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Comparing trunk/src/integrators/NPT.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 234107 (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 NPT.hpp
45		* @author tlin
46		* @date 11/19/2004
46	–	* @time 13:25am
47		* @version 1.0
48		*/
49
#	Line 52 | Line 52
52
53		#include "integrators/VelocityVerletIntegrator.hpp"
54
55	<	namespace oopse {
56	<	class NPT : public VelocityVerletIntegrator {
57	<	public:
55	>	namespace OpenMD {
56	>	class NPT : public VelocityVerletIntegrator {
57	>	public:
58
59	<	NPT(SimInfo * info);
60	<	virtual ~NPT();
59	>	NPT(SimInfo * info);
60	>	virtual ~NPT();
61
62
63	<	int getMaxIterationNumber() {
64	<	return maxIterNum_;
65	<	}
63	>	int getMaxIterationNumber() {
64	>	return maxIterNum_;
65	>	}
66
67	<	void setMaxIterationNumber(int maxIter) {
68	<	maxIterNum_ = maxIter;
69	<	}
70	<	double getTauThermostat() {
71	<	return tauThermostat;
72	<	}
67	>	void setMaxIterationNumber(int maxIter) {
68	>	maxIterNum_ = maxIter;
69	>	}
70	>	RealType getTauThermostat() {
71	>	return tauThermostat;
72	>	}
73
74	<	void setTauThermostat(double tt) {
75	<	tauThermostat = tt;
76	<	}
74	>	void setTauThermostat(RealType tt) {
75	>	tauThermostat = tt;
76	>	}
77
78	<	double getTauBarostat() {
79	<	return tauBarostat;
80	<	}
81	<	void setTauBarostat(double tb) {
82	<	tauBarostat = tb;
83	<	}
78	>	RealType getTauBarostat() {
79	>	return tauBarostat;
80	>	}
81	>	void setTauBarostat(RealType tb) {
82	>	tauBarostat = tb;
83	>	}
84
85	<	double getTargetTemp() {
86	<	return targetTemp;
87	<	}
85	>	RealType getTargetTemp() {
86	>	return targetTemp;
87	>	}
88
89	<	void setTargetTemp(double tt) {
90	<	targetTemp = tt;
91	<	}
89	>	void setTargetTemp(RealType tt) {
90	>	targetTemp = tt;
91	>	}
92
93	<	double getTargetPressure() {
94	<	return targetTemp;
95	<	}
93	>	RealType getTargetPressure() {
94	>	return targetTemp;
95	>	}
96
97	<	void setTargetPressure(double tp) {
98	<	targetPressure = tp;
99	<	}
97	>	void setTargetPressure(RealType tp) {
98	>	targetPressure = tp;
99	>	}
100
101	<	double getChiTolerance() {
102	<	return chiTolerance;
103	<	}
101	>	RealType getChiTolerance() {
102	>	return chiTolerance;
103	>	}
104
105	<	void setChiTolerance(double tol) {
106	<	chiTolerance = tol;
107	<	}
105	>	void setChiTolerance(RealType tol) {
106	>	chiTolerance = tol;
107	>	}
108
109	<	double getEtaTolerance() {
110	<	return etaTolerance;
111	<	}
109	>	RealType getEtaTolerance() {
110	>	return etaTolerance;
111	>	}
112
113	<	void setEtaTolerance(double tol) {
114	<	etaTolerance = tol;
115	<	}
113	>	void setEtaTolerance(RealType tol) {
114	>	etaTolerance = tol;
115	>	}
116
117	<	protected:
117	>	protected:
118
119	<	virtual void integrateStep() {
120	<	needStress= true;
121	<	VelocityVerletIntegrator::integrateStep();
122	<	}
119	>	virtual void integrateStep() {
120	>	needStress= true;
121	>	VelocityVerletIntegrator::integrateStep();
122	>	}
123
124	<	virtual void doUpdate();
125	<
126	<	double NkBT;
127	<	double fkBT;
124	>	virtual void doUpdateSizes();
125
126	<	double tt2;
127	<	double tb2;
126	>	virtual void resetIntegrator();
127	>
128	>	virtual void resetEta();
129	>
130	>	RealType NkBT;
131	>	RealType fkBT;
132	>
133	>	RealType tt2;
134	>	RealType tb2;
135
136	<	double instaTemp;
137	<	double instaPress;
138	<	double instaVol;
136	>	RealType instaTemp;
137	>	RealType instaPress;
138	>	RealType instaVol;
139
140
141	<	// targetTemp, targetPressure, and tauBarostat must be set.
142	<	// One of qmass or tauThermostat must be set;
141	>	// targetTemp, targetPressure, and tauBarostat must be set.
142	>	// One of qmass or tauThermostat must be set;
143
144	<	double targetTemp;
145	<	double targetPressure;
146	<	double tauThermostat;
147	<	double tauBarostat;
144	>	RealType targetTemp;
145	>	RealType targetPressure;
146	>	RealType tauThermostat;
147	>	RealType tauBarostat;
148
149	<	std::vector<Vector3d> oldPos;
150	<	std::vector<Vector3d> oldVel;
151	<	std::vector<Vector3d> oldJi;
149	>	std::vector<Vector3d> oldPos;
150	>	std::vector<Vector3d> oldVel;
151	>	std::vector<Vector3d> oldJi;
152
153	<	double etaTolerance;
153	>	RealType etaTolerance;
154
155	<	double chi;
156	<	double integralOfChidt;
153	<	Mat3x3d press;
155	>	pair<RealType, RealType> thermostat;
156	>	Mat3x3d press;
157
158	<	private:
158	>	private:
159
160	<	virtual void moveA();
161	<	virtual void moveB();
160	>	virtual void moveA();
161	>	virtual void moveB();
162
163	<	virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
163	>	virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
164
165	<	virtual void getVelScaleB(Vector3d& sc, int index) = 0;
165	>	virtual void getVelScaleB(Vector3d& sc, int index) = 0;
166
167	<	virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
168	<	int index, Vector3d& sc) = 0;
167	>	virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
168	>	int index, Vector3d& sc) = 0;
169
170	<	virtual void calcVelScale() = 0;
170	>	virtual void calcVelScale() = 0;
171
172	<	virtual bool etaConverged() = 0;
172	>	virtual bool etaConverged() = 0;
173
174	<	virtual void evolveEtaA() = 0;
174	>	virtual void evolveEtaA() = 0;
175
176	<	virtual void evolveEtaB() = 0;
176	>	virtual void evolveEtaB() = 0;
177
178	<	virtual void scaleSimBox() = 0;
178	>	virtual void scaleSimBox() = 0;
179
180	<	virtual double calcConservedQuantity() = 0;
180	>	virtual RealType calcConservedQuantity() = 0;
181
182	<	virtual void loadEta() = 0;
183	<	virtual void saveEta() = 0;
184	<
185	<	int maxIterNum_;
182	>	virtual void loadEta() = 0;
183	>	virtual void saveEta() = 0;
184	>	RealType chiTolerance;
185	>
186
187	<	double chiTolerance;
188	<	};
187	>	protected:
188	>	int maxIterNum_;
189
190	<	}      //end namespace oopse
190	>	};
191
192	+	}      //end namespace OpenMD
193	+
194		#endif //INTEGRATORS_NPT_HPP

Comparing trunk/src/integrators/NPT.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

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