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

Comparing trunk/src/constraints/Rattle.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1981 by gezelter, Mon Apr 14 18:32:51 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_->getNConstraints() > 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");
60		painCave.isFatal = 1;
61		simError();
62		}
57	–
63		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
64	+	if (simParams->haveConstraintTime()){
65	+	constraintTime_ = simParams->getConstraintTime();
66	+	} else {
67	+	constraintTime_ = simParams->getStatusTime();
68	+	}
69	+
70	+	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
71	+
72	+	// create ConstraintWriter
73	+	constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
74	+
75	+	if (!constraintWriter_){
76	+	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
77	+	painCave.isFatal = 1;
78	+	simError();
79	+	}
80		}
81
82		void Rattle::constraintA() {
83	<	if (info_->getNConstraints() > 0) {
84	<	doConstraint(&Rattle::constraintPairA);
64	<	}
83	>	if (!doRattle_) return;
84	>	doConstraint(&Rattle::constraintPairA);
85		}
86		void Rattle::constraintB() {
87	<	if (info_->getNConstraints() > 0) {
88	<	doConstraint(&Rattle::constraintPairB);
87	>	if (!doRattle_) return;
88	>	doConstraint(&Rattle::constraintPairB);
89	>
90	>	if (currentSnapshot_->getTime() >= currConstraintTime_){
91	>	Molecule* mol;
92	>	SimInfo::MoleculeIterator mi;
93	>	ConstraintPair* consPair;
94	>	Molecule::ConstraintPairIterator cpi;
95	>	std::list<ConstraintPair*> constraints;
96	>	for (mol = info_->beginMolecule(mi); mol != NULL;
97	>	mol = info_->nextMolecule(mi)) {
98	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
99	>	consPair = mol->nextConstraintPair(cpi)) {
100	>
101	>	constraints.push_back(consPair);
102	>	}
103	>	}
104	>
105	>	constraintWriter_->writeConstraintForces(constraints);
106	>	currConstraintTime_ += constraintTime_;
107		}
108		}
109
110		void Rattle::doConstraint(ConstraintPairFuncPtr func) {
111	+	if (!doRattle_) return;
112	+
113		Molecule* mol;
114		SimInfo::MoleculeIterator mi;
115		ConstraintElem* consElem;
#	Line 77 | Line 117 | namespace oopse {
117		ConstraintPair* consPair;
118		Molecule::ConstraintPairIterator cpi;
119
120	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
121	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
120	>	for (mol = info_->beginMolecule(mi); mol != NULL;
121	>	mol = info_->nextMolecule(mi)) {
122	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
123	>	consElem = mol->nextConstraintElem(cei)) {
124		consElem->setMoved(true);
125		consElem->setMoving(false);
126		}
#	Line 92 | Line 134 | namespace oopse {
134
135		//loop over every constraint pair
136
137	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
138	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
137	>	for (mol = info_->beginMolecule(mi); mol != NULL;
138	>	mol = info_->nextMolecule(mi)) {
139	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
140	>	consPair = mol->nextConstraintPair(cpi)) {
141
142
143		//dispatch constraint algorithm
#	Line 103 | Line 147 | namespace oopse {
147		switch(exeStatus){
148		case consFail:
149		sprintf(painCave.errMsg,
150	<	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
150	>	"Constraint failure in Rattle::constrainA, "
151	>	"Constraint Fail\n");
152		painCave.isFatal = 1;
153		simError();
154
155		break;
156		case consSuccess:
157	<	//constrain the pair by moving two elements
157	>	// constrain the pair by moving two elements
158		done = false;
159		consPair->getConsElem1()->setMoving(true);
160		consPair->getConsElem2()->setMoving(true);
161		break;
162		case consAlready:
163	<	//current pair is already constrained, do not need to move the elements
163	>	// current pair is already constrained, do not need to
164	>	// move the elements
165		break;
166		default:
167	<	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
167	>	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
168	>	"Error: unrecognized status");
169		painCave.isFatal = 1;
170		simError();
171		break;
#	Line 128 | Line 175 | namespace oopse {
175		}//end for(iter->first())
176
177
178	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
179	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
178	>	for (mol = info_->beginMolecule(mi); mol != NULL;
179	>	mol = info_->nextMolecule(mi)) {
180	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
181	>	consElem = mol->nextConstraintElem(cei)) {
182		consElem->setMoved(consElem->getMoving());
183		consElem->setMoving(false);
184		}
#	Line 140 | Line 189 | namespace oopse {
189
190		if (!done){
191		sprintf(painCave.errMsg,
192	<	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
192	>	"Constraint failure in Rattle::constrainA, "
193	>	"too many iterations: %d\n",
194		iteration);
195		painCave.isFatal = 1;
196		simError();
#	Line 148 | Line 198 | namespace oopse {
198		}
199
200		int Rattle::constraintPairA(ConstraintPair* consPair){
201	+
202		ConstraintElem* consElem1 = consPair->getConsElem1();
203		ConstraintElem* consElem2 = consPair->getConsElem2();
204
#	Line 208 | Line 259 | namespace oopse {
259		Vector3d velB = consElem2->getVel();
260		velB -= rmb * delta;
261		consElem2->setVel(velB);
262	<
262	>
263	>	// report the constraint force back to the constraint pair:
264	>	consPair->setConstraintForce(gab);
265		return consSuccess;
266		}
267		else
#	Line 250 | Line 303 | namespace oopse {
303		velB -= rmb * delta;
304		consElem2->setVel(velB);
305
306	+	// report the constraint force back to the constraint pair:
307	+	consPair->setConstraintForce(gab);
308		return consSuccess;
309		}
310		else

Comparing trunk/src/constraints/Rattle.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1981 by gezelter, Mon Apr 14 18:32:51 2014 UTC

#	Line 0 | Line 1
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