src/rnemd/RNEMD.hpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @file RNEMD.hpp
 * @author gezelter
 * @date 03/13/2009
 * @time 15:56pm
 * @version 1.0
 */

#ifndef INTEGRATORS_RNEMD_HPP
#define INTEGRATORS_RNEMD_HPP
#include "brains/SimInfo.hpp"
#include "math/RandNumGen.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include <iostream>

namespace oopse {

  /**
   * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
   * @todo document
   */
  class RNEMD {
  public:
    RNEMD(SimInfo* info);
    virtual ~RNEMD();
    
    void doRNEMD();
    void doSwap();
    void doScale();
    void collectData();
    void getStarted();
    void getStatus();
    void set_RNEMD_exchange_time(RealType exchangeTime) {
      exchangeTime_ = exchangeTime;
    }
    void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
    void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
    void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}

  private:

    enum RNEMDTypeEnum {
      rnemdKineticSwap,
      rnemdKineticScale,
      rnemdPxScale,
      rnemdPyScale,
      rnemdPzScale,
      rnemdPx,
      rnemdPy,
      rnemdPz,
      rnemdUnknown
    };
    
    SimInfo* info_;
    RandNumGen* randNumGen_;
    std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
    RNEMDTypeEnum rnemdType_;
    std::string rnemdObjectSelection_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    bool usePeriodicBoundaryConditions_;
    int nBins_;
    int midBin_;
    int rnemdLogWidth_;
    RealType exchangeTime_;
    RealType targetFlux_;
    RealType exchangeSum_;
    int failTrialCount_;
    int failRootCount_;
    std::ofstream rnemdLog_;
    // keeps track of what's being averaged
    std::vector<RealType> valueHist_;
    std::vector<int> valueCount_;
    // keeps track of the number of degrees of freedom being averaged
    std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
    std::ofstream xTempLog_, yTempLog_, zTempLog_;
  };

}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	1368
Committed:	Mon Oct 19 13:39:04 2009 UTC (15 years, 6 months ago) by skuang
Original Path:	*trunk/src/integrators/RNEMD.hpp*
File size:	4147 byte(s)
Log Message:	added RNEMD scaling
#	User	Rev	Content
1	gezelter	1329	/*
2			* Copyright (c) 2005 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file RNEMD.hpp
44			* @author gezelter
45			* @date 03/13/2009
46			* @time 15:56pm
47			* @version 1.0
48			*/
49
50			#ifndef INTEGRATORS_RNEMD_HPP
51			#define INTEGRATORS_RNEMD_HPP
52			#include "brains/SimInfo.hpp"
53			#include "math/RandNumGen.hpp"
54	gezelter	1331	#include "selection/SelectionEvaluator.hpp"
55			#include "selection/SelectionManager.hpp"
56	skuang	1368	#include <iostream>
57	gezelter	1329
58			namespace oopse {
59
60			/**
61			* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
62			* @todo document
63			*/
64			class RNEMD {
65			public:
66			RNEMD(SimInfo* info);
67			virtual ~RNEMD();
68	skuang	1368
69			void doRNEMD();
70	gezelter	1329	void doSwap();
71	skuang	1368	void doScale();
72			void collectData();
73			void getStarted();
74	skuang	1338	void getStatus();
75	skuang	1368	void set_RNEMD_exchange_time(RealType exchangeTime) {
76			exchangeTime_ = exchangeTime;
77			}
78	gezelter	1329	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
79			RealType get_RNEMD_exchange_total() { return exchangeSum_; }
80	skuang	1368	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
81			void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
82	gezelter	1331
83	gezelter	1329	private:
84	gezelter	1331
85	gezelter	1329	enum RNEMDTypeEnum {
86	skuang	1368	rnemdKineticSwap,
87			rnemdKineticScale,
88			rnemdPxScale,
89			rnemdPyScale,
90			rnemdPzScale,
91	gezelter	1329	rnemdPx,
92			rnemdPy,
93			rnemdPz,
94			rnemdUnknown
95			};
96	skuang	1368
97	gezelter	1329	SimInfo* info_;
98			RandNumGen* randNumGen_;
99	skuang	1368	std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
100	gezelter	1329	RNEMDTypeEnum rnemdType_;
101	gezelter	1331	std::string rnemdObjectSelection_;
102	skuang	1368	SelectionEvaluator evaluator_;
103	gezelter	1331	SelectionManager seleMan_;
104			bool usePeriodicBoundaryConditions_;
105	skuang	1368	int nBins_;
106			int midBin_;
107			int rnemdLogWidth_;
108			RealType exchangeTime_;
109			RealType targetFlux_;
110			RealType exchangeSum_;
111			int failTrialCount_;
112			int failRootCount_;
113			std::ofstream rnemdLog_;
114			// keeps track of what's being averaged
115			std::vector<RealType> valueHist_;
116			std::vector<int> valueCount_;
117			// keeps track of the number of degrees of freedom being averaged
118			std::vector<RealType> xTempHist_, yTempHist_, zTempHist_;
119			std::ofstream xTempLog_, yTempLog_, zTempLog_;
120	gezelter	1329	};
121
122			}
123	skuang	1368	#endif //INTEGRATORS_RNEMD_HPP