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 {
  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_;

  };
}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	1774
Committed:	Wed Aug 8 16:03:02 2012 UTC (13 years, 2 months ago) by gezelter
File size:	5500 byte(s)
Log Message:	Cleaning up RNEMD log, adding XY area to Snapshot
#	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	class RNEMD {
63	public:
64	RNEMD(SimInfo* info);
65	virtual ~RNEMD();
66
67	void doRNEMD();
68	void doSwap();
69	void doNIVS();
70	void doVSS();
71	void collectData();
72	void getStarted();
73	bool inSlabA(Vector3d pos);
74	bool inSlabB(Vector3d pos);
75	void parseOutputFileFormat(const std::string& format);
76	void writeOutputFile();
77	void writeReal(int index, unsigned int bin);
78	void writeVector(int index, unsigned int bin);
79	void writeRealStdDev(int index, unsigned int bin);
80	void writeVectorStdDev(int index, unsigned int bin);
81
82	private:
83
84	enum RNEMDMethod {
85	rnemdSwap,
86	rnemdNIVS,
87	rnemdVSS,
88	rnemdUnkownMethod
89	};
90	enum RNEMDFluxType {
91	rnemdKE, // translational kinetic energy flux
92	rnemdRotKE, // rotational kinetic energy flux
93	rnemdFullKE, // full kinetic energy flux
94	rnemdPx, // flux of momentum along x axis
95	rnemdPy, // flux of momentum along y axis
96	rnemdPz, // flux of momentum along z axis
97	rnemdPvector, // flux of momentum vector
98	rnemdKePx, // flux of translational KE and x-momentum
99	rnemdKePy, // flux of translational KE and y-momentum
100	rnemdKePvector, // full combo platter
101	rnemdUnknownFluxType
102	};
103
104	enum OutputFields {
105	BEGININDEX = 0,
106	Z = BEGININDEX,
107	TEMPERATURE,
108	VELOCITY,
109	DENSITY,
110	ENDINDEX
111	};
112
113	struct OutputData {
114	string title;
115	string units;
116	string dataType;
117	vector<Accumulator*> accumulator;
118	};
119
120	typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
121	typedef map<string, OutputFields> OutputMapType;
122
123	SimInfo* info_;
124
125	map<string, RNEMDMethod> stringToMethod_;
126	map<string, RNEMDFluxType> stringToFluxType_;
127	RNEMDMethod rnemdMethod_;
128	RNEMDFluxType rnemdFluxType_;
129	string rnemdObjectSelection_;
130	SelectionEvaluator evaluator_;
131	SelectionManager seleMan_;
132	bool usePeriodicBoundaryConditions_;
133	int nBins_;
134	RealType slabWidth_;
135	RealType slabACenter_;
136	RealType slabBCenter_;
137
138	RealType kineticFlux_; // target or desired flux
139	Vector3d momentumFluxVector_; // target or desired flux
140
141	RealType kineticTarget_; // target or desired one-time exchange energy
142	Vector3d momentumTarget_; // target or desired one-time exchange momentum
143
144	RealType kineticExchange_; // actual exchange energy (running total)
145	Vector3d momentumExchange_; // actual exchange momentum (running total)
146
147	RealType exchangeTime_;
148
149	RealType targetJzpz2_;
150
151	unsigned int trialCount_;
152	unsigned int failTrialCount_;
153	unsigned int failRootCount_;
154
155	string rnemdFileName_;
156	ofstream rnemdFile_;
157
158	RealType runTime_, statusTime_;
159
160	vector<OutputData> data_;
161	OutputBitSet outputMask_;
162	OutputMapType outputMap_;
163	Accumulator* areaAccumulator_;
164
165	};
166	}
167	#endif //INTEGRATORS_RNEMD_HPP