ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/integrators/NPT.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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, 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 {
57	<	class NPT : public VelocityVerletIntegrator {
58	<	public:
56	>	namespace OpenMD {
57	>	class NPT : public VelocityVerletIntegrator {
58	>	public:
59
60	<	NPT(SimInfo * info);
61	<	virtual ~NPT();
60	>	NPT(SimInfo * info);
61	>	virtual ~NPT();
62
63
64	<	int getMaxIterationNumber() {
65	<	return maxIterNum_;
66	<	}
64	>	int getMaxIterationNumber() {
65	>	return maxIterNum_;
66	>	}
67
68	<	void setMaxIterationNumber(int maxIter) {
69	<	maxIterNum_ = maxIter;
70	<	}
71	<	double getTauThermostat() {
72	<	return tauThermostat;
73	<	}
68	>	void setMaxIterationNumber(int maxIter) {
69	>	maxIterNum_ = maxIter;
70	>	}
71	>	RealType getTauThermostat() {
72	>	return tauThermostat;
73	>	}
74
75	<	void setTauThermostat(double tt) {
76	<	tauThermostat = tt;
77	<	}
75	>	void setTauThermostat(RealType tt) {
76	>	tauThermostat = tt;
77	>	}
78
79	<	double getTauBarostat() {
80	<	return tauBarostat;
81	<	}
82	<	void setTauBarostat(double tb) {
83	<	tauBarostat = tb;
84	<	}
79	>	RealType getTauBarostat() {
80	>	return tauBarostat;
81	>	}
82	>	void setTauBarostat(RealType tb) {
83	>	tauBarostat = tb;
84	>	}
85
86	<	double getTargetTemp() {
87	<	return targetTemp;
88	<	}
86	>	RealType getTargetTemp() {
87	>	return targetTemp;
88	>	}
89
90	<	void setTargetTemp(double tt) {
91	<	targetTemp = tt;
92	<	}
90	>	void setTargetTemp(RealType tt) {
91	>	targetTemp = tt;
92	>	}
93
94	<	double getTargetPressure() {
95	<	return targetTemp;
96	<	}
94	>	RealType getTargetPressure() {
95	>	return targetTemp;
96	>	}
97
98	<	void setTargetPressure(double tp) {
99	<	targetPressure = tp;
100	<	}
98	>	void setTargetPressure(RealType tp) {
99	>	targetPressure = tp;
100	>	}
101
102	<	double getChiTolerance() {
103	<	return chiTolerance;
104	<	}
102	>	RealType getChiTolerance() {
103	>	return chiTolerance;
104	>	}
105
106	<	void setChiTolerance(double tol) {
107	<	chiTolerance = tol;
108	<	}
106	>	void setChiTolerance(RealType tol) {
107	>	chiTolerance = tol;
108	>	}
109
110	<	double getEtaTolerance() {
111	<	return etaTolerance;
112	<	}
110	>	RealType getEtaTolerance() {
111	>	return etaTolerance;
112	>	}
113
114	<	void setEtaTolerance(double tol) {
115	<	etaTolerance = tol;
116	<	}
114	>	void setEtaTolerance(RealType tol) {
115	>	etaTolerance = tol;
116	>	}
117
118	<	protected:
118	>	protected:
119
120	<	virtual void integrateStep() {
121	<	needStress= true;
122	<	VelocityVerletIntegrator::integrateStep();
123	<	}
120	>	virtual void integrateStep() {
121	>	needStress= true;
122	>	VelocityVerletIntegrator::integrateStep();
123	>	}
124
125	<	virtual void doUpdate();
125	<
126	<	double NkBT;
127	<	double fkBT;
125	>	virtual void doUpdateSizes();
126
127	<	double tt2;
128	<	double tb2;
127	>	virtual void resetIntegrator();
128	>
129	>	virtual void resetEta();
130	>
131	>	RealType NkBT;
132	>	RealType fkBT;
133	>
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;
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;
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;
157	<	double integralOfChidt;
153	<	Mat3x3d press;
156	>	pair<RealType, RealType> thermostat;
157	>	Mat3x3d press;
158
159	<	private:
159	>	private:
160
161	<	virtual void moveA();
162	<	virtual void moveB();
161	>	virtual void moveA();
162	>	virtual void moveB();
163
164	<	virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
164	>	virtual void getVelScaleA(Vector3d& sc, const Vector3d& vel) = 0;
165
166	<	virtual void getVelScaleB(Vector3d& sc, int index) = 0;
166	>	virtual void getVelScaleB(Vector3d& sc, int index) = 0;
167
168	<	virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
169	<	int index, Vector3d& sc) = 0;
168	>	virtual void getPosScale(const Vector3d& pos, const Vector3d& COM,
169	>	int index, Vector3d& sc) = 0;
170
171	<	virtual void calcVelScale() = 0;
171	>	virtual void calcVelScale() = 0;
172
173	<	virtual bool etaConverged() = 0;
173	>	virtual bool etaConverged() = 0;
174
175	<	virtual void evolveEtaA() = 0;
175	>	virtual void evolveEtaA() = 0;
176
177	<	virtual void evolveEtaB() = 0;
177	>	virtual void evolveEtaB() = 0;
178
179	<	virtual void scaleSimBox() = 0;
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;
183	>	virtual void loadEta() = 0;
184	>	virtual void saveEta() = 0;
185
186	<	int maxIterNum_;
186	>	int maxIterNum_;
187
188	<	double chiTolerance;
189	<	};
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 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines