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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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);
    ~RNEMD();
    
    void doRNEMD();
    void doSwap(SelectionManager& smanA, SelectionManager& smanB);
    void doNIVS(SelectionManager& smanA, SelectionManager& smanB);
    void doVSS(SelectionManager& smanA, SelectionManager& smanB);
    RealType getDividingArea();
    void collectData();
    void getStarted();
    void parseOutputFileFormat(const std::string& format);
    void writeOutputFile();
    void writeReal(int index, unsigned int bin);
    void writeVector(int index, unsigned int bin);
    void writeRealErrorBars(int index, unsigned int bin);
    void writeVectorErrorBars(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
      rnemdLx,       // flux of angular momentum along x axis 
      rnemdLy,       // flux of angular momentum along y axis 
      rnemdLz,       // flux of angular momentum along z axis 
      rnemdLvector,  // flux of angular momentum vector
      rnemdKePx,     // flux of translational KE and x-momentum
      rnemdKePy,     // flux of translational KE and y-momentum
      rnemdKePvector, // full combo flying platter
      rnemdKeLx,     // flux of translational KE and x-angular momentum
      rnemdKeLy,     // flux of translational KE and y-angular momentum
      rnemdKeLz,     // flux of translational KE and z-angular momentum
      rnemdKeLvector, // full combo spinning platter
      rnemdUnknownFluxType
    };

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

    struct OutputData {
      string title;
      string units;
      string dataType;
      vector<BaseAccumulator*> 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_;

    // object selection for specifying a particular species:
    string rnemdObjectSelection_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;

    // Geometric selections for the two regions for the exchange:
    string selectionA_;
    SelectionEvaluator evaluatorA_;
    SelectionManager seleManA_;
    string selectionB_;
    SelectionEvaluator evaluatorB_;
    SelectionManager seleManB_;
    SelectionManager commonA_;
    SelectionManager commonB_;
    bool hasSelectionA_;
    bool hasSelectionB_;                      
    bool hasSphereBRadius_;

    bool usePeriodicBoundaryConditions_;
    bool hasDividingArea_;
    RealType dividingArea_;

    int nBins_;
    RealType binWidth_;
    RealType slabWidth_;
    RealType slabACenter_;
    RealType slabBCenter_;
    RealType sphereARadius_;
    RealType sphereBRadius_;
    RealType areaA_;
    bool AisHull_;
    RealType areaB_;
    bool BisHull_;

    Vector3d coordinateOrigin_;

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

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

    RealType kineticExchange_;    // actual exchange energy (running total)
    Vector3d momentumExchange_;   // actual exchange momentum (running total)
    Vector3d angularMomentumExchange_; // 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_;
    bool hasData_;

