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

Comparing trunk/src/selection/DistanceFinder.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
2	>	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
#	Line 35 | Line 35
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, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
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 "selection/DistanceFinder.hpp"
44		#include "primitives/Molecule.hpp"
45	<	namespace OpenMD {
45	>	#ifdef IS_MPI
46	>	#include <mpi.h>
47	>	#endif
48
49	+	namespace OpenMD {
50	+
51		DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
52	<
52	>
53		nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
54		stuntdoubles_.resize(nStuntDoubles_);
55
#	Line 54 | Line 59 | namespace OpenMD {
59		Atom* atom;
60		Molecule::RigidBodyIterator rbIter;
61		RigidBody* rb;
57	–
62
63	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
63	>
64	>	for (mol = info_->beginMolecule(mi); mol != NULL;
65	>	mol = info_->nextMolecule(mi)) {
66
67	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
67	>	for(atom = mol->beginAtom(ai); atom != NULL;
68	>	atom = mol->nextAtom(ai)) {
69		stuntdoubles_[atom->getGlobalIndex()] = atom;
70		}
71
72	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
72	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
73	>	rb = mol->nextRigidBody(rbIter)) {
74		stuntdoubles_[rb->getGlobalIndex()] = rb;
75		}
76	<
69	<	}
70	<
76	>	}
77		}
78
79		OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
80		StuntDouble * center;
81		Vector3d centerPos;
82		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
83	<	OpenMDBitSet bsResult(nStuntDoubles_);
83	>	OpenMDBitSet bsResult(nStuntDoubles_);
84		assert(bsResult.size() == bs.size());
85	<
86	<	for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
85	>
86	>	#ifdef IS_MPI
87	>	int mol;
88	>	int proc;
89	>	RealType data[3];
90	>	int worldRank = MPI::COMM_WORLD.Get_rank();
91	>	#endif
92	>
93	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
94	>	if (stuntdoubles_[j]->isRigidBody()) {
95	>	RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
96	>	rb->updateAtoms();
97	>	}
98	>	}
99	>
100	>	OpenMDBitSet bsTemp(nStuntDoubles_);
101	>	bsTemp = bs;
102	>	bsTemp.parallelReduce();
103	>
104	>	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
105	>
106	>	// Now, if we own stuntdouble i, we can use the position, but in
107	>	// parallel, we'll need to let everyone else know what that
108	>	// position is!
109	>
110	>	#ifdef IS_MPI
111	>	mol = info_->getGlobalMolMembership(i);
112	>	proc = info_->getMolToProc(mol);
113	>
114	>	if (proc == worldRank) {
115	>	center = stuntdoubles_[i];
116	>	centerPos = center->getPos();
117	>	data[0] = centerPos.x();
118	>	data[1] = centerPos.y();
119	>	data[2] = centerPos.z();
120	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
121	>	} else {
122	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
123	>	centerPos = Vector3d(data);
124	>	}
125	>	#else
126		center = stuntdoubles_[i];
127		centerPos = center->getPos();
128	<	for (int j = 0; j < stuntdoubles_.size(); ++j) {
128	>	#endif
129	>
130	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
131		Vector3d r =centerPos - stuntdoubles_[j]->getPos();
132		currSnapshot->wrapVector(r);
133		if (r.length() <= distance) {
#	Line 88 | Line 135 | namespace OpenMD {
135		}
136		}
137		}
91	–
138		return bsResult;
139		}
140
141	+
142	+	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
143	+	StuntDouble * center;
144	+	Vector3d centerPos;
145	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
146	+	OpenMDBitSet bsResult(nStuntDoubles_);
147	+	assert(bsResult.size() == bs.size());
148	+
149	+	#ifdef IS_MPI
150	+	int mol;
151	+	int proc;
152	+	RealType data[3];
153	+	int worldRank = MPI::COMM_WORLD.Get_rank();
154	+	#endif
155	+
156	+	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
157	+	if (stuntdoubles_[j]->isRigidBody()) {
158	+	RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
159	+	rb->updateAtoms(frame);
160	+	}
161	+	}
162	+
163	+	OpenMDBitSet bsTemp(nStuntDoubles_);
164	+	bsTemp = bs;
165	+	bsTemp.parallelReduce();
166	+
167	+	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
168	+
169	+	// Now, if we own stuntdouble i, we can use the position, but in
170	+	// parallel, we'll need to let everyone else know what that
171	+	// position is!
172	+
173	+	#ifdef IS_MPI
174	+	mol = info_->getGlobalMolMembership(i);
175	+	proc = info_->getMolToProc(mol);
176	+
177	+	if (proc == worldRank) {
178	+	center = stuntdoubles_[i];
179	+	centerPos = center->getPos(frame);
180	+	data[0] = centerPos.x();
181	+	data[1] = centerPos.y();
182	+	data[2] = centerPos.z();
183	+	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
184	+	} else {
185	+	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
186	+	centerPos = Vector3d(data);
187	+	}
188	+	#else
189	+	center = stuntdoubles_[i];
190	+	centerPos = center->getPos(frame);
191	+	#endif
192	+
193	+	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
194	+	Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
195	+	currSnapshot->wrapVector(r);
196	+	if (r.length() <= distance) {
197	+	bsResult.setBitOn(j);
198	+	}
199	+	}
200	+	}
201	+	return bsResult;
202	+	}
203		}

Comparing trunk/src/selection/DistanceFinder.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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