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, 5 months ago) by gezelter
File size:	5736 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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. 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