  };
}
#endif //INTEGRATORS_RNEMD_HPP
Revision:	2046
Committed:	Tue Dec 2 22:11:04 2014 UTC (10 years, 7 months ago) by gezelter
File size:	7157 byte(s)
Log Message:	Fixed some broken comments for use with Doxygen. Made changes to allow topology-based force-field overrides in include files. Fixed a calculation of box quadrupole moments for molecules with point dipoles.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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			#ifndef INTEGRATORS_RNEMD_HPP
44			#define INTEGRATORS_RNEMD_HPP
45			#include "brains/SimInfo.hpp"
46			#include "math/RandNumGen.hpp"
47	gezelter	1331	#include "selection/SelectionEvaluator.hpp"
48			#include "selection/SelectionManager.hpp"
49	skuang	1368	#include <iostream>
50	gezelter	1329
51	gezelter	1629	using namespace std;
52	gezelter	1390	namespace OpenMD {
53	gezelter	1329
54			class RNEMD {
55			public:
56			RNEMD(SimInfo* info);
57	gezelter	1879	~RNEMD();
58	skuang	1368
59			void doRNEMD();
60	gezelter	1879	void doSwap(SelectionManager& smanA, SelectionManager& smanB);
61			void doNIVS(SelectionManager& smanA, SelectionManager& smanB);
62			void doVSS(SelectionManager& smanA, SelectionManager& smanB);
63			RealType getDividingArea();
64	skuang	1368	void collectData();
65			void getStarted();
66	gezelter	1773	void parseOutputFileFormat(const std::string& format);
67			void writeOutputFile();
68			void writeReal(int index, unsigned int bin);
69			void writeVector(int index, unsigned int bin);
70	gezelter	1979	void writeRealErrorBars(int index, unsigned int bin);
71			void writeVectorErrorBars(int index, unsigned int bin);
72	gezelter	1331
73	gezelter	1329	private:
74	gezelter	1331
75	gezelter	1773	enum RNEMDMethod {
76			rnemdSwap,
77			rnemdNIVS,
78			rnemdVSS,
79			rnemdUnkownMethod
80	gezelter	1329	};
81	gezelter	1773	enum RNEMDFluxType {
82			rnemdKE, // translational kinetic energy flux
83			rnemdRotKE, // rotational kinetic energy flux
84			rnemdFullKE, // full kinetic energy flux
85			rnemdPx, // flux of momentum along x axis
86			rnemdPy, // flux of momentum along y axis
87			rnemdPz, // flux of momentum along z axis
88			rnemdPvector, // flux of momentum vector
89	gezelter	1879	rnemdLx, // flux of angular momentum along x axis
90			rnemdLy, // flux of angular momentum along y axis
91			rnemdLz, // flux of angular momentum along z axis
92			rnemdLvector, // flux of angular momentum vector
93	gezelter	1773	rnemdKePx, // flux of translational KE and x-momentum
94			rnemdKePy, // flux of translational KE and y-momentum
95	gezelter	1879	rnemdKePvector, // full combo flying platter
96			rnemdKeLx, // flux of translational KE and x-angular momentum
97			rnemdKeLy, // flux of translational KE and y-angular momentum
98			rnemdKeLz, // flux of translational KE and z-angular momentum
99			rnemdKeLvector, // full combo spinning platter
100	gezelter	1773	rnemdUnknownFluxType
101			};
102
103			enum OutputFields {
104			BEGININDEX = 0,
105			Z = BEGININDEX,
106	gezelter	1879	R,
107	gezelter	1773	TEMPERATURE,
108			VELOCITY,
109	gezelter	1879	ANGULARVELOCITY,
110	gezelter	1773	DENSITY,
111			ENDINDEX
112			};
113
114			struct OutputData {
115			string title;
116			string units;
117			string dataType;
118	gezelter	1791	vector<BaseAccumulator*> accumulator;
119	gezelter	1773	};
120
121			typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
122			typedef map<string, OutputFields> OutputMapType;
123	skuang	1368
124	gezelter	1329	SimInfo* info_;
125	gezelter	1773
126			map<string, RNEMDMethod> stringToMethod_;
127			map<string, RNEMDFluxType> stringToFluxType_;
128			RNEMDMethod rnemdMethod_;
129			RNEMDFluxType rnemdFluxType_;
130	gezelter	1879
131			// object selection for specifying a particular species:
132	gezelter	1629	string rnemdObjectSelection_;
133	skuang	1368	SelectionEvaluator evaluator_;
134	gezelter	1331	SelectionManager seleMan_;
135	gezelter	1879
136			// Geometric selections for the two regions for the exchange:
137			string selectionA_;
138			SelectionEvaluator evaluatorA_;
139			SelectionManager seleManA_;
140			string selectionB_;
141			SelectionEvaluator evaluatorB_;
142			SelectionManager seleManB_;
143			SelectionManager commonA_;
144			SelectionManager commonB_;
145			bool hasSelectionA_;
146			bool hasSelectionB_;
147			bool hasSphereBRadius_;
148
149	gezelter	1331	bool usePeriodicBoundaryConditions_;
150	gezelter	1879	bool hasDividingArea_;
151			RealType dividingArea_;
152
153			int nBins_;
154			RealType binWidth_;
155	gezelter	1773	RealType slabWidth_;
156			RealType slabACenter_;
157			RealType slabBCenter_;
158	gezelter	1879	RealType sphereARadius_;
159			RealType sphereBRadius_;
160	gezelter	1903	RealType areaA_;
161			bool AisHull_;
162			RealType areaB_;
163			bool BisHull_;
164	gezelter	1773
165	gezelter	1879	Vector3d coordinateOrigin_;
166
167	gezelter	1773	RealType kineticFlux_; // target or desired flux
168			Vector3d momentumFluxVector_; // target or desired flux
169	gezelter	1879	Vector3d angularMomentumFluxVector_; // target or desired flux
170	gezelter	1773
171			RealType kineticTarget_; // target or desired one-time exchange energy
172			Vector3d momentumTarget_; // target or desired one-time exchange momentum
173	gezelter	1879	Vector3d angularMomentumTarget_; // target or desired one-time
174			// exchange angular momentum
175	gezelter	1773
176			RealType kineticExchange_; // actual exchange energy (running total)
177			Vector3d momentumExchange_; // actual exchange momentum (running total)
178	gezelter	1879	Vector3d angularMomentumExchange_; // actual exchange momentum
179			// (running total)
180	skuang	1368	RealType exchangeTime_;
181	gezelter	1773
182	jmarr	1728	RealType targetJzpz2_;
183	gezelter	1773
184			unsigned int trialCount_;
185			unsigned int failTrialCount_;
186			unsigned int failRootCount_;
187
188			string rnemdFileName_;
189			ofstream rnemdFile_;
190
191			RealType runTime_, statusTime_;
192
193			vector<OutputData> data_;
194			OutputBitSet outputMask_;
195			OutputMapType outputMap_;
196	gezelter	1774	Accumulator* areaAccumulator_;
197	gezelter	1776	bool doRNEMD_;
198	gezelter	1879	bool hasData_;
199	gezelter	1773
200	gezelter	1329	};
201			}
202	skuang	1368	#endif //INTEGRATORS_RNEMD_HPP