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 doShiftScale();
    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;}
    void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;}
    void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;}
    void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;}
    void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;}
    void set_RNEMD_target_jzpz2(RealType targetJzpz2) {targetJzpz2_ = targetJzpz2;}
    RealType get_RNEMD_exchange_total() { return exchangeSum_; }

  private:

    enum RNEMDTypeEnum {
      rnemdKineticSwap,
      rnemdKineticScale,
      rnemdKineticScaleVAM,
      rnemdKineticScaleAM,
      rnemdPxScale,
      rnemdPyScale,
      rnemdPzScale,
      rnemdPx,
      rnemdPy,
      rnemdPz,
      rnemdShiftScaleV,
      rnemdShiftScaleVAM,
      rnemdUnknown
    };
    
    SimInfo* info_;
    RandNumGen* randNumGen_;
    map<string, RNEMDTypeEnum> stringToEnumMap_;
    RNEMDTypeEnum rnemdType_;
    string rnemdObjectSelection_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    bool usePeriodicBoundaryConditions_;
    bool outputTemp_;
    bool outputVx_;
    bool outputVy_;
    bool output3DTemp_;
    bool outputRotTemp_;
    // James put this in.
    bool outputDen_;
    bool outputVz_;
    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 targetJzKE_;
    RealType targetJzpx_;
    RealType targetJzpy_;
    RealType targetJzpz_;
    RealType targetJzpz2_;
    Vector3d jzp_, njzp_;
    RealType exchangeSum_;
    int failTrialCount_;
    int failRootCount_;
    ofstream rnemdLog_;
    int logFrameCount_;
    // James added denLog, vzzLog
    ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_;
    ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
    // keeps track of what's being averaged James added DenHist, pzzHist
    vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_, DenHist_, pzzHist_, DenHist2_;
    vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_;
    // keeps track of the number of degrees of freedom being averaged
    //vector<int> pxzCount_, pyzCount_;
    vector<int> tempCount_, xyzTempCount_, rotTempCount_;
  };

}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	1728
Committed:	Wed May 30 16:07:03 2012 UTC (12 years, 11 months ago) by jmarr
Original Path:	*branches/development/src/integrators/RNEMD.hpp*
File size:	5830 byte(s)
Log Message:	resolved
#	Content
1	/*
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. 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 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	#include "selection/SelectionEvaluator.hpp"
56	#include "selection/SelectionManager.hpp"
57	#include <iostream>
58
59	using namespace std;
60	namespace OpenMD {
61
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
71	void doRNEMD();
72	void doSwap();
73	void doScale();
74	void doShiftScale();
75	void collectData();
76	void getStarted();
77	void getStatus();
78	void set_RNEMD_exchange_time(RealType exchangeTime) {
79	exchangeTime_ = exchangeTime;
80	}
81	void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
82	void set_RNEMD_logWidth(int logWidth) { rnemdLogWidth_ = logWidth; }
83	void set_RNEMD_exchange_total(RealType et) { exchangeSum_ = et; }
84	void set_RNEMD_target_flux(RealType targetFlux) {targetFlux_ = targetFlux;}
85	void set_RNEMD_target_JzKE(RealType targetJzKE) {targetJzKE_ = targetJzKE;}
86	void set_RNEMD_target_jzpx(RealType targetJzpx) {targetJzpx_ = targetJzpx;}
87	void set_RNEMD_target_jzpy(RealType targetJzpy) {targetJzpy_ = targetJzpy;}
88	void set_RNEMD_target_jzpz(RealType targetJzpz) {targetJzpz_ = targetJzpz;}
89	void set_RNEMD_target_jzpz2(RealType targetJzpz2) {targetJzpz2_ = targetJzpz2;}
90	RealType get_RNEMD_exchange_total() { return exchangeSum_; }
91
92	private:
93
94	enum RNEMDTypeEnum {
95	rnemdKineticSwap,
96	rnemdKineticScale,
97	rnemdKineticScaleVAM,
98	rnemdKineticScaleAM,
99	rnemdPxScale,
100	rnemdPyScale,
101	rnemdPzScale,
102	rnemdPx,
103	rnemdPy,
104	rnemdPz,
105	rnemdShiftScaleV,
106	rnemdShiftScaleVAM,
107	rnemdUnknown
108	};
109
110	SimInfo* info_;
111	RandNumGen* randNumGen_;
112	map<string, RNEMDTypeEnum> stringToEnumMap_;
113	RNEMDTypeEnum rnemdType_;
114	string rnemdObjectSelection_;
115	SelectionEvaluator evaluator_;
116	SelectionManager seleMan_;
117	bool usePeriodicBoundaryConditions_;
118	bool outputTemp_;
119	bool outputVx_;
120	bool outputVy_;
121	bool output3DTemp_;
122	bool outputRotTemp_;
123	// James put this in.
124	bool outputDen_;
125	bool outputVz_;
126	int nBins_; /*< The number of bins to divide the simulation box into. /
127	/*!
128	The middle bin for the RNEMD method. midBin_ = nBins_/2;
129	Depending on the setting of the flux, this box should contain the minimum energy (temperature)
130	within the simulation.
131	*/
132	int midBin_;
133	int rnemdLogWidth_; /*< Number of elements to print out in logs /
134	RealType zShift_;
135	RealType exchangeTime_;
136	RealType targetFlux_;
137	RealType targetJzKE_;
138	RealType targetJzpx_;
139	RealType targetJzpy_;
140	RealType targetJzpz_;
141	RealType targetJzpz2_;
142	Vector3d jzp_, njzp_;
143	RealType exchangeSum_;
144	int failTrialCount_;
145	int failRootCount_;
146	ofstream rnemdLog_;
147	int logFrameCount_;
148	// James added denLog, vzzLog
149	ofstream tempLog_, vxzLog_, vyzLog_, denLog_, vzzLog_, denLog2_;
150	ofstream xTempLog_, yTempLog_, zTempLog_, rotTempLog_;
151	// keeps track of what's being averaged James added DenHist, pzzHist
152	vector<RealType> tempHist_, pxzHist_, pyzHist_, mHist_, DenHist_, pzzHist_, DenHist2_;
153	vector<RealType> xTempHist_, yTempHist_, zTempHist_, rotTempHist_;
154	// keeps track of the number of degrees of freedom being averaged
155	//vector<int> pxzCount_, pyzCount_;
156	vector<int> tempCount_, xyzTempCount_, rotTempCount_;
157	};
158
159	}
160	#endif //INTEGRATORS_RNEMD_HPP