src/integrators/NPT.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @file NPT.hpp
 * @author tlin
 * @date 11/19/2004
 * @time 13:25am
 * @version 1.0
 */

#ifndef INTEGRATORS_NPT_HPP
#define INTEGRATORS_NPT_HPP

#include "integrators/VelocityVerletIntegrator.hpp"

namespace oopse {
    class NPT : public VelocityVerletIntegrator {
        public:

            NPT(SimInfo * info);
            virtual ~NPT();


            int getMaxIterationNumber() {
                return maxIterNum_;
            }

            void setMaxIterationNumber(int maxIter) {
                maxIterNum_ = maxIter;
            }
            double getTauThermostat() {
                return tauThermostat;
            }

            void setTauThermostat(double tt) {
                tauThermostat = tt;
            }

            double getTauBarostat() {
                return tauBarostat;
            }
            void setTauBarostat(double tb) {
                tauBarostat = tb;
            }

            double getTargetTemp() {
                return targetTemp;
            }
            
            void setTargetTemp(double tt) {
                targetTemp = tt;
            }

            double getTargetPressure() {
                return targetTemp;
            }
            
            void setTargetPressure(double tp) {
                targetPressure = tp;
            }

            double getChiTolerance() {
                return chiTolerance;
            }
            
            void setChiTolerance(double tol) {
                chiTolerance = tol;
            }

            double getEtaTolerance() {
                return etaTolerance;
            }
            
            void setEtaTolerance(double tol) {
                etaTolerance = tol;
            }

        protected:

            virtual void integrateStep() {
                needStress= true;
                VelocityVerletIntegrator::integrateStep();
            }

            virtual void doUpdate();
            
            double NkBT;
            double fkBT;

            double tt2;            
            double tb2;
            
            double instaTemp;
            double instaPress;
            double instaVol;


            // targetTemp, targetPressure, and tauBarostat must be set.
            // One of qmass or tauThermostat must be set;

            double targetTemp;
            double targetPressure;
            double tauThermostat;
            double tauBarostat;

            std::vector<Vector3d> oldPos;
            std::vector<Vector3d> oldVel;
            std::vector<Vector3d> oldJi;

            double etaTolerance;
       
            double chi;
            double integralOfChidt;
            Mat3x3d press;
            
        private:

            virtual void moveA();
            virtual void moveB();
            
            virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
            
            virtual void getVelScaleB(Vector3d& sc, int index) = 0;
            
            virtual void getPosScale(const Vector3d& pos, const Vector3d& COM, 
                                                            int index, Vector3d& sc) = 0;

            virtual void calcVelScale() = 0;

            virtual bool etaConverged() = 0;

            virtual void evolveEtaA() = 0;

            virtual void evolveEtaB() = 0;

            virtual void scaleSimBox() = 0;
            
            virtual double calcConservedQuantity() = 0;      

            virtual void loadEta() = 0;
            virtual void saveEta() = 0;
            
            int maxIterNum_;

            double chiTolerance;    
    };

}      //end namespace oopse

#endif //INTEGRATORS_NPT_HPP
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 6 months ago) by gezelter
File size:	5736 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file NPT.hpp
44			* @author tlin
45			* @date 11/19/2004
46			* @time 13:25am
47			* @version 1.0
48			*/
49
50			#ifndef INTEGRATORS_NPT_HPP
51			#define INTEGRATORS_NPT_HPP
52
53			#include "integrators/VelocityVerletIntegrator.hpp"
54
55			namespace oopse {
56			class NPT : public VelocityVerletIntegrator {
57			public:
58
59			NPT(SimInfo * info);
60			virtual ~NPT();
61
62
63			int getMaxIterationNumber() {
64			return maxIterNum_;
65			}
66
67			void setMaxIterationNumber(int maxIter) {
68			maxIterNum_ = maxIter;
69			}
70			double getTauThermostat() {
71			return tauThermostat;
72			}
73
74			void setTauThermostat(double tt) {
75			tauThermostat = tt;
76			}
77
78			double getTauBarostat() {
79			return tauBarostat;
80			}
81			void setTauBarostat(double tb) {
82			tauBarostat = tb;
83			}
84
85			double getTargetTemp() {
86			return targetTemp;
87			}
88
89			void setTargetTemp(double tt) {
90			targetTemp = tt;
91			}
92
93			double getTargetPressure() {
94			return targetTemp;
95			}
96
97			void setTargetPressure(double tp) {
98			targetPressure = tp;
99			}
100
101			double getChiTolerance() {
102			return chiTolerance;
103			}
104
105			void setChiTolerance(double tol) {
106			chiTolerance = tol;
107			}
108
109			double getEtaTolerance() {
110			return etaTolerance;
111			}
112
113			void setEtaTolerance(double tol) {
114			etaTolerance = tol;
115			}
116
117			protected:
118
119			virtual void integrateStep() {
120			needStress= true;
121			VelocityVerletIntegrator::integrateStep();
122			}
123
124			virtual void doUpdate();
125
126			double NkBT;
127			double fkBT;
128
129			double tt2;
130			double tb2;
131
132			double instaTemp;
133			double instaPress;
134			double instaVol;
135
136
137			// targetTemp, targetPressure, and tauBarostat must be set.
138			// One of qmass or tauThermostat must be set;
139
140			double targetTemp;
141			double targetPressure;
142			double tauThermostat;
143			double tauBarostat;
144
145			std::vector<Vector3d> oldPos;
146			std::vector<Vector3d> oldVel;
147			std::vector<Vector3d> oldJi;
148
149			double etaTolerance;
150
151			double chi;
152			double integralOfChidt;
153			Mat3x3d press;
154
155			private:
156
157			virtual void moveA();
158			virtual void moveB();
159
160			virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
161
162			virtual void getVelScaleB(Vector3d& sc, int index) = 0;
163
164			virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
165			int index, Vector3d& sc) = 0;
166
167			virtual void calcVelScale() = 0;
168
169			virtual bool etaConverged() = 0;
170
171			virtual void evolveEtaA() = 0;
172
173			virtual void evolveEtaB() = 0;
174
175			virtual void scaleSimBox() = 0;
176
177			virtual double calcConservedQuantity() = 0;
178
179			virtual void loadEta() = 0;
180			virtual void saveEta() = 0;
181
182			int maxIterNum_;
183
184			double chiTolerance;
185			};
186
187			} //end namespace oopse
188
189			#endif //INTEGRATORS_NPT_HPP