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();

    virtual void resetIntegrator();

    virtual void resetEta();
    
    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:	2243
Committed:	Sun May 29 00:06:14 2005 UTC (19 years, 1 month ago) by tim
File size:	5016 byte(s)
Log Message:	adding resetIntegrator
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	class NPT : public VelocityVerletIntegrator {
57			public:
58	gezelter	1930
59	gezelter	2204	NPT(SimInfo * info);
60			virtual ~NPT();
61	gezelter	1930
62
63	gezelter	2204	int getMaxIterationNumber() {
64			return maxIterNum_;
65			}
66	gezelter	1930
67	gezelter	2204	void setMaxIterationNumber(int maxIter) {
68			maxIterNum_ = maxIter;
69			}
70			double getTauThermostat() {
71			return tauThermostat;
72			}
73	gezelter	1930
74	gezelter	2204	void setTauThermostat(double tt) {
75			tauThermostat = tt;
76			}
77	gezelter	1930
78	gezelter	2204	double getTauBarostat() {
79			return tauBarostat;
80			}
81			void setTauBarostat(double tb) {
82			tauBarostat = tb;
83			}
84	gezelter	1930
85	gezelter	2204	double getTargetTemp() {
86			return targetTemp;
87			}
88	gezelter	1930
89	gezelter	2204	void setTargetTemp(double tt) {
90			targetTemp = tt;
91			}
92	gezelter	1930
93	gezelter	2204	double getTargetPressure() {
94			return targetTemp;
95			}
96	gezelter	1930
97	gezelter	2204	void setTargetPressure(double tp) {
98			targetPressure = tp;
99			}
100	gezelter	1930
101	gezelter	2204	double getChiTolerance() {
102			return chiTolerance;
103			}
104	gezelter	1930
105	gezelter	2204	void setChiTolerance(double tol) {
106			chiTolerance = tol;
107			}
108	gezelter	1930
109	gezelter	2204	double getEtaTolerance() {
110			return etaTolerance;
111			}
112	gezelter	1930
113	gezelter	2204	void setEtaTolerance(double tol) {
114			etaTolerance = tol;
115			}
116	gezelter	1930
117	gezelter	2204	protected:
118	gezelter	1930
119	gezelter	2204	virtual void integrateStep() {
120			needStress= true;
121			VelocityVerletIntegrator::integrateStep();
122			}
123	gezelter	1930
124	gezelter	2204	virtual void doUpdate();
125	tim	2243
126			virtual void resetIntegrator();
127
128			virtual void resetEta();
129
130	gezelter	2204	double NkBT;
131			double fkBT;
132	gezelter	1930
133	gezelter	2204	double tt2;
134			double tb2;
135	gezelter	1930
136	gezelter	2204	double instaTemp;
137			double instaPress;
138			double instaVol;
139	gezelter	1930
140
141	gezelter	2204	// targetTemp, targetPressure, and tauBarostat must be set.
142			// One of qmass or tauThermostat must be set;
143	gezelter	1930
144	gezelter	2204	double targetTemp;
145			double targetPressure;
146			double tauThermostat;
147			double tauBarostat;
148	gezelter	1930
149	gezelter	2204	std::vector<Vector3d> oldPos;
150			std::vector<Vector3d> oldVel;
151			std::vector<Vector3d> oldJi;
152	gezelter	1930
153	gezelter	2204	double etaTolerance;
154	gezelter	1930
155	gezelter	2204	double chi;
156			double integralOfChidt;
157			Mat3x3d press;
158	gezelter	1930
159	gezelter	2204	private:
160	gezelter	1930
161	gezelter	2204	virtual void moveA();
162			virtual void moveB();
163	gezelter	1930
164	gezelter	2204	virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
165	gezelter	1930
166	gezelter	2204	virtual void getVelScaleB(Vector3d& sc, int index) = 0;
167	gezelter	1930
168	gezelter	2204	virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
169			int index, Vector3d& sc) = 0;
170	gezelter	1930
171	gezelter	2204	virtual void calcVelScale() = 0;
172	gezelter	1930
173	gezelter	2204	virtual bool etaConverged() = 0;
174	gezelter	1930
175	gezelter	2204	virtual void evolveEtaA() = 0;
176	gezelter	1930
177	gezelter	2204	virtual void evolveEtaB() = 0;
178	gezelter	1930
179	gezelter	2204	virtual void scaleSimBox() = 0;
180	gezelter	1930
181	gezelter	2204	virtual double calcConservedQuantity() = 0;
182	gezelter	1930
183	gezelter	2204	virtual void loadEta() = 0;
184			virtual void saveEta() = 0;
185	gezelter	1930
186	gezelter	2204	int maxIterNum_;
187	gezelter	1930
188	gezelter	2204	double chiTolerance;
189			};
190	gezelter	1930
191			} //end namespace oopse
192
193			#endif //INTEGRATORS_NPT_HPP