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 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 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	>	Globals* simParams = info_->getSimParams();
56	>
57	>	if (simParams->haveDt()) {
58	>	dt_ = simParams->getDt();
59		} else {
60		sprintf(painCave.errMsg,
61	<	"Integrator Error: dt is not set\n");
61	>	"Rattle Error: dt is not set\n");
62		painCave.isFatal = 1;
63		simError();
64		}
65	<
65	>
66		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
67	+	if (simParams->haveConstraintTime()){
68	+	constraintTime_ = simParams->getConstraintTime();
69	+	} else {
70	+	constraintTime_ = simParams->getStatusTime();
71	+	}
72	+
73	+	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
74	+	".constraintForces";
75	+
76	+	// create ConstraintWriter
77	+	constraintWriter_ = new ConstraintWriter(info_,
78	+	constraintOutputFile_.c_str());
79	+
80	+	if (!constraintWriter_){
81	+	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
82	+	painCave.isFatal = 1;
83	+	simError();
84	+	}
85		}
86
87		void Rattle::constraintA() {
88	<	if (info_->getNConstraints() > 0) {
89	<	doConstraint(&Rattle::constraintPairA);
64	<	}
88	>	if (!doRattle_) return;
89	>	doConstraint(&Rattle::constraintPairA);
90		}
91		void Rattle::constraintB() {
92	<	if (info_->getNConstraints() > 0) {
93	<	doConstraint(&Rattle::constraintPairB);
92	>	if (!doRattle_) return;
93	>	doConstraint(&Rattle::constraintPairB);
94	>
95	>	if (currentSnapshot_->getTime() >= currConstraintTime_){
96	>	Molecule* mol;
97	>	SimInfo::MoleculeIterator mi;
98	>	ConstraintPair* consPair;
99	>	Molecule::ConstraintPairIterator cpi;
100	>	std::list<ConstraintPair*> constraints;
101	>	for (mol = info_->beginMolecule(mi); mol != NULL;
102	>	mol = info_->nextMolecule(mi)) {
103	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
104	>	consPair = mol->nextConstraintPair(cpi)) {
105	>
106	>	constraints.push_back(consPair);
107	>	}
108	>	}
109	>	constraintWriter_->writeConstraintForces(constraints);
110	>	currConstraintTime_ += constraintTime_;
111		}
112		}
113
114		void Rattle::doConstraint(ConstraintPairFuncPtr func) {
115	+	if (!doRattle_) return;
116	+
117		Molecule* mol;
118		SimInfo::MoleculeIterator mi;
119		ConstraintElem* consElem;
#	Line 77 | Line 121 | namespace oopse {
121		ConstraintPair* consPair;
122		Molecule::ConstraintPairIterator cpi;
123
124	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
125	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
124	>	for (mol = info_->beginMolecule(mi); mol != NULL;
125	>	mol = info_->nextMolecule(mi)) {
126	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
127	>	consElem = mol->nextConstraintElem(cei)) {
128		consElem->setMoved(true);
129		consElem->setMoving(false);
130		}
#	Line 92 | Line 138 | namespace oopse {
138
139		//loop over every constraint pair
140
141	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
142	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
141	>	for (mol = info_->beginMolecule(mi); mol != NULL;
142	>	mol = info_->nextMolecule(mi)) {
143	>	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
144	>	consPair = mol->nextConstraintPair(cpi)) {
145
146
147		//dispatch constraint algorithm
#	Line 103 | Line 151 | namespace oopse {
151		switch(exeStatus){
152		case consFail:
153		sprintf(painCave.errMsg,
154	<	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
154	>	"Constraint failure in Rattle::constrainA, "
155	>	"Constraint Fail\n");
156		painCave.isFatal = 1;
157		simError();
158
159		break;
160		case consSuccess:
161	<	//constrain the pair by moving two elements
161	>	// constrain the pair by moving two elements
162		done = false;
163		consPair->getConsElem1()->setMoving(true);
164		consPair->getConsElem2()->setMoving(true);
165		break;
166		case consAlready:
167	<	//current pair is already constrained, do not need to move the elements
167	>	// current pair is already constrained, do not need to
168	>	// move the elements
169		break;
170		default:
171	<	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
171	>	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
172	>	"Error: unrecognized status");
173		painCave.isFatal = 1;
174		simError();
175		break;
#	Line 128 | Line 179 | namespace oopse {
179		}//end for(iter->first())
180
181
182	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
183	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
182	>	for (mol = info_->beginMolecule(mi); mol != NULL;
183	>	mol = info_->nextMolecule(mi)) {
184	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
185	>	consElem = mol->nextConstraintElem(cei)) {
186		consElem->setMoved(consElem->getMoving());
187		consElem->setMoving(false);
188		}
#	Line 140 | Line 193 | namespace oopse {
193
194		if (!done){
195		sprintf(painCave.errMsg,
196	<	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
196	>	"Constraint failure in Rattle::constrainA, "
197	>	"too many iterations: %d\n",
198		iteration);
199		painCave.isFatal = 1;
200		simError();
#	Line 148 | Line 202 | namespace oopse {
202		}
203
204		int Rattle::constraintPairA(ConstraintPair* consPair){
205	+
206		ConstraintElem* consElem1 = consPair->getConsElem1();
207		ConstraintElem* consElem2 = consPair->getConsElem2();
208
#	Line 208 | Line 263 | namespace oopse {
263		Vector3d velB = consElem2->getVel();
264		velB -= rmb * delta;
265		consElem2->setVel(velB);
266	<
266	>
267	>	// report the constraint force back to the constraint pair:
268	>	consPair->setConstraintForce(gab);
269		return consSuccess;
270		}
271		else
#	Line 250 | Line 307 | namespace oopse {
307		velB -= rmb * delta;
308		consElem2->setVel(velB);
309
310	+	// report the constraint force back to the constraint pair:
311	+	consPair->setConstraintForce(gab);
312		return consSuccess;
313		}
314		else

Comparing trunk/src/constraints/Rattle.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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

Diff Legend

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