ViewVC Help

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

root/OpenMD/trunk/src/constraints/Rattle.cpp

Comparing trunk/src/constraints/Rattle.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 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		#include "constraints/Rattle.hpp"
44		#include "primitives/Molecule.hpp"
45		#include "utils/simError.h"
46	<	namespace oopse {
46	>	namespace OpenMD {
47
48	<	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
48	>	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10),
49	>	consTolerance_(1.0e-6), doRattle_(false),
50	>	currConstraintTime_(0.0) {
51
52	<	if (info_->getSimParams()->haveDt()) {
53	<	dt_ = info_->getSimParams()->getDt();
52	>	if (info_->getNGlobalConstraints() > 0)
53	>	doRattle_ = true;
54	>
55	>	if (!doRattle_) return;
56	>
57	>	Globals* simParams = info_->getSimParams();
58	>
59	>	if (simParams->haveDt()) {
60	>	dt_ = simParams->getDt();
61		} else {
62		sprintf(painCave.errMsg,
63	<	"Integrator Error: dt is not set\n");
63	>	"Rattle Error: dt is not set\n");
64		painCave.isFatal = 1;
65		simError();
66		}
67	<
67	>
68		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
69	+	if (simParams->haveConstraintTime()){
70	+	constraintTime_ = simParams->getConstraintTime();
71	+	} else {
72	+	constraintTime_ = simParams->getStatusTime();
73	+	}
74	+
75	+	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
76	+	".constraintForces";
77	+
78	+
79	+	// create ConstraintWriter
80	+	constraintWriter_ = new ConstraintWriter(info_,
81	+	constraintOutputFile_.c_str());
82	+
83	+	if (!constraintWriter_){
84	+	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
85	+	painCave.isFatal = 1;
86	+	simError();
87	+	}
88		}
89
90		void Rattle::constraintA() {
91	<	if (info_->getNConstraints() > 0) {
92	<	doConstraint(&Rattle::constraintPairA);
64	<	}
91	>	if (!doRattle_) return;
92	>	doConstraint(&Rattle::constraintPairA);
93		}
94		void Rattle::constraintB() {
95	<	if (info_->getNConstraints() > 0) {
96	<	doConstraint(&Rattle::constraintPairB);
95	>	if (!doRattle_) return;
96	>	doConstraint(&Rattle::constraintPairB);
97	>
98	>	if (currentSnapshot_->getTime() >= currConstraintTime_){
99	>	Molecule* mol;
100	>	SimInfo::MoleculeIterator mi;
101	>	ConstraintPair* consPair;
102	>	Molecule::ConstraintPairIterator cpi;
103	>	std::list<ConstraintPair*> constraints;
104	>	for (mol = info_->beginMolecule(mi); mol != NULL;
105	>	mol = info_->nextMolecule(mi)) {
106	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
107	>	consPair = mol->nextConstraintPair(cpi)) {
108	>
109	>	constraints.push_back(consPair);
110	>	}
111	>	}
112	>	constraintWriter_->writeConstraintForces(constraints);
113	>	currConstraintTime_ += constraintTime_;
114		}
115		}
116
117		void Rattle::doConstraint(ConstraintPairFuncPtr func) {
118	+	if (!doRattle_) return;
119	+
120		Molecule* mol;
121		SimInfo::MoleculeIterator mi;
122		ConstraintElem* consElem;
#	Line 77 | Line 124 | namespace oopse {
124		ConstraintPair* consPair;
125		Molecule::ConstraintPairIterator cpi;
126
127	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
128	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
127	>	for (mol = info_->beginMolecule(mi); mol != NULL;
128	>	mol = info_->nextMolecule(mi)) {
129	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
130	>	consElem = mol->nextConstraintElem(cei)) {
131		consElem->setMoved(true);
132		consElem->setMoving(false);
133		}
#	Line 92 | Line 141 | namespace oopse {
141
142		//loop over every constraint pair
143
144	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
145	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
144	>	for (mol = info_->beginMolecule(mi); mol != NULL;
145	>	mol = info_->nextMolecule(mi)) {
146	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
147	>	consPair = mol->nextConstraintPair(cpi)) {
148
149
150		//dispatch constraint algorithm
#	Line 103 | Line 154 | namespace oopse {
154		switch(exeStatus){
155		case consFail:
156		sprintf(painCave.errMsg,
157	<	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
157	>	"Constraint failure in Rattle::constrainA, "
158	>	"Constraint Fail\n");
159		painCave.isFatal = 1;
160		simError();
161
162		break;
163		case consSuccess:
164	<	//constrain the pair by moving two elements
