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root/OpenMD/trunk/src/integrators/NPT.hpp

Comparing trunk/src/integrators/NPT.hpp (file contents):
Revision 546 by tim, Sun May 29 00:06:14 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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, 24107 (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		/**
#	Line 52 | Line 53
53
54		#include "integrators/VelocityVerletIntegrator.hpp"
55
56	<	namespace oopse {
56	>	namespace OpenMD {
57		class NPT : public VelocityVerletIntegrator {
58		public:
59
#	Line 67 | Line 68 | namespace oopse {
68		void setMaxIterationNumber(int maxIter) {
69		maxIterNum_ = maxIter;
70		}
71	<	double getTauThermostat() {
71	>	RealType getTauThermostat() {
72		return tauThermostat;
73		}
74
75	<	void setTauThermostat(double tt) {
75	>	void setTauThermostat(RealType tt) {
76		tauThermostat = tt;
77		}
78
79	<	double getTauBarostat() {
79	>	RealType getTauBarostat() {
80		return tauBarostat;
81		}
82	<	void setTauBarostat(double tb) {
82	>	void setTauBarostat(RealType tb) {
83		tauBarostat = tb;
84		}
85
86	<	double getTargetTemp() {
86	>	RealType getTargetTemp() {
87		return targetTemp;
88		}
89
90	<	void setTargetTemp(double tt) {
90	>	void setTargetTemp(RealType tt) {
91		targetTemp = tt;
92		}
93
94	<	double getTargetPressure() {
94	>	RealType getTargetPressure() {
95		return targetTemp;
96		}
97
98	<	void setTargetPressure(double tp) {
98	>	void setTargetPressure(RealType tp) {
99		targetPressure = tp;
100		}
101
102	<	double getChiTolerance() {
102	>	RealType getChiTolerance() {
103		return chiTolerance;
104		}
105
106	<	void setChiTolerance(double tol) {
106	>	void setChiTolerance(RealType tol) {
107		chiTolerance = tol;
108		}
109
110	<	double getEtaTolerance() {
110	>	RealType getEtaTolerance() {
111		return etaTolerance;
112		}
113
114	<	void setEtaTolerance(double tol) {
114	>	void setEtaTolerance(RealType tol) {
115		etaTolerance = tol;
116		}
117
#	Line 121 | Line 122 | namespace oopse {
122		VelocityVerletIntegrator::integrateStep();
123		}
124
125	<	virtual void doUpdate();
125	>	virtual void doUpdateSizes();
126
127		virtual void resetIntegrator();
128
129		virtual void resetEta();
130
131	<	double NkBT;
132	<	double fkBT;
131	>	RealType NkBT;
132	>	RealType fkBT;
133
134	<	double tt2;
135	<	double tb2;
134	>	RealType tt2;
135	>	RealType tb2;
136
137	<	double instaTemp;
138	<	double instaPress;
139	<	double instaVol;
137	>	RealType instaTemp;
138	>	RealType instaPress;
139	>	RealType instaVol;
140
141
142		// targetTemp, targetPressure, and tauBarostat must be set.
143		// One of qmass or tauThermostat must be set;
144
145	<	double targetTemp;
146	<	double targetPressure;
147	<	double tauThermostat;
148	<	double tauBarostat;
145	>	RealType targetTemp;
146	>	RealType targetPressure;
147	>	RealType tauThermostat;
148	>	RealType tauBarostat;
149
150		std::vector<Vector3d> oldPos;
151		std::vector<Vector3d> oldVel;
152		std::vector<Vector3d> oldJi;
153
154	<	double etaTolerance;
154	>	RealType etaTolerance;
155
156	<	double chi;
156	<	double integralOfChidt;
156	>	pair<RealType, RealType> thermostat;
157		Mat3x3d press;
158
159		private:
#	Line 178 | Line 178 | namespace oopse {
178
179		virtual void scaleSimBox() = 0;
180
181	<	virtual double calcConservedQuantity() = 0;
181	>	virtual RealType calcConservedQuantity() = 0;
182
183		virtual void loadEta() = 0;
184		virtual void saveEta() = 0;
185
186		int maxIterNum_;
187
188	<	double chiTolerance;
188	>	RealType chiTolerance;
189		};
190
191	<	}      //end namespace oopse
191	>	}      //end namespace OpenMD
192
193		#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 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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