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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 1982 by gezelter, Tue Apr 15 12:12:23 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), consTolerance_(1.0e-6), doRattle_(false) {
49
50	<	if (info_->getSimParams()->haveDt()) {
51	<	dt_ = info_->getSimParams()->getDt();
50	>	if (info_->getNGlobalConstraints() > 0)
51	>	doRattle_ = true;
52	>
53	>	Globals* simParams = info_->getSimParams();
54	>
55	>	if (simParams->haveDt()) {
56	>	dt_ = simParams->getDt();
57		} else {
58		sprintf(painCave.errMsg,
59	<	"Integrator Error: dt is not set\n");
59	>	"Rattle Error: dt is not set\n");
60		painCave.isFatal = 1;
61		simError();
62		}
63	<
63	>
64		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
65	+	if (simParams->haveConstraintTime()){
66	+	constraintTime_ = simParams->getConstraintTime();
67	+	} else {
68	+	constraintTime_ = simParams->getStatusTime();
69	+	}
70	+
71	+	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
72	+
73	+	// create ConstraintWriter
74	+	constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
75	+
76	+	if (!constraintWriter_){
77	+	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
78	+	painCave.isFatal = 1;
79	+	simError();
80	+	}
81		}
82
83		void Rattle::constraintA() {
84	<	if (info_->getNConstraints() > 0) {
85	<	doConstraint(&Rattle::constraintPairA);
64	<	}
84	>	if (!doRattle_) return;
85	>	doConstraint(&Rattle::constraintPairA);
86		}
87		void Rattle::constraintB() {
88	<	if (info_->getNConstraints() > 0) {
89	<	doConstraint(&Rattle::constraintPairB);
88	>	if (!doRattle_) return;
89	>	doConstraint(&Rattle::constraintPairB);
90	>
91	>	if (currentSnapshot_->getTime() >= currConstraintTime_){
92	>	Molecule* mol;
93	>	SimInfo::MoleculeIterator mi;
94	>	ConstraintPair* consPair;
95	>	Molecule::ConstraintPairIterator cpi;
96	>	std::list<ConstraintPair*> constraints;
97	>	for (mol = info_->beginMolecule(mi); mol != NULL;
98	>	mol = info_->nextMolecule(mi)) {
99	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
100	>	consPair = mol->nextConstraintPair(cpi)) {
101	>
102	>	constraints.push_back(consPair);
103	>	}
104	>	}
105	>
106	>	constraintWriter_->writeConstraintForces(constraints);
107	>	currConstraintTime_ += constraintTime_;
108		}
109		}
110
111		void Rattle::doConstraint(ConstraintPairFuncPtr func) {
112	+	if (!doRattle_) return;
113	+
114		Molecule* mol;
115		SimInfo::MoleculeIterator mi;
116		ConstraintElem* consElem;
#	Line 77 | Line 118 | namespace oopse {
118		ConstraintPair* consPair;
119		Molecule::ConstraintPairIterator cpi;
120
121	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
122	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
121	>	for (mol = info_->beginMolecule(mi); mol != NULL;
122	>	mol = info_->nextMolecule(mi)) {
123	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
124	>	consElem = mol->nextConstraintElem(cei)) {
125		consElem->setMoved(true);
126		consElem->setMoving(false);
127		}
#	Line 92 | Line 135 | namespace oopse {
135
136		//loop over every constraint pair
137
138	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
139	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
138	>	for (mol = info_->beginMolecule(mi); mol != NULL;
139	>	mol = info_->nextMolecule(mi)) {
140	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
141	>	consPair = mol->nextConstraintPair(cpi)) {
142
143
144		//dispatch constraint algorithm
#	Line 103 | Line 148 | namespace oopse {
148		switch(exeStatus){
149		case consFail:
150		sprintf(painCave.errMsg,
151	<	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
151	>	"Constraint failure in Rattle::constrainA, "
152	>	"Constraint Fail\n");
153		painCave.isFatal = 1;
154		simError();
155
156		break;
157		case consSuccess:
158	<	//constrain the pair by moving two elements
158	>	// constrain the pair by moving two elements
159		done = false;
160		consPair->getConsElem1()->setMoving(true);