164	>	// constrain the pair by moving two elements
165		done = false;
166		consPair->getConsElem1()->setMoving(true);
167		consPair->getConsElem2()->setMoving(true);
168		break;
169		case consAlready:
170	<	//current pair is already constrained, do not need to move the elements
170	>	// current pair is already constrained, do not need to
171	>	// move the elements
172		break;
173		default:
174	<	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
174	>	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
175	>	"Error: unrecognized status");
176		painCave.isFatal = 1;
177		simError();
178		break;
#	Line 128 | Line 182 | namespace oopse {
182		}//end for(iter->first())
183
184
185	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
186	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
185	>	for (mol = info_->beginMolecule(mi); mol != NULL;
186	>	mol = info_->nextMolecule(mi)) {
187	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
188	>	consElem = mol->nextConstraintElem(cei)) {
189		consElem->setMoved(consElem->getMoving());
190		consElem->setMoving(false);
191		}
#	Line 140 | Line 196 | namespace oopse {
196
197		if (!done){
198		sprintf(painCave.errMsg,
199	<	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
199	>	"Constraint failure in Rattle::constrainA, "
200	>	"too many iterations: %d\n",
201		iteration);
202		painCave.isFatal = 1;
203		simError();
#	Line 148 | Line 205 | namespace oopse {
205		}
206
207		int Rattle::constraintPairA(ConstraintPair* consPair){
208	+
209		ConstraintElem* consElem1 = consPair->getConsElem1();
210		ConstraintElem* consElem2 = consPair->getConsElem2();
211
#	Line 160 | Line 218 | namespace oopse {
218
219		currentSnapshot_->wrapVector(pab);
220
221	<	double pabsq = pab.lengthSquare();
221	>	RealType pabsq = pab.lengthSquare();
222
223	<	double rabsq = consPair->getConsDistSquare();
224	<	double diffsq = rabsq - pabsq;
223	>	RealType rabsq = consPair->getConsDistSquare();
224	>	RealType diffsq = rabsq - pabsq;
225
226	+
227		// the original rattle code from alan tidesley
228		if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
229
230		Vector3d oldPosA = consElem1->getPrevPos();
231		Vector3d oldPosB = consElem2->getPrevPos();
232
233	<	Vector3d rab = oldPosA - oldPosB;
233	>	Vector3d rab = oldPosA - oldPosB;
234
235		currentSnapshot_->wrapVector(rab);
236
237	<	double rpab = dot(rab, pab);
238	<	double rpabsq = rpab * rpab;
237	>	RealType rpab = dot(rab, pab);
238	>	RealType rpabsq = rpab * rpab;
239
240		if (rpabsq < (rabsq * -diffsq)){
241		return consFail;
242		}
243
244	<	double rma = 1.0 / consElem1->getMass();
245	<	double rmb = 1.0 / consElem2->getMass();
244	>	RealType rma = 1.0 / consElem1->getMass();
245	>	RealType rmb = 1.0 / consElem2->getMass();
246
247	<	double gab = diffsq / (2.0 * (rma + rmb) * rpab);
247	>	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
248
249		Vector3d delta = rab * gab;
250
#	Line 208 | Line 267 | namespace oopse {
267		Vector3d velB = consElem2->getVel();
268		velB -= rmb * delta;
269		consElem2->setVel(velB);
270	<
270	>
271	>	// report the constraint force back to the constraint pair:
272	>	consPair->setConstraintForce(gab);
273		return consSuccess;
274		}
275		else
#	Line 234 | Line 295 | namespace oopse {
295
296		currentSnapshot_->wrapVector(rab);
297
298	<	double rma = 1.0 / consElem1->getMass();
299	<	double rmb = 1.0 / consElem2->getMass();
298	>	RealType rma = 1.0 / consElem1->getMass();
299	>	RealType rmb = 1.0 / consElem2->getMass();
300
301	<	double rvab = dot(rab, dv);
301	>	RealType rvab = dot(rab, dv);
302
303	<	double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
303	>	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
304
305		if (fabs(gab) > consTolerance_){
306		Vector3d delta = rab * gab;
#	Line 250 | Line 311 | namespace oopse {
311		velB -= rmb * delta;
312		consElem2->setVel(velB);
313
314	+	// report the constraint force back to the constraint pair:
315	+	consPair->setConstraintForce(gab);
316		return consSuccess;
317		}
318		else

Comparing trunk/src/constraints/Rattle.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 UTC

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

Diff Legend

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