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

Comparing trunk/src/selection/HullFinder.cpp (file contents):
Revision 1438 by chuckv, Wed Apr 21 19:05:04 2010 UTC vs.
Revision 2056 by gezelter, Fri Feb 20 15:12:07 2015 UTC

#	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/HullFinder.hpp"
#	Line 47 | Line 48 | namespace OpenMD {
48
49		HullFinder::HullFinder(SimInfo* info) : info_(info) {
50
51	<	nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
52	<	stuntdoubles_.resize(nStuntDoubles_);
51	>	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
52	>	nObjects_.push_back(info_->getNGlobalBonds());
53	>	nObjects_.push_back(info_->getNGlobalBends());
54	>	nObjects_.push_back(info_->getNGlobalTorsions());
55	>	nObjects_.push_back(info_->getNGlobalInversions());
56	>	nObjects_.push_back(info_->getNGlobalMolecules());
57	>
58	>	stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
59	>	bonds_.resize(nObjects_[BOND]);
60	>	bends_.resize(nObjects_[BEND]);
61	>	torsions_.resize(nObjects_[TORSION]);
62	>	inversions_.resize(nObjects_[INVERSION]);
63	>	molecules_.resize(nObjects_[MOLECULE]);
64
65		SimInfo::MoleculeIterator mi;
66	<	Molecule* mol;
55	<	StuntDouble* integrableObject;
56	<	Molecule::IntegrableObjectIterator  ioi;
66	>	Molecule::IntegrableObjectIterator ioi;
67		Molecule::AtomIterator ai;
58	–	Atom* atom;
68		Molecule::RigidBodyIterator rbIter;
69	<	RigidBody* rb;
69	>	Molecule::BondIterator bondIter;
70	>	Molecule::BendIterator bendIter;
71	>	Molecule::TorsionIterator torsionIter;
72	>	Molecule::InversionIterator inversionIter;
73
74	+	Molecule* mol;
75	+	StuntDouble* sd;
76	+	Atom* atom;
77	+	RigidBody* rb;
78	+	Bond* bond;
79	+	Bend* bend;
80	+	Torsion* torsion;
81	+	Inversion* inversion;
82	+
83		for (mol = info_->beginMolecule(mi); mol != NULL;
84		mol = info_->nextMolecule(mi)) {
85	<
85	>
86	>	molecules_[mol->getGlobalIndex()] = mol;
87	>
88		// Hull is constructed from all known integrable objects.
89	<	for (integrableObject = mol->beginIntegrableObject(ioi);
90	<	integrableObject != NULL;
91	<	integrableObject = mol->nextIntegrableObject(ioi)) {
92	<	localSites_.push_back(integrableObject);
89	>	for (sd = mol->beginIntegrableObject(ioi);
90	>	sd != NULL;
91	>	sd = mol->nextIntegrableObject(ioi)) {
92	>	localSites_.push_back(sd);
93		}
94
95		// selection can include atoms (which may be a subset of the IOs)
#	Line 80 | Line 103 | namespace OpenMD {
103		rb = mol->nextRigidBody(rbIter)) {
104		stuntdoubles_[rb->getGlobalIndex()] = rb;
105		}
106	<
106	>
107	>	// These others are going to be inferred from the objects on the hull:
108	>	for (bond = mol->beginBond(bondIter); bond != NULL;
109	>	bond = mol->nextBond(bondIter)) {
110	>	bonds_[bond->getGlobalIndex()] = bond;
111	>	}
112	>	for (bend = mol->beginBend(bendIter); bend != NULL;
113	>	bend = mol->nextBend(bendIter)) {
114	>	bends_[bend->getGlobalIndex()] = bend;
115	>	}
116	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
117	>	torsion = mol->nextTorsion(torsionIter)) {
118	>	torsions_[torsion->getGlobalIndex()] = torsion;
119	>	}
120	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
121	>	inversion = mol->nextInversion(inversionIter)) {
122	>	inversions_[inversion->getGlobalIndex()] = inversion;
123	>	}
124	>
125		}
126		#ifdef HAVE_QHULL
