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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 1979 by gezelter, Sat Apr 5 20:56:01 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_->getNConstraints() > 0)
51	+	doRattle_ = true;
52	+
53	+
54		if (info_->getSimParams()->haveDt()) {
55		dt_ = info_->getSimParams()->getDt();
56		} else {
#	Line 54 | Line 59 | namespace oopse {
59		painCave.isFatal = 1;
60		simError();
61		}
57	–
62		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
63		}
64
65		void Rattle::constraintA() {
66	<	if (info_->getNConstraints() > 0) {
67	<	doConstraint(&Rattle::constraintPairA);
64	<	}
66	>	if (!doRattle_) return;
67	>	doConstraint(&Rattle::constraintPairA);
68		}
69		void Rattle::constraintB() {
70	<	if (info_->getNConstraints() > 0) {
71	<	doConstraint(&Rattle::constraintPairB);
69	<	}
70	>	if (!doRattle_) return;
71	>	doConstraint(&Rattle::constraintPairB);
72		}
73
74		void Rattle::doConstraint(ConstraintPairFuncPtr func) {
75	+	if (!doRattle_) return;
76	+
77		Molecule* mol;
78		SimInfo::MoleculeIterator mi;
79		ConstraintElem* consElem;
#	Line 77 | Line 81 | namespace oopse {
81		ConstraintPair* consPair;
82		Molecule::ConstraintPairIterator cpi;
83
84	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
85	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
84	>	for (mol = info_->beginMolecule(mi); mol != NULL;
85	>	mol = info_->nextMolecule(mi)) {
86	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
87	>	consElem = mol->nextConstraintElem(cei)) {
88		consElem->setMoved(true);
89		consElem->setMoving(false);
90		}
#	Line 92 | Line 98 | namespace oopse {
98
99		//loop over every constraint pair
100
101	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
102	<	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
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
107		//dispatch constraint algorithm
#	Line 103 | Line 111 | namespace oopse {
111		switch(exeStatus){
112		case consFail:
113		sprintf(painCave.errMsg,
114	<	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
114	>	"Constraint failure in Rattle::constrainA, "
115	>	"Constraint Fail\n");
116		painCave.isFatal = 1;
117		simError();
118
119		break;
120		case consSuccess:
121	<	//constrain the pair by moving two elements
121	>	// constrain the pair by moving two elements
122		done = false;
123		consPair->getConsElem1()->setMoving(true);
124		consPair->getConsElem2()->setMoving(true);
125		break;
126		case consAlready:
127	<	//current pair is already constrained, do not need to move the elements
127	>	// current pair is already constrained, do not need to
128	>	// move the elements
129		break;
130		default:
131	<	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
131	>	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
132	>	"Error: unrecognized status");
133		painCave.isFatal = 1;
134		simError();
135		break;
#	Line 128 | Line 139 | namespace oopse {
139		}//end for(iter->first())
140
141
142	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
143	<	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
142	>	for (mol = info_->beginMolecule(mi); mol != NULL;
143	>	mol = info_->nextMolecule(mi)) {
144	>	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
145	>	consElem = mol->nextConstraintElem(cei)) {
146		consElem->setMoved(consElem->getMoving());
147		consElem->setMoving(false);
148		}
#	Line 140 | Line 153 | namespace oopse {
153
154		if (!done){
155		sprintf(painCave.errMsg,
156	<	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
156	>	"Constraint failure in Rattle::constrainA, "
157	>	"too many iterations: %d\n",
158		iteration);
159		painCave.isFatal = 1;
160		simError();
#	Line 148 | Line 162 | namespace oopse {
162		}
163
164		int Rattle::constraintPairA(ConstraintPair* consPair){
165	+
166		ConstraintElem* consElem1 = consPair->getConsElem1();
167		ConstraintElem* consElem2 = consPair->getConsElem2();
168
#	Line 208 | Line 223 | namespace oopse {
223		Vector3d velB = consElem2->getVel();
224		velB -= rmb * delta;
225		consElem2->setVel(velB);
226	<
226	>
227	>	// report the constraint force back to the constraint pair:
228	>	consPair->setConstraintForce(gab);
229		return consSuccess;
230		}
231		else
#	Line 250 | Line 267 | namespace oopse {
267		velB -= rmb * delta;
268		consElem2->setVel(velB);
269
270	+	// report the constraint force back to the constraint pair:
271	+	consPair->setConstraintForce(gab);
272		return consSuccess;
273		}
274		else

Comparing trunk/src/constraints/Rattle.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1979 by gezelter, Sat Apr 5 20:56:01 2014 UTC

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

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