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root/OpenMD/branches/development/src/integrators/Velocitizer.cpp

Comparing:
trunk/src/integrators/Velocitizer.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/integrators/Velocitizer.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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	<
42	>
43		#include "integrators/Velocitizer.hpp"
44		#include "math/SquareMatrix3.hpp"
45		#include "primitives/Molecule.hpp"
46		#include "primitives/StuntDouble.hpp"
46	–	#include "math/randomSPRNG.hpp"
47
48	<	namespace oopse {
48	>	#ifndef IS_MPI
49	>	#include "math/SeqRandNumGen.hpp"
50	>	#else
51	>	#include "math/ParallelRandNumGen.hpp"
52	>	#endif
53
54	<	void Velocitizer::velocitize(double temperature) {
54	>	/* Remove me after testing*/
55	>	/*
56	>	#include <cstdio>
57	>	#include <iostream>
58	>	*/
59	>	/*End remove me*/
60	>
61	>	namespace OpenMD {
62	>
63	>	Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
64	>
65	>	int seedValue;
66	>	Globals * simParams = info->getSimParams();
67	>
68	>	#ifndef IS_MPI
69	>	if (simParams->haveSeed()) {
70	>	seedValue = simParams->getSeed();
71	>	randNumGen_ = new SeqRandNumGen(seedValue);
72	>	}else {
73	>	randNumGen_ = new SeqRandNumGen();
74	>	}
75	>	#else
76	>	if (simParams->haveSeed()) {
77	>	seedValue = simParams->getSeed();
78	>	randNumGen_ = new ParallelRandNumGen(seedValue);
79	>	}else {
80	>	randNumGen_ = new ParallelRandNumGen();
81	>	}
82	>	#endif
83	>	}
84	>
85	>	Velocitizer::~Velocitizer() {
86	>	delete randNumGen_;
87	>	}
88	>
89	>	void Velocitizer::velocitize(RealType temperature) {
90		Vector3d aVel;
91		Vector3d aJ;
92		Mat3x3d I;
#	Line 55 | Line 94 | void Velocitizer::velocitize(double temperature) {
94		int m;
95		int n;
96		Vector3d vdrift;
97	<	double vbar;
97	>	RealType vbar;
98		/**@todo refactory kb */
99	<	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
100	<	double av2;
101	<	double kebar;
102	<
99	>	const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
100	>	RealType av2;
101	>	RealType kebar;
102	>
103	>	Globals * simParams = info_->getSimParams();
104	>
105		SimInfo::MoleculeIterator i;
106		Molecule::IntegrableObjectIterator j;
107		Molecule * mol;
108		StuntDouble * integrableObject;
68	–	gaussianSPRNG gaussStream(info_->getSeed());
109
110		kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
71	–
111		for( mol = info_->beginMolecule(i); mol != NULL;
112	<	mol = info_->nextMolecule(i) ) {
113	<	for( integrableObject = mol->beginIntegrableObject(j);
114	<	integrableObject != NULL;
115	<	integrableObject = mol->nextIntegrableObject(j) ) {
116	<
117	<	// uses equipartition theory to solve for vbar in angstrom/fs
118	<
119	<	av2 = 2.0 * kebar / integrableObject->getMass();
120	<	vbar = sqrt(av2);
121	<
122	<	// picks random velocities from a gaussian distribution
123	<	// centered on vbar
124	<
125	<	for( int k = 0; k < 3; k++ ) {
126	<	aVel[k] = vbar * gaussStream.getGaussian();
127	<	}
128	<
129	<	integrableObject->setVel(aVel);
130	<
131	<	if (integrableObject->isDirectional()) {
132	<	I = integrableObject->getI();
133	<
134	<	if (integrableObject->isLinear()) {
135	<	l = integrableObject->linearAxis();
136	<	m = (l + 1) % 3;
137	<	n = (l + 2) % 3;
138	<
139	<	aJ[l] = 0.0;
140	<	vbar = sqrt(2.0 * kebar * I(m, m));
141	<	aJ[m] = vbar * gaussStream.getGaussian();
142	<	vbar = sqrt(2.0 * kebar * I(n, n));
143	<	aJ[n] = vbar * gaussStream.getGaussian();
144	<	} else {
145	<	for( int k = 0; k < 3; k++ ) {
146	<	vbar = sqrt(2.0 * kebar * I(k, k));
147	<	aJ[k] = vbar * gaussStream.getGaussian();
148	<	}
149	<	} // else isLinear
150	<
151	<	integrableObject->setJ(aJ);
152	<	}     //isDirectional
114	<	}
112	>	mol = info_->nextMolecule(i) ) {
113	>	for( integrableObject = mol->beginIntegrableObject(j);
114	>	integrableObject != NULL;
115	>	integrableObject = mol->nextIntegrableObject(j) ) {
116	>
117	>	// uses equipartition theory to solve for vbar in angstrom/fs
118	>
119	>	av2 = 2.0 * kebar / integrableObject->getMass();
120	>	vbar = sqrt(av2);
121	>
122	>	// picks random velocities from a gaussian distribution
123	>	// centered on vbar
124	>
125	>	for( int k = 0; k < 3; k++ ) {
126	>	aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
127	>	}
128	>	integrableObject->setVel(aVel);
129	>
130	>	if (integrableObject->isDirectional()) {
131	>	I = integrableObject->getI();
132	>
133	>	if (integrableObject->isLinear()) {
134	>	l = integrableObject->linearAxis();
135	>	m = (l + 1) % 3;
136	>	n = (l + 2) % 3;
137	>
138	>	aJ[l] = 0.0;
139	>	vbar = sqrt(2.0 * kebar * I(m, m));
140	>	aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
141	>	vbar = sqrt(2.0 * kebar * I(n, n));
142	>	aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
143	>	} else {
144	>	for( int k = 0; k < 3; k++ ) {
145	>	vbar = sqrt(2.0 * kebar * I(k, k));
146	>	aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
147	>	}
148	>	} // else isLinear
149	>
150	>	integrableObject->setJ(aJ);
151	>	}     //isDirectional
152	>	}
153		}             //end for (mol = beginMolecule(i); ...)
