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
 * @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 {
  public:
    RNEMD(SimInfo* info);
    virtual ~RNEMD();
    
    void doRNEMD();
    void doSwap();
    void doNIVS();
    void doVSS();
    void collectData();
    void getStarted();
    bool inSlabA(Vector3d pos);
    bool inSlabB(Vector3d pos);
    void parseOutputFileFormat(const std::string& format);
    void writeOutputFile();
    void writeReal(int index, unsigned int bin);
    void writeVector(int index, unsigned int bin);
    void writeRealStdDev(int index, unsigned int bin);
    void writeVectorStdDev(int index, unsigned int bin);

  private:

    enum RNEMDMethod {
      rnemdSwap,
      rnemdNIVS,
      rnemdVSS,
      rnemdUnkownMethod
    };
    enum RNEMDFluxType {
      rnemdKE,       // translational kinetic energy flux
      rnemdRotKE,    // rotational kinetic energy flux
      rnemdFullKE,   // full kinetic energy flux
      rnemdPx,       // flux of momentum along x axis 
      rnemdPy,       // flux of momentum along y axis 
      rnemdPz,       // flux of momentum along z axis 
      rnemdPvector,  // flux of momentum vector
      rnemdKePx,     // flux of translational KE and x-momentum
      rnemdKePy,     // flux of translational KE and y-momentum
      rnemdKePvector, // full combo platter
      rnemdUnknownFluxType
    };

    enum OutputFields {
      BEGININDEX = 0,
      Z = BEGININDEX,
      TEMPERATURE,
      VELOCITY,
      DENSITY,
      ENDINDEX 
    };

    struct OutputData {
      string title;
      string units;
      string dataType;
      vector<Accumulator*> accumulator;
    };

    typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
    typedef map<string, OutputFields> OutputMapType;
    
    SimInfo* info_;

    map<string, RNEMDMethod> stringToMethod_;
    map<string, RNEMDFluxType> stringToFluxType_;
    RNEMDMethod rnemdMethod_;
    RNEMDFluxType rnemdFluxType_;
    string rnemdObjectSelection_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    bool usePeriodicBoundaryConditions_;
    int nBins_; 
    RealType slabWidth_;
    RealType slabACenter_;
    RealType slabBCenter_;

    RealType kineticFlux_;        // target or desired *flux*
    Vector3d momentumFluxVector_; // target or desired *flux*

    RealType kineticTarget_;     // target or desired one-time exchange energy
    Vector3d momentumTarget_;    // target or desired one-time exchange momentum

    RealType kineticExchange_;    // actual exchange energy (running total)
    Vector3d momentumExchange_;   // actual exchange momentum (running total)

    RealType exchangeTime_;

    RealType targetJzpz2_;

    unsigned int trialCount_;
    unsigned int failTrialCount_;
    unsigned int failRootCount_;

    string rnemdFileName_;
    ofstream rnemdFile_;

    RealType runTime_, statusTime_;

    vector<OutputData> data_;
    OutputBitSet outputMask_;
    OutputMapType outputMap_;
    Accumulator* areaAccumulator_;
    bool doRNEMD_;

  };
}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	5502 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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	jmarr	1728	* [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			* @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	gezelter	1629	using namespace std;
59	gezelter	1390	namespace OpenMD {
60	gezelter	1329
61			class RNEMD {
62			public:
63			RNEMD(SimInfo* info);
64			virtual ~RNEMD();
65	skuang	1368
66			void doRNEMD();
67	gezelter	1329	void doSwap();
68	gezelter	1773	void doNIVS();
69			void doVSS();
70	skuang	1368	void collectData();
71			void getStarted();
72	gezelter	1773	bool inSlabA(Vector3d pos);
73			bool inSlabB(Vector3d pos);
74			void parseOutputFileFormat(const std::string& format);
75			void writeOutputFile();
76			void writeReal(int index, unsigned int bin);
77			void writeVector(int index, unsigned int bin);
78	gezelter	1774	void writeRealStdDev(int index, unsigned int bin);
79			void writeVectorStdDev(int index, unsigned int bin);
80	gezelter	1331
81	gezelter	1329	private:
82	gezelter	1331
83	gezelter	1773	enum RNEMDMethod {
84			rnemdSwap,
85			rnemdNIVS,
86			rnemdVSS,
87			rnemdUnkownMethod
88	gezelter	1329	};
89	gezelter	1773	enum RNEMDFluxType {
90			rnemdKE, // translational kinetic energy flux
91			rnemdRotKE, // rotational kinetic energy flux
92			rnemdFullKE, // full kinetic energy flux
93			rnemdPx, // flux of momentum along x axis
94			rnemdPy, // flux of momentum along y axis
95			rnemdPz, // flux of momentum along z axis
96			rnemdPvector, // flux of momentum vector
97			rnemdKePx, // flux of translational KE and x-momentum
98			rnemdKePy, // flux of translational KE and y-momentum
99			rnemdKePvector, // full combo platter
100			rnemdUnknownFluxType
101			};
102
103			enum OutputFields {
104			BEGININDEX = 0,
105			Z = BEGININDEX,
106			TEMPERATURE,
107			VELOCITY,
108			DENSITY,
109			ENDINDEX
110			};
111
112			struct OutputData {
113			string title;
114			string units;
115			string dataType;
116			vector<Accumulator*> accumulator;
117			};
118
119			typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
120			typedef map<string, OutputFields> OutputMapType;
121	skuang	1368
122	gezelter	1329	SimInfo* info_;
123	gezelter	1773
124			map<string, RNEMDMethod> stringToMethod_;
125			map<string, RNEMDFluxType> stringToFluxType_;
126			RNEMDMethod rnemdMethod_;
127			RNEMDFluxType rnemdFluxType_;
128	gezelter	1629	string rnemdObjectSelection_;
129	skuang	1368	SelectionEvaluator evaluator_;
130	gezelter	1331	SelectionManager seleMan_;
131			bool usePeriodicBoundaryConditions_;
132	gezelter	1773	int nBins_;
133			RealType slabWidth_;
134			RealType slabACenter_;
135			RealType slabBCenter_;
136
137			RealType kineticFlux_; // target or desired flux
138			Vector3d momentumFluxVector_; // target or desired flux
139
140			RealType kineticTarget_; // target or desired one-time exchange energy
141			Vector3d momentumTarget_; // target or desired one-time exchange momentum
142
143			RealType kineticExchange_; // actual exchange energy (running total)
144			Vector3d momentumExchange_; // actual exchange momentum (running total)
145
146	skuang	1368	RealType exchangeTime_;
147	gezelter	1773
148	jmarr	1728	RealType targetJzpz2_;
149	gezelter	1773
150			unsigned int trialCount_;
151			unsigned int failTrialCount_;
152			unsigned int failRootCount_;
153
154			string rnemdFileName_;
155			ofstream rnemdFile_;
156
157			RealType runTime_, statusTime_;
158
159			vector<OutputData> data_;
160			OutputBitSet outputMask_;
161			OutputMapType outputMap_;
162	gezelter	1774	Accumulator* areaAccumulator_;
163	gezelter	1776	bool doRNEMD_;
164	gezelter	1773
165	gezelter	1329	};
166			}
167	skuang	1368	#endif //INTEGRATORS_RNEMD_HPP