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

Comparing trunk/src/selection/DistanceFinder.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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
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	+	#ifdef IS_MPI
44	+	#include <mpi.h>
45	+	#endif
46	+
47		#include "selection/DistanceFinder.hpp"
48		#include "primitives/Molecule.hpp"
44	–	namespace oopse {
49
50	+	namespace OpenMD {
51	+
52		DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
53	<
53	>
54		nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
55		stuntdoubles_.resize(nStuntDoubles_);
56
#	Line 54 | Line 60 | namespace oopse {
60		Atom* atom;
61		Molecule::RigidBodyIterator rbIter;
62		RigidBody* rb;
57	–
63
64	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
64	>
65	>	for (mol = info_->beginMolecule(mi); mol != NULL;
66	>	mol = info_->nextMolecule(mi)) {
67
68	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
68	>	for(atom = mol->beginAtom(ai); atom != NULL;
69	>	atom = mol->nextAtom(ai)) {
70		stuntdoubles_[atom->getGlobalIndex()] = atom;
71		}
72
73	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
73	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
74	>	rb = mol->nextRigidBody(rbIter)) {
75		stuntdoubles_[rb->getGlobalIndex()] = rb;
76		}
77	<
69	<	}
70	<
77	>	}
78		}
79
80	<	OOPSEBitSet DistanceFinder::find(const OOPSEBitSet& bs, RealType distance) {
80	>	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
81		StuntDouble * center;
82		Vector3d centerPos;
83		Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
84	<	OOPSEBitSet bsResult(nStuntDoubles_);
84	>	OpenMDBitSet bsResult(nStuntDoubles_);
85		assert(bsResult.size() == bs.size());
86	<
87	<	for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
86	>
87	>	#ifdef IS_MPI
88	>	int mol;
89	>	int proc;
90	>	RealType data[3];
91	>	int worldRank = MPI::COMM_WORLD.Get_rank();
92	>	#endif
93	>
94	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
95	>	if (stuntdoubles_[j]->isRigidBody()) {
96	>	RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
97	>	rb->updateAtoms();
98	>	}
99	>	}
100	>
101	>	OpenMDBitSet bsTemp(nStuntDoubles_);
102	>	bsTemp = bs;
103	>	bsTemp.parallelReduce();
104	>
105	>	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
106	>
107	>	// Now, if we own stuntdouble i, we can use the position, but in
108	>	// parallel, we'll need to let everyone else know what that
109	>	// position is!
110	>
111	>	#ifdef IS_MPI
112	>	mol = info_->getGlobalMolMembership(i);
113	>	proc = info_->getMolToProc(mol);
114	>
115	>	if (proc == worldRank) {
116	>	center = stuntdoubles_[i];
117	>	centerPos = center->getPos();
118	>	data[0] = centerPos.x();
119	>	data[1] = centerPos.y();
120	>	data[2] = centerPos.z();
121	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
122	>	} else {
123	>	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
124	>	centerPos = Vector3d(data);
125	>	}
126	>	#else
127		center = stuntdoubles_[i];
128		centerPos = center->getPos();
129	<	for (int j = 0; j < stuntdoubles_.size(); ++j) {
129	>	#endif
130	>
131	>	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
132		Vector3d r =centerPos - stuntdoubles_[j]->getPos();
133		currSnapshot->wrapVector(r);
134		if (r.length() <= distance) {
#	Line 88 | Line 136 | namespace oopse {
136		}
137		}
138		}
91	–
139		return bsResult;
140		}
141
142	+
143	+	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
144	+	StuntDouble * center;
145	+	Vector3d centerPos;
146	+	Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
147	+	OpenMDBitSet bsResult(nStuntDoubles_);
148	+	assert(bsResult.size() == bs.size());
149	+
150	+	#ifdef IS_MPI
151	+	int mol;
152	+	int proc;
153	+	RealType data[3];
154	+	int worldRank = MPI::COMM_WORLD.Get_rank();
155	+	#endif
156	+
157	+	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
158	+	if (stuntdoubles_[j]->isRigidBody()) {
159	+	RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
160	+	rb->updateAtoms(frame);
161	+	}
162	+	}
163	+
164	+	OpenMDBitSet bsTemp(nStuntDoubles_);
165	+	bsTemp = bs;
166	+	bsTemp.parallelReduce();
167	+
168	+	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
169	+
170	+	// Now, if we own stuntdouble i, we can use the position, but in
171	+	// parallel, we'll need to let everyone else know what that
172	+	// position is!
173	+
174	+	#ifdef IS_MPI
175	+	mol = info_->getGlobalMolMembership(i);
176	+	proc = info_->getMolToProc(mol);
177	+
178	+	if (proc == worldRank) {
179	+	center = stuntdoubles_[i];
180	+	centerPos = center->getPos(frame);
181	+	data[0] = centerPos.x();
182	+	data[1] = centerPos.y();
183	+	data[2] = centerPos.z();
184	+	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
185	+	} else {
186	+	MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
187	+	centerPos = Vector3d(data);
188	+	}
189	+	#else
190	+	center = stuntdoubles_[i];
191	+	centerPos = center->getPos(frame);
192	+	#endif
193	+
194	+	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
195	+	Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
196	+	currSnapshot->wrapVector(r);
197	+	if (r.length() <= distance) {
198	+	bsResult.setBitOn(j);
199	+	}
200	+	}
201	+	}
202	+	return bsResult;
203	+	}
204		}

Comparing trunk/src/selection/DistanceFinder.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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