127		surfaceMesh_ = new ConvexHull();
128	+	#endif
129	+	}
130	+
131	+	HullFinder::~HullFinder() {
132	+	delete surfaceMesh_;
133	+	}
134	+
135	+	SelectionSet HullFinder::findHull() {
136	+	SelectionSet ssResult(nObjects_);
137	+	#ifdef HAVE_QHULL
138	+	surfaceMesh_->computeHull(localSites_);
139		#else
140		sprintf( painCave.errMsg,
141	<	"Hullfinder error: Hull calculation not possible without libqhull.\n",
142	<	"Please rebuild with Qhull");
143	<	painCave.severity = OPENMD_ERROR;
144	<	painCave.isFatal = 1;
145	<	simError();
94	<
141	>	"HullFinder : Hull calculation is not possible without libqhull.\n"
142	>	"\tPlease rebuild OpenMD with qhull enabled.");
143	>	painCave.severity = OPENMD_ERROR;
144	>	painCave.isFatal = 1;
145	>	simError();
146		#endif
147	+
148	+	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
149	+	// Loop over the mesh faces
150	+	std::vector<Triangle>::iterator face;
151	+	std::vector<StuntDouble*>::iterator vertex;
152	+
153	+	// This will work in parallel because the triangles returned by the mesh
154	+	// have a NULL stuntDouble if this processor doesn't own the
155	+
156	+	for (face = sMesh.begin(); face != sMesh.end(); ++face) {
157	+	Triangle thisTriangle = *face;
158	+	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
159	+	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
160	+	if ((*vertex) != NULL) {
161	+	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
162	+	}
163	+	}
164	+	}
165	+	surfaceArea_ = surfaceMesh_->getArea();
166	+	return ssResult;
167		}
168
169	<	OpenMDBitSet HullFinder::findHull() {
170	<	StuntDouble* sd;
171	<	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
101	<	OpenMDBitSet bsResult(nStuntDoubles_);
102	<
169	>	SelectionSet HullFinder::findHull(int frame) {
170	>	SelectionSet ssResult(nObjects_);
171	>	#ifdef HAVE_QHULL
172		surfaceMesh_->computeHull(localSites_);
173	+	#else
174	+	sprintf( painCave.errMsg,
175	+	"HullFinder : Hull calculation is not possible without libqhull.\n"
176	+	"\tPlease rebuild OpenMD with qhull enabled.");
177	+	painCave.severity = OPENMD_ERROR;
178	+	painCave.isFatal = 1;
179	+	simError();
180	+	#endif
181	+
182		std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
105	–	int nTriangles = sMesh.size();
183		// Loop over the mesh faces
184		std::vector<Triangle>::iterator face;
185		std::vector<StuntDouble*>::iterator vertex;
186
187	+	// This will work in parallel because the triangles returned by the mesh
188	+	// have a NULL stuntDouble if this processor doesn't own the
189	+
190		for (face = sMesh.begin(); face != sMesh.end(); ++face) {
191		Triangle thisTriangle = *face;
192		std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
193		for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
194		if ((*vertex) != NULL) {
195	<	bsResult.setBitOn((*vertex)->getGlobalIndex());
195	>	ssResult.bitsets_[STUNTDOUBLE].setBitOn((*vertex)->getGlobalIndex());
196		}
197		}
198		}
199	<	return bsResult;
199	>	surfaceArea_ = surfaceMesh_->getArea();
200	>	return ssResult;
201		}
202
203		}

Comparing trunk/src/selection/HullFinder.cpp (property svn:keywords):
Revision 1438 by chuckv, Wed Apr 21 19:05:04 2010 UTC vs.
Revision 2056 by gezelter, Fri Feb 20 15:12:07 2015 UTC

#	Line 0 | Line 1
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