAL,
93	gezelter	1764	PRESSURE_TENSOR,
94			SYSTEM_DIPOLE,
95	gezelter	1710	TAGGED_PAIR_DISTANCE,
96			SHADOWH,
97	gezelter	1764	HELFANDMOMENT,
98			HEATFLUX,
99			ELECTRONIC_TEMPERATURE,
100	gezelter	1710	ENDINDEX //internal use
101			};
102
103	gezelter	1764	struct StatsData {
104			string title;
105			string units;
106			string dataType;
107			Accumulator* accumulator;
108			};
109
110			typedef bitset<ENDINDEX-BEGININDEX> StatsBitSet;
111			typedef map<string, StatsIndex> StatsMapType;
112	gezelter	1710
113	gezelter	1764	Stats(SimInfo* info);
114			void parseStatFileFormat(const std::string& format);
115			void collectStats();
116	gezelter	1710
117	gezelter	1764	StatsBitSet getStatsMask();
118			StatsMapType getStatsMap();
119			void setStatsMask(StatsBitSet mask);
120	gezelter	1710
121	gezelter	1764	string getTitle(int index);
122			string getUnits(int index);
123			string getDataType(int index);
124
125			int getIntData(int index);
126			RealType getRealData(int index);
127			Vector3d getVectorData(int index);
128			Mat3x3d getMatrixData(int index);
129
130	gezelter	1710	private:
131	gezelter	1764	SimInfo* info_;
132			void init();
133			bool isInit_;
134			vector<StatsData> data_;
135			StatsBitSet statsMask_;
136			StatsMapType statsMap_;
137	gezelter	1710	};
138			} //end namespace OpenMD
139			#endif //BRAINS_STATS_HPP