154	<
155	<
156	<
154	>
155	>
156	>
157		removeComDrift();
158	<
159	<	}
160	<
161	<
162	<
163	<	void Velocitizer::removeComDrift() {
158	>	// Remove angular drift if we are not using periodic boundary conditions.
159	>	if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift();
160	>
161	>	}
162	>
163	>
164	>
165	>	void Velocitizer::removeComDrift() {
166		// Get the Center of Mass drift velocity.
167		Vector3d vdrift = info_->getComVel();
168
#	Line 134 | Line 174 | void Velocitizer::removeComDrift() {
174		//  Corrects for the center of mass drift.
175		// sums all the momentum and divides by total mass.
176		for( mol = info_->beginMolecule(i); mol != NULL;
177	<	mol = info_->nextMolecule(i) ) {
178	<	for( integrableObject = mol->beginIntegrableObject(j);
179	<	integrableObject != NULL;
180	<	integrableObject = mol->nextIntegrableObject(j) ) {
181	<	integrableObject->setVel(integrableObject->getVel() - vdrift);
182	<	}
177	>	mol = info_->nextMolecule(i) ) {
178	>	for( integrableObject = mol->beginIntegrableObject(j);
179	>	integrableObject != NULL;
180	>	integrableObject = mol->nextIntegrableObject(j) ) {
181	>	integrableObject->setVel(integrableObject->getVel() - vdrift);
182	>	}
183		}
184	<
184	>
185	>	}
186	>
187	>
188	>	void Velocitizer::removeAngularDrift() {
189	>	// Get the Center of Mass drift velocity.
190	>
191	>	Vector3d vdrift;
192	>	Vector3d com;
193	>
194	>	info_->getComAll(com,vdrift);
195	>
196	>	Mat3x3d inertiaTensor;
197	>	Vector3d angularMomentum;
198	>	Vector3d omega;
199	>
200	>
201	>
202	>	info_->getInertiaTensor(inertiaTensor,angularMomentum);
203	>	// We now need the inverse of the inertia tensor.
204	>	/*
205	>	std::cerr << "Angular Momentum before is "
206	>	<< angularMomentum <<  std::endl;
207	>	std::cerr << "Inertia Tensor before is "
208	>	<< inertiaTensor <<  std::endl;
209	>	*/
210	>	inertiaTensor =inertiaTensor.inverse();
211	>	/*
212	>	std::cerr << "Inertia Tensor after inverse is "
213	>	<< inertiaTensor <<  std::endl;
214	>	*/
215	>	omega = inertiaTensor*angularMomentum;
216	>
217	>	SimInfo::MoleculeIterator i;
218	>	Molecule::IntegrableObjectIterator j;
219	>	Molecule * mol;
220	>	StuntDouble * integrableObject;
221	>	Vector3d tempComPos;
222	>
223	>	//  Corrects for the center of mass angular drift.
224	>	// sums all the angular momentum and divides by total mass.
225	>	for( mol = info_->beginMolecule(i); mol != NULL;
226	>	mol = info_->nextMolecule(i) ) {
227	>	for( integrableObject = mol->beginIntegrableObject(j);
228	>	integrableObject != NULL;
229	>	integrableObject = mol->nextIntegrableObject(j) ) {
230	>	tempComPos = integrableObject->getPos()-com;
231	>	integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos));
232	>	}
233	>	}
234	>
235	>	angularMomentum = info_->getAngularMomentum();
236	>	/*
237	>	std::cerr << "Angular Momentum after is "
238	>	<< angularMomentum <<  std::endl;
239	>	*/
240	>	}
241	>
242	>
243	>
244	>
245		}
146	–
147	–	}

Comparing:
trunk/src/integrators/Velocitizer.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/integrators/Velocitizer.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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