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Comparing trunk/src/integrators/NPT.hpp (file contents):
Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

#	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 {
55	>	namespace OpenMD {
56		class NPT : public VelocityVerletIntegrator {
57		public:
58
#	Line 67 | Line 67 | namespace oopse {
67		void setMaxIterationNumber(int maxIter) {
68		maxIterNum_ = maxIter;
69		}
70	<	double getTauThermostat() {
70	>	RealType getTauThermostat() {
71		return tauThermostat;
72		}
73
74	<	void setTauThermostat(double tt) {
74	>	void setTauThermostat(RealType tt) {
75		tauThermostat = tt;
76		}
77
78	<	double getTauBarostat() {
78	>	RealType getTauBarostat() {
79		return tauBarostat;
80		}
81	<	void setTauBarostat(double tb) {
81	>	void setTauBarostat(RealType tb) {
82		tauBarostat = tb;
83		}
84
85	<	double getTargetTemp() {
85	>	RealType getTargetTemp() {
86		return targetTemp;
87		}
88
89	<	void setTargetTemp(double tt) {
89	>	void setTargetTemp(RealType tt) {
90		targetTemp = tt;
91		}
92
93	<	double getTargetPressure() {
93	>	RealType getTargetPressure() {
94		return targetTemp;
95		}
96
97	<	void setTargetPressure(double tp) {
97	>	void setTargetPressure(RealType tp) {
98		targetPressure = tp;
99		}
100
101	<	double getChiTolerance() {
101	>	RealType getChiTolerance() {
102		return chiTolerance;
103		}
104
105	<	void setChiTolerance(double tol) {
105	>	void setChiTolerance(RealType tol) {
106		chiTolerance = tol;
107		}
108
109	<	double getEtaTolerance() {
109	>	RealType getEtaTolerance() {
110		return etaTolerance;
111		}
112
113	<	void setEtaTolerance(double tol) {
113	>	void setEtaTolerance(RealType tol) {
114		etaTolerance = tol;
115		}
116
#	Line 121 | Line 121 | namespace oopse {
121		VelocityVerletIntegrator::integrateStep();
122		}
123
124	<	virtual void doUpdate();
124	>	virtual void doUpdateSizes();
125
126		virtual void resetIntegrator();
127
128		virtual void resetEta();
129
130	<	double NkBT;
131	<	double fkBT;
130	>	RealType NkBT;
131	>	RealType fkBT;
132
133	<	double tt2;
134	<	double tb2;
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;
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;
152
153	<	double etaTolerance;
153	>	RealType etaTolerance;
154
155	<	double chi;
156	<	double integralOfChidt;
155	>	pair<RealType, RealType> thermostat;
156		Mat3x3d press;
157
158		private:
#	Line 178 | Line 177 | namespace oopse {
177
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	<
184	>	RealType chiTolerance;
185	>
186	>
187	>	protected:
188		int maxIterNum_;
189
188	–	double chiTolerance;
190		};
191
192	<	}      //end namespace oopse
192	>	}      //end namespace OpenMD
193
194		#endif //INTEGRATORS_NPT_HPP

Comparing trunk/src/integrators/NPT.hpp (property svn:keywords):
Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

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