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root/OpenMD/trunk/src/selection/DistanceFinder.cpp

Comparing trunk/src/selection/DistanceFinder.cpp (file contents):
Revision 1434 by chuckv, Wed Apr 14 14:41:33 2010 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

#	Line 36 | Line 36
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, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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 "selection/DistanceFinder.hpp"
#	Line 56 | Line 57 | namespace OpenMD {
57		RigidBody* rb;
58
59
60	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
60	>	for (mol = info_->beginMolecule(mi); mol != NULL;
61	>	mol = info_->nextMolecule(mi)) {
62
63	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
63	>	for(atom = mol->beginAtom(ai); atom != NULL;
64	>	atom = mol->nextAtom(ai)) {
65		stuntdoubles_[atom->getGlobalIndex()] = atom;
66		}
67
68	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
69	>	rb = mol->nextRigidBody(rbIter)) {
70		stuntdoubles_[rb->getGlobalIndex()] = rb;
71		}
72	<
69	<	}
70	<
72	>	}
73		}
74
75		OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
#	Line 77 | Line 79 | namespace OpenMD {
79		OpenMDBitSet bsResult(nStuntDoubles_);
80		assert(bsResult.size() == bs.size());
81
82	<	for (int j = 0; j < stuntdoubles_.size(); ++j) {
82	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
83		if (stuntdoubles_[j]->isRigidBody()) {
84		RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
85		rb->updateAtoms();
86		}
87		}
88
89	+	// This will fail in parallel because i might not be on this processor.
90	+
91		for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
92		center = stuntdoubles_[i];
93		centerPos = center->getPos();
94	<	for (int j = 0; j < stuntdoubles_.size(); ++j) {
94	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
95		Vector3d r =centerPos - stuntdoubles_[j]->getPos();
96		currSnapshot->wrapVector(r);
97		if (r.length() <= distance) {

Comparing trunk/src/selection/DistanceFinder.cpp (property svn:keywords):
Revision 1434 by chuckv, Wed Apr 14 14:41:33 2010 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

#	Line 0 | Line 1
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