161		consPair->getConsElem2()->setMoving(true);
162		break;
163		case consAlready:
164	<	//current pair is already constrained, do not need to move the elements
164	>	// current pair is already constrained, do not need to
165	>	// move the elements
166		break;
167		default:
168	<	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
168	>	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
169	>	"Error: unrecognized status");
170		painCave.isFatal = 1;
171		simError();
172		break;
#	Line 128 | Line 176 | namespace oopse {
176		}//end for(iter->first())
177
178
179	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
180	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
179	>	for (mol = info_->beginMolecule(mi); mol != NULL;
180	>	mol = info_->nextMolecule(mi)) {
181	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
182	>	consElem = mol->nextConstraintElem(cei)) {
183		consElem->setMoved(consElem->getMoving());
184		consElem->setMoving(false);
185		}
#	Line 140 | Line 190 | namespace oopse {
190
191		if (!done){
192		sprintf(painCave.errMsg,
193	<	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
193	>	"Constraint failure in Rattle::constrainA, "
194	>	"too many iterations: %d\n",
195		iteration);
196		painCave.isFatal = 1;
197		simError();
#	Line 148 | Line 199 | namespace oopse {
199		}
200
201		int Rattle::constraintPairA(ConstraintPair* consPair){
202	+
203		ConstraintElem* consElem1 = consPair->getConsElem1();
204		ConstraintElem* consElem2 = consPair->getConsElem2();
205
#	Line 160 | Line 212 | namespace oopse {
212
213		currentSnapshot_->wrapVector(pab);
214
215	<	double pabsq = pab.lengthSquare();
215	>	RealType pabsq = pab.lengthSquare();
216
217	<	double rabsq = consPair->getConsDistSquare();
218	<	double diffsq = rabsq - pabsq;
217	>	RealType rabsq = consPair->getConsDistSquare();
218	>	RealType diffsq = rabsq - pabsq;
219
220		// the original rattle code from alan tidesley
221		if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
#	Line 175 | Line 227 | namespace oopse {
227
228		currentSnapshot_->wrapVector(rab);
229
230	<	double rpab = dot(rab, pab);
231	<	double rpabsq = rpab * rpab;
230	>	RealType rpab = dot(rab, pab);
231	>	RealType rpabsq = rpab * rpab;
232
233		if (rpabsq < (rabsq * -diffsq)){
234		return consFail;
235		}
236
237	<	double rma = 1.0 / consElem1->getMass();
238	<	double rmb = 1.0 / consElem2->getMass();
237	>	RealType rma = 1.0 / consElem1->getMass();
238	>	RealType rmb = 1.0 / consElem2->getMass();
239
240	<	double gab = diffsq / (2.0 * (rma + rmb) * rpab);
240	>	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
241
242		Vector3d delta = rab * gab;
243
#	Line 208 | Line 260 | namespace oopse {
260		Vector3d velB = consElem2->getVel();
261		velB -= rmb * delta;
262		consElem2->setVel(velB);
263	<
263	>
264	>	// report the constraint force back to the constraint pair:
265	>	consPair->setConstraintForce(gab);
266		return consSuccess;
267		}
268		else
#	Line 234 | Line 288 | namespace oopse {
288
289		currentSnapshot_->wrapVector(rab);
290
291	<	double rma = 1.0 / consElem1->getMass();
292	<	double rmb = 1.0 / consElem2->getMass();
291	>	RealType rma = 1.0 / consElem1->getMass();
292	>	RealType rmb = 1.0 / consElem2->getMass();
293
294	<	double rvab = dot(rab, dv);
294	>	RealType rvab = dot(rab, dv);
295
296	<	double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
296	>	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
297
298		if (fabs(gab) > consTolerance_){
299		Vector3d delta = rab * gab;
#	Line 250 | Line 304 | namespace oopse {
304		velB -= rmb * delta;
305		consElem2->setVel(velB);
306
307	+	// report the constraint force back to the constraint pair:
308	+	consPair->setConstraintForce(gab);
309		return consSuccess;
310		}
311		else

Comparing trunk/src/constraints/Rattle.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1982 by gezelter, Tue Apr 15 12:12:23 2014 UTC

#	Line 0 | Line 1
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