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. 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 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>

using namespace std;
namespace OpenMD {

  /**
   * @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; }
    void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
    void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
    void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
    RealType get_RNEMD_exchange_total() { return exchangeSum_; }

  private:

    enum RNEMDTypeEnum {
      rnemdKineticSwap,
      rnemdKineticScale,
      rnemdPxScale,
      rnemdPyScale,
      rnemdPzScale,
      rnemdPx,
      rnemdPy,
      rnemdPz,
      rnemdUnknown
    };
    
    SimInfo* info_;
    RandNumGen* randNumGen_;
    map<string, RNEMDTypeEnum> stringToEnumMap_;
    RNEMDTypeEnum rnemdType_;
    string rnemdObjectSelection_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    bool usePeriodicBoundaryConditions_;
    bool output3DTemp_;
    int nBins_; /**< The number of bins to divide the simulation box into.  */
    /*!
      The middle bin for the RNEMD method. midBin_ = nBins_/2;
      Depending on the setting of the flux, this box should contain the minimum energy (temperature)
      within the simulation. 
    */
    int midBin_;
    int rnemdLogWidth_; /**< Number of elements to print out in logs */
    RealType zShift_;
    RealType exchangeTime_;
    RealType targetFlux_;
    RealType exchangeSum_;
    int failTrialCount_;
    int failRootCount_;
    ofstream rnemdLog_;
    // keeps track of what's being averaged
    vector<RealType> valueHist_;
    vector<int> valueCount_, xyzTempCount_;
    // keeps track of the number of degrees of freedom being averaged
    vector<RealType> xTempHist_, yTempHist_, zTempHist_;
    ofstream xTempLog_, yTempLog_, zTempLog_;
  };

}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
Original Path:	*branches/development/src/integrators/RNEMD.hpp*
File size:	4690 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	1329	* 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	1329	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1329	*/
42
43			/**
44			* @file RNEMD.hpp
45			* @author gezelter
46			* @date 03/13/2009
47			* @time 15:56pm
48			* @version 1.0
49			*/
50
51			#ifndef INTEGRATORS_RNEMD_HPP
52			#define INTEGRATORS_RNEMD_HPP
53			#include "brains/SimInfo.hpp"
54			#include "math/RandNumGen.hpp"
55	gezelter	1331	#include "selection/SelectionEvaluator.hpp"
56			#include "selection/SelectionManager.hpp"
57	skuang	1368	#include <iostream>
58	gezelter	1329
59	gezelter	1629	using namespace std;
60	gezelter	1390	namespace OpenMD {
61	gezelter	1329
62			/**
63			* @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
64			* @todo document
65			*/
66			class RNEMD {
67			public:
68			RNEMD(SimInfo* info);
69			virtual ~RNEMD();
70	skuang	1368
71			void doRNEMD();
72	gezelter	1329	void doSwap();
73	skuang	1368	void doScale();
74			void collectData();
75			void getStarted();
76	skuang	1338	void getStatus();
77	skuang	1368	void set_RNEMD_exchange_time(RealType exchangeTime) {
78			exchangeTime_ = exchangeTime;
79			}
80	gezelter	1329	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
81	gezelter	1629	void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
82	skuang	1368	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
83			void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
84	gezelter	1629	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
85	gezelter	1331
86	gezelter	1329	private:
87	gezelter	1331
88	gezelter	1329	enum RNEMDTypeEnum {
89	skuang	1368	rnemdKineticSwap,
90			rnemdKineticScale,
91			rnemdPxScale,
92			rnemdPyScale,
93			rnemdPzScale,
94	gezelter	1329	rnemdPx,
95			rnemdPy,
96			rnemdPz,
97			rnemdUnknown
98			};
99	skuang	1368
100	gezelter	1329	SimInfo* info_;
101			RandNumGen* randNumGen_;
102	gezelter	1629	map<string, RNEMDTypeEnum> stringToEnumMap_;
103	gezelter	1329	RNEMDTypeEnum rnemdType_;
104	gezelter	1629	string rnemdObjectSelection_;
105	skuang	1368	SelectionEvaluator evaluator_;
106	gezelter	1331	SelectionManager seleMan_;
107			bool usePeriodicBoundaryConditions_;
108	gezelter	1629	bool output3DTemp_;
109			int nBins_; /*< The number of bins to divide the simulation box into. /
110			/*!
111			The middle bin for the RNEMD method. midBin_ = nBins_/2;
112			Depending on the setting of the flux, this box should contain the minimum energy (temperature)
113			within the simulation.
114			*/
115	skuang	1368	int midBin_;
116	gezelter	1629	int rnemdLogWidth_; /*< Number of elements to print out in logs /
117			RealType zShift_;
118	skuang	1368	RealType exchangeTime_;
119			RealType targetFlux_;
120			RealType exchangeSum_;
121			int failTrialCount_;
122			int failRootCount_;
123	gezelter	1629	ofstream rnemdLog_;
124	skuang	1368	// keeps track of what's being averaged
125	gezelter	1629	vector<RealType> valueHist_;
126			vector<int> valueCount_, xyzTempCount_;
127	skuang	1368	// keeps track of the number of degrees of freedom being averaged
128	gezelter	1629	vector<RealType> xTempHist_, yTempHist_, zTempHist_;
129			ofstream xTempLog_, yTempLog_, zTempLog_;
130	gezelter	1329	};
131
132			}
133	skuang	1368	#endif //INTEGRATORS_RNEMD_HPP